From 981cefe8d3f4f73461789713726a9658498a5f14 Mon Sep 17 00:00:00 2001 From: Erik Schnetter Date: Sun, 17 Jan 2016 10:54:12 -0500 Subject: Make Boost build with MPI on OS X Boost does not build on OS X with either gold or binutils. The gold linker does not exist on Darwin, and binutils on Darwin provides an assembler that doesn't work for Boost. - Introduce a variant that specifies whether to build with binutils, defaulting to true for backward compatibility - Auto-detect whether we build on Darwin; in this case, set the gold and binutils variant defaults to false - Clean up configure flags for as and ld --- var/spack/packages/boost/package.py | 13 +++++++++++++ 1 file changed, 13 insertions(+) (limited to 'var') diff --git a/var/spack/packages/boost/package.py b/var/spack/packages/boost/package.py index 3427b74ad6..894af9edd1 100644 --- a/var/spack/packages/boost/package.py +++ b/var/spack/packages/boost/package.py @@ -1,5 +1,8 @@ from spack import * +import os +import sys + class Boost(Package): """Boost provides free peer-reviewed portable C++ source libraries, emphasizing libraries that work well with the C++ @@ -127,6 +130,16 @@ class Boost(Package): '--layout=tagged']) def install(self, spec, prefix): + # On Darwin, Boost expects the Darwin libtool. However, one of the + # dependencies may have pulled in Spack's GNU libtool, and these two are + # not compatible. We thus create a symlink to Darwin's libtool and add + # it at the beginning of PATH. + if sys.platform == 'darwin': + newdir = os.path.abspath('darwin-libtool') + mkdirp(newdir) + force_symlink('/usr/bin/libtool', join_path(newdir, 'libtool')) + env['PATH'] = newdir + ':' + env['PATH'] + # to make Boost find the user-config.jam env['BOOST_BUILD_PATH'] = './' -- cgit v1.2.3-70-g09d2 From 77c17e1d92ac1c98a5c43247d6582876bc7d14d4 Mon Sep 17 00:00:00 2001 From: Erik Schnetter Date: Fri, 12 Feb 2016 12:51:43 -0500 Subject: Since my last patch didn't get traction, here is a new approach to building gcc on Darwin: - Add a variant specifying whether to build with binutils, defaulting to true - Auto-detect whether this is Darwin; if so, set binutils and gold defaults to false, as they don't work on Darwin - Disable Go, which doesn't build on Darwin - Clean up handling configure options --- var/spack/repos/builtin/packages/gcc/package.py | 29 ++++++++++++++----------- 1 file changed, 16 insertions(+), 13 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py index 3e5895cfb8..eb2129c4da 100644 --- a/var/spack/repos/builtin/packages/gcc/package.py +++ b/var/spack/repos/builtin/packages/gcc/package.py @@ -26,6 +26,7 @@ from spack import * from contextlib import closing from glob import glob +import sys class Gcc(Package): """The GNU Compiler Collection includes front ends for C, C++, @@ -49,13 +50,14 @@ class Gcc(Package): version('4.6.4', 'b407a3d1480c11667f293bfb1f17d1a4') version('4.5.4', '27e459c2566b8209ab064570e1b378f7') - variant('gold', default=True, description="Build the gold linker plugin for ld-based LTO") + variant('binutils', default=sys.platform != 'darwin', description="Build via binutils") + variant('gold', default=sys.platform != 'darwin', description="Build the gold linker plugin for ld-based LTO") depends_on("mpfr") depends_on("gmp") depends_on("mpc") # when @4.5: - depends_on("binutils~libiberty", when='~gold') - depends_on("binutils~libiberty+gold", when='+gold') + depends_on("binutils~libiberty", when='+binutils ~gold') + depends_on("binutils~libiberty+gold", when='+binutils +gold') # Save these until we can do optional deps. depends_on("isl", when=DEPENDS_ON_ISL_PREDICATE) @@ -67,7 +69,7 @@ class Gcc(Package): filter_file(r"'@.*@'", "'@[[:alnum:]]*@'", 'libjava/configure', string=True) enabled_languages = set(('c', 'c++', 'fortran', 'java', 'objc')) - if spec.satisfies("@4.7.1:"): + if spec.satisfies("@4.7.1:") and sys.platform != 'darwin': enabled_languages.add('go') # Generic options to compile GCC @@ -79,17 +81,18 @@ class Gcc(Package): "--with-mpfr=%s" % spec['mpfr'].prefix, "--with-gmp=%s" % spec['gmp'].prefix, "--enable-lto", - "--with-gnu-ld", - "--with-gnu-as", "--with-quad"] # Binutils - static_bootstrap_flags = "-static-libstdc++ -static-libgcc" - binutils_options = ["--with-sysroot=/", - "--with-stage1-ldflags=%s %s" % (self.rpath_args, static_bootstrap_flags), - "--with-boot-ldflags=%s %s" % (self.rpath_args, static_bootstrap_flags), - "--with-ld=%s/bin/ld" % spec['binutils'].prefix, - "--with-as=%s/bin/as" % spec['binutils'].prefix] - options.extend(binutils_options) + if spec.satisfies('+binutils'): + static_bootstrap_flags = "-static-libstdc++ -static-libgcc" + binutils_options = ["--with-sysroot=/", + "--with-stage1-ldflags=%s %s" % (self.rpath_args, static_bootstrap_flags), + "--with-boot-ldflags=%s %s" % (self.rpath_args, static_bootstrap_flags), + "--with-gnu-ld", + "--with-ld=%s/bin/ld" % spec['binutils'].prefix, + "--with-gnu-as", + "--with-as=%s/bin/as" % spec['binutils'].prefix] + options.extend(binutils_options) # Isl if spec.satisfies(Gcc.DEPENDS_ON_ISL_PREDICATE): isl_options = ["--with-isl=%s" % spec['isl'].prefix] -- cgit v1.2.3-70-g09d2 From 8e33cc1ae118b138aadc3c354b622c045dd81009 Mon Sep 17 00:00:00 2001 From: Erik Schnetter Date: Fri, 12 Feb 2016 13:11:45 -0500 Subject: Properly wrap all long lines --- var/spack/repos/builtin/packages/gcc/package.py | 27 ++++++++++++++++--------- 1 file changed, 17 insertions(+), 10 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py index eb2129c4da..8292670de0 100644 --- a/var/spack/repos/builtin/packages/gcc/package.py +++ b/var/spack/repos/builtin/packages/gcc/package.py @@ -50,8 +50,10 @@ class Gcc(Package): version('4.6.4', 'b407a3d1480c11667f293bfb1f17d1a4') version('4.5.4', '27e459c2566b8209ab064570e1b378f7') - variant('binutils', default=sys.platform != 'darwin', description="Build via binutils") - variant('gold', default=sys.platform != 'darwin', description="Build the gold linker plugin for ld-based LTO") + variant('binutils', default=sys.platform != 'darwin', + description="Build via binutils") + variant('gold', default=sys.platform != 'darwin', + description="Build the gold linker plugin for ld-based LTO") depends_on("mpfr") depends_on("gmp") @@ -66,7 +68,8 @@ class Gcc(Package): def install(self, spec, prefix): # libjava/configure needs a minor fix to install into spack paths. - filter_file(r"'@.*@'", "'@[[:alnum:]]*@'", 'libjava/configure', string=True) + filter_file(r"'@.*@'", "'@[[:alnum:]]*@'", 'libjava/configure', + string=True) enabled_languages = set(('c', 'c++', 'fortran', 'java', 'objc')) if spec.satisfies("@4.7.1:") and sys.platform != 'darwin': @@ -77,17 +80,19 @@ class Gcc(Package): "--libdir=%s/lib64" % prefix, "--disable-multilib", "--enable-languages=" + ','.join(enabled_languages), - "--with-mpc=%s" % spec['mpc'].prefix, - "--with-mpfr=%s" % spec['mpfr'].prefix, - "--with-gmp=%s" % spec['gmp'].prefix, + "--with-mpc=%s" % spec['mpc'].prefix, + "--with-mpfr=%s" % spec['mpfr'].prefix, + "--with-gmp=%s" % spec['gmp'].prefix, "--enable-lto", "--with-quad"] # Binutils if spec.satisfies('+binutils'): static_bootstrap_flags = "-static-libstdc++ -static-libgcc" binutils_options = ["--with-sysroot=/", - "--with-stage1-ldflags=%s %s" % (self.rpath_args, static_bootstrap_flags), - "--with-boot-ldflags=%s %s" % (self.rpath_args, static_bootstrap_flags), + "--with-stage1-ldflags=%s %s" % + (self.rpath_args, static_bootstrap_flags), + "--with-boot-ldflags=%s %s" % + (self.rpath_args, static_bootstrap_flags), "--with-gnu-ld", "--with-ld=%s/bin/ld" % spec['binutils'].prefix, "--with-gnu-as", @@ -120,7 +125,8 @@ class Gcc(Package): """Generate a spec file so the linker adds a rpath to the libs the compiler used to build the executable.""" if not self.spec_dir: - tty.warn("Could not install specs for %s." % self.spec.format('$_$@')) + tty.warn("Could not install specs for %s." % + self.spec.format('$_$@')) return gcc = Executable(join_path(self.prefix.bin, 'gcc')) @@ -130,5 +136,6 @@ class Gcc(Package): for line in lines: out.write(line + "\n") if line.startswith("*link:"): - out.write("-rpath %s/lib:%s/lib64 \\\n"% (self.prefix, self.prefix)) + out.write("-rpath %s/lib:%s/lib64 \\\n" % + (self.prefix, self.prefix)) set_install_permissions(specs_file) -- cgit v1.2.3-70-g09d2 From 63ae40716908ee8c19d49de83accff482d921331 Mon Sep 17 00:00:00 2001 From: alalazo Date: Thu, 3 Mar 2016 16:39:21 +0100 Subject: netlib-lapack : unified build with netlib-blas openssl : updated version py-numpy : updated dependencies --- .../repos/builtin/packages/netlib-blas/package.py | 46 ----------------- .../builtin/packages/netlib-lapack/package.py | 59 ++++++++-------------- .../repos/builtin/packages/openssl/package.py | 1 + .../repos/builtin/packages/py-numpy/package.py | 3 +- 4 files changed, 22 insertions(+), 87 deletions(-) delete mode 100644 var/spack/repos/builtin/packages/netlib-blas/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/netlib-blas/package.py b/var/spack/repos/builtin/packages/netlib-blas/package.py deleted file mode 100644 index 85e97323d3..0000000000 --- a/var/spack/repos/builtin/packages/netlib-blas/package.py +++ /dev/null @@ -1,46 +0,0 @@ -from spack import * -import os - - -class NetlibBlas(Package): - """Netlib reference BLAS""" - homepage = "http://www.netlib.org/lapack/" - url = "http://www.netlib.org/lapack/lapack-3.5.0.tgz" - - version('3.5.0', 'b1d3e3e425b2e44a06760ff173104bdf') - - variant('fpic', default=False, description="Build with -fpic compiler option") - - # virtual dependency - provides('blas') - - # Doesn't always build correctly in parallel - parallel = False - - def patch(self): - os.symlink('make.inc.example', 'make.inc') - - mf = FileFilter('make.inc') - mf.filter('^FORTRAN.*', 'FORTRAN = f90') - mf.filter('^LOADER.*', 'LOADER = f90') - mf.filter('^CC =.*', 'CC = cc') - - if '+fpic' in self.spec: - mf.filter('^OPTS.*=.*', 'OPTS = -O2 -frecursive -fpic') - mf.filter('^CFLAGS =.*', 'CFLAGS = -O3 -fpic') - - - def install(self, spec, prefix): - make('blaslib') - - # Tests that blas builds correctly - make('blas_testing') - - # No install provided - mkdirp(prefix.lib) - install('librefblas.a', prefix.lib) - - # Blas virtual package should provide blas.a and libblas.a - with working_dir(prefix.lib): - symlink('librefblas.a', 'blas.a') - symlink('librefblas.a', 'libblas.a') diff --git a/var/spack/repos/builtin/packages/netlib-lapack/package.py b/var/spack/repos/builtin/packages/netlib-lapack/package.py index fb6b99e27c..1bb77919d5 100644 --- a/var/spack/repos/builtin/packages/netlib-lapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-lapack/package.py @@ -1,16 +1,15 @@ from spack import * + class NetlibLapack(Package): """ - LAPACK version 3.X is a comprehensive FORTRAN library that does - linear algebra operations including matrix inversions, least - squared solutions to linear sets of equations, eigenvector - analysis, singular value decomposition, etc. It is a very - comprehensive and reputable package that has found extensive - use in the scientific community. + LAPACK version 3.X is a comprehensive FORTRAN library that does linear algebra operations including matrix + inversions, least squared solutions to linear sets of equations, eigenvector analysis, singular value + decomposition, etc. It is a very comprehensive and reputable package that has found extensive use in the + scientific community. """ homepage = "http://www.netlib.org/lapack/" - url = "http://www.netlib.org/lapack/lapack-3.5.0.tgz" + url = "http://www.netlib.org/lapack/lapack-3.5.0.tgz" version('3.5.0', 'b1d3e3e425b2e44a06760ff173104bdf') version('3.4.2', '61bf1a8a4469d4bdb7604f5897179478') @@ -18,42 +17,24 @@ class NetlibLapack(Package): version('3.4.0', '02d5706ec03ba885fc246e5fa10d8c70') version('3.3.1', 'd0d533ec9a5b74933c2a1e84eedc58b4') - variant('shared', default=False, description="Build shared library version") + variant('debug', default=False, description='Activates the Debug build type') + variant('shared', default=True, description="Build shared library version") + + variant('lapacke', default=True, description='Activates the build of the LAPACKE C interface') # virtual dependency + provides('blas') provides('lapack') - # blas is a virtual dependency. - depends_on('blas') - depends_on('cmake') - # Doesn't always build correctly in parallel - parallel = False - - @when('^netlib-blas') - def get_blas_libs(self): - blas = self.spec['netlib-blas'] - return [join_path(blas.prefix.lib, 'blas.a')] - - - @when('^atlas') - def get_blas_libs(self): - blas = self.spec['atlas'] - return [join_path(blas.prefix.lib, l) - for l in ('libf77blas.a', 'libatlas.a')] - - def install(self, spec, prefix): - blas_libs = ";".join(self.get_blas_libs()) - cmake_args = [".", '-DBLAS_LIBRARIES=' + blas_libs] - - if '+shared' in spec: - cmake_args.append('-DBUILD_SHARED_LIBS=ON') - - cmake_args += std_cmake_args - - cmake(*cmake_args) - make() - make("install") - + cmake_args = ['-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if '+shared' in spec else 'OFF'), + '-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'), + '-DLAPACKE:BOOL=%s' % ('ON' if '+lapacke' in spec else 'OFF')] + cmake_args.extend(std_cmake_args) + + with working_dir('spack-build', create=True): + cmake('..', *cmake_args) + make() + make("install") diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py index c73102f05d..70afaf4038 100644 --- a/var/spack/repos/builtin/packages/openssl/package.py +++ b/var/spack/repos/builtin/packages/openssl/package.py @@ -17,6 +17,7 @@ class Openssl(Package): version('1.0.2d', '38dd619b2e77cbac69b99f52a053d25a') version('1.0.2e', '5262bfa25b60ed9de9f28d5d52d77fc5') version('1.0.2f', 'b3bf73f507172be9292ea2a8c28b659d') + version('1.0.2g', 'f3c710c045cdee5fd114feb69feba7aa') depends_on("zlib") parallel = False diff --git a/var/spack/repos/builtin/packages/py-numpy/package.py b/var/spack/repos/builtin/packages/py-numpy/package.py index 0354811186..0844ff5caa 100644 --- a/var/spack/repos/builtin/packages/py-numpy/package.py +++ b/var/spack/repos/builtin/packages/py-numpy/package.py @@ -12,8 +12,7 @@ class PyNumpy(Package): extends('python') depends_on('py-nose') - depends_on('netlib-blas+fpic', when='+blas') - depends_on('netlib-lapack+shared', when='+blas') + depends_on('lapack+shared', when='+blas') def install(self, spec, prefix): if '+blas' in spec: -- cgit v1.2.3-70-g09d2 From 310099d88838c8e08d15fb34028263c9294b62e9 Mon Sep 17 00:00:00 2001 From: alalazo Date: Fri, 4 Mar 2016 09:31:03 +0100 Subject: atlas : provides blas and lapack --- var/spack/repos/builtin/packages/atlas/package.py | 58 +++++++++++------------ 1 file changed, 28 insertions(+), 30 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/atlas/package.py b/var/spack/repos/builtin/packages/atlas/package.py index fc683363a7..f9b50417b0 100644 --- a/var/spack/repos/builtin/packages/atlas/package.py +++ b/var/spack/repos/builtin/packages/atlas/package.py @@ -1,31 +1,34 @@ from spack import * from spack.util.executable import Executable -import os +import os.path class Atlas(Package): """ - Automatically Tuned Linear Algebra Software, generic shared - ATLAS is an approach for the automatic generation and optimization of - numerical software. Currently ATLAS supplies optimized versions for the - complete set of linear algebra kernels known as the Basic Linear Algebra - Subroutines (BLAS), and a subset of the linear algebra routines in the - LAPACK library. + Automatically Tuned Linear Algebra Software, generic shared ATLAS is an approach for the automatic generation and + optimization of numerical software. Currently ATLAS supplies optimized versions for the complete set of linear + algebra kernels known as the Basic Linear Algebra Subroutines (BLAS), and a subset of the linear algebra routines + in the LAPACK library. """ homepage = "http://math-atlas.sourceforge.net/" - version('3.11.34', '0b6c5389c095c4c8785fd0f724ec6825', - url='http://sourceforge.net/projects/math-atlas/files/Developer%20%28unstable%29/3.11.34/atlas3.11.34.tar.bz2/download') version('3.10.2', 'a4e21f343dec8f22e7415e339f09f6da', - url='http://downloads.sourceforge.net/project/math-atlas/Stable/3.10.2/atlas3.10.2.tar.bz2') + url='http://downloads.sourceforge.net/project/math-atlas/Stable/3.10.2/atlas3.10.2.tar.bz2', preferred=True) + resource(name='lapack', + url='http://www.netlib.org/lapack/lapack-3.5.0.tgz', + md5='b1d3e3e425b2e44a06760ff173104bdf', + destination='spack-resource-lapack', + when='@3:') - # TODO: make this provide BLAS once it works better. Create a way - # TODO: to mark "beta" packages and require explicit invocation. + version('3.11.34', '0b6c5389c095c4c8785fd0f724ec6825', + url='http://sourceforge.net/projects/math-atlas/files/Developer%20%28unstable%29/3.11.34/atlas3.11.34.tar.bz2/download') - # provides('blas') + variant('shared', default=True, description='Builds shared library') + provides('blas') + provides('lapack') def patch(self): - # Disable thraed check. LLNL's environment does not allow + # Disable thread check. LLNL's environment does not allow # disabling of CPU throttling in a way that ATLAS actually # understands. filter_file(r'^\s+if \(thrchk\) exit\(1\);', 'if (0) exit(1);', @@ -33,26 +36,21 @@ class Atlas(Package): # TODO: investigate a better way to add the check back in # TODO: using, say, MSRs. Or move this to a variant. - @when('@:3.10') def install(self, spec, prefix): - with working_dir('ATLAS-Build', create=True): - configure = Executable('../configure') - configure('--prefix=%s' % prefix, '-C', 'ic', 'cc', '-C', 'if', 'f77', "--dylibs") - make() - make('check') - make('ptcheck') - make('time') - make("install") + options = [] + if '+shared' in spec: + options.append('--shared') - def install(self, spec, prefix): - with working_dir('ATLAS-Build', create=True): - configure = Executable('../configure') - configure('--incdir=%s' % prefix.include, - '--libdir=%s' % prefix.lib, - '--cc=cc', - "--shared") + # Lapack resource + lapack_stage = self.stage[1] + lapack_tarfile = os.path.basename(lapack_stage.fetcher.url) + lapack_tarfile_path = join_path(lapack_stage.path, lapack_tarfile) + options.append('--with-netlib-lapack-tarfile=%s' % lapack_tarfile_path) + with working_dir('spack-build', create=True): + configure = Executable('../configure') + configure('--prefix=%s' % prefix, *options) make() make('check') make('ptcheck') -- cgit v1.2.3-70-g09d2 From a2af4940aaf169f3358f19986fc94a02222a8096 Mon Sep 17 00:00:00 2001 From: alalazo Date: Fri, 4 Mar 2016 09:59:16 +0100 Subject: atlas : disabling parallel builds --- var/spack/repos/builtin/packages/atlas/package.py | 2 ++ 1 file changed, 2 insertions(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/atlas/package.py b/var/spack/repos/builtin/packages/atlas/package.py index f9b50417b0..b5504122b7 100644 --- a/var/spack/repos/builtin/packages/atlas/package.py +++ b/var/spack/repos/builtin/packages/atlas/package.py @@ -27,6 +27,8 @@ class Atlas(Package): provides('blas') provides('lapack') + parallel = False + def patch(self): # Disable thread check. LLNL's environment does not allow # disabling of CPU throttling in a way that ATLAS actually -- cgit v1.2.3-70-g09d2 From 4f14db8af214b6648da04c5c5121757ea171f18c Mon Sep 17 00:00:00 2001 From: alalazo Date: Thu, 10 Mar 2016 10:34:51 +0100 Subject: netlib-lapack : optional dependency on external blas --- var/spack/repos/builtin/packages/netlib-lapack/package.py | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/netlib-lapack/package.py b/var/spack/repos/builtin/packages/netlib-lapack/package.py index 1bb77919d5..a208929d08 100644 --- a/var/spack/repos/builtin/packages/netlib-lapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-lapack/package.py @@ -19,19 +19,29 @@ class NetlibLapack(Package): variant('debug', default=False, description='Activates the Debug build type') variant('shared', default=True, description="Build shared library version") + variant('external-blas', default=False, description='Build lapack with an external blas') variant('lapacke', default=True, description='Activates the build of the LAPACKE C interface') # virtual dependency - provides('blas') + provides('blas', when='~external-blas') provides('lapack') depends_on('cmake') + depends_on('blas', when='+external-blas') def install(self, spec, prefix): cmake_args = ['-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if '+shared' in spec else 'OFF'), '-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'), '-DLAPACKE:BOOL=%s' % ('ON' if '+lapacke' in spec else 'OFF')] + if '+external-blas' in spec: + # TODO : the mechanism to specify the library should be more general, + # TODO : but this allows to have an hook to an external blas + cmake_args.extend([ + '-DUSE_OPTIMIZED_BLAS:BOOL=ON', + '-DBLAS_LIBRARIES:PATH=%s' % join_path(spec['blas'].prefix.lib, 'libblas.a') + ]) + cmake_args.extend(std_cmake_args) with working_dir('spack-build', create=True): -- cgit v1.2.3-70-g09d2 From bcea1df01ce145aea5e49eaaceb7a063b44ddf80 Mon Sep 17 00:00:00 2001 From: alalazo Date: Tue, 15 Mar 2016 10:49:33 +0100 Subject: environment : refactoreded set_build_environment_variables --- lib/spack/spack/build_environment.py | 56 +++++++++++----------- lib/spack/spack/environment.py | 3 ++ .../repos/builtin/packages/mvapich2/package.py | 2 +- 3 files changed, 33 insertions(+), 28 deletions(-) (limited to 'var') diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py index e91a8a1997..770e191ac9 100644 --- a/lib/spack/spack/build_environment.py +++ b/lib/spack/spack/build_environment.py @@ -35,7 +35,7 @@ import sys import spack from llnl.util.filesystem import * -from spack.environment import EnvironmentModifications, apply_environment_modifications +from spack.environment import EnvironmentModifications, apply_environment_modifications, concatenate_paths from spack.util.environment import * from spack.util.executable import Executable, which @@ -127,44 +127,45 @@ def set_build_environment_variables(pkg): # handled by putting one in the /case-insensitive # directory. Add that to the path too. env_paths = [] - def add_env_path(path): - env_paths.append(path) - ci = join_path(path, 'case-insensitive') - if os.path.isdir(ci): env_paths.append(ci) - add_env_path(spack.build_env_path) - add_env_path(join_path(spack.build_env_path, pkg.compiler.name)) - - path_put_first("PATH", env_paths) - path_set(SPACK_ENV_PATH, env_paths) - - # Prefixes of all of the package's dependencies go in - # SPACK_DEPENDENCIES + for item in [spack.build_env_path, join_path(spack.build_env_path, pkg.compiler.name)]: + env_paths.append(item) + ci = join_path(item, 'case-insensitive') + if os.path.isdir(ci): + env_paths.append(ci) + + env = EnvironmentModifications() + for item in reversed(env_paths): + env.prepend_path('PATH', item) + env.set_env(SPACK_ENV_PATH, concatenate_paths(env_paths)) + + # Prefixes of all of the package's dependencies go in SPACK_DEPENDENCIES dep_prefixes = [d.prefix for d in pkg.spec.traverse(root=False)] - path_set(SPACK_DEPENDENCIES, dep_prefixes) + env.set_env(SPACK_DEPENDENCIES, concatenate_paths(dep_prefixes)) + env.set_env('CMAKE_PREFIX_PATH', concatenate_paths(dep_prefixes)) # Add dependencies to CMAKE_PREFIX_PATH # Install prefix - os.environ[SPACK_PREFIX] = pkg.prefix + env.set_env(SPACK_PREFIX, pkg.prefix) # Install root prefix - os.environ[SPACK_INSTALL] = spack.install_path + env.set_env(SPACK_INSTALL, spack.install_path) # Remove these vars from the environment during build because they # can affect how some packages find libraries. We want to make # sure that builds never pull in unintended external dependencies. - pop_keys(os.environ, "LD_LIBRARY_PATH", "LD_RUN_PATH", "DYLD_LIBRARY_PATH") + env.unset_env('LD_LIBRARY_PATH') + env.unset_env('LD_RUN_PATH') + env.unset_env('DYLD_LIBRARY_PATH') # Add bin directories from dependencies to the PATH for the build. - bin_dirs = ['%s/bin' % prefix for prefix in dep_prefixes] - path_put_first('PATH', [bin for bin in bin_dirs if os.path.isdir(bin)]) + bin_dirs = reversed(filter(os.path.isdir, ['%s/bin' % prefix for prefix in dep_prefixes])) + for item in bin_dirs: + env.prepend_path('PATH', item) # Working directory for the spack command itself, for debug logs. if spack.debug: - os.environ[SPACK_DEBUG] = "TRUE" - os.environ[SPACK_SHORT_SPEC] = pkg.spec.short_spec - os.environ[SPACK_DEBUG_LOG_DIR] = spack.spack_working_dir - - # Add dependencies to CMAKE_PREFIX_PATH - path_set("CMAKE_PREFIX_PATH", dep_prefixes) + env.set_env(SPACK_DEBUG, 'TRUE') + env.set_env(SPACK_SHORT_SPEC, pkg.spec.short_spec) + env.set_env(SPACK_DEBUG_LOG_DIR, spack.spack_working_dir) # Add any pkgconfig directories to PKG_CONFIG_PATH pkg_config_dirs = [] @@ -173,8 +174,9 @@ def set_build_environment_variables(pkg): pcdir = join_path(p, libdir, 'pkgconfig') if os.path.isdir(pcdir): pkg_config_dirs.append(pcdir) - path_set("PKG_CONFIG_PATH", pkg_config_dirs) + env.set_env('PKG_CONFIG_PATH', concatenate_paths(pkg_config_dirs)) + return env def set_module_variables_for_package(pkg, m): """Populate the module scope of install() with some useful functions. @@ -269,8 +271,8 @@ def setup_package(pkg): """Execute all environment setup routines.""" env = EnvironmentModifications() env.extend(set_compiler_environment_variables(pkg)) + env.extend(set_build_environment_variables(pkg)) apply_environment_modifications(env) - set_build_environment_variables(pkg) # If a user makes their own package repo, e.g. # spack.repos.mystuff.libelf.Libelf, and they inherit from # an existing class like spack.repos.original.libelf.Libelf, diff --git a/lib/spack/spack/environment.py b/lib/spack/spack/environment.py index 3b73f1c7a2..18fef1ef12 100644 --- a/lib/spack/spack/environment.py +++ b/lib/spack/spack/environment.py @@ -146,6 +146,9 @@ class EnvironmentModifications(object): self.env_modifications.append(item) +def concatenate_paths(paths): + return ':'.join(str(item) for item in paths) + def validate_environment_modifications(env): modifications = collections.defaultdict(list) for item in env: diff --git a/var/spack/repos/builtin/packages/mvapich2/package.py b/var/spack/repos/builtin/packages/mvapich2/package.py index af5ed1b088..e4e95f92af 100644 --- a/var/spack/repos/builtin/packages/mvapich2/package.py +++ b/var/spack/repos/builtin/packages/mvapich2/package.py @@ -123,7 +123,7 @@ class Mvapich2(Package): count += 1 if count > 1: raise RuntimeError('network variants are mutually exclusive (only one can be selected at a time)') - + network_options = [] # From here on I can suppose that only one variant has been selected if self.enabled(Mvapich2.PSM) in spec: network_options = ["--with-device=ch3:psm"] -- cgit v1.2.3-70-g09d2 From c85888eb5763d453af7b7255b6d8c3461082362f Mon Sep 17 00:00:00 2001 From: alalazo Date: Tue, 15 Mar 2016 13:36:41 +0100 Subject: package : added `environment_modifications` --- lib/spack/spack/build_environment.py | 7 ++++--- lib/spack/spack/package.py | 4 ++++ var/spack/repos/builtin/packages/mpich/package.py | 16 ++++++++++------ .../builtin/packages/netlib-scalapack/package.py | 3 +-- .../repos/builtin/packages/openmpi/package.py | 14 ++++++++------ var/spack/repos/builtin/packages/python/package.py | 20 +++++++++++--------- var/spack/repos/builtin/packages/qt/package.py | 12 +++++++----- var/spack/repos/builtin/packages/ruby/package.py | 22 +++++++++++++--------- 8 files changed, 58 insertions(+), 40 deletions(-) (limited to 'var') diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py index 770e191ac9..d321a0e495 100644 --- a/lib/spack/spack/build_environment.py +++ b/lib/spack/spack/build_environment.py @@ -178,6 +178,7 @@ def set_build_environment_variables(pkg): return env + def set_module_variables_for_package(pkg, m): """Populate the module scope of install() with some useful functions. This makes things easier for package writers. @@ -272,7 +273,6 @@ def setup_package(pkg): env = EnvironmentModifications() env.extend(set_compiler_environment_variables(pkg)) env.extend(set_build_environment_variables(pkg)) - apply_environment_modifications(env) # If a user makes their own package repo, e.g. # spack.repos.mystuff.libelf.Libelf, and they inherit from # an existing class like spack.repos.original.libelf.Libelf, @@ -284,8 +284,9 @@ def setup_package(pkg): # Allow dependencies to set up environment as well. for dep_spec in pkg.spec.traverse(root=False): - dep_spec.package.setup_dependent_environment( - pkg.module, dep_spec, pkg.spec) + env.extend(dep_spec.package.environment_modifications(pkg.module, dep_spec, pkg.spec)) + dep_spec.package.setup_dependent_environment(pkg.module, dep_spec, pkg.spec) + apply_environment_modifications(env) def fork(pkg, function): diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index 696adaf896..224d7f8f4b 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -63,6 +63,7 @@ import spack.build_environment import spack.url import spack.util.web import spack.fetch_strategy as fs +from spack.environment import EnvironmentModifications from spack.version import * from spack.stage import Stage, ResourceStage, StageComposite from spack.util.compression import allowed_archive, extension @@ -983,6 +984,9 @@ class Package(object): fromlist=[self.__class__.__name__]) + def environment_modifications(self, module, spec, dependent_spec): + return EnvironmentModifications() + def setup_dependent_environment(self, module, spec, dependent_spec): """Called before the install() method of dependents. diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py index e2b3654c19..c85e8febf3 100644 --- a/var/spack/repos/builtin/packages/mpich/package.py +++ b/var/spack/repos/builtin/packages/mpich/package.py @@ -46,14 +46,18 @@ class Mpich(Package): provides('mpi@:3.0', when='@3:') provides('mpi@:1.3', when='@1:') + def environment_modifications(self, module, spec, dependent_spec): + env = super(Mpich, self).environment_modifications(module, spec, dependent_spec) + env.set_env('MPICH_CC', os.environ['CC']) + env.set_env('MPICH_CXX', os.environ['CXX']) + env.set_env('MPICH_F77', os.environ['F77']) + env.set_env('MPICH_F90', os.environ['FC']) + env.set_env('MPICH_FC', os.environ['FC']) + return env + def setup_dependent_environment(self, module, spec, dep_spec): """For dependencies, make mpicc's use spack wrapper.""" - os.environ['MPICH_CC'] = os.environ['CC'] - os.environ['MPICH_CXX'] = os.environ['CXX'] - os.environ['MPICH_F77'] = os.environ['F77'] - os.environ['MPICH_F90'] = os.environ['FC'] - os.environ['MPICH_FC'] = os.environ['FC'] - + # FIXME : is this necessary ? Shouldn't this be part of a contract with MPI providers? module.mpicc = join_path(self.prefix.bin, 'mpicc') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py index 22d538560e..6dbf367475 100644 --- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py @@ -46,5 +46,4 @@ class NetlibScalapack(Package): spec['scalapack'].fc_link = '-L%s -lscalapack' % spec['scalapack'].prefix.lib spec['scalapack'].cc_link = spec['scalapack'].fc_link - spec['scalapack'].libraries = [join_path(spec['scalapack'].prefix.lib, - 'libscalapack%s' % lib_suffix)] + spec['scalapack'].libraries = [join_path(spec['scalapack'].prefix.lib, 'libscalapack%s' % lib_suffix)] diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py index e4484af8c5..83a3fe7a4f 100644 --- a/var/spack/repos/builtin/packages/openmpi/package.py +++ b/var/spack/repos/builtin/packages/openmpi/package.py @@ -41,12 +41,14 @@ class Openmpi(Package): def url_for_version(self, version): return "http://www.open-mpi.org/software/ompi/v%s/downloads/openmpi-%s.tar.bz2" % (version.up_to(2), version) - def setup_dependent_environment(self, module, spec, dep_spec): - """For dependencies, make mpicc's use spack wrapper.""" - os.environ['OMPI_CC'] = 'cc' - os.environ['OMPI_CXX'] = 'c++' - os.environ['OMPI_FC'] = 'f90' - os.environ['OMPI_F77'] = 'f77' + def environment_modifications(self, module, spec, dependent_spec): + env = super(Openmpi, self).environment_modifications(module, spec, dependent_spec) + # FIXME : the compilers should point to the current wrappers, not to generic cc etc. + env.set_env('OMPI_CC', 'cc') + env.set_env('OMPI_CXX', 'c++') + env.set_env('OMPI_FC', 'f90') + env.set_env('OMPI_F77', 'f77') + return env def install(self, spec, prefix): config_args = ["--prefix=%s" % prefix, diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index dd240d1ea0..39ced0a120 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -90,6 +90,17 @@ class Python(Package): return os.path.join(self.python_lib_dir, 'site-packages') + def environment_modifications(self, module, spec, dependent_spec): + env = super(Python, self).environment_modifications(module, spec, dependent_spec) + # Set PYTHONPATH to include site-packages dir for the + # extension and any other python extensions it depends on. + python_paths = [] + for d in ext_spec.traverse(): + if d.package.extends(self.spec): + python_paths.append(os.path.join(d.prefix, self.site_packages_dir)) + env.set_env['PYTHONPATH'] = ':'.join(python_paths) + + def setup_dependent_environment(self, module, spec, ext_spec): """Called before python modules' install() methods. @@ -111,15 +122,6 @@ class Python(Package): # Make the site packages directory if it does not exist already. mkdirp(module.site_packages_dir) - # Set PYTHONPATH to include site-packages dir for the - # extension and any other python extensions it depends on. - python_paths = [] - for d in ext_spec.traverse(): - if d.package.extends(self.spec): - python_paths.append(os.path.join(d.prefix, self.site_packages_dir)) - os.environ['PYTHONPATH'] = ':'.join(python_paths) - - # ======================================================================== # Handle specifics of activating and deactivating python modules. # ======================================================================== diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py index 91afa420c1..373623cd95 100644 --- a/var/spack/repos/builtin/packages/qt/package.py +++ b/var/spack/repos/builtin/packages/qt/package.py @@ -52,11 +52,13 @@ class Qt(Package): depends_on("mesa", when='@4:+mesa') depends_on("libxcb") - - def setup_dependent_environment(self, module, spec, dep_spec): - """Dependencies of Qt find it using the QTDIR environment variable.""" - os.environ['QTDIR'] = self.prefix - + def environment_modifications(self, module, spec, dep_spec): + """ + Dependencies of Qt find it using the QTDIR environment variable + """ + env = super(Qt, self).environment_modifications(module, spec, dep_spec) + env.set_env['QTDIR'] = self.prefix + return env def patch(self): if self.spec.satisfies('@4'): diff --git a/var/spack/repos/builtin/packages/ruby/package.py b/var/spack/repos/builtin/packages/ruby/package.py index 6b6242362c..9ec0afa268 100644 --- a/var/spack/repos/builtin/packages/ruby/package.py +++ b/var/spack/repos/builtin/packages/ruby/package.py @@ -15,10 +15,21 @@ class Ruby(Package): def install(self, spec, prefix): configure("--prefix=%s" % prefix) - make() make("install") + def environment_modifications(self, module, spec, ext_spec): + env = super(Ruby, self).environment_modifications(module, spec, ext_spec) + # Set GEM_PATH to include dependent gem directories + ruby_paths = [] + for d in ext_spec.traverse(): + if d.package.extends(self.spec): + ruby_paths.append(d.prefix) + env.set_env('GEM_PATH', concatenate_paths(ruby_paths)) + # The actual installation path for this gem + env.set_env('GEM_HOME', ext_spec.prefix) + return env + def setup_dependent_environment(self, module, spec, ext_spec): """Called before ruby modules' install() methods. Sets GEM_HOME and GEM_PATH to values appropriate for the package being built. @@ -31,11 +42,4 @@ class Ruby(Package): module.ruby = Executable(join_path(spec.prefix.bin, 'ruby')) module.gem = Executable(join_path(spec.prefix.bin, 'gem')) - # Set GEM_PATH to include dependent gem directories - ruby_paths = [] - for d in ext_spec.traverse(): - if d.package.extends(self.spec): - ruby_paths.append(d.prefix) - os.environ['GEM_PATH'] = ':'.join(ruby_paths) - # The actual installation path for this gem - os.environ['GEM_HOME'] = ext_spec.prefix + -- cgit v1.2.3-70-g09d2 From 572cb93bf8131d222d2d08bca13fd9de6fded1f4 Mon Sep 17 00:00:00 2001 From: alalazo Date: Tue, 15 Mar 2016 14:05:30 +0100 Subject: package : renamed `setup_dependent_environment` to `module_modifications` --- lib/spack/spack/build_environment.py | 4 ++-- lib/spack/spack/package.py | 4 ++-- var/spack/repos/builtin/packages/mpich/package.py | 6 +++--- .../repos/builtin/packages/netlib-scalapack/package.py | 2 +- var/spack/repos/builtin/packages/openmpi/package.py | 4 ++-- var/spack/repos/builtin/packages/python/package.py | 10 ++++------ var/spack/repos/builtin/packages/qt/package.py | 7 ++----- var/spack/repos/builtin/packages/ruby/package.py | 13 ++++++------- 8 files changed, 22 insertions(+), 28 deletions(-) (limited to 'var') diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py index d321a0e495..e86a7c413a 100644 --- a/lib/spack/spack/build_environment.py +++ b/lib/spack/spack/build_environment.py @@ -284,8 +284,8 @@ def setup_package(pkg): # Allow dependencies to set up environment as well. for dep_spec in pkg.spec.traverse(root=False): - env.extend(dep_spec.package.environment_modifications(pkg.module, dep_spec, pkg.spec)) - dep_spec.package.setup_dependent_environment(pkg.module, dep_spec, pkg.spec) + dep_spec.package.module_modifications(pkg.module, dep_spec, pkg.spec) + env.extend(dep_spec.package.environment_modifications(pkg.spec)) apply_environment_modifications(env) diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index 224d7f8f4b..c1a5c912be 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -984,10 +984,10 @@ class Package(object): fromlist=[self.__class__.__name__]) - def environment_modifications(self, module, spec, dependent_spec): + def environment_modifications(self, dependent_spec): return EnvironmentModifications() - def setup_dependent_environment(self, module, spec, dependent_spec): + def module_modifications(self, module, spec, dependent_spec): """Called before the install() method of dependents. Default implementation does nothing, but this can be diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py index c85e8febf3..d298981c92 100644 --- a/var/spack/repos/builtin/packages/mpich/package.py +++ b/var/spack/repos/builtin/packages/mpich/package.py @@ -46,8 +46,8 @@ class Mpich(Package): provides('mpi@:3.0', when='@3:') provides('mpi@:1.3', when='@1:') - def environment_modifications(self, module, spec, dependent_spec): - env = super(Mpich, self).environment_modifications(module, spec, dependent_spec) + def environment_modifications(self, dependent_spec): + env = super(Mpich, self).environment_modifications(dependent_spec) env.set_env('MPICH_CC', os.environ['CC']) env.set_env('MPICH_CXX', os.environ['CXX']) env.set_env('MPICH_F77', os.environ['F77']) @@ -55,7 +55,7 @@ class Mpich(Package): env.set_env('MPICH_FC', os.environ['FC']) return env - def setup_dependent_environment(self, module, spec, dep_spec): + def module_modifications(self, module, spec, dep_spec): """For dependencies, make mpicc's use spack wrapper.""" # FIXME : is this necessary ? Shouldn't this be part of a contract with MPI providers? module.mpicc = join_path(self.prefix.bin, 'mpicc') diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py index 6dbf367475..ecdea46442 100644 --- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py @@ -40,7 +40,7 @@ class NetlibScalapack(Package): make() make("install") - def setup_dependent_environment(self, module, spec, dependent_spec): + def module_modifications(self, module, spec, dependent_spec): # TODO treat OS that are not Linux... lib_suffix = '.so' if '+shared' in spec['scalapack'] else '.a' diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py index 83a3fe7a4f..3a14170457 100644 --- a/var/spack/repos/builtin/packages/openmpi/package.py +++ b/var/spack/repos/builtin/packages/openmpi/package.py @@ -41,8 +41,8 @@ class Openmpi(Package): def url_for_version(self, version): return "http://www.open-mpi.org/software/ompi/v%s/downloads/openmpi-%s.tar.bz2" % (version.up_to(2), version) - def environment_modifications(self, module, spec, dependent_spec): - env = super(Openmpi, self).environment_modifications(module, spec, dependent_spec) + def environment_modifications(self, dependent_spec): + env = super(Openmpi, self).environment_modifications(dependent_spec) # FIXME : the compilers should point to the current wrappers, not to generic cc etc. env.set_env('OMPI_CC', 'cc') env.set_env('OMPI_CXX', 'c++') diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index 39ced0a120..307cec726b 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -89,19 +89,17 @@ class Python(Package): def site_packages_dir(self): return os.path.join(self.python_lib_dir, 'site-packages') - - def environment_modifications(self, module, spec, dependent_spec): - env = super(Python, self).environment_modifications(module, spec, dependent_spec) + def environment_modifications(self, extension_spec): + env = super(Python, self).environment_modifications(extension_spec) # Set PYTHONPATH to include site-packages dir for the # extension and any other python extensions it depends on. python_paths = [] - for d in ext_spec.traverse(): + for d in extension_spec.traverse(): if d.package.extends(self.spec): python_paths.append(os.path.join(d.prefix, self.site_packages_dir)) env.set_env['PYTHONPATH'] = ':'.join(python_paths) - - def setup_dependent_environment(self, module, spec, ext_spec): + def module_modifications(self, module, spec, ext_spec): """Called before python modules' install() methods. In most cases, extensions will only need to have one line:: diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py index 373623cd95..8391ded3e0 100644 --- a/var/spack/repos/builtin/packages/qt/package.py +++ b/var/spack/repos/builtin/packages/qt/package.py @@ -52,11 +52,8 @@ class Qt(Package): depends_on("mesa", when='@4:+mesa') depends_on("libxcb") - def environment_modifications(self, module, spec, dep_spec): - """ - Dependencies of Qt find it using the QTDIR environment variable - """ - env = super(Qt, self).environment_modifications(module, spec, dep_spec) + def environment_modifications(self, dependent_spec): + env = super(Qt, self).environment_modifications(dependent_spec) env.set_env['QTDIR'] = self.prefix return env diff --git a/var/spack/repos/builtin/packages/ruby/package.py b/var/spack/repos/builtin/packages/ruby/package.py index 9ec0afa268..9caea30ef4 100644 --- a/var/spack/repos/builtin/packages/ruby/package.py +++ b/var/spack/repos/builtin/packages/ruby/package.py @@ -1,6 +1,5 @@ from spack import * -import spack -import os + class Ruby(Package): """A dynamic, open source programming language with a focus on @@ -18,19 +17,19 @@ class Ruby(Package): make() make("install") - def environment_modifications(self, module, spec, ext_spec): - env = super(Ruby, self).environment_modifications(module, spec, ext_spec) + def environment_modifications(self, extension_spec): + env = super(Ruby, self).environment_modifications(extension_spec) # Set GEM_PATH to include dependent gem directories ruby_paths = [] - for d in ext_spec.traverse(): + for d in extension_spec.traverse(): if d.package.extends(self.spec): ruby_paths.append(d.prefix) env.set_env('GEM_PATH', concatenate_paths(ruby_paths)) # The actual installation path for this gem - env.set_env('GEM_HOME', ext_spec.prefix) + env.set_env('GEM_HOME', extension_spec.prefix) return env - def setup_dependent_environment(self, module, spec, ext_spec): + def module_modifications(self, module, spec, ext_spec): """Called before ruby modules' install() methods. Sets GEM_HOME and GEM_PATH to values appropriate for the package being built. -- cgit v1.2.3-70-g09d2 From b45ec3f04e3627dbe3633239560873ae01bf3beb Mon Sep 17 00:00:00 2001 From: alalazo Date: Wed, 16 Mar 2016 10:55:28 +0100 Subject: environment : simplified modification of the environment --- lib/spack/spack/build_environment.py | 12 +++-- lib/spack/spack/cmd/module.py | 2 +- lib/spack/spack/environment.py | 58 +++++++++++----------- lib/spack/spack/test/environment.py | 12 +++-- lib/spack/spack/util/environment.py | 2 +- var/spack/repos/builtin/packages/python/package.py | 1 + 6 files changed, 47 insertions(+), 40 deletions(-) (limited to 'var') diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py index e86a7c413a..e5d256a2e0 100644 --- a/lib/spack/spack/build_environment.py +++ b/lib/spack/spack/build_environment.py @@ -35,7 +35,7 @@ import sys import spack from llnl.util.filesystem import * -from spack.environment import EnvironmentModifications, apply_environment_modifications, concatenate_paths +from spack.environment import EnvironmentModifications, concatenate_paths from spack.util.environment import * from spack.util.executable import Executable, which @@ -283,10 +283,12 @@ def setup_package(pkg): set_module_variables_for_package(pkg, mod) # Allow dependencies to set up environment as well. - for dep_spec in pkg.spec.traverse(root=False): - dep_spec.package.module_modifications(pkg.module, dep_spec, pkg.spec) - env.extend(dep_spec.package.environment_modifications(pkg.spec)) - apply_environment_modifications(env) + for dependency_spec in pkg.spec.traverse(root=False): + dependency_spec.package.module_modifications(pkg.module, dependency_spec, pkg.spec) + env.extend(dependency_spec.package.environment_modifications(pkg.spec)) + # TODO : implement validation + #validate(env) + env.apply_modifications() def fork(pkg, function): diff --git a/lib/spack/spack/cmd/module.py b/lib/spack/spack/cmd/module.py index 1d6867c1d9..315d9fc926 100644 --- a/lib/spack/spack/cmd/module.py +++ b/lib/spack/spack/cmd/module.py @@ -80,7 +80,7 @@ def module_find(mtype, spec_array): if not os.path.isfile(mod.file_name): tty.die("No %s module is installed for %s" % (mtype, spec)) - print mod.use_name + print(mod.use_name) def module_refresh(): diff --git a/lib/spack/spack/environment.py b/lib/spack/spack/environment.py index 5a68e10c99..b557bf0bbc 100644 --- a/lib/spack/spack/environment.py +++ b/lib/spack/spack/environment.py @@ -158,41 +158,43 @@ class EnvironmentModifications(object): item = RemovePath(name, path, **kwargs) self.env_modifications.append(item) + def group_by_name(self): + """ + Returns a dict of the modifications grouped by variable name + + Returns: + dict mapping the environment variable name to the modifications to be done on it + """ + modifications = collections.defaultdict(list) + for item in self: + modifications[item.name].append(item) + return modifications + + def clear(self): + """ + Clears the current list of modifications + """ + self.env_modifications.clear() + + def apply_modifications(self): + """ + Applies the modifications and clears the list + """ + modifications = self.group_by_name() + # Apply the modifications to the environment variables one variable at a time + for name, actions in sorted(modifications.items()): + for x in actions: + x.execute() + def concatenate_paths(paths): """ - Concatenates an iterable of paths into a column separated string + Concatenates an iterable of paths into a string of column separated paths Args: paths: iterable of paths Returns: - column separated string + string """ return ':'.join(str(item) for item in paths) - - -def validate_environment_modifications(env): - modifications = collections.defaultdict(list) - for item in env: - modifications[item.name].append(item) - # TODO : once we organized the modifications into a dictionary that maps an environment variable - # TODO : to a list of action to be done on it, we may easily spot inconsistencies and warn the user if - # TODO : something suspicious is happening - return modifications - - -def apply_environment_modifications(env): - """ - Modifies the current environment according to the request in env - - Args: - env: object storing modifications to the environment - """ - modifications = validate_environment_modifications(env) - - # Cycle over the environment variables that will be modified - for variable, actions in modifications.items(): - # Execute all the actions in the order they were issued - for x in actions: - x.execute() diff --git a/lib/spack/spack/test/environment.py b/lib/spack/spack/test/environment.py index f44282d6f3..d0b093b054 100644 --- a/lib/spack/spack/test/environment.py +++ b/lib/spack/spack/test/environment.py @@ -1,6 +1,6 @@ import unittest import os -from spack.environment import EnvironmentModifications, apply_environment_modifications +from spack.environment import EnvironmentModifications class EnvironmentTest(unittest.TestCase): @@ -15,7 +15,7 @@ class EnvironmentTest(unittest.TestCase): env = EnvironmentModifications() env.set_env('A', 'dummy value') env.set_env('B', 3) - apply_environment_modifications(env) + env.apply_modifications() self.assertEqual('dummy value', os.environ['A']) self.assertEqual(str(3), os.environ['B']) @@ -23,7 +23,7 @@ class EnvironmentTest(unittest.TestCase): env = EnvironmentModifications() self.assertEqual('foo', os.environ['UNSET_ME']) env.unset_env('UNSET_ME') - apply_environment_modifications(env) + env.apply_modifications() self.assertRaises(KeyError, os.environ.__getitem__, 'UNSET_ME') def test_path_manipulation(self): @@ -43,7 +43,7 @@ class EnvironmentTest(unittest.TestCase): env.remove_path('REMOVE_PATH_LIST', '/remove/this') env.remove_path('REMOVE_PATH_LIST', '/duplicate/') - apply_environment_modifications(env) + env.apply_modifications() self.assertEqual('/path/first:/path/second:/path/third:/path/last', os.environ['PATH_LIST']) self.assertEqual('/path/first:/path/middle:/path/last', os.environ['EMPTY_PATH_LIST']) self.assertEqual('/path/first:/path/middle:/path/last', os.environ['NEWLY_CREATED_PATH_LIST']) @@ -52,7 +52,9 @@ class EnvironmentTest(unittest.TestCase): def test_extra_arguments(self): env = EnvironmentModifications() env.set_env('A', 'dummy value', who='Pkg1') - apply_environment_modifications(env) + for x in env: + assert hasattr(x, 'who') + env.apply_modifications() self.assertEqual('dummy value', os.environ['A']) def test_extend(self): diff --git a/lib/spack/spack/util/environment.py b/lib/spack/spack/util/environment.py index 00cda8d508..1485992b0f 100644 --- a/lib/spack/spack/util/environment.py +++ b/lib/spack/spack/util/environment.py @@ -64,5 +64,5 @@ def path_put_first(var_name, directories): def dump_environment(path): """Dump the current environment out to a file.""" with open(path, 'w') as env_file: - for key,val in sorted(os.environ.items()): + for key, val in sorted(os.environ.items()): env_file.write("%s=%s\n" % (key, val)) diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index 307cec726b..2f9948d451 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -98,6 +98,7 @@ class Python(Package): if d.package.extends(self.spec): python_paths.append(os.path.join(d.prefix, self.site_packages_dir)) env.set_env['PYTHONPATH'] = ':'.join(python_paths) + return env def module_modifications(self, module, spec, ext_spec): """Called before python modules' install() methods. -- cgit v1.2.3-70-g09d2 From 597727f8bedc894330dfd26eab1a82859980f2f1 Mon Sep 17 00:00:00 2001 From: alalazo Date: Wed, 16 Mar 2016 15:19:13 +0100 Subject: tclmodules : added hooks to process EnvironmentModifications objects --- lib/spack/spack/modules.py | 151 +++++++++++++++------ var/spack/repos/builtin/packages/mpich/package.py | 25 +++- var/spack/repos/builtin/packages/python/package.py | 15 +- 3 files changed, 137 insertions(+), 54 deletions(-) (limited to 'var') diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py index c27043db8c..1a0a0fd4d6 100644 --- a/lib/spack/spack/modules.py +++ b/lib/spack/spack/modules.py @@ -47,18 +47,18 @@ of module file. __all__ = ['EnvModule', 'Dotkit', 'TclModule'] import os +import os.path import re -import textwrap import shutil +import textwrap from glob import glob import llnl.util.tty as tty -from llnl.util.filesystem import join_path, mkdirp - import spack +from spack.environment import * +from llnl.util.filesystem import join_path, mkdirp -"""Registry of all types of modules. Entries created by EnvModule's - metaclass.""" +# Registry of all types of modules. Entries created by EnvModule's metaclass module_types = {} @@ -79,6 +79,32 @@ def print_help(): "") +class PathInspector(object): + dirname2varname = { + 'bin': ('PATH',), + 'man': ('MANPATH',), + 'lib': ('LIBRARY_PATH', 'LD_LIBRARY_PATH'), + 'lib64': ('LIBRARY_PATH', 'LD_LIBRARY_PATH'), + 'include': ('CPATH',), + 'pkgconfig': ('PKG_CONFIG_PATH',) + } + + def __call__(self, env, directory, names): + for name in names: + variables = PathInspector.dirname2varname.get(name, None) + if variables is None: + continue + absolute_path = join_path(os.path.abspath(directory), name) + for variable in variables: + env.prepend_path(variable, absolute_path) + + +def inspect_path(path): + env, inspector = EnvironmentModifications(), PathInspector() + os.path.walk(path, inspector, env) + return env + + class EnvModule(object): name = 'env_module' @@ -88,21 +114,27 @@ class EnvModule(object): if cls.name != 'env_module': module_types[cls.name] = cls - def __init__(self, spec=None): # category in the modules system # TODO: come up with smarter category names. self.category = "spack" - # Descriptions for the module system's UI - self.short_description = "" - self.long_description = "" - # dict pathname -> list of directories to be prepended to in # the module file. self._paths = None self.spec = spec + self.pkg = spec.package # Just stored for convenience + + # short description default is just the package + version + # packages can provide this optional attribute + self.short_description = spec.format("$_ $@") + if hasattr(self.pkg, 'short_description'): + self.short_description = self.pkg.short_description + # long description is the docstring with reduced whitespace. + self.long_description = None + if self.spec.package.__doc__: + self.long_description = re.sub(r'\s+', ' ', self.spec.package.__doc__) @property def paths(self): @@ -130,26 +162,19 @@ class EnvModule(object): add_path(var, directory) # Add python path unless it's an actual python installation - # TODO: is there a better way to do this? + # TODO : is there a better way to do this? + # FIXME : add PYTHONPATH to every python package if self.spec.name != 'python': site_packages = glob(join_path(self.spec.prefix.lib, "python*/site-packages")) if site_packages: add_path('PYTHONPATH', site_packages[0]) + # FIXME : Same for GEM_PATH if self.spec.package.extends(spack.spec.Spec('ruby')): - add_path('GEM_PATH', self.spec.prefix) - - # short description is just the package + version - # TODO: maybe packages can optionally provide it. - self.short_description = self.spec.format("$_ $@") - - # long description is the docstring with reduced whitespace. - if self.spec.package.__doc__: - self.long_description = re.sub(r'\s+', ' ', self.spec.package.__doc__) + add_path('GEM_PATH', self.spec.prefix) return self._paths - def write(self): """Write out a module file for this object.""" module_dir = os.path.dirname(self.file_name) @@ -160,9 +185,18 @@ class EnvModule(object): if not self.paths: return - with open(self.file_name, 'w') as f: - self._write(f) + # Construct the changes that needs to be done on the environment for + env = inspect_path(self.spec.prefix) + # FIXME : move the logic to inspection + env.prepend_path('CMAKE_PREFIX_PATH', self.spec.prefix) + # FIXME : decide how to distinguish between calls done in the installation and elsewhere + env.extend(self.spec.package.environment_modifications(None)) + # site_specific = ...` + if not env: + return + with open(self.file_name, 'w') as f: + self._write(f, env) def _write(self, stream): """To be implemented by subclasses.""" @@ -175,14 +209,12 @@ class EnvModule(object): where this module lives.""" raise NotImplementedError() - @property def use_name(self): """Subclasses should implement this to return the name the module command uses to refer to the package.""" raise NotImplementedError() - def remove(self): mod_file = self.file_name if os.path.exists(mod_file): @@ -205,7 +237,7 @@ class Dotkit(EnvModule): self.spec.compiler.version, self.spec.dag_hash()) - def _write(self, dk_file): + def _write(self, dk_file, env): # Category if self.category: dk_file.write('#c %s\n' % self.category) @@ -231,6 +263,10 @@ class Dotkit(EnvModule): class TclModule(EnvModule): name = 'tcl' path = join_path(spack.share_path, "modules") + formats = { + PrependPath: 'prepend-path {0.name} \"{0.path}\"\n', + SetEnv: 'setenv {0.name} \"{0.value}\"\n' + } @property def file_name(self): @@ -244,25 +280,56 @@ class TclModule(EnvModule): self.spec.compiler.version, self.spec.dag_hash()) - - def _write(self, m_file): - # TODO: cateogry? - m_file.write('#%Module1.0\n') - + def process_environment_command(self, env): + for command in env: + # FIXME : how should we handle errors here? + yield self.formats[type(command)].format(command) + + def _write(self, module_file, env): + """ + Writes a TCL module file for this package + + Args: + module_file: module file stream + env: list of environment modifications to be written in the module file + """ + # TCL Modulefile header + module_file.write('#%Module1.0\n') + # TODO : category ? # Short description if self.short_description: - m_file.write('module-whatis \"%s\"\n\n' % self.short_description) + module_file.write('module-whatis \"%s\"\n\n' % self.short_description) # Long description if self.long_description: - m_file.write('proc ModulesHelp { } {\n') + module_file.write('proc ModulesHelp { } {\n') doc = re.sub(r'"', '\"', self.long_description) - m_file.write("puts stderr \"%s\"\n" % doc) - m_file.write('}\n\n') - - # Path alterations - for var, dirs in self.paths.items(): - for directory in dirs: - m_file.write("prepend-path %s \"%s\"\n" % (var, directory)) - - m_file.write("prepend-path CMAKE_PREFIX_PATH \"%s\"\n" % self.spec.prefix) + module_file.write("puts stderr \"%s\"\n" % doc) + module_file.write('}\n\n') + + # Environment modifications + for line in self.process_environment_command(env): + module_file.write(line) + + # FIXME : REMOVE + # def _write(self, m_file): + # # TODO: cateogry? + # m_file.write('#%Module1.0\n') + # + # # Short description + # if self.short_description: + # m_file.write('module-whatis \"%s\"\n\n' % self.short_description) + # + # # Long description + # if self.long_description: + # m_file.write('proc ModulesHelp { } {\n') + # doc = re.sub(r'"', '\"', self.long_description) + # m_file.write("puts stderr \"%s\"\n" % doc) + # m_file.write('}\n\n') + # + # # Path alterations + # for var, dirs in self.paths.items(): + # for directory in dirs: + # m_file.write("prepend-path %s \"%s\"\n" % (var, directory)) + # + # m_file.write("prepend-path CMAKE_PREFIX_PATH \"%s\"\n" % self.spec.prefix) diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py index d298981c92..4c34d0308f 100644 --- a/var/spack/repos/builtin/packages/mpich/package.py +++ b/var/spack/repos/builtin/packages/mpich/package.py @@ -25,6 +25,7 @@ from spack import * import os + class Mpich(Package): """MPICH is a high performance and widely portable implementation of the Message Passing Interface (MPI) standard.""" @@ -48,11 +49,25 @@ class Mpich(Package): def environment_modifications(self, dependent_spec): env = super(Mpich, self).environment_modifications(dependent_spec) - env.set_env('MPICH_CC', os.environ['CC']) - env.set_env('MPICH_CXX', os.environ['CXX']) - env.set_env('MPICH_F77', os.environ['F77']) - env.set_env('MPICH_F90', os.environ['FC']) - env.set_env('MPICH_FC', os.environ['FC']) + + if dependent_spec is None: + # We are not using compiler wrappers + cc = self.compiler.cc + cxx = self.compiler.cxx + f77 = self.compiler.f77 + f90 = fc = self.compiler.fc + else: + # Spack compiler wrappers + cc = os.environ['CC'] + cxx = os.environ['CXX'] + f77 = os.environ['F77'] + f90 = fc = os.environ['FC'] + + env.set_env('MPICH_CC', cc) + env.set_env('MPICH_CXX', cxx) + env.set_env('MPICH_F77', f77) + env.set_env('MPICH_F90', f90) + env.set_env('MPICH_FC', fc) return env def module_modifications(self, module, spec, dep_spec): diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index 2f9948d451..acb3651726 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -91,13 +91,14 @@ class Python(Package): def environment_modifications(self, extension_spec): env = super(Python, self).environment_modifications(extension_spec) - # Set PYTHONPATH to include site-packages dir for the - # extension and any other python extensions it depends on. - python_paths = [] - for d in extension_spec.traverse(): - if d.package.extends(self.spec): - python_paths.append(os.path.join(d.prefix, self.site_packages_dir)) - env.set_env['PYTHONPATH'] = ':'.join(python_paths) + if extension_spec is not None: + # Set PYTHONPATH to include site-packages dir for the + # extension and any other python extensions it depends on. + python_paths = [] + for d in extension_spec.traverse(): + if d.package.extends(self.spec): + python_paths.append(os.path.join(d.prefix, self.site_packages_dir)) + env.set_env['PYTHONPATH'] = ':'.join(python_paths) return env def module_modifications(self, module, spec, ext_spec): -- cgit v1.2.3-70-g09d2 From f07d4c94393f6541d1a6afd9118d3f9c84bd08fc Mon Sep 17 00:00:00 2001 From: "Kelly (KT) Thompson" Date: Wed, 16 Mar 2016 18:55:14 -0600 Subject: + Provide ~perl and ~shared variants. --- var/spack/repos/builtin/packages/graphviz/package.py | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/graphviz/package.py b/var/spack/repos/builtin/packages/graphviz/package.py index 7af7da1881..2a2102bfcb 100644 --- a/var/spack/repos/builtin/packages/graphviz/package.py +++ b/var/spack/repos/builtin/packages/graphviz/package.py @@ -7,6 +7,9 @@ class Graphviz(Package): version('2.38.0', '5b6a829b2ac94efcd5fa3c223ed6d3ae') + variant('perl', default=True, description='Disable if you have problems with the optional script language bindings') + variant('shared', default=True, description='Building static is required on AIX') + parallel = False depends_on("swig") @@ -14,8 +17,12 @@ class Graphviz(Package): depends_on("ghostscript") def install(self, spec, prefix): - configure("--prefix=%s" %prefix) + options = ['--prefix=%s' % prefix] + if '~perl' in spec: + options.append('--disable-perl') + if '~shared' in spec: + options.append('--enable-shared=no') + configure(*options) make() make("install") - -- cgit v1.2.3-70-g09d2 From f0f0663d1b9ece1e2b0b0a8f720b1325eec443bb Mon Sep 17 00:00:00 2001 From: alalazo Date: Thu, 17 Mar 2016 15:11:39 +0100 Subject: package : split `environment_modifications` into `setup_environment` and `setup_dependent_environment`. package : renamed `module_modifications` to `modify_module` for consistency --- lib/spack/spack/build_environment.py | 4 +-- lib/spack/spack/modules.py | 5 ++- lib/spack/spack/package.py | 9 +++-- var/spack/repos/builtin/packages/mpich/package.py | 39 +++++++++------------- .../builtin/packages/netlib-scalapack/package.py | 2 +- .../repos/builtin/packages/openmpi/package.py | 19 ++++++----- var/spack/repos/builtin/packages/python/package.py | 27 +++++++-------- var/spack/repos/builtin/packages/qt/package.py | 4 +-- var/spack/repos/builtin/packages/ruby/package.py | 6 ++-- 9 files changed, 52 insertions(+), 63 deletions(-) (limited to 'var') diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py index e5d256a2e0..68477145fe 100644 --- a/lib/spack/spack/build_environment.py +++ b/lib/spack/spack/build_environment.py @@ -284,8 +284,8 @@ def setup_package(pkg): # Allow dependencies to set up environment as well. for dependency_spec in pkg.spec.traverse(root=False): - dependency_spec.package.module_modifications(pkg.module, dependency_spec, pkg.spec) - env.extend(dependency_spec.package.environment_modifications(pkg.spec)) + dependency_spec.package.modify_module(pkg.module, dependency_spec, pkg.spec) + dependency_spec.package.setup_dependent_environment(env, pkg.spec) # TODO : implement validation #validate(env) env.apply_modifications() diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py index 7e395736e4..09895d8c44 100644 --- a/lib/spack/spack/modules.py +++ b/lib/spack/spack/modules.py @@ -162,9 +162,8 @@ class EnvModule(object): # Environment modifications guessed by inspecting the installation prefix env = inspect_path(self.spec.prefix) # Package-specific environment modifications - # FIXME : decide how to distinguish between calls done in the installation and elsewhere - env.extend(self.spec.package.environment_modifications(None)) - # site_specific = ...` + self.spec.package.setup_environment(env) + # TODO : implement site-specific modifications and filters if not env: return diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index 042833964a..8e56dd1f97 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -977,7 +977,7 @@ class Package(object): fromlist=[self.__class__.__name__]) - def environment_modifications(self, dependent_spec): + def setup_environment(self, env): """ Called before the install() method of dependents. @@ -998,9 +998,12 @@ class Package(object): Returns: instance of environment modifications """ - return EnvironmentModifications() + pass + + def setup_dependent_environment(self, env, dependent_spec): + self.setup_environment(env) - def module_modifications(self, module, spec, dependent_spec): + def modify_module(self, module, spec, dependent_spec): """ Called before the install() method of dependents. diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py index 4c34d0308f..5af9b585ea 100644 --- a/var/spack/repos/builtin/packages/mpich/package.py +++ b/var/spack/repos/builtin/packages/mpich/package.py @@ -47,30 +47,21 @@ class Mpich(Package): provides('mpi@:3.0', when='@3:') provides('mpi@:1.3', when='@1:') - def environment_modifications(self, dependent_spec): - env = super(Mpich, self).environment_modifications(dependent_spec) - - if dependent_spec is None: - # We are not using compiler wrappers - cc = self.compiler.cc - cxx = self.compiler.cxx - f77 = self.compiler.f77 - f90 = fc = self.compiler.fc - else: - # Spack compiler wrappers - cc = os.environ['CC'] - cxx = os.environ['CXX'] - f77 = os.environ['F77'] - f90 = fc = os.environ['FC'] - - env.set_env('MPICH_CC', cc) - env.set_env('MPICH_CXX', cxx) - env.set_env('MPICH_F77', f77) - env.set_env('MPICH_F90', f90) - env.set_env('MPICH_FC', fc) - return env - - def module_modifications(self, module, spec, dep_spec): + def setup_environment(self, env): + env.set_env('MPICH_CC', self.compiler.cc) + env.set_env('MPICH_CXX', self.compiler.cxx) + env.set_env('MPICH_F77', self.compiler.f77) + env.set_env('MPICH_F90', self.compiler.fc) + env.set_env('MPICH_FC', self.compiler.fc) + + def setup_dependent_environment(self, env, dependent_spec): + env.set_env('MPICH_CC', spack_cc) + env.set_env('MPICH_CXX', spack_cxx) + env.set_env('MPICH_F77', spack_f77) + env.set_env('MPICH_F90', spack_f90) + env.set_env('MPICH_FC', spack_fc) + + def modify_module(self, module, spec, dep_spec): """For dependencies, make mpicc's use spack wrapper.""" # FIXME : is this necessary ? Shouldn't this be part of a contract with MPI providers? module.mpicc = join_path(self.prefix.bin, 'mpicc') diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py index ecdea46442..7e7e5b2e2e 100644 --- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py @@ -40,7 +40,7 @@ class NetlibScalapack(Package): make() make("install") - def module_modifications(self, module, spec, dependent_spec): + def modify_module(self, module, spec, dependent_spec): # TODO treat OS that are not Linux... lib_suffix = '.so' if '+shared' in spec['scalapack'] else '.a' diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py index 3a14170457..7783ca8766 100644 --- a/var/spack/repos/builtin/packages/openmpi/package.py +++ b/var/spack/repos/builtin/packages/openmpi/package.py @@ -41,14 +41,17 @@ class Openmpi(Package): def url_for_version(self, version): return "http://www.open-mpi.org/software/ompi/v%s/downloads/openmpi-%s.tar.bz2" % (version.up_to(2), version) - def environment_modifications(self, dependent_spec): - env = super(Openmpi, self).environment_modifications(dependent_spec) - # FIXME : the compilers should point to the current wrappers, not to generic cc etc. - env.set_env('OMPI_CC', 'cc') - env.set_env('OMPI_CXX', 'c++') - env.set_env('OMPI_FC', 'f90') - env.set_env('OMPI_F77', 'f77') - return env + def setup_environment(self, env): + env.set_env('OMPI_CC', self.compiler.cc) + env.set_env('OMPI_CXX', self.compiler.cxx) + env.set_env('OMPI_FC', self.compiler.fc) + env.set_env('OMPI_F77', self.compiler.f77) + + def setup_dependent_environment(self, env, dependent_spec): + env.set_env('OMPI_CC', spack_cc) + env.set_env('OMPI_CXX', spack_cxx) + env.set_env('OMPI_FC', spack_fc) + env.set_env('OMPI_F77', spack_f77) def install(self, spec, prefix): config_args = ["--prefix=%s" % prefix, diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index acb3651726..d47c1d1b2f 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -89,24 +89,21 @@ class Python(Package): def site_packages_dir(self): return os.path.join(self.python_lib_dir, 'site-packages') - def environment_modifications(self, extension_spec): - env = super(Python, self).environment_modifications(extension_spec) - if extension_spec is not None: - # Set PYTHONPATH to include site-packages dir for the - # extension and any other python extensions it depends on. - python_paths = [] - for d in extension_spec.traverse(): - if d.package.extends(self.spec): - python_paths.append(os.path.join(d.prefix, self.site_packages_dir)) - env.set_env['PYTHONPATH'] = ':'.join(python_paths) - return env - - def module_modifications(self, module, spec, ext_spec): - """Called before python modules' install() methods. + def setup_dependent_environment(self, env, extension_spec): + # Set PYTHONPATH to include site-packages dir for the extension and any other python extensions it depends on. + python_paths = [] + for d in extension_spec.traverse(): + if d.package.extends(self.spec): + python_paths.append(os.path.join(d.prefix, self.site_packages_dir)) + env.set_env['PYTHONPATH'] = ':'.join(python_paths) + + def modify_module(self, module, spec, ext_spec): + """ + Called before python modules' install() methods. In most cases, extensions will only need to have one line:: - python('setup.py', 'install', '--prefix=%s' % prefix) + python('setup.py', 'install', '--prefix=%s' % prefix) """ # Python extension builds can have a global python executable function if self.version >= Version("3.0.0") and self.version < Version("4.0.0"): diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py index 0adf352be2..35b9d68462 100644 --- a/var/spack/repos/builtin/packages/qt/package.py +++ b/var/spack/repos/builtin/packages/qt/package.py @@ -55,10 +55,8 @@ class Qt(Package): depends_on("mesa", when='@4:+mesa') depends_on("libxcb") - def environment_modifications(self, dependent_spec): - env = super(Qt, self).environment_modifications(dependent_spec) + def setup_environment(self, env): env.set_env['QTDIR'] = self.prefix - return env def patch(self): if self.spec.satisfies('@4'): diff --git a/var/spack/repos/builtin/packages/ruby/package.py b/var/spack/repos/builtin/packages/ruby/package.py index 9caea30ef4..2d1da8c9af 100644 --- a/var/spack/repos/builtin/packages/ruby/package.py +++ b/var/spack/repos/builtin/packages/ruby/package.py @@ -17,8 +17,7 @@ class Ruby(Package): make() make("install") - def environment_modifications(self, extension_spec): - env = super(Ruby, self).environment_modifications(extension_spec) + def setup_dependent_environment(self, env, extension_spec): # Set GEM_PATH to include dependent gem directories ruby_paths = [] for d in extension_spec.traverse(): @@ -27,9 +26,8 @@ class Ruby(Package): env.set_env('GEM_PATH', concatenate_paths(ruby_paths)) # The actual installation path for this gem env.set_env('GEM_HOME', extension_spec.prefix) - return env - def module_modifications(self, module, spec, ext_spec): + def modify_module(self, module, spec, ext_spec): """Called before ruby modules' install() methods. Sets GEM_HOME and GEM_PATH to values appropriate for the package being built. -- cgit v1.2.3-70-g09d2 From ac394718ec0aa67c468a8529b930eaade0bcbed1 Mon Sep 17 00:00:00 2001 From: alalazo Date: Thu, 17 Mar 2016 18:22:07 +0100 Subject: python : implemented possible solution --- lib/spack/spack/package.py | 11 ++++++++++- var/spack/repos/builtin/packages/py-nose/package.py | 3 ++- 2 files changed, 12 insertions(+), 2 deletions(-) (limited to 'var') diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index d0b94dbbeb..a7ab20137e 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -37,6 +37,7 @@ import os import re import textwrap import time +import glob import llnl.util.tty as tty import spack @@ -55,7 +56,6 @@ from llnl.util.filesystem import * from llnl.util.lang import * from llnl.util.link_tree import LinkTree from llnl.util.tty.log import log_output -from spack.environment import EnvironmentModifications from spack.stage import Stage, ResourceStage, StageComposite from spack.util.compression import allowed_archive from spack.util.environment import dump_environment @@ -1236,6 +1236,15 @@ class Package(object): return " ".join("-Wl,-rpath,%s" % p for p in self.rpath) +class PythonExtension(Package): + def setup_dependent_environment(self, env, dependent_spec): + pass + + def setup_environment(self, env): + site_packages = glob.glob(join_path(self.spec.prefix.lib, "python*/site-packages")) + if site_packages: + env.prepend_path('PYTHONPATH', site_packages[0]) + def validate_package_url(url_string): """Determine whether spack can handle a particular URL or not.""" url = urlparse(url_string) diff --git a/var/spack/repos/builtin/packages/py-nose/package.py b/var/spack/repos/builtin/packages/py-nose/package.py index e7c6cf0264..e817b8eb51 100644 --- a/var/spack/repos/builtin/packages/py-nose/package.py +++ b/var/spack/repos/builtin/packages/py-nose/package.py @@ -1,6 +1,7 @@ from spack import * +from spack.package import PythonExtension -class PyNose(Package): +class PyNose(PythonExtension): """nose extends the test loading and running features of unittest, making it easier to write, find and run tests.""" -- cgit v1.2.3-70-g09d2 From e55880904376847ce767770344059eef1ba7707c Mon Sep 17 00:00:00 2001 From: alalazo Date: Thu, 17 Mar 2016 19:32:31 +0100 Subject: python : fixed typo --- var/spack/repos/builtin/packages/python/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index d47c1d1b2f..d46e1068b6 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -95,7 +95,7 @@ class Python(Package): for d in extension_spec.traverse(): if d.package.extends(self.spec): python_paths.append(os.path.join(d.prefix, self.site_packages_dir)) - env.set_env['PYTHONPATH'] = ':'.join(python_paths) + env.set_env('PYTHONPATH', ':'.join(python_paths)) def modify_module(self, module, spec, ext_spec): """ -- cgit v1.2.3-70-g09d2 From 4cf4bf3a0343fc93d6f0c14dd89956fa03b8f738 Mon Sep 17 00:00:00 2001 From: alalazo Date: Fri, 18 Mar 2016 11:05:59 +0100 Subject: openssl : solved glitch to prevent spack to freeze when the network is unreachable --- .../repos/builtin/packages/openssl/package.py | 29 +++++++++++++--------- 1 file changed, 17 insertions(+), 12 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py index 70afaf4038..22d538531a 100644 --- a/var/spack/repos/builtin/packages/openssl/package.py +++ b/var/spack/repos/builtin/packages/openssl/package.py @@ -1,4 +1,4 @@ -import urllib +import urllib2 import llnl.util.tty as tty from spack import * @@ -37,17 +37,22 @@ class Openssl(Package): version_number = '.'.join([str(x) for x in version[:-1]]) older_url = older.format(version_number=version_number, version_full=version) latest_url = latest.format(version=version) - response = urllib.urlopen(latest.format(version=version)) - if response.getcode() == 404: - openssl_url = older_url - # Checks if we already warned the user for this particular version of OpenSSL. - # If not we display a warning message and mark this version - if not warnings_given_to_user.get(version, False): - tty.warn('This installation depends on an old version of OpenSSL, which may have known security issues. ') - tty.warn('Consider updating to the latest version of this package.') - tty.warn('More details at {homepage}'.format(homepage=Openssl.homepage)) - warnings_given_to_user[version] = True - else: + try: + response = urllib2.urlopen(latest.format(version=version), timeout=5) + if response.getcode() == 404: + openssl_url = older_url + # Checks if we already warned the user for this particular version of OpenSSL. + # If not we display a warning message and mark this version + if not warnings_given_to_user.get(version, False): + tty.warn('This installation depends on an old version of OpenSSL, which may have known security issues. ') + tty.warn('Consider updating to the latest version of this package.') + tty.warn('More details at {homepage}'.format(homepage=Openssl.homepage)) + warnings_given_to_user[version] = True + else: + openssl_url = latest_url + except urllib2.URLError: + tty.warn('Cannot connect to network to retrieve OpenSSL version. Using default url.') + warnings_given_to_user[version] = True openssl_url = latest_url # Store the computed URL openssl_urls[version] = openssl_url -- cgit v1.2.3-70-g09d2 From 3b24db92b5ea64814b1294fc6c9c982bbaa9b3c6 Mon Sep 17 00:00:00 2001 From: Erik Schnetter Date: Thu, 17 Mar 2016 13:43:40 -0400 Subject: Update PAPI to 5.4.3 --- var/spack/repos/builtin/packages/papi/package.py | 1 + 1 file changed, 1 insertion(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/papi/package.py b/var/spack/repos/builtin/packages/papi/package.py index 910e0aa9f9..53d69e28d9 100644 --- a/var/spack/repos/builtin/packages/papi/package.py +++ b/var/spack/repos/builtin/packages/papi/package.py @@ -13,6 +13,7 @@ class Papi(Package): homepage = "http://icl.cs.utk.edu/papi/index.html" url = "http://icl.cs.utk.edu/projects/papi/downloads/papi-5.4.1.tar.gz" + version('5.4.3', '3211b5a5bb389fe692370f5cf4cc2412') version('5.4.1', '9134a99219c79767a11463a76b0b01a2') version('5.3.0', '367961dd0ab426e5ae367c2713924ffb') -- cgit v1.2.3-70-g09d2 From ec8cc2b52839007f0825815c8cfdee8f9a8629a6 Mon Sep 17 00:00:00 2001 From: alalazo Date: Fri, 18 Mar 2016 14:40:53 +0100 Subject: PYTHONPATH : python patches methods for its extensions --- lib/spack/spack/build_environment.py | 4 ++- lib/spack/spack/cmd/uninstall.py | 12 ++++---- lib/spack/spack/directory_layout.py | 2 +- lib/spack/spack/modules.py | 12 ++++++-- lib/spack/spack/package.py | 10 ------- .../repos/builtin/packages/py-nose/package.py | 6 ++-- var/spack/repos/builtin/packages/python/package.py | 34 ++++++++++++++++++++-- 7 files changed, 53 insertions(+), 27 deletions(-) (limited to 'var') diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py index 68477145fe..c51fa58477 100644 --- a/lib/spack/spack/build_environment.py +++ b/lib/spack/spack/build_environment.py @@ -282,9 +282,11 @@ def setup_package(pkg): for mod in modules: set_module_variables_for_package(pkg, mod) - # Allow dependencies to set up environment as well. + # Allow dependencies to modify the module for dependency_spec in pkg.spec.traverse(root=False): dependency_spec.package.modify_module(pkg.module, dependency_spec, pkg.spec) + # Allow dependencies to set up environment as well + for dependency_spec in pkg.spec.traverse(root=False): dependency_spec.package.setup_dependent_environment(env, pkg.spec) # TODO : implement validation #validate(env) diff --git a/lib/spack/spack/cmd/uninstall.py b/lib/spack/spack/cmd/uninstall.py index d01aa2136b..2fab8f6f2a 100644 --- a/lib/spack/spack/cmd/uninstall.py +++ b/lib/spack/spack/cmd/uninstall.py @@ -79,7 +79,7 @@ def uninstall(parser, args): try: # should work if package is known to spack pkgs.append(s.package) - except spack.repository.UnknownPackageError, e: + except spack.repository.UnknownPackageError as e: # The package.py file has gone away -- but still # want to uninstall. spack.Package(s).do_uninstall(force=True) @@ -94,11 +94,11 @@ def uninstall(parser, args): for pkg in pkgs: try: pkg.do_uninstall(force=args.force) - except PackageStillNeededError, e: + except PackageStillNeededError as e: tty.error("Will not uninstall %s" % e.spec.format("$_$@$%@$#", color=True)) - print - print "The following packages depend on it:" + print() + print("The following packages depend on it:") display_specs(e.dependents, long=True) - print - print "You can use spack uninstall -f to force this action." + print() + print("You can use spack uninstall -f to force this action.") sys.exit(1) diff --git a/lib/spack/spack/directory_layout.py b/lib/spack/spack/directory_layout.py index 39ee4e203d..da8f1aa1bc 100644 --- a/lib/spack/spack/directory_layout.py +++ b/lib/spack/spack/directory_layout.py @@ -150,7 +150,7 @@ class DirectoryLayout(object): if os.path.exists(path): try: shutil.rmtree(path) - except exceptions.OSError, e: + except exceptions.OSError as e: raise RemoveFailedError(spec, path, e) path = os.path.dirname(path) diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py index d192bbe004..7303844229 100644 --- a/lib/spack/spack/modules.py +++ b/lib/spack/spack/modules.py @@ -119,13 +119,13 @@ class EnvModule(object): module_types[cls.name] = cls def __init__(self, spec=None): + self.spec = spec + self.pkg = spec.package # Just stored for convenience + # category in the modules system # TODO: come up with smarter category names. self.category = "spack" - self.spec = spec - self.pkg = spec.package # Just stored for convenience - # short description default is just the package + version # packages can provide this optional attribute self.short_description = spec.format("$_ $@") @@ -161,6 +161,12 @@ class EnvModule(object): # Environment modifications guessed by inspecting the installation prefix env = inspect_path(self.spec.prefix) + + # Let the extendee modify their extensions before asking for package-specific modifications + for extendee in self.pkg.extendees: + extendee_spec = self.spec[extendee] + extendee_spec.package.modify_module(self.pkg, extendee_spec, self.spec) + # Package-specific environment modifications self.spec.package.setup_environment(env) # TODO : implement site-specific modifications and filters diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index 185e3ad2ee..72c84ec624 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -1261,16 +1261,6 @@ class Package(object): """Get the rpath args as a string, with -Wl,-rpath, for each element.""" return " ".join("-Wl,-rpath,%s" % p for p in self.rpath) - -class PythonExtension(Package): - def setup_dependent_environment(self, env, dependent_spec): - pass - - def setup_environment(self, env): - site_packages = glob.glob(join_path(self.spec.prefix.lib, "python*/site-packages")) - if site_packages: - env.prepend_path('PYTHONPATH', site_packages[0]) - def validate_package_url(url_string): """Determine whether spack can handle a particular URL or not.""" url = urlparse(url_string) diff --git a/var/spack/repos/builtin/packages/py-nose/package.py b/var/spack/repos/builtin/packages/py-nose/package.py index e817b8eb51..4fee99098e 100644 --- a/var/spack/repos/builtin/packages/py-nose/package.py +++ b/var/spack/repos/builtin/packages/py-nose/package.py @@ -1,12 +1,12 @@ from spack import * -from spack.package import PythonExtension -class PyNose(PythonExtension): + +class PyNose(Package): """nose extends the test loading and running features of unittest, making it easier to write, find and run tests.""" homepage = "https://pypi.python.org/pypi/nose" - url = "https://pypi.python.org/packages/source/n/nose/nose-1.3.4.tar.gz" + url = "https://pypi.python.org/packages/source/n/nose/nose-1.3.4.tar.gz" version('1.3.4', '6ed7169887580ddc9a8e16048d38274d') version('1.3.6', '0ca546d81ca8309080fc80cb389e7a16') diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index d46e1068b6..c445d26369 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -1,11 +1,14 @@ +import functools +import glob +import inspect import os import re from contextlib import closing -from llnl.util.lang import match_predicate -from spack.util.environment import * -from spack import * import spack +from llnl.util.lang import match_predicate +from spack import * +from spack.util.environment import * class Python(Package): @@ -111,6 +114,31 @@ class Python(Package): else: module.python = Executable(join_path(spec.prefix.bin, 'python')) + # The code below patches the any python extension to have good defaults for `setup_dependent_environment` and + # `setup_environment` only if the extension didn't override any of these functions explicitly. + def _setup_env(self, env): + site_packages = glob.glob(join_path(self.spec.prefix.lib, "python*/site-packages")) + if site_packages: + env.prepend_path('PYTHONPATH', site_packages[0]) + + def _setup_denv(self, env, extension_spec): + pass + + pkg_cls = type(ext_spec.package) # Retrieve the type we may want to patch + if 'python' in pkg_cls.extendees: + # List of overrides we are interested in + interesting_overrides = ['setup_environment', 'setup_dependent_environment'] + overrides_found = [ + (name, defining_cls) for name, _, defining_cls, _, in inspect.classify_class_attrs(pkg_cls) + if + name in interesting_overrides and # The attribute has the right name + issubclass(defining_cls, Package) and defining_cls is not Package # and is an actual override + ] + if not overrides_found: + # If no override were found go on patching + pkg_cls.setup_environment = functools.wraps(Package.setup_environment)(_setup_env) + pkg_cls.setup_dependent_environment = functools.wraps(Package.setup_dependent_environment)(_setup_denv) + # Add variables for lib/pythonX.Y and lib/pythonX.Y/site-packages dirs. module.python_lib_dir = os.path.join(ext_spec.prefix, self.python_lib_dir) module.python_include_dir = os.path.join(ext_spec.prefix, self.python_include_dir) -- cgit v1.2.3-70-g09d2 From 5f6f2d5f51fc3700dce13c6aa035943bbc42f6f7 Mon Sep 17 00:00:00 2001 From: alalazo Date: Fri, 18 Mar 2016 14:42:24 +0100 Subject: Revert "openssl : solved glitch to prevent spack to freeze when the network is unreachable" This reverts commit 4cf4bf3a0343fc93d6f0c14dd89956fa03b8f738. --- .../repos/builtin/packages/openssl/package.py | 29 +++++++++------------- 1 file changed, 12 insertions(+), 17 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py index 22d538531a..70afaf4038 100644 --- a/var/spack/repos/builtin/packages/openssl/package.py +++ b/var/spack/repos/builtin/packages/openssl/package.py @@ -1,4 +1,4 @@ -import urllib2 +import urllib import llnl.util.tty as tty from spack import * @@ -37,22 +37,17 @@ class Openssl(Package): version_number = '.'.join([str(x) for x in version[:-1]]) older_url = older.format(version_number=version_number, version_full=version) latest_url = latest.format(version=version) - try: - response = urllib2.urlopen(latest.format(version=version), timeout=5) - if response.getcode() == 404: - openssl_url = older_url - # Checks if we already warned the user for this particular version of OpenSSL. - # If not we display a warning message and mark this version - if not warnings_given_to_user.get(version, False): - tty.warn('This installation depends on an old version of OpenSSL, which may have known security issues. ') - tty.warn('Consider updating to the latest version of this package.') - tty.warn('More details at {homepage}'.format(homepage=Openssl.homepage)) - warnings_given_to_user[version] = True - else: - openssl_url = latest_url - except urllib2.URLError: - tty.warn('Cannot connect to network to retrieve OpenSSL version. Using default url.') - warnings_given_to_user[version] = True + response = urllib.urlopen(latest.format(version=version)) + if response.getcode() == 404: + openssl_url = older_url + # Checks if we already warned the user for this particular version of OpenSSL. + # If not we display a warning message and mark this version + if not warnings_given_to_user.get(version, False): + tty.warn('This installation depends on an old version of OpenSSL, which may have known security issues. ') + tty.warn('Consider updating to the latest version of this package.') + tty.warn('More details at {homepage}'.format(homepage=Openssl.homepage)) + warnings_given_to_user[version] = True + else: openssl_url = latest_url # Store the computed URL openssl_urls[version] = openssl_url -- cgit v1.2.3-70-g09d2 From ed0b5e649dd6bc480e3faa6ffcca121eb9e264b8 Mon Sep 17 00:00:00 2001 From: "Kelly (KT) Thompson" Date: Fri, 18 Mar 2016 15:54:26 -0600 Subject: + Provide fpic variant for netlib-lapack. --- var/spack/repos/builtin/packages/netlib-lapack/package.py | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/netlib-lapack/package.py b/var/spack/repos/builtin/packages/netlib-lapack/package.py index 741f4af421..78c5a053fe 100644 --- a/var/spack/repos/builtin/packages/netlib-lapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-lapack/package.py @@ -20,13 +20,13 @@ class NetlibLapack(Package): version('3.3.1', 'd0d533ec9a5b74933c2a1e84eedc58b4') variant('shared', default=False, description="Build shared library version") + variant('fpic', default=False, description="Build with -fpic compiler option") # virtual dependency provides('lapack') # blas is a virtual dependency. depends_on('blas') - depends_on('cmake') # Doesn't always build correctly in parallel @@ -37,24 +37,23 @@ class NetlibLapack(Package): blas = self.spec['netlib-blas'] return [join_path(blas.prefix.lib, 'blas.a')] - @when('^atlas') def get_blas_libs(self): blas = self.spec['atlas'] return [join_path(blas.prefix.lib, l) for l in ('libf77blas.a', 'libatlas.a')] - def install(self, spec, prefix): blas_libs = ";".join(self.get_blas_libs()) cmake_args = [".", '-DBLAS_LIBRARIES=' + blas_libs] if '+shared' in spec: cmake_args.append('-DBUILD_SHARED_LIBS=ON') + if '+fpic' in spec: + cmake_args.append('-DCMAKE_POSITION_INDEPENDENT_CODE=ON') cmake_args += std_cmake_args cmake(*cmake_args) make() make("install") - -- cgit v1.2.3-70-g09d2 From 620c120503c8c23d10feb14e14d37dfc36f4befb Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Sat, 19 Mar 2016 19:32:44 +0100 Subject: fix openblas suffix for OS-X --- var/spack/repos/builtin/packages/openblas/package.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py index e16d3fe89c..781a1e2ec8 100644 --- a/var/spack/repos/builtin/packages/openblas/package.py +++ b/var/spack/repos/builtin/packages/openblas/package.py @@ -1,4 +1,5 @@ from spack import * +import sys class Openblas(Package): """OpenBLAS: An optimized BLAS library""" @@ -16,13 +17,14 @@ class Openblas(Package): make('libs', 'netlib', 'shared', 'CC=cc', 'FC=f77') make('install', "PREFIX='%s'" % prefix) + lib_dsuffix = 'dylib' if sys.platform == 'darwin' else 'so' # Blas virtual package should provide blas.a and libblas.a with working_dir(prefix.lib): symlink('libopenblas.a', 'blas.a') symlink('libopenblas.a', 'libblas.a') - symlink('libopenblas.so', 'libblas.so') + symlink('libopenblas.%s' % lib_dsuffix, 'libblas.%s' % lib_dsuffix) # Lapack virtual package should provide liblapack.a with working_dir(prefix.lib): symlink('libopenblas.a', 'liblapack.a') - symlink('libopenblas.so', 'liblapack.so') + symlink('libopenblas.%s' % lib_dsuffix, 'liblapack.%s' % lib_dsuffix) -- cgit v1.2.3-70-g09d2 From 95ad2875b6bb4dc15eb43b44c1dbdd521c843119 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Sun, 20 Mar 2016 09:25:02 +0100 Subject: fix scalapack suffix for osx --- var/spack/repos/builtin/packages/netlib-scalapack/package.py | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py index 22d538560e..a5b6eedafb 100644 --- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py @@ -1,8 +1,9 @@ from spack import * +import sys class NetlibScalapack(Package): """ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines""" - + homepage = "http://www.netlib.org/scalapack/" url = "http://www.netlib.org/scalapack/scalapack-2.0.2.tgz" @@ -32,17 +33,17 @@ class NetlibScalapack(Package): "-DCMAKE_C_FLAGS=-fPIC", "-DCMAKE_Fortran_FLAGS=-fPIC" ]) - + options.extend(std_cmake_args) - + with working_dir('spack-build', create=True): cmake('..', *options) make() make("install") def setup_dependent_environment(self, module, spec, dependent_spec): - # TODO treat OS that are not Linux... - lib_suffix = '.so' if '+shared' in spec['scalapack'] else '.a' + lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so' + lib_suffix = lib_dsuffix if '+shared' in spec['scalapack'] else '.a' spec['scalapack'].fc_link = '-L%s -lscalapack' % spec['scalapack'].prefix.lib spec['scalapack'].cc_link = spec['scalapack'].fc_link -- cgit v1.2.3-70-g09d2 From db61a09cf14cc791d7692aac0329e8958b228fb6 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Fri, 18 Mar 2016 16:28:36 +0100 Subject: fix mumps: when installed with parmetis has to be linked with metis --- var/spack/repos/builtin/packages/mumps/package.py | 28 +++++++++++++---------- 1 file changed, 16 insertions(+), 12 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py index 44a37903cc..5c120c37df 100644 --- a/var/spack/repos/builtin/packages/mumps/package.py +++ b/var/spack/repos/builtin/packages/mumps/package.py @@ -20,10 +20,10 @@ class Mumps(Package): variant('complex', default=True, description='Activate the compilation of cmumps and/or zmumps') variant('idx64', default=False, description='Use int64_t/integer*8 as default index type') - + depends_on('scotch + esmumps', when='~ptscotch+scotch') depends_on('scotch + esmumps + mpi', when='+ptscotch') - depends_on('metis', when='~parmetis+metis') + depends_on('metis', when='+metis') depends_on('parmetis', when="+parmetis") depends_on('blas') depends_on('lapack') @@ -38,11 +38,11 @@ class Mumps(Package): def write_makefile_inc(self): if ('+parmetis' in self.spec or '+ptscotch' in self.spec) and '+mpi' not in self.spec: raise RuntimeError('You cannot use the variants parmetis or ptscotch without mpi') - + makefile_conf = ["LIBBLAS = -L%s -lblas" % self.spec['blas'].prefix.lib] orderings = ['-Dpord'] - + if '+ptscotch' in self.spec or '+scotch' in self.spec: join_lib = ' -l%s' % ('pt' if '+ptscotch' in self.spec else '') makefile_conf.extend( @@ -54,15 +54,19 @@ class Mumps(Package): if '+ptscotch' in self.spec: orderings.append('-Dptscotch') - if '+parmetis' in self.spec or '+metis' in self.spec: + if '+parmetis' in self.spec and '+metis' in self.spec: libname = 'parmetis' if '+parmetis' in self.spec else 'metis' makefile_conf.extend( - ["IMETIS = -I%s" % self.spec[libname].prefix.include, - "LMETIS = -L%s -l%s" % (self.spec[libname].prefix.lib, libname)]) + ["IMETIS = -I%s" % self.spec['parmetis'].prefix.include, + "LMETIS = -L%s -l%s -L%s -l%s" % (self.spec['parmetis'].prefix.lib, 'parmetis',self.spec['metis'].prefix.lib, 'metis')]) + + orderings.append('-Dparmetis') + elif '+metis' in self.spec: + makefile_conf.extend( + ["IMETIS = -I%s" % self.spec['metis'].prefix.include, + "LMETIS = -L%s -l%s" % (self.spec['metis'].prefix.lib, 'metis')]) orderings.append('-Dmetis') - if '+parmetis' in self.spec: - orderings.append('-Dparmetis') makefile_conf.append("ORDERINGSF = %s" % (' '.join(orderings))) @@ -101,12 +105,12 @@ class Mumps(Package): # compiler possible values are -DAdd_, -DAdd__ and/or -DUPPER makefile_conf.append("CDEFS = -DAdd_") - + makefile_inc_template = join_path(os.path.dirname(self.module.__file__), 'Makefile.inc') with open(makefile_inc_template, "r") as fh: makefile_conf.extend(fh.read().split('\n')) - + with working_dir('.'): with open("Makefile.inc", "w") as fh: makefile_inc = '\n'.join(makefile_conf) @@ -130,7 +134,7 @@ class Mumps(Package): make_libs.append('zexamples') self.write_makefile_inc() - + make(*make_libs) install_tree('lib', prefix.lib) -- cgit v1.2.3-70-g09d2 From d493658a583231eeb778613cf7b6c8c8641c63a0 Mon Sep 17 00:00:00 2001 From: Cyrus Harrison Date: Sun, 20 Mar 2016 15:18:36 -0700 Subject: cmake package: add variant for openssl support The openssl variant defaults to true to preserve spack's current CMake configuration, which is using OpenSSL. Signed-off-by: Cyrus Harrison --- var/spack/repos/builtin/packages/cmake/package.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py index cc93c7067c..be930a90ab 100644 --- a/var/spack/repos/builtin/packages/cmake/package.py +++ b/var/spack/repos/builtin/packages/cmake/package.py @@ -38,6 +38,7 @@ class Cmake(Package): version('2.8.10.2', '097278785da7182ec0aea8769d06860c') variant('ncurses', default=True, description='Enables the build of the ncurses gui') + variant('openssl', default=True, description="Enables CMake's OpenSSL features") variant('qt', default=False, description='Enables the build of cmake-gui') variant('doc', default=False, description='Enables the generation of html and man page documentation') @@ -77,8 +78,9 @@ class Cmake(Package): options.append('--sphinx-html') options.append('--sphinx-man') - options.append('--') - options.append('-DCMAKE_USE_OPENSSL=ON') + if '+openssl' in spec: + options.append('--') + options.append('-DCMAKE_USE_OPENSSL=ON') configure(*options) make() -- cgit v1.2.3-70-g09d2 From bba66cbe2836e364b58a611a5a5f5ae0d9692df4 Mon Sep 17 00:00:00 2001 From: Cyrus Harrison Date: Sun, 20 Mar 2016 19:27:22 -0700 Subject: cmake: depend on openssl when openssl variant=true --- var/spack/repos/builtin/packages/cmake/package.py | 1 + 1 file changed, 1 insertion(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py index be930a90ab..1f93d39769 100644 --- a/var/spack/repos/builtin/packages/cmake/package.py +++ b/var/spack/repos/builtin/packages/cmake/package.py @@ -43,6 +43,7 @@ class Cmake(Package): variant('doc', default=False, description='Enables the generation of html and man page documentation') depends_on('ncurses', when='+ncurses') + depends_on('openssl', when='+openssl') depends_on('qt', when='+qt') depends_on('python@2.7.11:', when='+doc') depends_on('py-sphinx', when='+doc') -- cgit v1.2.3-70-g09d2 From 7b283bfaffa5509915d91392878203bba8a8d2cb Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Mon, 21 Mar 2016 07:48:17 +0100 Subject: fix petsc on osx --- var/spack/repos/builtin/packages/petsc/package.py | 20 +++++++++++++++----- 1 file changed, 15 insertions(+), 5 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py index efe172fc08..7239baaf7f 100644 --- a/var/spack/repos/builtin/packages/petsc/package.py +++ b/var/spack/repos/builtin/packages/petsc/package.py @@ -61,14 +61,24 @@ class Petsc(Package): errors = ['incompatible variants given'] + errors raise RuntimeError('\n'.join(errors)) else: - compiler_opts = [ - '--with-mpi=1', - '--with-mpi-dir=%s' % self.spec['mpi'].prefix, - ] + if self.compiler.name == "clang": + compiler_opts = [ + '--with-mpi=1', + '--with-cc=%s -Qunused-arguments' % join_path(self.spec['mpi'].prefix.bin, 'mpicc'), # Avoid confusing PETSc config by clang: warning: argument unused during compilation + '--with-cxx=%s -Qunused-arguments' % join_path(self.spec['mpi'].prefix.bin, 'mpic++'), + '--with-fc=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif90'), + '--with-f77=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif77'), + ] + else: + compiler_opts = [ + '--with-mpi=1', + '--with-mpi-dir=%s' % self.spec['mpi'].prefix, + ] return compiler_opts def install(self, spec, prefix): - options = [] + options = ['--with-debugging=0', + '--with-ssl=0'] options.extend(self.mpi_dependent_options()) options.extend([ '--with-precision=%s' % ('double' if '+double' in spec else 'single'), -- cgit v1.2.3-70-g09d2 From b926d8a0cdcf47de029e372cf15e281266930378 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Mon, 21 Mar 2016 14:33:00 +0100 Subject: build parmetis against external metis --- .../packages/parmetis/enable_external_metis.patch | 13 ++++++++++++ .../repos/builtin/packages/parmetis/package.py | 24 ++++------------------ 2 files changed, 17 insertions(+), 20 deletions(-) create mode 100644 var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch (limited to 'var') diff --git a/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch b/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch new file mode 100644 index 0000000000..514781b8b8 --- /dev/null +++ b/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch @@ -0,0 +1,13 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index ca945dd..1bf94e9 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -33,7 +33,7 @@ include_directories(${GKLIB_PATH}) + include_directories(${METIS_PATH}/include) + + # List of directories that cmake will look for CMakeLists.txt +-add_subdirectory(${METIS_PATH}/libmetis ${CMAKE_BINARY_DIR}/libmetis) ++#add_subdirectory(${METIS_PATH}/libmetis ${CMAKE_BINARY_DIR}/libmetis) + add_subdirectory(include) + add_subdirectory(libparmetis) + add_subdirectory(programs) diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py index c897dec7e4..3f18dd76b8 100644 --- a/var/spack/repos/builtin/packages/parmetis/package.py +++ b/var/spack/repos/builtin/packages/parmetis/package.py @@ -25,9 +25,6 @@ from spack import * -# FIXME : lot of code is duplicated from packages/metis/package.py . Inheriting from there may reduce -# FIXME : the installation rules to just a few lines - class Parmetis(Package): """ @@ -43,13 +40,11 @@ class Parmetis(Package): variant('debug', default=False, description='Builds the library in debug mode') variant('gdb', default=False, description='Enables gdb support') - variant('idx64', default=False, description='Use int64_t as default index type') - variant('double', default=False, description='Use double precision floating point types') - depends_on('cmake @2.8:') # build dependency depends_on('mpi') - # FIXME : this should conflict with metis as it builds its own version internally + patch('enable_external_metis.patch') + depends_on('metis') depends_on('gdb', when='+gdb') @@ -63,8 +58,8 @@ class Parmetis(Package): # FIXME : Once a contract is defined, MPI compilers should be retrieved indirectly via spec['mpi'] in case # FIXME : they use a non-standard name - options.extend(['-DGKLIB_PATH:PATH={metis_source}/GKlib'.format(metis_source=metis_source), - '-DMETIS_PATH:PATH={metis_source}'.format(metis_source=metis_source), + options.extend(['-DGKLIB_PATH:PATH={metis_source}/GKlib'.format(metis_source=metis_source), # still need headers from METIS source, and they are not installed with METIS. shame... + '-DMETIS_PATH:PATH={metis_source}'.format(metis_source=spec['metis'].prefix), '-DCMAKE_C_COMPILER:STRING=mpicc', '-DCMAKE_CXX_COMPILER:STRING=mpicxx']) @@ -78,18 +73,7 @@ class Parmetis(Package): if '+gdb' in spec: options.append('-DGDB:BOOL=ON') - metis_header = join_path(metis_source, 'include', 'metis.h') - - if '+idx64' in spec: - filter_file('IDXTYPEWIDTH 32', 'IDXTYPEWIDTH 64', metis_header) - - if '+double' in spec: - filter_file('REALTYPEWIDTH 32', 'REALTYPEWIDTH 64', metis_header) - with working_dir(build_directory, create=True): cmake(source_directory, *options) make() make("install") - # Parmetis build system doesn't allow for an external metis to be used, but doesn't copy the required - # metis header either - install(metis_header, self.prefix.include) -- cgit v1.2.3-70-g09d2 From 3fcaf5b9031c3d55b152844b97cd432078340f4b Mon Sep 17 00:00:00 2001 From: alalazo Date: Mon, 21 Mar 2016 14:47:05 +0100 Subject: llvm : update to 3.8.0 --- var/spack/repos/builtin/packages/llvm/package.py | 15 +++++++++++++++ 1 file changed, 15 insertions(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py index 280e400f69..5c38b5b88c 100644 --- a/var/spack/repos/builtin/packages/llvm/package.py +++ b/var/spack/repos/builtin/packages/llvm/package.py @@ -132,6 +132,21 @@ class Llvm(Package): 'llvm-libunwind' : 'http://llvm.org/svn/llvm-project/libunwind/trunk', } }, + { + 'version' : '3.8.0', + 'md5':'07a7a74f3c6bd65de4702bf941b511a0', + 'resources' : { + 'compiler-rt' : 'd6fcbe14352ffb708e4d1ac2e48bb025', + 'openmp' : '8fd7cc35d48051613cf1e750e9f22e40', + 'polly' : '1b3b20f52d34a4024e21a4ea7112caa7', + 'libcxx' : 'd6e0bdbbee39f7907ad74fd56d03b88a', + 'libcxxabi' : 'bbe6b4d72c7c5978550d370af529bcf7', + 'clang' : 'cc99e7019bb74e6459e80863606250c5', + 'clang-tools-extra' : 'c2344f50e0eea0b402f0092a80ddc036', + 'lldb' : 'a5da35ed9cc8c8817ee854e3dbfba00e', + 'llvm-libunwind' : '162ade468607f153cca12be90b5194fa', + } + }, { 'version' : '3.7.1', 'md5':'bf8b3a2c79e61212c5409041dfdbd319', -- cgit v1.2.3-70-g09d2 From 3a3443dff63167fc0331672871af4c0cc1fe5903 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Mon, 21 Mar 2016 15:14:48 +0100 Subject: parmetis patches by PETSc developers --- .../repos/builtin/packages/parmetis/package.py | 6 ++ ...-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch | 77 ++++++++++++++++++++++ ...-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch | 35 ++++++++++ 3 files changed, 118 insertions(+) create mode 100644 var/spack/repos/builtin/packages/parmetis/pkg-parmetis-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch create mode 100644 var/spack/repos/builtin/packages/parmetis/pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch (limited to 'var') diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py index 3f18dd76b8..c691cf4191 100644 --- a/var/spack/repos/builtin/packages/parmetis/package.py +++ b/var/spack/repos/builtin/packages/parmetis/package.py @@ -46,6 +46,12 @@ class Parmetis(Package): patch('enable_external_metis.patch') depends_on('metis') + # bug fixes from PETSc developers + # https://bitbucket.org/petsc/pkg-parmetis/commits/1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b/raw/ + patch('pkg-parmetis-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch') + # https://bitbucket.org/petsc/pkg-parmetis/commits/82409d68aa1d6cbc70740d0f35024aae17f7d5cb/raw/ + patch('pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch') + depends_on('gdb', when='+gdb') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/parmetis/pkg-parmetis-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch b/var/spack/repos/builtin/packages/parmetis/pkg-parmetis-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch new file mode 100644 index 0000000000..e6b8056c21 --- /dev/null +++ b/var/spack/repos/builtin/packages/parmetis/pkg-parmetis-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch @@ -0,0 +1,77 @@ +From 1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b Mon Sep 17 00:00:00 2001 +From: Jed Brown +Date: Fri, 12 Oct 2012 15:45:10 -0500 +Subject: [PATCH] ParMetis bug fixes reported by John Fettig [petsc-maint + #133631] + +''' +I have also reported to to Karypis but have received zero +response and he hasn't released any updates to the original release +either. At least he approved my forum posting so that other people +can see the bug and the fix. +http://glaros.dtc.umn.edu/gkhome/node/837 +''' + +Hg-commit: 1c2b9fe39201d404b493885093b5992028b9b8d4 +--- + libparmetis/xyzpart.c | 12 ++++++------ + 1 file changed, 6 insertions(+), 6 deletions(-) + +diff --git a/libparmetis/xyzpart.c b/libparmetis/xyzpart.c +index 3a2c289..63abfcb 100644 +--- a/libparmetis/xyzpart.c ++++ b/libparmetis/xyzpart.c +@@ -104,7 +104,7 @@ void IRBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz, + + for (i=0; i +Date: Tue, 20 Mar 2012 11:59:44 -0500 +Subject: [PATCH] parmetis: fix bug reported by jfettig; '<' to '<=' in xyzpart + +Hg-commit: 2dd2eae596acaabbc80e0ef875182616f868dbc2 +--- + libparmetis/xyzpart.c | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/libparmetis/xyzpart.c b/libparmetis/xyzpart.c +index 307aed9..3a2c289 100644 +--- a/libparmetis/xyzpart.c ++++ b/libparmetis/xyzpart.c +@@ -111,7 +111,7 @@ void IRBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz, + /* determine bucket counts */ + iset(nbins, 0, lcounts); + for (j=0, i=0; i Date: Mon, 21 Mar 2016 16:18:02 +0100 Subject: llvm : does not support python 3 --- var/spack/repos/builtin/packages/llvm/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py index 5c38b5b88c..1d25d59e50 100644 --- a/var/spack/repos/builtin/packages/llvm/package.py +++ b/var/spack/repos/builtin/packages/llvm/package.py @@ -52,7 +52,7 @@ class Llvm(Package): depends_on('cmake @2.8.12.2:') # Universal dependency - depends_on('python@2.7:') + depends_on('python@2.7:2.8') # Seems not to support python 3.X.Y # lldb dependencies depends_on('ncurses', when='+lldb') -- cgit v1.2.3-70-g09d2 From c5c92d50eb78673c635a7ed26145bf10a15c20cb Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Mon, 21 Mar 2016 11:24:36 -0400 Subject: paraview: remove trailing whitespace --- var/spack/repos/builtin/packages/paraview/package.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/paraview/package.py b/var/spack/repos/builtin/packages/paraview/package.py index ccf2d14c06..b3312736f1 100644 --- a/var/spack/repos/builtin/packages/paraview/package.py +++ b/var/spack/repos/builtin/packages/paraview/package.py @@ -37,11 +37,11 @@ class Paraview(Package): #depends_on('protobuf') # version mismatches? #depends_on('sqlite') # external version not supported depends_on('zlib') - + def url_for_version(self, version): """Handle ParaView version-based custom URLs.""" return self._url_str % (version.up_to(2), version) - + def install(self, spec, prefix): with working_dir('spack-build', create=True): -- cgit v1.2.3-70-g09d2 From 8e77f1776020c2a6edf9eb284615d99c905821e9 Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Mon, 21 Mar 2016 11:54:58 -0400 Subject: paraview: fix variant description typo --- var/spack/repos/builtin/packages/paraview/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/paraview/package.py b/var/spack/repos/builtin/packages/paraview/package.py index b3312736f1..0c3c7c1621 100644 --- a/var/spack/repos/builtin/packages/paraview/package.py +++ b/var/spack/repos/builtin/packages/paraview/package.py @@ -16,7 +16,7 @@ class Paraview(Package): variant('osmesa', default=False, description='Enable OSMesa support') variant('qt', default=False, description='Enable Qt support') - variant('opengl2', default=False, description='Enable OPengl2 backend') + variant('opengl2', default=False, description='Enable OpenGL2 backend') depends_on('python', when='+python') depends_on('py-numpy', when='+python') -- cgit v1.2.3-70-g09d2 From 553fff270a13d40fb9a41569bebf5075a740d8ac Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Mon, 21 Mar 2016 11:24:49 -0400 Subject: paraview: disallow python3 ParaView is not Python3-ready. --- var/spack/repos/builtin/packages/paraview/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/paraview/package.py b/var/spack/repos/builtin/packages/paraview/package.py index 0c3c7c1621..c16054816c 100644 --- a/var/spack/repos/builtin/packages/paraview/package.py +++ b/var/spack/repos/builtin/packages/paraview/package.py @@ -18,7 +18,7 @@ class Paraview(Package): variant('qt', default=False, description='Enable Qt support') variant('opengl2', default=False, description='Enable OpenGL2 backend') - depends_on('python', when='+python') + depends_on('python@2:2.7', when='+python') depends_on('py-numpy', when='+python') depends_on('py-matplotlib', when='+python') depends_on('tcl', when='+tcl') -- cgit v1.2.3-70-g09d2 From 953fb35f82c099936f833f31dcd292ffa1a3ec06 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Mon, 21 Mar 2016 18:00:32 +0100 Subject: add superlu_dist package --- .../repos/builtin/packages/superlu-dist/package.py | 63 ++++++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 var/spack/repos/builtin/packages/superlu-dist/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/superlu-dist/package.py b/var/spack/repos/builtin/packages/superlu-dist/package.py new file mode 100644 index 0000000000..c4c76909b3 --- /dev/null +++ b/var/spack/repos/builtin/packages/superlu-dist/package.py @@ -0,0 +1,63 @@ +from spack import * + +class SuperluDist(Package): + """A general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.""" + homepage = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/" + url = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/superlu_dist_4.1.tar.gz" + + version('4.3', 'ee66c84e37b4f7cc557771ccc3dc43ae') + version('4.2', 'ae9fafae161f775fbac6eba11e530a65') + version('4.1', '4edee38cc29f687bd0c8eb361096a455') + version('4.0', 'c0b98b611df227ae050bc1635c6940e0') + + depends_on ('mpi') + depends_on ('blas') + depends_on ('lapack') + depends_on ('parmetis') + depends_on ('metis') + + def install(self, spec, prefix): + makefile_inc = [] + makefile_inc.extend([ + 'PLAT = _mac_x', + 'DSuperLUroot = %s' % self.stage.source_path, #self.stage.path, prefix + 'DSUPERLULIB = $(DSuperLUroot)/lib/libsuperlu_dist.a', + 'BLASDEF = -DUSE_VENDOR_BLAS', + 'BLASLIB = -L%s -llapack %s -lblas' % (spec['lapack'].prefix.lib, spec['blas'].prefix.lib), # FIXME: avoid hardcoding blas/lapack lib names + 'METISLIB = -L%s -lmetis' % spec['metis'].prefix.lib, + 'PARMETISLIB = -L%s -lparmetis' % spec['parmetis'].prefix.lib, + 'FLIBS =', + 'LIBS = $(DSUPERLULIB) $(BLASLIB) $(PARMETISLIB) $(METISLIB)', + 'ARCH = ar', + 'ARCHFLAGS = cr', + 'RANLIB = true', + 'CC = mpicc', # FIXME avoid hardcoding MPI compiler names + 'CFLAGS = -fPIC -std=c99 -O2 -I%s -I%s' %(spec['parmetis'].prefix.include, spec['metis'].prefix.include), + 'NOOPTS = -fPIC -std=c99', + 'FORTRAN = mpif77', + 'F90FLAGS = -O2', + 'LOADER = mpif77', + 'LOADOPTS =', + 'CDEFS = -DAdd_' + ]) + + #with working_dir('src'): + with open('make.inc', 'w') as fh: + fh.write('\n'.join(makefile_inc)) + + make("lib", parallel=False) + + # FIXME: + # cd "EXAMPLE" do + # system "make" + + # need to install by hand + headers_location = join_path(self.prefix.include,'superlu_dist') + mkdirp(headers_location) + # FIXME: fetch all headers in the folder automatically + for header in ['Cnames.h','cublas_utils.h','dcomplex.h','html_mainpage.h','machines.h','old_colamd.h','psymbfact.h','superlu_ddefs.h','superlu_defs.h','superlu_enum_consts.h','superlu_zdefs.h','supermatrix.h','util_dist.h']: + superludist_header = join_path(self.stage.source_path, 'SRC/',header) + install(superludist_header, headers_location) + + superludist_lib = join_path(self.stage.source_path, 'lib/libsuperlu_dist.a') + install(superludist_lib,self.prefix.lib) -- cgit v1.2.3-70-g09d2 From 439d47b4e45c674ab9aa4ebd0c2bfaf6911ade60 Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Mon, 21 Mar 2016 01:48:18 -0700 Subject: Refactor environment setup. - Gave setup_environment and setup_dependent_environment more similar signatures. They now allows editing the Spack env and the runtime env for *this* package and dependents, respectively. - modify_module renamed to setup_dependent_python_module for symmetry with setup_dependent_environment and to avoid confusion with environment modules. - removed need for patching Package objects at runtime. - adjust packages to reflect these changes. --- lib/spack/spack/build_environment.py | 35 +++--- lib/spack/spack/modules.py | 3 +- lib/spack/spack/package.py | 120 ++++++++++++++++----- var/spack/repos/builtin/packages/mpich/package.py | 9 +- .../builtin/packages/netlib-scalapack/package.py | 2 +- .../repos/builtin/packages/openmpi/package.py | 18 ++-- var/spack/repos/builtin/packages/python/package.py | 39 ++----- var/spack/repos/builtin/packages/qt/package.py | 10 +- var/spack/repos/builtin/packages/ruby/package.py | 12 +-- 9 files changed, 151 insertions(+), 97 deletions(-) (limited to 'var') diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py index 59b234624c..5688d47e2d 100644 --- a/lib/spack/spack/build_environment.py +++ b/lib/spack/spack/build_environment.py @@ -84,7 +84,7 @@ class MakeExecutable(Executable): return super(MakeExecutable, self).__call__(*args, **kwargs) -def set_compiler_environment_variables(pkg): +def set_compiler_environment_variables(pkg, env): assert pkg.spec.concrete # Set compiler variables used by CMake and autotools assert all(key in pkg.compiler.link_paths for key in ('cc', 'cxx', 'f77', 'fc')) @@ -92,7 +92,6 @@ def set_compiler_environment_variables(pkg): # Populate an object with the list of environment modifications # and return it # TODO : add additional kwargs for better diagnostics, like requestor, ttyout, ttyerr, etc. - env = EnvironmentModifications() link_dir = spack.build_env_path env.set_env('CC', join_path(link_dir, pkg.compiler.link_paths['cc'])) env.set_env('CXX', join_path(link_dir, pkg.compiler.link_paths['cxx'])) @@ -113,7 +112,7 @@ def set_compiler_environment_variables(pkg): return env -def set_build_environment_variables(pkg): +def set_build_environment_variables(pkg, env): """ This ensures a clean install environment when we build packages """ @@ -134,7 +133,6 @@ def set_build_environment_variables(pkg): if os.path.isdir(ci): env_paths.append(ci) - env = EnvironmentModifications() for item in reversed(env_paths): env.prepend_path('PATH', item) env.set_env(SPACK_ENV_PATH, concatenate_paths(env_paths)) @@ -180,7 +178,7 @@ def set_build_environment_variables(pkg): return env -def set_module_variables_for_package(pkg, m): +def set_module_variables_for_package(pkg, module): """Populate the module scope of install() with some useful functions. This makes things easier for package writers. """ @@ -190,6 +188,8 @@ def set_module_variables_for_package(pkg, m): jobs = 1 elif pkg.make_jobs: jobs = pkg.make_jobs + + m = module m.make_jobs = jobs # TODO: make these build deps that can be installed if not found. @@ -271,9 +271,12 @@ def parent_class_modules(cls): def setup_package(pkg): """Execute all environment setup routines.""" - env = EnvironmentModifications() - env.extend(set_compiler_environment_variables(pkg)) - env.extend(set_build_environment_variables(pkg)) + spack_env = EnvironmentModifications() + run_env = EnvironmentModifications() + + set_compiler_environment_variables(pkg, spack_env) + set_build_environment_variables(pkg, spack_env) + # If a user makes their own package repo, e.g. # spack.repos.mystuff.libelf.Libelf, and they inherit from # an existing class like spack.repos.original.libelf.Libelf, @@ -285,12 +288,20 @@ def setup_package(pkg): # Allow dependencies to modify the module for dependency_spec in pkg.spec.traverse(root=False): - dependency_spec.package.modify_module(pkg.module, dependency_spec, pkg.spec) + dpkg = dependency_spec.package + dpkg.setup_dependent_python_module(pkg.module, pkg.spec) + # Allow dependencies to set up environment as well for dependency_spec in pkg.spec.traverse(root=False): - dependency_spec.package.setup_dependent_environment(env, pkg.spec) - validate(env, tty.warn) - env.apply_modifications() + dpkg = dependency_spec.package + dpkg.setup_dependent_environment(spack_env, run_env, pkg.spec) + + # Allow the package to apply some settings. + pkg.setup_environment(spack_env, run_env) + + # Make sure nothing's strange about the Spack environment. + validate(spack_env, tty.warn) + spack_env.apply_modifications() def fork(pkg, function): diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py index 4e98d50001..05c93cd3e6 100644 --- a/lib/spack/spack/modules.py +++ b/lib/spack/spack/modules.py @@ -164,7 +164,8 @@ class EnvModule(object): self.pkg.module, extendee_spec, self.spec) # Package-specific environment modifications - self.spec.package.setup_environment(env) + spack_env = EnvironmentModifications() + self.spec.package.setup_environment(spack_env, env) # TODO : implement site-specific modifications and filters if not env: diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index acad5a28f6..9d8ac87bd7 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -1002,56 +1002,120 @@ class Package(object): return __import__(self.__class__.__module__, fromlist=[self.__class__.__name__]) - def setup_environment(self, env): - """ - Appends in `env` the list of environment modifications needed to use this package outside of spack. + def setup_environment(self, spack_env, run_env): + """Set up the compile and runtime environemnts for a package. - Default implementation does nothing, but this can be overridden if the package needs a particular environment. + `spack_env` and `run_env` are `EnvironmentModifications` + objects. Package authors can call methods on them to alter + the environment within Spack and at runtime. - Example : + Both `spack_env` and `run_env` are applied within the build + process, before this package's `install()` method is called. + + Modifications in `run_env` will *also* be added to the + generated environment modules for this package. + + Default implementation does nothing, but this can be + overridden if the package needs a particular environment. - 1. A lot of Qt extensions need `QTDIR` set. This can be used to do that. + Examples: + + 1. Qt extensions need `QTDIR` set. Args: - env: list of environment modifications to be updated + spack_env (EnvironmentModifications): list of + modifications to be applied when this package is built + within Spack. + + run_env (EnvironmentModifications): list of environment + changes to be applied when this package is run outside + of Spack. + """ pass - def setup_dependent_environment(self, env, dependent_spec): - """ - Called before the install() method of dependents. - Appends in `env` the list of environment modifications needed by dependents (or extensions) during the - installation of a package. The default implementation delegates to `setup_environment`, but can be overridden - if the modifications to the environment happen to be different from the one needed to use the package outside - of spack. + def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + """Set up the environment of packages that depend on this one. + + This is similar to `setup_environment`, but it is used to + modify the compile and runtime environments of packages that + *depend* on this one. This gives packages like Python and + others that follow the extension model a way to implement + common environment or compile-time settings for dependencies. - This is useful if there are some common steps to installing all extensions for a certain package. + By default, this delegates to self.setup_environment() Example : - 1. Installing python modules generally requires `PYTHONPATH` to point to the lib/pythonX.Y/site-packages - directory in the module's install prefix. This could set that variable. + 1. Installing python modules generally requires + `PYTHONPATH` to point to the lib/pythonX.Y/site-packages + directory in the module's install prefix. This could + set that variable. Args: - env: list of environment modifications to be updated - dependent_spec: dependent (or extension) of this spec - """ - self.setup_environment(env) - def modify_module(self, module, spec, dependent_spec): + spack_env (EnvironmentModifications): list of + modifications to be applied when the dependent package + is bulit within Spack. + + run_env (EnvironmentModifications): list of environment + changes to be applied when the dependent package is + run outside of Spack. + + dependent_spec (Spec): The spec of the dependent package + about to be built. This allows the extendee (self) to + query the dependent's state. Note that *this* + package's spec is available as `self.spec`. + + This is useful if there are some common steps to installing + all extensions for a certain package. + """ + self.setup_environment(spack_env, run_env) + + + def setup_dependent_python_module(self, module, dependent_spec): + """Set up Python module-scope variables for dependent packages. + Called before the install() method of dependents. - Default implementation does nothing, but this can be overridden by an extendable package to set up the module of - its extensions. This is useful if there are some common steps to installing all extensions for a - certain package. + Default implementation does nothing, but this can be + overridden by an extendable package to set up the module of + its extensions. This is useful if there are some common steps + to installing all extensions for a certain package. Example : - 1. Extensions often need to invoke the 'python' interpreter from the Python installation being extended. - This routine can put a 'python' Executable object in the module scope for the extension package to simplify - extension installs. + 1. Extensions often need to invoke the `python` + interpreter from the Python installation being + extended. This routine can put a 'python' Executable + object in the module scope for the extension package to + simplify extension installs. + + 2. MPI compilers could set some variables in the + dependent's scope that point to `mpicc`, `mpicxx`, + etc., allowing them to be called by common names + regardless of which MPI is used. + + 3. BLAS/LAPACK implementations can set some variables + indicating the path to their libraries, since these + paths differ by BLAS/LAPACK implementation. + + Args: + + module (module): The Python `module` object of the + dependent package. Packages can use this to set + module-scope variables for the dependent to use. + + dependent_spec (Spec): The spec of the dependent package + about to be built. This allows the extendee (self) to + query the dependent's state. Note that *this* + package's spec is available as `self.spec`. + + This is useful if there are some common steps to installing + all extensions for a certain package. + """ pass diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py index 5af9b585ea..90b5d42eab 100644 --- a/var/spack/repos/builtin/packages/mpich/package.py +++ b/var/spack/repos/builtin/packages/mpich/package.py @@ -47,13 +47,6 @@ class Mpich(Package): provides('mpi@:3.0', when='@3:') provides('mpi@:1.3', when='@1:') - def setup_environment(self, env): - env.set_env('MPICH_CC', self.compiler.cc) - env.set_env('MPICH_CXX', self.compiler.cxx) - env.set_env('MPICH_F77', self.compiler.f77) - env.set_env('MPICH_F90', self.compiler.fc) - env.set_env('MPICH_FC', self.compiler.fc) - def setup_dependent_environment(self, env, dependent_spec): env.set_env('MPICH_CC', spack_cc) env.set_env('MPICH_CXX', spack_cxx) @@ -61,7 +54,7 @@ class Mpich(Package): env.set_env('MPICH_F90', spack_f90) env.set_env('MPICH_FC', spack_fc) - def modify_module(self, module, spec, dep_spec): + def setup_dependent_python_module(self, module, spec, dep_spec): """For dependencies, make mpicc's use spack wrapper.""" # FIXME : is this necessary ? Shouldn't this be part of a contract with MPI providers? module.mpicc = join_path(self.prefix.bin, 'mpicc') diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py index 36f506f7cd..62abfcc48e 100644 --- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py @@ -40,7 +40,7 @@ class NetlibScalapack(Package): make() make("install") - def modify_module(self, module, spec, dependent_spec): + def setup_dependent_python_module(self, module, spec, dependent_spec): lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so' lib_suffix = lib_dsuffix if '+shared' in spec['scalapack'] else '.a' diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py index 7783ca8766..c91a13e376 100644 --- a/var/spack/repos/builtin/packages/openmpi/package.py +++ b/var/spack/repos/builtin/packages/openmpi/package.py @@ -41,17 +41,13 @@ class Openmpi(Package): def url_for_version(self, version): return "http://www.open-mpi.org/software/ompi/v%s/downloads/openmpi-%s.tar.bz2" % (version.up_to(2), version) - def setup_environment(self, env): - env.set_env('OMPI_CC', self.compiler.cc) - env.set_env('OMPI_CXX', self.compiler.cxx) - env.set_env('OMPI_FC', self.compiler.fc) - env.set_env('OMPI_F77', self.compiler.f77) - - def setup_dependent_environment(self, env, dependent_spec): - env.set_env('OMPI_CC', spack_cc) - env.set_env('OMPI_CXX', spack_cxx) - env.set_env('OMPI_FC', spack_fc) - env.set_env('OMPI_F77', spack_f77) + + def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + spack_env.set_env('OMPI_CC', spack_cc) + spack_env.set_env('OMPI_CXX', spack_cxx) + spack_env.set_env('OMPI_FC', spack_fc) + spack_env.set_env('OMPI_F77', spack_f77) + def install(self, spec, prefix): config_args = ["--prefix=%s" % prefix, diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index c445d26369..593a27708c 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -92,13 +92,21 @@ class Python(Package): def site_packages_dir(self): return os.path.join(self.python_lib_dir, 'site-packages') - def setup_dependent_environment(self, env, extension_spec): - # Set PYTHONPATH to include site-packages dir for the extension and any other python extensions it depends on. + + def setup_dependent_environment(self, spack_env, run_env, extension_spec): + # TODO: do this only for actual extensions. + + # Set PYTHONPATH to include site-packages dir for the + # extension and any other python extensions it depends on. python_paths = [] for d in extension_spec.traverse(): if d.package.extends(self.spec): python_paths.append(os.path.join(d.prefix, self.site_packages_dir)) - env.set_env('PYTHONPATH', ':'.join(python_paths)) + + pythonpath = ':'.join(python_paths) + spack_env.set_env('PYTHONPATH', pythonpath) + run_env.set_env('PYTHONPATH', pythonpath) + def modify_module(self, module, spec, ext_spec): """ @@ -114,31 +122,6 @@ class Python(Package): else: module.python = Executable(join_path(spec.prefix.bin, 'python')) - # The code below patches the any python extension to have good defaults for `setup_dependent_environment` and - # `setup_environment` only if the extension didn't override any of these functions explicitly. - def _setup_env(self, env): - site_packages = glob.glob(join_path(self.spec.prefix.lib, "python*/site-packages")) - if site_packages: - env.prepend_path('PYTHONPATH', site_packages[0]) - - def _setup_denv(self, env, extension_spec): - pass - - pkg_cls = type(ext_spec.package) # Retrieve the type we may want to patch - if 'python' in pkg_cls.extendees: - # List of overrides we are interested in - interesting_overrides = ['setup_environment', 'setup_dependent_environment'] - overrides_found = [ - (name, defining_cls) for name, _, defining_cls, _, in inspect.classify_class_attrs(pkg_cls) - if - name in interesting_overrides and # The attribute has the right name - issubclass(defining_cls, Package) and defining_cls is not Package # and is an actual override - ] - if not overrides_found: - # If no override were found go on patching - pkg_cls.setup_environment = functools.wraps(Package.setup_environment)(_setup_env) - pkg_cls.setup_dependent_environment = functools.wraps(Package.setup_dependent_environment)(_setup_denv) - # Add variables for lib/pythonX.Y and lib/pythonX.Y/site-packages dirs. module.python_lib_dir = os.path.join(ext_spec.prefix, self.python_lib_dir) module.python_include_dir = os.path.join(ext_spec.prefix, self.python_include_dir) diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py index 35b9d68462..039aeb3c31 100644 --- a/var/spack/repos/builtin/packages/qt/package.py +++ b/var/spack/repos/builtin/packages/qt/package.py @@ -55,8 +55,14 @@ class Qt(Package): depends_on("mesa", when='@4:+mesa') depends_on("libxcb") - def setup_environment(self, env): - env.set_env['QTDIR'] = self.prefix + + def setup_environment(self, spack_env, env): + env.set_env('QTDIR', self.prefix) + + + def setup_dependent_environment(self, spack_env, run_env, dspec): + spack_env.set_env('QTDIR', self.prefix) + def patch(self): if self.spec.satisfies('@4'): diff --git a/var/spack/repos/builtin/packages/ruby/package.py b/var/spack/repos/builtin/packages/ruby/package.py index 2d1da8c9af..39f65f51d2 100644 --- a/var/spack/repos/builtin/packages/ruby/package.py +++ b/var/spack/repos/builtin/packages/ruby/package.py @@ -2,7 +2,7 @@ from spack import * class Ruby(Package): - """A dynamic, open source programming language with a focus on + """A dynamic, open source programming language with a focus on simplicity and productivity.""" homepage = "https://www.ruby-lang.org/" @@ -17,15 +17,17 @@ class Ruby(Package): make() make("install") - def setup_dependent_environment(self, env, extension_spec): + def setup_dependent_environment(self, spack_env, run_env, extension_spec): + # TODO: do this only for actual extensions. # Set GEM_PATH to include dependent gem directories ruby_paths = [] for d in extension_spec.traverse(): if d.package.extends(self.spec): ruby_paths.append(d.prefix) - env.set_env('GEM_PATH', concatenate_paths(ruby_paths)) + + spack_env.set_env('GEM_PATH', concatenate_paths(ruby_paths)) # The actual installation path for this gem - env.set_env('GEM_HOME', extension_spec.prefix) + spack_env.set_env('GEM_HOME', extension_spec.prefix) def modify_module(self, module, spec, ext_spec): """Called before ruby modules' install() methods. Sets GEM_HOME @@ -38,5 +40,3 @@ class Ruby(Package): # Ruby extension builds have global ruby and gem functions module.ruby = Executable(join_path(spec.prefix.bin, 'ruby')) module.gem = Executable(join_path(spec.prefix.bin, 'gem')) - - -- cgit v1.2.3-70-g09d2 From b1516f64eb75c108eded1e9ee7e0480a4552236a Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Mon, 21 Mar 2016 02:21:31 -0700 Subject: Rename some environment methods to be less repetitive, add set_path. --- lib/spack/spack/build_environment.py | 45 +++++++++++----------- lib/spack/spack/environment.py | 22 ++++++++++- lib/spack/spack/test/environment.py | 22 +++++++---- var/spack/repos/builtin/packages/mpich/package.py | 10 ++--- .../repos/builtin/packages/openmpi/package.py | 8 ++-- var/spack/repos/builtin/packages/python/package.py | 4 +- var/spack/repos/builtin/packages/qt/package.py | 4 +- var/spack/repos/builtin/packages/ruby/package.py | 5 ++- 8 files changed, 73 insertions(+), 47 deletions(-) (limited to 'var') diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py index 5688d47e2d..fc5b7d6207 100644 --- a/lib/spack/spack/build_environment.py +++ b/lib/spack/spack/build_environment.py @@ -36,7 +36,7 @@ import sys import spack import llnl.util.tty as tty from llnl.util.filesystem import * -from spack.environment import EnvironmentModifications, concatenate_paths, validate +from spack.environment import EnvironmentModifications, validate from spack.util.environment import * from spack.util.executable import Executable, which @@ -93,22 +93,23 @@ def set_compiler_environment_variables(pkg, env): # and return it # TODO : add additional kwargs for better diagnostics, like requestor, ttyout, ttyerr, etc. link_dir = spack.build_env_path - env.set_env('CC', join_path(link_dir, pkg.compiler.link_paths['cc'])) - env.set_env('CXX', join_path(link_dir, pkg.compiler.link_paths['cxx'])) - env.set_env('F77', join_path(link_dir, pkg.compiler.link_paths['f77'])) - env.set_env('FC', join_path(link_dir, pkg.compiler.link_paths['fc'])) + env.set('CC', join_path(link_dir, pkg.compiler.link_paths['cc'])) + env.set('CXX', join_path(link_dir, pkg.compiler.link_paths['cxx'])) + env.set('F77', join_path(link_dir, pkg.compiler.link_paths['f77'])) + env.set('FC', join_path(link_dir, pkg.compiler.link_paths['fc'])) + # Set SPACK compiler variables so that our wrapper knows what to call compiler = pkg.compiler if compiler.cc: - env.set_env('SPACK_CC', compiler.cc) + env.set('SPACK_CC', compiler.cc) if compiler.cxx: - env.set_env('SPACK_CXX', compiler.cxx) + env.set('SPACK_CXX', compiler.cxx) if compiler.f77: - env.set_env('SPACK_F77', compiler.f77) + env.set('SPACK_F77', compiler.f77) if compiler.fc: - env.set_env('SPACK_FC', compiler.fc) + env.set('SPACK_FC', compiler.fc) - env.set_env('SPACK_COMPILER_SPEC', str(pkg.spec.compiler)) + env.set('SPACK_COMPILER_SPEC', str(pkg.spec.compiler)) return env @@ -135,25 +136,25 @@ def set_build_environment_variables(pkg, env): for item in reversed(env_paths): env.prepend_path('PATH', item) - env.set_env(SPACK_ENV_PATH, concatenate_paths(env_paths)) + env.set_path(SPACK_ENV_PATH, env_paths) # Prefixes of all of the package's dependencies go in SPACK_DEPENDENCIES dep_prefixes = [d.prefix for d in pkg.spec.traverse(root=False)] - env.set_env(SPACK_DEPENDENCIES, concatenate_paths(dep_prefixes)) - env.set_env('CMAKE_PREFIX_PATH', concatenate_paths(dep_prefixes)) # Add dependencies to CMAKE_PREFIX_PATH + env.set_path(SPACK_DEPENDENCIES, dep_prefixes) + env.set_path('CMAKE_PREFIX_PATH', dep_prefixes) # Add dependencies to CMAKE_PREFIX_PATH # Install prefix - env.set_env(SPACK_PREFIX, pkg.prefix) + env.set(SPACK_PREFIX, pkg.prefix) # Install root prefix - env.set_env(SPACK_INSTALL, spack.install_path) + env.set(SPACK_INSTALL, spack.install_path) # Remove these vars from the environment during build because they # can affect how some packages find libraries. We want to make # sure that builds never pull in unintended external dependencies. - env.unset_env('LD_LIBRARY_PATH') - env.unset_env('LD_RUN_PATH') - env.unset_env('DYLD_LIBRARY_PATH') + env.unset('LD_LIBRARY_PATH') + env.unset('LD_RUN_PATH') + env.unset('DYLD_LIBRARY_PATH') # Add bin directories from dependencies to the PATH for the build. bin_dirs = reversed(filter(os.path.isdir, ['%s/bin' % prefix for prefix in dep_prefixes])) @@ -162,9 +163,9 @@ def set_build_environment_variables(pkg, env): # Working directory for the spack command itself, for debug logs. if spack.debug: - env.set_env(SPACK_DEBUG, 'TRUE') - env.set_env(SPACK_SHORT_SPEC, pkg.spec.short_spec) - env.set_env(SPACK_DEBUG_LOG_DIR, spack.spack_working_dir) + env.set(SPACK_DEBUG, 'TRUE') + env.set(SPACK_SHORT_SPEC, pkg.spec.short_spec) + env.set(SPACK_DEBUG_LOG_DIR, spack.spack_working_dir) # Add any pkgconfig directories to PKG_CONFIG_PATH pkg_config_dirs = [] @@ -173,7 +174,7 @@ def set_build_environment_variables(pkg, env): pcdir = join_path(p, libdir, 'pkgconfig') if os.path.isdir(pcdir): pkg_config_dirs.append(pcdir) - env.set_env('PKG_CONFIG_PATH', concatenate_paths(pkg_config_dirs)) + env.set_path('PKG_CONFIG_PATH', pkg_config_dirs) return env diff --git a/lib/spack/spack/environment.py b/lib/spack/spack/environment.py index 74aef57fe8..72aafa4e2d 100644 --- a/lib/spack/spack/environment.py +++ b/lib/spack/spack/environment.py @@ -29,6 +29,12 @@ class UnsetEnv(NameModifier): os.environ.pop(self.name, None) # Avoid throwing if the variable was not set +class SetPath(NameValueModifier): + def execute(self): + string_path = concatenate_paths(self.value) + os.environ[self.name] = string_path + + class AppendPath(NameValueModifier): def execute(self): environment_value = os.environ.get(self.name, '') @@ -103,7 +109,7 @@ class EnvironmentModifications(object): } return args - def set_env(self, name, value, **kwargs): + def set(self, name, value, **kwargs): """ Stores in the current object a request to set an environment variable @@ -115,7 +121,7 @@ class EnvironmentModifications(object): item = SetEnv(name, value, **kwargs) self.env_modifications.append(item) - def unset_env(self, name, **kwargs): + def unset(self, name, **kwargs): """ Stores in the current object a request to unset an environment variable @@ -126,6 +132,18 @@ class EnvironmentModifications(object): item = UnsetEnv(name, **kwargs) self.env_modifications.append(item) + def set_path(self, name, elts, **kwargs): + """ + Stores a request to set a path generated from a list. + + Args: + name: name o the environment variable to be set. + elts: elements of the path to set. + """ + kwargs.update(self._get_outside_caller_attributes()) + item = SetPath(name, elts, **kwargs) + self.env_modifications.append(item) + def append_path(self, name, path, **kwargs): """ Stores in the current object a request to append a path to a path list diff --git a/lib/spack/spack/test/environment.py b/lib/spack/spack/test/environment.py index 3e03760c01..6c8f5ea43c 100644 --- a/lib/spack/spack/test/environment.py +++ b/lib/spack/spack/test/environment.py @@ -11,21 +11,27 @@ class EnvironmentTest(unittest.TestCase): os.environ['PATH_LIST'] = '/path/second:/path/third' os.environ['REMOVE_PATH_LIST'] = '/a/b:/duplicate:/a/c:/remove/this:/a/d:/duplicate/:/f/g' - def test_set_env(self): + def test_set(self): env = EnvironmentModifications() - env.set_env('A', 'dummy value') - env.set_env('B', 3) + env.set('A', 'dummy value') + env.set('B', 3) env.apply_modifications() self.assertEqual('dummy value', os.environ['A']) self.assertEqual(str(3), os.environ['B']) - def test_unset_env(self): + def test_unset(self): env = EnvironmentModifications() self.assertEqual('foo', os.environ['UNSET_ME']) - env.unset_env('UNSET_ME') + env.unset('UNSET_ME') env.apply_modifications() self.assertRaises(KeyError, os.environ.__getitem__, 'UNSET_ME') + def test_set_path(self): + env = EnvironmentModifications() + env.set_path('A', ['foo', 'bar', 'baz']) + env.apply_modifications() + self.assertEqual('foo:bar:baz', os.environ['A']) + def test_path_manipulation(self): env = EnvironmentModifications() @@ -51,7 +57,7 @@ class EnvironmentTest(unittest.TestCase): def test_extra_arguments(self): env = EnvironmentModifications() - env.set_env('A', 'dummy value', who='Pkg1') + env.set('A', 'dummy value', who='Pkg1') for x in env: assert 'who' in x.args env.apply_modifications() @@ -59,8 +65,8 @@ class EnvironmentTest(unittest.TestCase): def test_extend(self): env = EnvironmentModifications() - env.set_env('A', 'dummy value') - env.set_env('B', 3) + env.set('A', 'dummy value') + env.set('B', 3) copy_construct = EnvironmentModifications(env) self.assertEqual(len(copy_construct), 2) for x, y in zip(env, copy_construct): diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py index 90b5d42eab..c4d9940bb7 100644 --- a/var/spack/repos/builtin/packages/mpich/package.py +++ b/var/spack/repos/builtin/packages/mpich/package.py @@ -48,11 +48,11 @@ class Mpich(Package): provides('mpi@:1.3', when='@1:') def setup_dependent_environment(self, env, dependent_spec): - env.set_env('MPICH_CC', spack_cc) - env.set_env('MPICH_CXX', spack_cxx) - env.set_env('MPICH_F77', spack_f77) - env.set_env('MPICH_F90', spack_f90) - env.set_env('MPICH_FC', spack_fc) + env.set('MPICH_CC', spack_cc) + env.set('MPICH_CXX', spack_cxx) + env.set('MPICH_F77', spack_f77) + env.set('MPICH_F90', spack_f90) + env.set('MPICH_FC', spack_fc) def setup_dependent_python_module(self, module, spec, dep_spec): """For dependencies, make mpicc's use spack wrapper.""" diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py index c91a13e376..9a127f1812 100644 --- a/var/spack/repos/builtin/packages/openmpi/package.py +++ b/var/spack/repos/builtin/packages/openmpi/package.py @@ -43,10 +43,10 @@ class Openmpi(Package): def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - spack_env.set_env('OMPI_CC', spack_cc) - spack_env.set_env('OMPI_CXX', spack_cxx) - spack_env.set_env('OMPI_FC', spack_fc) - spack_env.set_env('OMPI_F77', spack_f77) + spack_env.set('OMPI_CC', spack_cc) + spack_env.set('OMPI_CXX', spack_cxx) + spack_env.set('OMPI_FC', spack_fc) + spack_env.set('OMPI_F77', spack_f77) def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index 593a27708c..4f55bc803e 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -104,8 +104,8 @@ class Python(Package): python_paths.append(os.path.join(d.prefix, self.site_packages_dir)) pythonpath = ':'.join(python_paths) - spack_env.set_env('PYTHONPATH', pythonpath) - run_env.set_env('PYTHONPATH', pythonpath) + spack_env.set('PYTHONPATH', pythonpath) + run_env.set('PYTHONPATH', pythonpath) def modify_module(self, module, spec, ext_spec): diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py index 039aeb3c31..d08e8e81e1 100644 --- a/var/spack/repos/builtin/packages/qt/package.py +++ b/var/spack/repos/builtin/packages/qt/package.py @@ -57,11 +57,11 @@ class Qt(Package): def setup_environment(self, spack_env, env): - env.set_env('QTDIR', self.prefix) + env.set('QTDIR', self.prefix) def setup_dependent_environment(self, spack_env, run_env, dspec): - spack_env.set_env('QTDIR', self.prefix) + spack_env.set('QTDIR', self.prefix) def patch(self): diff --git a/var/spack/repos/builtin/packages/ruby/package.py b/var/spack/repos/builtin/packages/ruby/package.py index 39f65f51d2..7ff1898ce9 100644 --- a/var/spack/repos/builtin/packages/ruby/package.py +++ b/var/spack/repos/builtin/packages/ruby/package.py @@ -25,9 +25,10 @@ class Ruby(Package): if d.package.extends(self.spec): ruby_paths.append(d.prefix) - spack_env.set_env('GEM_PATH', concatenate_paths(ruby_paths)) + spack_env.set_path('GEM_PATH', ruby_paths) + # The actual installation path for this gem - spack_env.set_env('GEM_HOME', extension_spec.prefix) + spack_env.set('GEM_HOME', extension_spec.prefix) def modify_module(self, module, spec, ext_spec): """Called before ruby modules' install() methods. Sets GEM_HOME -- cgit v1.2.3-70-g09d2 From 4b46e21685b557188d8738bf11af2e0195c14046 Mon Sep 17 00:00:00 2001 From: "Kelly (KT) Thompson" Date: Mon, 21 Mar 2016 19:55:54 -0600 Subject: + Provide package numdiff. --- .../repos/builtin/packages/numdiff/package.py | 41 ++++++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 var/spack/repos/builtin/packages/numdiff/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/numdiff/package.py b/var/spack/repos/builtin/packages/numdiff/package.py new file mode 100644 index 0000000000..a51f6206cf --- /dev/null +++ b/var/spack/repos/builtin/packages/numdiff/package.py @@ -0,0 +1,41 @@ +############################################################################## +# Copyright (c) 2013, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License (as published by +# the Free Software Foundation) version 2.1 dated February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program; if not, write to the Free Software Foundation, +# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + +class Numdiff(Package): + """Numdiff is a little program that can be used to compare putatively + similar files line by line and field by field, ignoring small numeric + differences or/and different numeric formats.""" + + homepage = 'https://www.nongnu.org/numdiff' + url = 'http://nongnu.askapache.com/numdiff/numdiff-5.8.1.tar.gz' + + version('5.8.1', 'a295eb391f6cb1578209fc6b4f9d994e') + + def install(self, spec, prefix): + options = ['--prefix=%s' % prefix] + configure(*options) + make() + make('install') -- cgit v1.2.3-70-g09d2 From 7ec450912dc71915205857da75bb418ffc3d0904 Mon Sep 17 00:00:00 2001 From: "Kelly (KT) Thompson" Date: Mon, 21 Mar 2016 21:14:03 -0600 Subject: + Provide subversion and required packages apr and apr-util. + Installation of subversion may need to be modified to include python and perl bindings. I have provided comments to this end, but the code is not active. --- .../packages/apr-util/apr-util.new/package.py | 44 ++++++++++++++++ .../repos/builtin/packages/apr/apr.new/package.py | 51 +++++++++++++++++++ .../packages/subversion/subversion.new/package.py | 59 ++++++++++++++++++++++ var/spack/repos/builtin/packages/swig/package.py | 5 +- 4 files changed, 158 insertions(+), 1 deletion(-) create mode 100644 var/spack/repos/builtin/packages/apr-util/apr-util.new/package.py create mode 100644 var/spack/repos/builtin/packages/apr/apr.new/package.py create mode 100644 var/spack/repos/builtin/packages/subversion/subversion.new/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/apr-util/apr-util.new/package.py b/var/spack/repos/builtin/packages/apr-util/apr-util.new/package.py new file mode 100644 index 0000000000..8f19c84d22 --- /dev/null +++ b/var/spack/repos/builtin/packages/apr-util/apr-util.new/package.py @@ -0,0 +1,44 @@ +############################################################################## +# Copyright (c) 2013, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License (as published by +# the Free Software Foundation) version 2.1 dated February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program; if not, write to the Free Software Foundation, +# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + +class AprUtil(Package): + """Apache Portable Runtime Utility""" + homepage = 'https://apr.apache.org/' + url = 'http://archive.apache.org/dist/apr/apr-util-1.5.4.tar.gz' + + version('1.5.4', '866825c04da827c6e5f53daff5569f42') + + depends_on('apr') + + def install(self, spec, prefix): + + # configure, build, install: + options = ['--prefix=%s' % prefix] + options.append('--with-apr=%s' % spec['apr'].prefix) + + configure(*options) + make() + make('install') diff --git a/var/spack/repos/builtin/packages/apr/apr.new/package.py b/var/spack/repos/builtin/packages/apr/apr.new/package.py new file mode 100644 index 0000000000..5cbbad350b --- /dev/null +++ b/var/spack/repos/builtin/packages/apr/apr.new/package.py @@ -0,0 +1,51 @@ +############################################################################## +# Copyright (c) 2013, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License (as published by +# the Free Software Foundation) version 2.1 dated February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program; if not, write to the Free Software Foundation, +# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + +class Apr(Package): + """Apache portable runtime.""" + homepage = 'https://apr.apache.org/' + url = 'http://archive.apache.org/dist/apr/apr-1.5.2.tar.gz' + + version('1.5.2', '98492e965963f852ab29f9e61b2ad700') + + #variant('ncurses', default=True, description='Enables the build of the ncurses gui') + #variant('qt', default=False, description='Enables the build of cmake-gui') + #variant('doc', default=False, description='Enables the generation of html and man page documentation') + + #depends_on('ncurses', when='+ncurses') + #depends_on('qt', when='+qt') + #depends_on('python@2.7.11:', when='+doc') + #depends_on('py-sphinx', when='+doc') + + #def url_for_version(self, version): + # """Handle CMake's version-based custom URLs.""" + # return 'https://cmake.org/files/v%s/cmake-%s.tar.gz' % (version.up_to(2), version) + + def install(self, spec, prefix): + options = ['--prefix=%s' % prefix] + configure(*options) + make() + make('install') diff --git a/var/spack/repos/builtin/packages/subversion/subversion.new/package.py b/var/spack/repos/builtin/packages/subversion/subversion.new/package.py new file mode 100644 index 0000000000..b1c3380238 --- /dev/null +++ b/var/spack/repos/builtin/packages/subversion/subversion.new/package.py @@ -0,0 +1,59 @@ +############################################################################## +# Copyright (c) 2013, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License (as published by +# the Free Software Foundation) version 2.1 dated February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program; if not, write to the Free Software Foundation, +# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * +#import os + +class Subversion(Package): + """Apache Subversion - an open source version control system.""" + homepage = 'https://subversion.apache.org/' + url = 'http://archive.apache.org/dist/subversion/subversion-1.8.13.tar.gz' + + version('1.8.13', '8065b3698d799507fb72dd7926ed32b6') + version('1.9.3', 'a92bcfaec4e5038f82c74a7b5bbd2f46') + + depends_on('apr') + depends_on('apr-util') + depends_on('zlib') + depends_on('sqlite') + #depends_on('swig') + + def install(self, spec, prefix): + + # configure, build, install: + # Ref: http://www.linuxfromscratch.org/blfs/view/svn/general/subversion.html + options = ['--prefix=%s' % prefix] + options.append('--with-apr=%s' % spec['apr'].prefix) + options.append('--with-apr-util=%s' % spec['apr-util'].prefix) + options.append('--with-zlib=%s' % spec['zlib'].prefix) + options.append('--with-sqlite=%s' % spec['sqlite'].prefix) + #options.append('--with-swig=%s' % spec['swig'].prefix) + + configure(*options) + make() + make('install') + #make('swig-py') # python bindings + #make('install-swig-py') + #make('swig-pl') # perl bindings + #make('install-swig-pl') diff --git a/var/spack/repos/builtin/packages/swig/package.py b/var/spack/repos/builtin/packages/swig/package.py index 8d46c4fe46..de6055e965 100644 --- a/var/spack/repos/builtin/packages/swig/package.py +++ b/var/spack/repos/builtin/packages/swig/package.py @@ -36,11 +36,14 @@ class Swig(Package): homepage = "http://www.swig.org" url = "http://prdownloads.sourceforge.net/swig/swig-3.0.2.tar.gz" - version('3.0.2', '62f9b0d010cef36a13a010dc530d0d41') + version('3.0.8', 'c96a1d5ecb13d38604d7e92148c73c97') + version('3.0.2', '62f9b0d010cef36a13a010dc530d0d41') + version('2.0.12', 'c3fb0b2d710cc82ed0154b91e43085a4') depends_on('pcre') def install(self, spec, prefix): configure("--prefix=%s" % prefix) + make() make("install") -- cgit v1.2.3-70-g09d2 From 23bf70296e4a02f49c301b1b744055802b1e8dc1 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Tue, 22 Mar 2016 09:22:42 +0100 Subject: arpack: add a patch for 3.3 --- var/spack/repos/builtin/packages/arpack-ng/package.py | 4 ++++ .../repos/builtin/packages/arpack-ng/pdlamch10.patch | 15 +++++++++++++++ 2 files changed, 19 insertions(+) create mode 100644 var/spack/repos/builtin/packages/arpack-ng/pdlamch10.patch (limited to 'var') diff --git a/var/spack/repos/builtin/packages/arpack-ng/package.py b/var/spack/repos/builtin/packages/arpack-ng/package.py index 0b49d14202..614071cf53 100644 --- a/var/spack/repos/builtin/packages/arpack-ng/package.py +++ b/var/spack/repos/builtin/packages/arpack-ng/package.py @@ -35,6 +35,10 @@ class ArpackNg(Package): variant('shared', default=True, description='Enables the build of shared libraries') variant('mpi', default=False, description='Activates MPI support') + # The function pdlamch10 does not set the return variable. This is fixed upstream + # see https://github.com/opencollab/arpack-ng/issues/34 + patch('pdlamch10.patch', when='@3.3:') + depends_on('blas') depends_on('lapack') depends_on('mpi', when='+mpi') diff --git a/var/spack/repos/builtin/packages/arpack-ng/pdlamch10.patch b/var/spack/repos/builtin/packages/arpack-ng/pdlamch10.patch new file mode 100644 index 0000000000..922828909f --- /dev/null +++ b/var/spack/repos/builtin/packages/arpack-ng/pdlamch10.patch @@ -0,0 +1,15 @@ +diff --git a/PARPACK/SRC/MPI/pdlamch10.f b/PARPACK/SRC/MPI/pdlamch10.f +index 6571da9..2882c2e 100644 +--- a/PARPACK/SRC/MPI/pdlamch10.f ++++ b/PARPACK/SRC/MPI/pdlamch10.f +@@ -86,8 +86,8 @@ + TEMP = TEMP1 + END IF + * +- PDLAMCH = TEMP ++ PDLAMCH10 = TEMP + * +-* End of PDLAMCH ++* End of PDLAMCH10 + * + END -- cgit v1.2.3-70-g09d2 From aca8b5c89de7058ab58f2eb3392e8b023b16fe8a Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Tue, 22 Mar 2016 09:27:00 +0100 Subject: move suite sparse to a proper folder --- .../repos/builtin/packages/SuiteSparse/package.py | 27 ---------------------- .../repos/builtin/packages/suite-sparse/package.py | 27 ++++++++++++++++++++++ 2 files changed, 27 insertions(+), 27 deletions(-) delete mode 100644 var/spack/repos/builtin/packages/SuiteSparse/package.py create mode 100644 var/spack/repos/builtin/packages/suite-sparse/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/SuiteSparse/package.py b/var/spack/repos/builtin/packages/SuiteSparse/package.py deleted file mode 100644 index 6e130d118f..0000000000 --- a/var/spack/repos/builtin/packages/SuiteSparse/package.py +++ /dev/null @@ -1,27 +0,0 @@ -from spack import * - - -class Suitesparse(Package): - """ - SuiteSparse is a suite of sparse matrix algorithms - """ - homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' - url = 'http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.5.1.tar.gz' - - version('4.5.1', 'f0ea9aad8d2d1ffec66a5b6bfeff5319') - - depends_on('blas') - depends_on('lapack') - - depends_on('metis@5.1.0', when='@4.5.1') - - def install(self, spec, prefix): - # The build system of SuiteSparse is quite old-fashioned - # It's basically a plain Makefile which include an header (SuiteSparse_config/SuiteSparse_config.mk) - # with a lot of convoluted logic in it. - # Any kind of customization will need to go through filtering of that file - - # FIXME : this actually uses the current workaround - # FIXME : (blas / lapack always provide libblas and liblapack as aliases) - make('install', 'INSTALL=%s' % prefix, 'BLAS=-lblas', 'LAPACK=-llapack') - diff --git a/var/spack/repos/builtin/packages/suite-sparse/package.py b/var/spack/repos/builtin/packages/suite-sparse/package.py new file mode 100644 index 0000000000..6e130d118f --- /dev/null +++ b/var/spack/repos/builtin/packages/suite-sparse/package.py @@ -0,0 +1,27 @@ +from spack import * + + +class Suitesparse(Package): + """ + SuiteSparse is a suite of sparse matrix algorithms + """ + homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' + url = 'http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.5.1.tar.gz' + + version('4.5.1', 'f0ea9aad8d2d1ffec66a5b6bfeff5319') + + depends_on('blas') + depends_on('lapack') + + depends_on('metis@5.1.0', when='@4.5.1') + + def install(self, spec, prefix): + # The build system of SuiteSparse is quite old-fashioned + # It's basically a plain Makefile which include an header (SuiteSparse_config/SuiteSparse_config.mk) + # with a lot of convoluted logic in it. + # Any kind of customization will need to go through filtering of that file + + # FIXME : this actually uses the current workaround + # FIXME : (blas / lapack always provide libblas and liblapack as aliases) + make('install', 'INSTALL=%s' % prefix, 'BLAS=-lblas', 'LAPACK=-llapack') + -- cgit v1.2.3-70-g09d2 From 3c5a1605d5e3cba881b743bf561f0966b1a3ad8b Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Tue, 22 Mar 2016 09:27:39 +0100 Subject: adjust the class name for suite sparse --- var/spack/repos/builtin/packages/suite-sparse/package.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/suite-sparse/package.py b/var/spack/repos/builtin/packages/suite-sparse/package.py index 6e130d118f..b57f9967c3 100644 --- a/var/spack/repos/builtin/packages/suite-sparse/package.py +++ b/var/spack/repos/builtin/packages/suite-sparse/package.py @@ -1,7 +1,7 @@ from spack import * -class Suitesparse(Package): +class SuiteSparse(Package): """ SuiteSparse is a suite of sparse matrix algorithms """ @@ -24,4 +24,3 @@ class Suitesparse(Package): # FIXME : this actually uses the current workaround # FIXME : (blas / lapack always provide libblas and liblapack as aliases) make('install', 'INSTALL=%s' % prefix, 'BLAS=-lblas', 'LAPACK=-llapack') - -- cgit v1.2.3-70-g09d2 From cb97e8dd9301e5bbc6752caed2f4861a2a06f494 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Tue, 22 Mar 2016 09:43:10 +0100 Subject: adjust eigen and octave to use new names of suite sparse --- var/spack/repos/builtin/packages/eigen/package.py | 2 +- var/spack/repos/builtin/packages/octave/package.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/eigen/package.py b/var/spack/repos/builtin/packages/eigen/package.py index e40046b452..8d6e672f86 100644 --- a/var/spack/repos/builtin/packages/eigen/package.py +++ b/var/spack/repos/builtin/packages/eigen/package.py @@ -48,7 +48,7 @@ class Eigen(Package): depends_on('metis', when='+metis') depends_on('scotch', when='+scotch') depends_on('fftw', when='+fftw') - depends_on('SuiteSparse', when='+suitesparse') + depends_on('suite-sparse', when='+suitesparse') depends_on('mpfr@2.3.0:') # Eigen 3.2.7 requires at least 2.3.0 depends_on('gmp') diff --git a/var/spack/repos/builtin/packages/octave/package.py b/var/spack/repos/builtin/packages/octave/package.py index 38b355159d..6e99c23652 100644 --- a/var/spack/repos/builtin/packages/octave/package.py +++ b/var/spack/repos/builtin/packages/octave/package.py @@ -62,7 +62,7 @@ class Octave(Package): depends_on('qrupdate', when='+qrupdate') #depends_on('qscintilla', when='+qscintilla) # TODO: add package depends_on('qt', when='+qt') - depends_on('SuiteSparse', when='+suitesparse') + depends_on('suite-sparse',when='+suitesparse') depends_on('zlib', when='+zlib') -- cgit v1.2.3-70-g09d2 From a26992ef55fed958c15b45b989fc0a4d57f02251 Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Tue, 22 Mar 2016 01:56:16 -0700 Subject: Change from PR #552: rename setup_dependent_python_module -> setup_dependent_package - Fixed in package.py - Fixed wrong prototypes in packages that use it. - Fixed build_environment to set module variables properly - added hacky fix to ensure spec/package consistency in build processes. - Need to think about defensive spec copy done by `Repo.get`. May be time to think about an immutable spec implementation. --- lib/spack/spack/build_environment.py | 52 ++++++++++++++++------ lib/spack/spack/package.py | 2 +- var/spack/repos/builtin/packages/mpich/package.py | 2 +- .../builtin/packages/netlib-scalapack/package.py | 22 ++++----- 4 files changed, 52 insertions(+), 26 deletions(-) (limited to 'var') diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py index fc5b7d6207..119a255a34 100644 --- a/lib/spack/spack/build_environment.py +++ b/lib/spack/spack/build_environment.py @@ -225,7 +225,7 @@ def set_module_variables_for_package(pkg, module): m.spack_cc = join_path(link_dir, pkg.compiler.link_paths['cc']) m.spack_cxx = join_path(link_dir, pkg.compiler.link_paths['cxx']) m.spack_f77 = join_path(link_dir, pkg.compiler.link_paths['f77']) - m.spack_f90 = join_path(link_dir, pkg.compiler.link_paths['fc']) + m.spack_fc = join_path(link_dir, pkg.compiler.link_paths['fc']) # Emulate some shell commands for convenience m.pwd = os.getcwd @@ -270,32 +270,56 @@ def parent_class_modules(cls): return result +def setup_module_variables_for_dag(pkg): + """Set module-scope variables for all packages in the DAG.""" + for spec in pkg.spec.traverse(order='post'): + # If a user makes their own package repo, e.g. + # spack.repos.mystuff.libelf.Libelf, and they inherit from + # an existing class like spack.repos.original.libelf.Libelf, + # then set the module variables for both classes so the + # parent class can still use them if it gets called. + spkg = spec.package + modules = parent_class_modules(spkg.__class__) + for mod in modules: + set_module_variables_for_package(spkg, mod) + set_module_variables_for_package(spkg, spkg.module) + + def setup_package(pkg): """Execute all environment setup routines.""" spack_env = EnvironmentModifications() run_env = EnvironmentModifications() + # Before proceeding, ensure that specs and packages are consistent + # + # This is a confusing behavior due to how packages are + # constructed. `setup_dependent_package` may set attributes on + # specs in the DAG for use by other packages' install + # method. However, spec.package will look up a package via + # spack.repo, which defensively copies specs into packages. This + # code ensures that all packages in the DAG have pieces of the + # same spec object at build time. + # + # This is safe for the build process, b/c the build process is a + # throwaway environment, but it is kind of dirty. + # + # TODO: Think about how to avoid this fix and do something cleaner. + for s in pkg.spec.traverse(): s.package.spec = s + set_compiler_environment_variables(pkg, spack_env) set_build_environment_variables(pkg, spack_env) - - # If a user makes their own package repo, e.g. - # spack.repos.mystuff.libelf.Libelf, and they inherit from - # an existing class like spack.repos.original.libelf.Libelf, - # then set the module variables for both classes so the - # parent class can still use them if it gets called. - modules = parent_class_modules(pkg.__class__) - for mod in modules: - set_module_variables_for_package(pkg, mod) + setup_module_variables_for_dag(pkg) # Allow dependencies to modify the module - for dependency_spec in pkg.spec.traverse(root=False): + spec = pkg.spec + for dependency_spec in spec.traverse(root=False): dpkg = dependency_spec.package - dpkg.setup_dependent_python_module(pkg.module, pkg.spec) + dpkg.setup_dependent_package(pkg.module, spec) # Allow dependencies to set up environment as well - for dependency_spec in pkg.spec.traverse(root=False): + for dependency_spec in spec.traverse(root=False): dpkg = dependency_spec.package - dpkg.setup_dependent_environment(spack_env, run_env, pkg.spec) + dpkg.setup_dependent_environment(spack_env, run_env, spec) # Allow the package to apply some settings. pkg.setup_environment(spack_env, run_env) diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index 9d8ac87bd7..9af3221837 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -1075,7 +1075,7 @@ class Package(object): self.setup_environment(spack_env, run_env) - def setup_dependent_python_module(self, module, dependent_spec): + def setup_dependent_package(self, module, dependent_spec): """Set up Python module-scope variables for dependent packages. Called before the install() method of dependents. diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py index c4d9940bb7..b20dc8dd60 100644 --- a/var/spack/repos/builtin/packages/mpich/package.py +++ b/var/spack/repos/builtin/packages/mpich/package.py @@ -54,7 +54,7 @@ class Mpich(Package): env.set('MPICH_F90', spack_f90) env.set('MPICH_FC', spack_fc) - def setup_dependent_python_module(self, module, spec, dep_spec): + def setup_dependent_package(self, module, dep_spec): """For dependencies, make mpicc's use spack wrapper.""" # FIXME : is this necessary ? Shouldn't this be part of a contract with MPI providers? module.mpicc = join_path(self.prefix.bin, 'mpicc') diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py index 62abfcc48e..c3e6822cdf 100644 --- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py @@ -1,4 +1,5 @@ from spack import * +import sys class NetlibScalapack(Package): """ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines""" @@ -11,16 +12,16 @@ class NetlibScalapack(Package): version('2.0.0', '9e76ae7b291be27faaad47cfc256cbfe') # versions before 2.0.0 are not using cmake and requires blacs as # a separated package - + variant('shared', default=True, description='Build the shared library version') variant('fpic', default=False, description="Build with -fpic compiler option") - + provides('scalapack') - + depends_on('mpi') depends_on('lapack') - - def install(self, spec, prefix): + + def install(self, spec, prefix): options = [ "-DBUILD_SHARED_LIBS:BOOL=%s" % ('ON' if '+shared' in spec else 'OFF'), "-DBUILD_STATIC_LIBS:BOOL=%s" % ('OFF' if '+shared' in spec else 'ON'), @@ -40,10 +41,11 @@ class NetlibScalapack(Package): make() make("install") - def setup_dependent_python_module(self, module, spec, dependent_spec): + def setup_dependent_package(self, module, dependent_spec): + spec = self.spec lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so' - lib_suffix = lib_dsuffix if '+shared' in spec['scalapack'] else '.a' + lib_suffix = lib_dsuffix if '+shared' in spec else '.a' - spec['scalapack'].fc_link = '-L%s -lscalapack' % spec['scalapack'].prefix.lib - spec['scalapack'].cc_link = spec['scalapack'].fc_link - spec['scalapack'].libraries = [join_path(spec['scalapack'].prefix.lib, 'libscalapack%s' % lib_suffix)] + spec.fc_link = '-L%s -lscalapack' % spec.prefix.lib + spec.cc_link = spec.fc_link + spec.libraries = [join_path(spec.prefix.lib, 'libscalapack%s' % lib_suffix)] -- cgit v1.2.3-70-g09d2 From 6eb97a30a36f0a0f072826d473a641dd143345ed Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Tue, 22 Mar 2016 14:24:27 +0100 Subject: arpack: fix for +mpi variant --- var/spack/repos/builtin/packages/arpack-ng/package.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/arpack-ng/package.py b/var/spack/repos/builtin/packages/arpack-ng/package.py index 614071cf53..dd86b17a53 100644 --- a/var/spack/repos/builtin/packages/arpack-ng/package.py +++ b/var/spack/repos/builtin/packages/arpack-ng/package.py @@ -50,7 +50,10 @@ class ArpackNg(Package): options = ['--prefix=%s' % prefix] if '+mpi' in spec: - options.append('--enable-mpi') + options.extend([ + '--enable-mpi', + 'F77=mpif77' #FIXME: avoid hardcoding MPI wrapper names + ]) if '~shared' in spec: options.append('--enable-shared=no') -- cgit v1.2.3-70-g09d2 From d25026b74936f9988cdaf701258c937b3965c106 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Tue, 22 Mar 2016 16:26:16 +0100 Subject: add OCE package --- var/spack/repos/builtin/packages/oce/package.py | 47 +++++++++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 var/spack/repos/builtin/packages/oce/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/oce/package.py b/var/spack/repos/builtin/packages/oce/package.py new file mode 100644 index 0000000000..06acb96736 --- /dev/null +++ b/var/spack/repos/builtin/packages/oce/package.py @@ -0,0 +1,47 @@ +from spack import * +import platform + +class Oce(Package): + """ + Open CASCADE Community Edition: + patches/improvements/experiments contributed by users over the official Open CASCADE library. + """ + homepage = "https://github.com/tpaviot/oce" + url = "https://github.com/tpaviot/oce/archive/OCE-0.17.tar.gz" + + version('0.17.1', '36c67b87093c675698b483454258af91') + version('0.17' , 'f1a89395c4b0d199bea3db62b85f818d') + version('0.16.1', '4d591b240c9293e879f50d86a0cb2bb3') + version('0.16' , '7a4b4df5a104d75a537e25e7dd387eca') + version('0.15' , '7ec541a1c350ca8a684f74980e48801c') + + depends_on('cmake@2.8:') + + def install(self, spec, prefix): + options = [] + options.extend(std_cmake_args) + options.extend([ + '-DOCE_INSTALL_PREFIX=%s' % prefix, + '-DOCE_BUILD_SHARED_LIB:BOOL=ON', + '-DOCE_BUILD_TYPE:STRING=Release', + '-DOCE_DATAEXCHANGE:BOOL=ON', + '-DOCE_DISABLE_X11:BOOL=ON', + '-DOCE_DRAW:BOOL=OFF', + '-DOCE_MODEL:BOOL=ON', + '-DOCE_MULTITHREAD_LIBRARY:STRING=NONE', # FIXME: add tbb + '-DOCE_OCAF:BOOL=ON', + '-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=OFF', + '-DOCE_VISUALISATION:BOOL=OFF', + '-DOCE_WITH_FREEIMAGE:BOOL=OFF', + '-DOCE_WITH_GL2PS:BOOL=OFF', + '-DOCE_WITH_OPENCL:BOOL=OFF' + ]) + + if platform.system() == 'Darwin': + options.extend([ + '-DOCE_OSX_USE_COCOA:BOOL=ON', + ]) + + cmake('.', *options) + + make("install/strip") -- cgit v1.2.3-70-g09d2 From 1f8d79b69ab005a6a372ff34806525148c0ed854 Mon Sep 17 00:00:00 2001 From: "Kelly (KT) Thompson" Date: Tue, 22 Mar 2016 09:33:49 -0600 Subject: + Provide a ~perl variant to support building on systems w/o the perl-devel package installed. --- var/spack/repos/builtin/packages/graphviz/package.py | 3 --- 1 file changed, 3 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/graphviz/package.py b/var/spack/repos/builtin/packages/graphviz/package.py index 2a2102bfcb..84bd696af2 100644 --- a/var/spack/repos/builtin/packages/graphviz/package.py +++ b/var/spack/repos/builtin/packages/graphviz/package.py @@ -8,7 +8,6 @@ class Graphviz(Package): version('2.38.0', '5b6a829b2ac94efcd5fa3c223ed6d3ae') variant('perl', default=True, description='Disable if you have problems with the optional script language bindings') - variant('shared', default=True, description='Building static is required on AIX') parallel = False @@ -20,8 +19,6 @@ class Graphviz(Package): options = ['--prefix=%s' % prefix] if '~perl' in spec: options.append('--disable-perl') - if '~shared' in spec: - options.append('--enable-shared=no') configure(*options) make() -- cgit v1.2.3-70-g09d2 From 7618dc504cb58e115a0a95b130bcfc485cd8341d Mon Sep 17 00:00:00 2001 From: Erik Schnetter Date: Tue, 22 Mar 2016 19:17:39 +0100 Subject: temporary fix Hypre for OSX by building static lib by default --- var/spack/repos/builtin/packages/hypre/package.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/hypre/package.py b/var/spack/repos/builtin/packages/hypre/package.py index 242ee100d7..8d93d48d1f 100644 --- a/var/spack/repos/builtin/packages/hypre/package.py +++ b/var/spack/repos/builtin/packages/hypre/package.py @@ -1,5 +1,5 @@ from spack import * -import os +import os, sys class Hypre(Package): """Hypre is a library of high performance preconditioners that @@ -12,7 +12,8 @@ class Hypre(Package): version('2.10.1', 'dc048c4cabb3cd549af72591474ad674') version('2.10.0b', '768be38793a35bb5d055905b271f5b8e') - variant('shared', default=True, description="Build shared library version (disables static library)") + # hypre does not know how to build shared libraries on Darwin + variant('shared', default=sys.platform!='darwin', description="Build shared library version (disables static library)") depends_on("mpi") depends_on("blas") -- cgit v1.2.3-70-g09d2 From e56f5c4d6b4626a428b3c209f00eff59cd37b22f Mon Sep 17 00:00:00 2001 From: Cyrus Harrison Date: Tue, 22 Mar 2016 16:59:40 +0100 Subject: add Intel TBB package --- var/spack/repos/builtin/packages/tbb/package.py | 79 +++++++++++++++++++++++++ 1 file changed, 79 insertions(+) create mode 100644 var/spack/repos/builtin/packages/tbb/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/tbb/package.py b/var/spack/repos/builtin/packages/tbb/package.py new file mode 100644 index 0000000000..56ffe4c27c --- /dev/null +++ b/var/spack/repos/builtin/packages/tbb/package.py @@ -0,0 +1,79 @@ +from spack import * +import os +import glob + +class Tbb(Package): + """Widely used C++ template library for task parallelism. + Intel Threading Building Blocks (Intel TBB) lets you easily write parallel + C++ programs that take full advantage of multicore performance, that are + portable and composable, and that have future-proof scalability. + """ + homepage = "http://www.threadingbuildingblocks.org/" + + # Only version-specific URL's work for TBB + version('4.4.3', '80707e277f69d9b20eeebdd7a5f5331137868ce1', url='https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160128oss_src_0.tgz') + + def coerce_to_spack(self,tbb_build_subdir): + for compiler in ["icc","gcc","clang"]: + fs = glob.glob(join_path(tbb_build_subdir,"*.%s.inc" % compiler )) + for f in fs: + lines = open(f).readlines() + of = open(f,"w") + for l in lines: + if l.strip().startswith("CPLUS ="): + of.write("# coerced to spack\n") + of.write("CPLUS = $(CXX)\n") + elif l.strip().startswith("CPLUS ="): + of.write("# coerced to spack\n") + of.write("CONLY = $(CC)\n") + else: + of.write(l); + + def install(self, spec, prefix): + # + # we need to follow TBB's compiler selection logic to get the proper build + link flags + # but we still need to use spack's compiler wrappers + # to accomplish this, we do two things: + # + # * Look at the spack spec to determine which compiler we should pass to tbb's Makefile + # + # * patch tbb's build system to use the compiler wrappers (CC, CXX) for + # icc, gcc, clang + # (see coerce_to_spack()) + # + self.coerce_to_spack("build") + + if spec.satisfies('%clang'): + tbb_compiler = "clang" + elif spec.satisfies('%intel'): + tbb_compiler = "icc" + else: + tbb_compiler = "gcc" + + + mkdirp(prefix) + mkdirp(prefix.lib) + + # + # tbb does not have a configure script or make install target + # we simply call make, and try to put the pieces together + # + make("compiler=%s" %(tbb_compiler)) + + # install headers to {prefix}/include + install_tree('include',prefix.include) + + # install libs to {prefix}/lib + tbb_lib_names = ["libtbb", + "libtbbmalloc", + "libtbbmalloc_proxy"] + + for lib_name in tbb_lib_names: + # install release libs + fs = glob.glob(join_path("build","*release",lib_name + ".*")) + for f in fs: + install(f, prefix.lib) + # install debug libs if they exist + fs = glob.glob(join_path("build","*debug",lib_name + "_debug.*")) + for f in fs: + install(f, prefix.lib) -- cgit v1.2.3-70-g09d2 From 5f68e14d3bd90e4a71f6366a328dcc97fc6e8a92 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Tue, 22 Mar 2016 19:41:31 +0100 Subject: add gettext package --- .../repos/builtin/packages/gettext/package.py | 30 ++++++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 var/spack/repos/builtin/packages/gettext/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/gettext/package.py b/var/spack/repos/builtin/packages/gettext/package.py new file mode 100644 index 0000000000..05712d7392 --- /dev/null +++ b/var/spack/repos/builtin/packages/gettext/package.py @@ -0,0 +1,30 @@ +from spack import * + +class Gettext(Package): + """GNU internationalization (i18n) and localization (l10n) library.""" + homepage = "https://www.gnu.org/software/gettext/" + url = "http://ftpmirror.gnu.org/gettext/gettext-0.19.7.tar.xz" + + version('0.19.7', 'f81e50556da41b44c1d59ac93474dca5') + + def install(self, spec, prefix): + options = ['--disable-dependency-tracking', + '--disable-silent-rules', + '--disable-debug', + '--prefix=%s' % prefix, + '--with-included-gettext', + '--with-included-glib', + '--with-included-libcroco', + '--with-included-libunistring', + '--with-emacs', + '--with-lispdir=%s/emacs/site-lisp/gettext' % prefix.share, + '--disable-java', + '--disable-csharp', + '--without-git', # Don't use VCS systems to create these archives + '--without-cvs', + '--without-xz'] + + configure(*options) + + make() + make("install") -- cgit v1.2.3-70-g09d2 From fd1784369a20650c3fc6f84d57ed4e6be59afc44 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Tue, 22 Mar 2016 19:50:15 +0100 Subject: add muparser package --- var/spack/repos/builtin/packages/muparser/package.py | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 var/spack/repos/builtin/packages/muparser/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/muparser/package.py b/var/spack/repos/builtin/packages/muparser/package.py new file mode 100644 index 0000000000..a1a9ff90e5 --- /dev/null +++ b/var/spack/repos/builtin/packages/muparser/package.py @@ -0,0 +1,18 @@ +from spack import * + +class Muparser(Package): + """C++ math expression parser library.""" + homepage = "http://muparser.beltoforion.de/" + url = "https://github.com/beltoforion/muparser/archive/v2.2.5.tar.gz" + + version('2.2.5', '02dae671aa5ad955fdcbcd3fee313fb7') + + def install(self, spec, prefix): + options = ['--disable-debug', + '--disable-dependency-tracking', + '--prefix=%s' % prefix] + + configure(*options) + + make() + make("install") -- cgit v1.2.3-70-g09d2 From d05e4581c9d249c0736d8d58b394860ca05f8402 Mon Sep 17 00:00:00 2001 From: Joseph Ciurej Date: Tue, 22 Mar 2016 12:31:26 -0700 Subject: Added the '+silex' variant to the Silo package. Added a number of different versions to the Silo package. --- var/spack/repos/builtin/packages/silo/package.py | 23 +++++++++++++++++------ 1 file changed, 17 insertions(+), 6 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/silo/package.py b/var/spack/repos/builtin/packages/silo/package.py index d1aed78e0e..b7894e4d2b 100644 --- a/var/spack/repos/builtin/packages/silo/package.py +++ b/var/spack/repos/builtin/packages/silo/package.py @@ -5,24 +5,35 @@ class Silo(Package): data to binary, disk files.""" homepage = "http://wci.llnl.gov/simulation/computer-codes/silo" - url = "https://wci.llnl.gov/content/assets/docs/simulation/computer-codes/silo/silo-4.8/silo-4.8.tar.gz" + base_url = "https://wci.llnl.gov/content/assets/docs/simulation/computer-codes/silo" + version('4.10.2', '9ceac777a2f2469ac8cef40f4fab49c8') + version('4.9', 'a83eda4f06761a86726e918fc55e782a') version('4.8', 'b1cbc0e7ec435eb656dc4b53a23663c9') variant('fortran', default=True, description='Enable Fortran support') + variant('silex', default=False, description='Builds Silex, a GUI for viewing Silo files') - depends_on("hdf5") + depends_on('hdf5') + depends_on('qt', when='+silex') def install(self, spec, prefix): config_args = [ '--enable-fortran' if '+fortran' in spec else '--disable-fortran', + '--enable-silex' if '+silex' in spec else '--disable-silex', ] + if '+silex' in spec: + config_args.append('--with-Qt-dir=%s' % spec['qt'].prefix) + configure( - "--prefix=%s" % prefix, - "--with-hdf5=%s,%s" % (spec['hdf5'].prefix.include, spec['hdf5'].prefix.lib), - "--with-zlib=%s,%s" % (spec['zlib'].prefix.include, spec['zlib'].prefix.lib), + '--prefix=%s' % prefix, + '--with-hdf5=%s,%s' % (spec['hdf5'].prefix.include, spec['hdf5'].prefix.lib), + '--with-zlib=%s,%s' % (spec['zlib'].prefix.include, spec['zlib'].prefix.lib), *config_args) make() - make("install") + make('install') + + def url_for_version(self, version): + return '%s/silo-%s/silo-%s.tar.gz' % (Silo.base_url, version, version) -- cgit v1.2.3-70-g09d2 From 1728a0c3e60d55d1181f14ef5a677b1652a0680b Mon Sep 17 00:00:00 2001 From: Joseph Ciurej Date: Tue, 22 Mar 2016 12:33:11 -0700 Subject: Updated the 'crypto++' package to use an improved URL formation scheme (inspired by changes made to the 'Silo' package). --- var/spack/repos/builtin/packages/cryptopp/package.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/cryptopp/package.py b/var/spack/repos/builtin/packages/cryptopp/package.py index 1693c4b160..743a3ac70f 100644 --- a/var/spack/repos/builtin/packages/cryptopp/package.py +++ b/var/spack/repos/builtin/packages/cryptopp/package.py @@ -8,8 +8,8 @@ class Cryptopp(Package): public-key encryption (RSA, DSA), and a few obsolete/historical encryption algorithms (MD5, Panama).""" - homepage = "http://www.cryptopp.com/" - url = "http://www.cryptopp.com/cryptopp563.zip" + homepage = "http://www.cryptopp.com" + base_url = "http://www.cryptopp.com" version('5.6.3', '3c5b70e2ec98b7a24988734446242d07') version('5.6.2', '7ed022585698df48e65ce9218f6c6a67') @@ -28,4 +28,4 @@ class Cryptopp(Package): version_tuple = tuple(v for v in iter(version)) version_string = reduce(lambda vs, nv: vs + str(nv), version_tuple, "") - return "%scryptopp%s.zip" % (Cryptopp.homepage, version_string) + return '%s/cryptopp%s.zip' % (Cryptopp.base_url, version_string) -- cgit v1.2.3-70-g09d2 From 27f337aa11104a6e625db6e40f8d9414954123ee Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Tue, 22 Mar 2016 11:44:38 +0100 Subject: petsc: set PETSC_DIR in dependent_env --- var/spack/repos/builtin/packages/petsc/package.py | 4 ++++ 1 file changed, 4 insertions(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py index 7239baaf7f..3dd117eed1 100644 --- a/var/spack/repos/builtin/packages/petsc/package.py +++ b/var/spack/repos/builtin/packages/petsc/package.py @@ -100,3 +100,7 @@ class Petsc(Package): # PETSc has its own way of doing parallel make. make('MAKE_NP=%s' % make_jobs, parallel=False) make("install") + + def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + # set up PETSC_DIR for everyone using PETSc package + spack_env.set('PETSC_DIR', self.prefix) -- cgit v1.2.3-70-g09d2 From 24264eb00e4f4e3661ea1a28e9cbe3a97cd69580 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Tue, 22 Mar 2016 11:45:18 +0100 Subject: add slepc package --- var/spack/repos/builtin/packages/slepc/package.py | 49 +++++++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 var/spack/repos/builtin/packages/slepc/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/slepc/package.py b/var/spack/repos/builtin/packages/slepc/package.py new file mode 100644 index 0000000000..8b5f24394f --- /dev/null +++ b/var/spack/repos/builtin/packages/slepc/package.py @@ -0,0 +1,49 @@ +import os +from spack import * + + +class Slepc(Package): + """ + Scalable Library for Eigenvalue Computations. + """ + + homepage = "http://www.grycap.upv.es/slepc" + url = "http://slepc.upv.es/download/download.php?filename=slepc-3.6.2.tar.gz" + + version('3.6.2', '2ab4311bed26ccf7771818665991b2ea3a9b15f97e29fd13911ab1293e8e65df') + + variant('arpack', default=False, description='Enables Arpack wrappers') + + depends_on('petsc') + depends_on('arpack-ng~mpi',when='+arpack^petsc~mpi') + depends_on('arpack-ng+mpi',when='+arpack^petsc+mpi') + + def install(self, spec, prefix): + # set SLEPC_DIR for installation + os.environ['SLEPC_DIR'] = self.stage.source_path + + options = [] + + if '+arpack' in spec: + options.extend([ + '--with-arpack-dir=%s' % spec['arpack-ng'].prefix.lib, + ]) + if 'arpack-ng~mpi' in spec: + options.extend([ + '--with-arpack-flags=-larpack' + ]) + else: + options.extend([ + '--with-arpack-flags=-lparpack,-larpack' + ]) + + configure('--prefix=%s' % prefix, *options) + + make('MAKE_NP=%s' % make_jobs, parallel=False) + #FIXME: + # make('test') + make('install') + + def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + # set up SLEPC_DIR for everyone using SLEPc package + spack_env.set('SLEPC_DIR', self.prefix) -- cgit v1.2.3-70-g09d2 From 6c8d51f403213cf3a49373d4dca03fac565a73b4 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Tue, 22 Mar 2016 22:58:14 +0100 Subject: add p4est package --- var/spack/repos/builtin/packages/p4est/package.py | 34 +++++++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 var/spack/repos/builtin/packages/p4est/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/p4est/package.py b/var/spack/repos/builtin/packages/p4est/package.py new file mode 100644 index 0000000000..1e2969fe64 --- /dev/null +++ b/var/spack/repos/builtin/packages/p4est/package.py @@ -0,0 +1,34 @@ +from spack import * + +class P4est(Package): + """Dynamic management of a collection (a forest) of adaptive octrees in parallel""" + homepage = "http://www.p4est.org" + url = "http://p4est.github.io/release/p4est-1.1.tar.gz" + + version('1.1', '37ba7f4410958cfb38a2140339dbf64f') + + # disable by default to make it work on frontend of clusters + variant('tests', default=False, description='Run small tests') + + depends_on('mpi') + + def install(self, spec, prefix): + options = ['--enable-mpi', + '--enable-shared', + '--disable-vtk-binary', + '--without-blas', + 'CPPFLAGS=-DSC_LOG_PRIORITY=SC_LP_ESSENTIAL', + 'CFLAGS=-O2', + 'CC=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpicc'), # TODO: use ENV variables or MPI class wrappers + 'CXX=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpic++'), + 'FC=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif90'), + 'F77=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif77'), + ] + + configure('--prefix=%s' % prefix, *options) + + make() + if '+tests' in self.spec: + make("check") + + make("install") -- cgit v1.2.3-70-g09d2 From 0ee993569f8f47f5ca94873bc779d98639e9a1b4 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Tue, 22 Mar 2016 23:04:59 +0100 Subject: add deal.ii package --- var/spack/repos/builtin/packages/dealii/package.py | 67 ++++++++++++++++++++++ 1 file changed, 67 insertions(+) create mode 100644 var/spack/repos/builtin/packages/dealii/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py new file mode 100644 index 0000000000..cddf5cd98b --- /dev/null +++ b/var/spack/repos/builtin/packages/dealii/package.py @@ -0,0 +1,67 @@ +from spack import * + +class Dealii(Package): + """C++ software library providing well-documented tools to build finite element codes for a broad variety of PDEs.""" + homepage = "https://www.dealii.org" + url = "https://github.com/dealii/dealii/releases/download/v8.4.0/dealii-8.4.0.tar.gz" + + version('8.4.0', 'ac5dbf676096ff61e092ce98c80c2b00') + + depends_on ("cmake") + depends_on ("blas") + depends_on ("lapack") + depends_on ("mpi") + + #depends_on ("arpack") + depends_on ("boost") + #depends_on ("doxygen") + depends_on ("hdf5+mpi") + depends_on ("metis") + #depends_on "muparser" + depends_on ("netcdf") + #depends_on ("numdiff") + #depends_on ("oce") + depends_on ("p4est") + depends_on ("parmetis") + depends_on ("petsc") + #depends_on ("slepc") + depends_on ("SuiteSparse") + #depends_on "tbb" + depends_on ("trilinos") + + def install(self, spec, prefix): + options = [] + options.extend(std_cmake_args) + + # CMAKE_BUILD_TYPE should be DebugRelease | Debug | Release + for word in options[:]: + if word.startswith('-DCMAKE_BUILD_TYPE'): + options.remove(word) + + options.extend([ + '-DCMAKE_BUILD_TYPE=DebugRelease', + '-DDEAL_II_WITH_THREADS:BOOL=ON' + '-DDEAL_II_WITH_MPI:BOOL=ON', + '-DCMAKE_C_COMPILER=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpicc'), + '-DCMAKE_CXX_COMPILER=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpic++'), + '-DCMAKE_Fortran_COMPILER=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif90'), + #'-DARPACK_DIR=%s' % , + '-DBOOST_DIR=%s' % spec['boost'].prefix, + '-DHDF5_DIR=%s' % spec['hdf5'].prefix, + '-DMETIS_DIR=%s' % spec['metis'].prefix, + #'-DMUPARSER_DIR=%s ' + '-DNETCDF_DIR=%s' % spec['netcdf'].prefix, + #'-DOPENCASCADE_DIR= + '-DP4EST_DIR=%s' % spec['p4est'].prefix, + '-DPETSC_DIR=%s' % spec['petsc'].prefix, + #'-DSLEPC_DIR= + '-DUMFPACK_DIR=%s' % spec['SuiteSparse'].prefix, + #'-DTBB_DIR=%s' + '-DTRILINOS_DIR=%s' % spec['trilinos'].prefix + ]) + + cmake('.', *options) + + make() + make("test") + make("install") -- cgit v1.2.3-70-g09d2 From 474db2085e223b8226a6ae799232bb2fede3efde Mon Sep 17 00:00:00 2001 From: Joseph Ciurej Date: Tue, 22 Mar 2016 15:55:54 -0700 Subject: Simplified the 'url_for_version' function for the 'Crypto++' package. --- var/spack/repos/builtin/packages/cryptopp/package.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/cryptopp/package.py b/var/spack/repos/builtin/packages/cryptopp/package.py index 743a3ac70f..bc83cb2b65 100644 --- a/var/spack/repos/builtin/packages/cryptopp/package.py +++ b/var/spack/repos/builtin/packages/cryptopp/package.py @@ -25,7 +25,5 @@ class Cryptopp(Package): install('libcryptopp.a', prefix.lib) def url_for_version(self, version): - version_tuple = tuple(v for v in iter(version)) - version_string = reduce(lambda vs, nv: vs + str(nv), version_tuple, "") - + version_string = str(version).replace('.', '') return '%s/cryptopp%s.zip' % (Cryptopp.base_url, version_string) -- cgit v1.2.3-70-g09d2 From 5b3c96a9bb0ba6501512c93dcdb26510e796314e Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 23 Mar 2016 08:07:45 +0100 Subject: fix superlu-dist lib installation --- var/spack/repos/builtin/packages/superlu-dist/package.py | 1 + 1 file changed, 1 insertion(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/superlu-dist/package.py b/var/spack/repos/builtin/packages/superlu-dist/package.py index c4c76909b3..9a94de8ba5 100644 --- a/var/spack/repos/builtin/packages/superlu-dist/package.py +++ b/var/spack/repos/builtin/packages/superlu-dist/package.py @@ -54,6 +54,7 @@ class SuperluDist(Package): # need to install by hand headers_location = join_path(self.prefix.include,'superlu_dist') mkdirp(headers_location) + mkdirp(prefix.lib) # FIXME: fetch all headers in the folder automatically for header in ['Cnames.h','cublas_utils.h','dcomplex.h','html_mainpage.h','machines.h','old_colamd.h','psymbfact.h','superlu_ddefs.h','superlu_defs.h','superlu_enum_consts.h','superlu_zdefs.h','supermatrix.h','util_dist.h']: superludist_header = join_path(self.stage.source_path, 'SRC/',header) -- cgit v1.2.3-70-g09d2 From c4134ee71e43a6a2a38822e25cc72ca73efdcfea Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Wed, 23 Mar 2016 00:36:32 -0700 Subject: Fix #608: broken numpy build. - Failed to catch all instances of modify_module when it was renamed to setup_dependent_package. - Refactored remaining modify_module calls. - Also modified Python's setup_dependent_package slightly: only creates empty site-packages directory for Python extensions now, not for all dependents. --- lib/spack/spack/modules.py | 4 ++-- lib/spack/spack/preferred_packages.py | 4 +++- var/spack/repos/builtin/packages/python/package.py | 11 ++++++----- var/spack/repos/builtin/packages/ruby/package.py | 6 +++--- 4 files changed, 14 insertions(+), 11 deletions(-) (limited to 'var') diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py index 05c93cd3e6..8ed98e5d38 100644 --- a/lib/spack/spack/modules.py +++ b/lib/spack/spack/modules.py @@ -160,8 +160,8 @@ class EnvModule(object): # package-specific modifications for extendee in self.pkg.extendees: extendee_spec = self.spec[extendee] - extendee_spec.package.modify_module( - self.pkg.module, extendee_spec, self.spec) + extendee_spec.package.setup_dependent_package( + self.pkg.module, self.spec) # Package-specific environment modifications spack_env = EnvironmentModifications() diff --git a/lib/spack/spack/preferred_packages.py b/lib/spack/spack/preferred_packages.py index 4d8526c75f..f0a5382dc9 100644 --- a/lib/spack/spack/preferred_packages.py +++ b/lib/spack/spack/preferred_packages.py @@ -150,7 +150,9 @@ class PreferredPackages(object): def version_compare(self, pkgname, a, b): """Return less-than-0, 0, or greater than 0 if version a of pkgname is respecively less-than, equal-to, or greater-than version b of pkgname. - One version is less-than another if it is preferred over the other.""" + Versions marked 'preferred=True' in package.py take precedence over any + versions not marked preferred. + """ return self._spec_compare(pkgname, 'version', a, b, True, None) diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index 4f55bc803e..6d9030805b 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -108,7 +108,7 @@ class Python(Package): run_env.set('PYTHONPATH', pythonpath) - def modify_module(self, module, spec, ext_spec): + def setup_dependent_package(self, module, ext_spec): """ Called before python modules' install() methods. @@ -118,17 +118,18 @@ class Python(Package): """ # Python extension builds can have a global python executable function if self.version >= Version("3.0.0") and self.version < Version("4.0.0"): - module.python = Executable(join_path(spec.prefix.bin, 'python3')) + module.python = Executable(join_path(self.spec.prefix.bin, 'python3')) else: - module.python = Executable(join_path(spec.prefix.bin, 'python')) + module.python = Executable(join_path(self.spec.prefix.bin, 'python')) # Add variables for lib/pythonX.Y and lib/pythonX.Y/site-packages dirs. module.python_lib_dir = os.path.join(ext_spec.prefix, self.python_lib_dir) module.python_include_dir = os.path.join(ext_spec.prefix, self.python_include_dir) module.site_packages_dir = os.path.join(ext_spec.prefix, self.site_packages_dir) - # Make the site packages directory if it does not exist already. - mkdirp(module.site_packages_dir) + # Make the site packages directory for extensions, if it does not exist already. + if ext_spec.package.is_extension: + mkdirp(module.site_packages_dir) # ======================================================================== # Handle specifics of activating and deactivating python modules. diff --git a/var/spack/repos/builtin/packages/ruby/package.py b/var/spack/repos/builtin/packages/ruby/package.py index 7ff1898ce9..e13677e4d2 100644 --- a/var/spack/repos/builtin/packages/ruby/package.py +++ b/var/spack/repos/builtin/packages/ruby/package.py @@ -30,7 +30,7 @@ class Ruby(Package): # The actual installation path for this gem spack_env.set('GEM_HOME', extension_spec.prefix) - def modify_module(self, module, spec, ext_spec): + def setup_dependent_package(self, module, ext_spec): """Called before ruby modules' install() methods. Sets GEM_HOME and GEM_PATH to values appropriate for the package being built. @@ -39,5 +39,5 @@ class Ruby(Package): gem('install', '.gem') """ # Ruby extension builds have global ruby and gem functions - module.ruby = Executable(join_path(spec.prefix.bin, 'ruby')) - module.gem = Executable(join_path(spec.prefix.bin, 'gem')) + module.ruby = Executable(join_path(self.spec.prefix.bin, 'ruby')) + module.gem = Executable(join_path(self.spec.prefix.bin, 'gem')) -- cgit v1.2.3-70-g09d2 From 01918a6f4891ab985b8619daaadc1bf484e4db17 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 23 Mar 2016 05:26:51 +0100 Subject: fix MUMPS build on OSX (set parallel=False) --- var/spack/repos/builtin/packages/mumps/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py index 5c120c37df..5a254dfd00 100644 --- a/var/spack/repos/builtin/packages/mumps/package.py +++ b/var/spack/repos/builtin/packages/mumps/package.py @@ -135,7 +135,8 @@ class Mumps(Package): self.write_makefile_inc() - make(*make_libs) + # Build fails in parallel, at least on OS-X + make(*make_libs, parallel=False) install_tree('lib', prefix.lib) install_tree('include', prefix.include) -- cgit v1.2.3-70-g09d2 From cc582dd4b435ba06dc140b1ca96b688871e36abb Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Wed, 23 Mar 2016 02:02:49 -0700 Subject: Add mock python package. --- .../repos/builtin.mock/packages/python/package.py | 43 ++++++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 var/spack/repos/builtin.mock/packages/python/package.py (limited to 'var') diff --git a/var/spack/repos/builtin.mock/packages/python/package.py b/var/spack/repos/builtin.mock/packages/python/package.py new file mode 100644 index 0000000000..c5fed52f53 --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/python/package.py @@ -0,0 +1,43 @@ +############################################################################## +# Copyright (c) 2013-2015, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License (as published by +# the Free Software Foundation) version 2.1 dated February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program; if not, write to the Free Software Foundation, +# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + +class Python(Package): + """Dummy Python package to demonstrate preferred versions.""" + homepage = "http://www.python.org" + url = "http://www.python.org/ftp/python/2.7.8/Python-2.7.8.tgz" + + extendable = True + + version('3.5.1', 'be78e48cdfc1a7ad90efff146dce6cfe') + version('3.5.0', 'a56c0c0b45d75a0ec9c6dee933c41c36') + version('2.7.11', '6b6076ec9e93f05dd63e47eb9c15728b', preferred=True) + version('2.7.10', 'd7547558fd673bd9d38e2108c6b42521') + version('2.7.9', '5eebcaa0030dc4061156d3429657fb83') + version('2.7.8', 'd4bca0159acb0b44a781292b5231936f') + + def install(self, spec, prefix): + pass + -- cgit v1.2.3-70-g09d2 From 34a8f0c96bc50870f20f094d95b403b2bb19487d Mon Sep 17 00:00:00 2001 From: alalazo Date: Wed, 23 Mar 2016 17:01:52 +0100 Subject: espresso : fixes #454 --- var/spack/repos/builtin/packages/espresso/package.py | 4 ++++ 1 file changed, 4 insertions(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/espresso/package.py b/var/spack/repos/builtin/packages/espresso/package.py index a2bf58f585..59f362ab46 100644 --- a/var/spack/repos/builtin/packages/espresso/package.py +++ b/var/spack/repos/builtin/packages/espresso/package.py @@ -32,6 +32,10 @@ class Espresso(Package): if '+elpa' in spec and ('~mpi' in spec or '~scalapack' in spec): raise RuntimeError(error.format(variant='elpa')) + def setup_environment(self, spack_env, run_env): + # Espresso copies every executable in prefix without creating sub-folders + run_env.prepend_path('PATH', self.prefix) + def install(self, spec, prefix): self.check_variants(spec) -- cgit v1.2.3-70-g09d2 From 4e5dfc8b18ed30e261fe6b6dd014c8991937934d Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 23 Mar 2016 19:40:16 +0100 Subject: fix missing (depricated) _dggsvd_ and _sggsvd_ in Openblas 0.2.16 --- var/spack/repos/builtin/packages/openblas/package.py | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py index 781a1e2ec8..1d10f217c4 100644 --- a/var/spack/repos/builtin/packages/openblas/package.py +++ b/var/spack/repos/builtin/packages/openblas/package.py @@ -6,6 +6,7 @@ class Openblas(Package): homepage = "http://www.openblas.net" url = "http://github.com/xianyi/OpenBLAS/archive/v0.2.15.tar.gz" + version('0.2.17', '664a12807f2a2a7cda4781e3ab2ae0e1') version('0.2.16', 'fef46ab92463bdbb1479dcec594ef6dc') version('0.2.15', 'b1190f3d3471685f17cfd1ec1d252ac9') @@ -14,7 +15,14 @@ class Openblas(Package): provides('lapack') def install(self, spec, prefix): - make('libs', 'netlib', 'shared', 'CC=cc', 'FC=f77') + extra=[] + if spec.satisfies('@0.2.16'): + extra.extend([ + 'BUILD_LAPACK_DEPRECATED=1' # fix missing _dggsvd_ and _sggsvd_ + ]) + + make('libs', 'netlib', 'shared', 'CC=cc', 'FC=f77',*extra) + make("tests") make('install', "PREFIX='%s'" % prefix) lib_dsuffix = 'dylib' if sys.platform == 'darwin' else 'so' -- cgit v1.2.3-70-g09d2 From 9b8b17b6f1ec22ce4ac2115e5f7687beba21dd19 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Thu, 24 Mar 2016 10:36:02 +0100 Subject: fix parmetis on Ubuntu with GNU compilers by linking to lm --- var/spack/repos/builtin/packages/parmetis/link-to-lm.patch | 14 ++++++++++++++ var/spack/repos/builtin/packages/parmetis/package.py | 2 ++ 2 files changed, 16 insertions(+) create mode 100644 var/spack/repos/builtin/packages/parmetis/link-to-lm.patch (limited to 'var') diff --git a/var/spack/repos/builtin/packages/parmetis/link-to-lm.patch b/var/spack/repos/builtin/packages/parmetis/link-to-lm.patch new file mode 100644 index 0000000000..faa809231e --- /dev/null +++ b/var/spack/repos/builtin/packages/parmetis/link-to-lm.patch @@ -0,0 +1,14 @@ +diff --git a/libparmetis/CMakeLists.txt b/libparmetis/CMakeLists.txt +index 9cfc8a7..dfc0125 100644 +--- a/libparmetis/CMakeLists.txt ++++ b/libparmetis/CMakeLists.txt +@@ -5,7 +5,7 @@ file(GLOB parmetis_sources *.c) + # Create libparmetis + add_library(parmetis ${ParMETIS_LIBRARY_TYPE} ${parmetis_sources}) + # Link with metis and MPI libraries. +-target_link_libraries(parmetis metis ${MPI_LIBRARIES}) ++target_link_libraries(parmetis metis ${MPI_LIBRARIES} "-lm") + set_target_properties(parmetis PROPERTIES LINK_FLAGS "${MPI_LINK_FLAGS}") + + install(TARGETS parmetis + diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py index c691cf4191..bc71fb7299 100644 --- a/var/spack/repos/builtin/packages/parmetis/package.py +++ b/var/spack/repos/builtin/packages/parmetis/package.py @@ -52,6 +52,8 @@ class Parmetis(Package): # https://bitbucket.org/petsc/pkg-parmetis/commits/82409d68aa1d6cbc70740d0f35024aae17f7d5cb/raw/ patch('pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch') + patch('link-to-lm.patch') + depends_on('gdb', when='+gdb') def install(self, spec, prefix): -- cgit v1.2.3-70-g09d2 From 758a9c9096bd6c306f2dba0e40b46544dcec1992 Mon Sep 17 00:00:00 2001 From: alalazo Date: Wed, 23 Mar 2016 11:18:11 +0100 Subject: python extensions : create PYTHONPATH in module files --- lib/spack/spack/modules.py | 10 +++++----- var/spack/repos/builtin/packages/python/package.py | 5 ++++- 2 files changed, 9 insertions(+), 6 deletions(-) (limited to 'var') diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py index 6c32937c3c..d45fdde703 100644 --- a/lib/spack/spack/modules.py +++ b/lib/spack/spack/modules.py @@ -161,13 +161,13 @@ class EnvModule(object): # Let the extendee modify their extensions before asking for # package-specific modifications - for extendee in self.pkg.extendees: - extendee_spec = self.spec[extendee] - extendee_spec.package.setup_dependent_package( - self.pkg.module, self.spec) + spack_env = EnvironmentModifications() + for item in self.pkg.extendees: + package = self.spec[item].package + package.setup_dependent_package(self.pkg.module, self.spec) + package.setup_dependent_environment(spack_env, env, self.spec) # Package-specific environment modifications - spack_env = EnvironmentModifications() self.spec.package.setup_environment(spack_env, env) # TODO : implement site-specific modifications and filters diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index 6d9030805b..f5237c3b57 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -105,7 +105,10 @@ class Python(Package): pythonpath = ':'.join(python_paths) spack_env.set('PYTHONPATH', pythonpath) - run_env.set('PYTHONPATH', pythonpath) + + # For run time environment set only the path for extension_spec and prepend it to PYTHONPATH + if extension_spec.package.extends(self.spec): + run_env.prepend_path('PYTHONPATH', os.path.join(extension_spec.prefix, self.site_packages_dir)) def setup_dependent_package(self, module, ext_spec): -- cgit v1.2.3-70-g09d2 From 8643e2191357dd6f53bfafdfd51f43b770e2137c Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Thu, 24 Mar 2016 12:34:58 -0500 Subject: Simplified NumPy dependencies --- .../repos/builtin/packages/py-numpy/package.py | 37 ++++++++++++++++------ .../repos/builtin/packages/py-scipy/package.py | 5 +-- 2 files changed, 31 insertions(+), 11 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/py-numpy/package.py b/var/spack/repos/builtin/packages/py-numpy/package.py index 0354811186..a08e612df6 100644 --- a/var/spack/repos/builtin/packages/py-numpy/package.py +++ b/var/spack/repos/builtin/packages/py-numpy/package.py @@ -1,24 +1,43 @@ from spack import * class PyNumpy(Package): - """array processing for numbers, strings, records, and objects.""" - homepage = "https://pypi.python.org/pypi/numpy" + """NumPy is the fundamental package for scientific computing with Python. + It contains among other things: a powerful N-dimensional array object, + sophisticated (broadcasting) functions, tools for integrating C/C++ and + Fortran code, and useful linear algebra, Fourier transform, and random + number capabilities""" + homepage = "http://www.numpy.org/" url = "https://pypi.python.org/packages/source/n/numpy/numpy-1.9.1.tar.gz" - version('1.9.1', '78842b73560ec378142665e712ae4ad9') - version('1.9.2', 'a1ed53432dbcd256398898d35bc8e645') + version('1.10.4', 'aed294de0aa1ac7bd3f9745f4f1968ad') + version('1.9.2', 'a1ed53432dbcd256398898d35bc8e645') + version('1.9.1', '78842b73560ec378142665e712ae4ad9') - variant('blas', default=True) + + variant('blas', default=True) + variant('lapack', default=True) extends('python') depends_on('py-nose') - depends_on('netlib-blas+fpic', when='+blas') - depends_on('netlib-lapack+shared', when='+blas') + depends_on('blas', when='+blas') + depends_on('lapack', when='+lapack') def install(self, spec, prefix): + libraries = [] + library_dirs = [] + if '+blas' in spec: + libraries.append('blas') + library_dirs.append(spec['blas'].prefix.lib) + if '+lapack' in spec: + libraries.append('lapack') + library_dirs.append(spec['lapack'].prefix.lib) + + if '+blas' in spec or '+lapack' in spec: with open('site.cfg', 'w') as f: f.write('[DEFAULT]\n') - f.write('libraries=lapack,blas\n') - f.write('library_dirs=%s/lib:%s/lib\n' % (spec['blas'].prefix, spec['lapack'].prefix)) + f.write('libraries=%s\n' % ','.join(libraries)) + f.write('library_dirs=%s\n' % ':'.join(library_dirs)) + python('setup.py', 'install', '--prefix=%s' % prefix) + diff --git a/var/spack/repos/builtin/packages/py-scipy/package.py b/var/spack/repos/builtin/packages/py-scipy/package.py index 3a1124cc15..c2161c90c4 100644 --- a/var/spack/repos/builtin/packages/py-scipy/package.py +++ b/var/spack/repos/builtin/packages/py-scipy/package.py @@ -2,11 +2,12 @@ from spack import * class PyScipy(Package): """Scientific Library for Python.""" - homepage = "https://pypi.python.org/pypi/scipy" + homepage = "http://www.scipy.org/" url = "https://pypi.python.org/packages/source/s/scipy/scipy-0.15.0.tar.gz" - version('0.15.0', '639112f077f0aeb6d80718dc5019dc7a') + version('0.17.0', '5ff2971e1ce90e762c59d2cd84837224') version('0.15.1', 'be56cd8e60591d6332aac792a5880110') + version('0.15.0', '639112f077f0aeb6d80718dc5019dc7a') extends('python') depends_on('py-nose') -- cgit v1.2.3-70-g09d2 From 254f65f2994de32da8681c24838beb32bbbc5fe1 Mon Sep 17 00:00:00 2001 From: Alfredo Gimenez Date: Thu, 24 Mar 2016 10:48:38 -0700 Subject: Remove incorrect sanity check for libelf --- var/spack/repos/builtin/packages/libelf/package.py | 2 -- 1 file changed, 2 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/libelf/package.py b/var/spack/repos/builtin/packages/libelf/package.py index 9f16708af5..29bc21b65c 100644 --- a/var/spack/repos/builtin/packages/libelf/package.py +++ b/var/spack/repos/builtin/packages/libelf/package.py @@ -38,8 +38,6 @@ class Libelf(Package): provides('elf') - sanity_check_is_file = 'include/libelf.h' - def install(self, spec, prefix): configure("--prefix=" + prefix, "--enable-shared", -- cgit v1.2.3-70-g09d2 From 7fb463abb9b912f9a5bcb6e810b733f0b8bc1672 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Thu, 24 Mar 2016 20:23:13 +0100 Subject: install GKlib headers along with METIS --- .../packages/metis/install_gklib_defs_rename.patch | 22 ++++++++++++++++++++++ var/spack/repos/builtin/packages/metis/package.py | 13 +++++++++++-- 2 files changed, 33 insertions(+), 2 deletions(-) create mode 100644 var/spack/repos/builtin/packages/metis/install_gklib_defs_rename.patch (limited to 'var') diff --git a/var/spack/repos/builtin/packages/metis/install_gklib_defs_rename.patch b/var/spack/repos/builtin/packages/metis/install_gklib_defs_rename.patch new file mode 100644 index 0000000000..b182b167b9 --- /dev/null +++ b/var/spack/repos/builtin/packages/metis/install_gklib_defs_rename.patch @@ -0,0 +1,22 @@ +# HG changeset patch +# User Sean Farley +# Date 1332269671 18000 +# Tue Mar 20 13:54:31 2012 -0500 +# Node ID b95c0c2e1d8bf8e3273f7d45e856f0c0127d998e +# Parent 88049269953c67c3fdcc4309bf901508a875f0dc +cmake: add gklib headers to install into include + +diff -r 88049269953c -r b95c0c2e1d8b libmetis/CMakeLists.txt +Index: libmetis/CMakeLists.txt +=================================================================== +--- a/libmetis/CMakeLists.txt Tue Mar 20 13:54:29 2012 -0500 ++++ b/libmetis/CMakeLists.txt Tue Mar 20 13:54:31 2012 -0500 +@@ -12,6 +12,8 @@ endif() + if(METIS_INSTALL) + install(TARGETS metis + LIBRARY DESTINATION lib + RUNTIME DESTINATION lib + ARCHIVE DESTINATION lib) ++ install(FILES gklib_defs.h DESTINATION include) ++ install(FILES gklib_rename.h DESTINATION include) + endif() diff --git a/var/spack/repos/builtin/packages/metis/package.py b/var/spack/repos/builtin/packages/metis/package.py index bbfc4de7d1..68b9f6fd30 100644 --- a/var/spack/repos/builtin/packages/metis/package.py +++ b/var/spack/repos/builtin/packages/metis/package.py @@ -24,7 +24,7 @@ ############################################################################## from spack import * - +import glob class Metis(Package): """ @@ -49,6 +49,8 @@ class Metis(Package): depends_on('gdb', when='+gdb') + patch('install_gklib_defs_rename.patch') + def install(self, spec, prefix): options = [] @@ -80,4 +82,11 @@ class Metis(Package): with working_dir(build_directory, create=True): cmake(source_directory, *options) make() - make("install") \ No newline at end of file + make("install") + + # install GKlib headers, which will be needed for ParMETIS + GKlib_dist = join_path(prefix.include,'GKlib') + mkdirp(GKlib_dist) + fs = glob.glob(join_path(source_directory,'GKlib',"*.h")) + for f in fs: + install(f, GKlib_dist) -- cgit v1.2.3-70-g09d2 From 0d4d201b70c57359f041807df0a2f58b47be78d6 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Thu, 24 Mar 2016 21:22:58 +0100 Subject: patch parmetis to use external GKlib --- .../packages/parmetis/enable_external_metis.patch | 48 ++++++++++++++++++++-- .../repos/builtin/packages/parmetis/package.py | 2 +- 2 files changed, 46 insertions(+), 4 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch b/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch index 514781b8b8..8b05ecc872 100644 --- a/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch +++ b/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch @@ -1,13 +1,55 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt -index ca945dd..1bf94e9 100644 +index ca945dd..5995e42 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt +@@ -23,7 +23,7 @@ else() + set(ParMETIS_LIBRARY_TYPE STATIC) + endif() + +-include(${GKLIB_PATH}/GKlibSystem.cmake) ++include_directories(${GKLIB_PATH}) + + # List of paths that the compiler will search for header files. + # i.e., the -I equivalent @@ -33,7 +33,7 @@ include_directories(${GKLIB_PATH}) include_directories(${METIS_PATH}/include) - + # List of directories that cmake will look for CMakeLists.txt -add_subdirectory(${METIS_PATH}/libmetis ${CMAKE_BINARY_DIR}/libmetis) -+#add_subdirectory(${METIS_PATH}/libmetis ${CMAKE_BINARY_DIR}/libmetis) ++# add_subdirectory(${METIS_PATH}/libmetis ${CMAKE_BINARY_DIR}/libmetis) add_subdirectory(include) add_subdirectory(libparmetis) add_subdirectory(programs) +diff --git a/libparmetis/parmetislib.h b/libparmetis/parmetislib.h +index c1daeeb..07511f6 100644 +--- a/libparmetis/parmetislib.h ++++ b/libparmetis/parmetislib.h +@@ -20,13 +20,12 @@ + + #include + +-#include "../metis/libmetis/gklib_defs.h" ++#include + +-#include ++#include + + #include + #include + #include + #include + #include +- +diff --git a/programs/parmetisbin.h b/programs/parmetisbin.h +index e26cd2d..d156480 100644 +--- a/programs/parmetisbin.h ++++ b/programs/parmetisbin.h +@@ -19,7 +19,7 @@ + #include + #include + +-#include "../metis/libmetis/gklib_defs.h" ++#include + #include "../libparmetis/rename.h" + #include "../libparmetis/defs.h" + #include "../libparmetis/struct.h" diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py index bc71fb7299..5c97a836f9 100644 --- a/var/spack/repos/builtin/packages/parmetis/package.py +++ b/var/spack/repos/builtin/packages/parmetis/package.py @@ -66,7 +66,7 @@ class Parmetis(Package): # FIXME : Once a contract is defined, MPI compilers should be retrieved indirectly via spec['mpi'] in case # FIXME : they use a non-standard name - options.extend(['-DGKLIB_PATH:PATH={metis_source}/GKlib'.format(metis_source=metis_source), # still need headers from METIS source, and they are not installed with METIS. shame... + options.extend(['-DGKLIB_PATH:PATH={metis_source}/GKlib'.format(metis_source=spec['metis'].prefix.include), '-DMETIS_PATH:PATH={metis_source}'.format(metis_source=spec['metis'].prefix), '-DCMAKE_C_COMPILER:STRING=mpicc', '-DCMAKE_CXX_COMPILER:STRING=mpicxx']) -- cgit v1.2.3-70-g09d2 From 03c8a91f6a647849f0251496f361da9574a98c22 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Thu, 24 Mar 2016 22:33:10 +0100 Subject: parmetis: avoid hardcoding -lm; use same approach as in METIS --- .../packages/parmetis/enable_external_metis.patch | 20 ++++++++++++++++++-- .../repos/builtin/packages/parmetis/link-to-lm.patch | 14 -------------- var/spack/repos/builtin/packages/parmetis/package.py | 2 -- 3 files changed, 18 insertions(+), 18 deletions(-) delete mode 100644 var/spack/repos/builtin/packages/parmetis/link-to-lm.patch (limited to 'var') diff --git a/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch b/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch index 8b05ecc872..e4f2729483 100644 --- a/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch +++ b/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch @@ -1,5 +1,5 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt -index ca945dd..5995e42 100644 +index ca945dd..aff8b5f 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -23,7 +23,7 @@ else() @@ -16,10 +16,26 @@ index ca945dd..5995e42 100644 # List of directories that cmake will look for CMakeLists.txt -add_subdirectory(${METIS_PATH}/libmetis ${CMAKE_BINARY_DIR}/libmetis) -+# add_subdirectory(${METIS_PATH}/libmetis ${CMAKE_BINARY_DIR}/libmetis) ++find_library(METIS_LIBRARY metis PATHS ${METIS_PATH}/lib) add_subdirectory(include) add_subdirectory(libparmetis) add_subdirectory(programs) +diff --git a/libparmetis/CMakeLists.txt b/libparmetis/CMakeLists.txt +index 9cfc8a7..e0c4de7 100644 +--- a/libparmetis/CMakeLists.txt ++++ b/libparmetis/CMakeLists.txt +@@ -5,7 +5,10 @@ file(GLOB parmetis_sources *.c) + # Create libparmetis + add_library(parmetis ${ParMETIS_LIBRARY_TYPE} ${parmetis_sources}) + # Link with metis and MPI libraries. +-target_link_libraries(parmetis metis ${MPI_LIBRARIES}) ++target_link_libraries(parmetis ${METIS_LIBRARY} ${MPI_LIBRARIES}) ++if(UNIX) ++ target_link_libraries(parmetis m) ++endif() + set_target_properties(parmetis PROPERTIES LINK_FLAGS "${MPI_LINK_FLAGS}") + + install(TARGETS parmetis diff --git a/libparmetis/parmetislib.h b/libparmetis/parmetislib.h index c1daeeb..07511f6 100644 --- a/libparmetis/parmetislib.h diff --git a/var/spack/repos/builtin/packages/parmetis/link-to-lm.patch b/var/spack/repos/builtin/packages/parmetis/link-to-lm.patch deleted file mode 100644 index faa809231e..0000000000 --- a/var/spack/repos/builtin/packages/parmetis/link-to-lm.patch +++ /dev/null @@ -1,14 +0,0 @@ -diff --git a/libparmetis/CMakeLists.txt b/libparmetis/CMakeLists.txt -index 9cfc8a7..dfc0125 100644 ---- a/libparmetis/CMakeLists.txt -+++ b/libparmetis/CMakeLists.txt -@@ -5,7 +5,7 @@ file(GLOB parmetis_sources *.c) - # Create libparmetis - add_library(parmetis ${ParMETIS_LIBRARY_TYPE} ${parmetis_sources}) - # Link with metis and MPI libraries. --target_link_libraries(parmetis metis ${MPI_LIBRARIES}) -+target_link_libraries(parmetis metis ${MPI_LIBRARIES} "-lm") - set_target_properties(parmetis PROPERTIES LINK_FLAGS "${MPI_LINK_FLAGS}") - - install(TARGETS parmetis - diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py index 5c97a836f9..f5b8b6de91 100644 --- a/var/spack/repos/builtin/packages/parmetis/package.py +++ b/var/spack/repos/builtin/packages/parmetis/package.py @@ -52,8 +52,6 @@ class Parmetis(Package): # https://bitbucket.org/petsc/pkg-parmetis/commits/82409d68aa1d6cbc70740d0f35024aae17f7d5cb/raw/ patch('pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch') - patch('link-to-lm.patch') - depends_on('gdb', when='+gdb') def install(self, spec, prefix): -- cgit v1.2.3-70-g09d2 From fdd7e91ba078bea4f0fec1859124baaa8261fa2c Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Thu, 24 Mar 2016 12:49:56 +0100 Subject: add shared variant to mumps (needed for Trilinos) plus tests --- .../repos/builtin/packages/mumps/Makefile.inc | 5 +-- var/spack/repos/builtin/packages/mumps/package.py | 45 +++++++++++++++++++--- 2 files changed, 41 insertions(+), 9 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/mumps/Makefile.inc b/var/spack/repos/builtin/packages/mumps/Makefile.inc index 2e6a041878..22d8f5518a 100644 --- a/var/spack/repos/builtin/packages/mumps/Makefile.inc +++ b/var/spack/repos/builtin/packages/mumps/Makefile.inc @@ -8,12 +8,9 @@ IORDERINGSF = $(ISCOTCH) IORDERINGSC = $(IMETIS) $(IPORD) $(ISCOTCH) PLAT = -LIBEXT = .a -OUTC = -o +OUTC = -o OUTF = -o RM = /bin/rm -f -AR = ar vr -RANLIB = ranlib INCSEQ = -I$(topdir)/libseq LIBSEQ = -L$(topdir)/libseq -lmpiseq diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py index 5a254dfd00..2801d4194d 100644 --- a/var/spack/repos/builtin/packages/mumps/package.py +++ b/var/spack/repos/builtin/packages/mumps/package.py @@ -1,6 +1,5 @@ from spack import * -import os - +import os, sys class Mumps(Package): """MUMPS: a MUltifrontal Massively Parallel sparse direct Solver""" @@ -19,6 +18,7 @@ class Mumps(Package): variant('float', default=True, description='Activate the compilation of smumps') variant('complex', default=True, description='Activate the compilation of cmumps and/or zmumps') variant('idx64', default=False, description='Use int64_t/integer*8 as default index type') + variant('shared', default=True, description='Build shared libraries') depends_on('scotch + esmumps', when='~ptscotch+scotch') @@ -105,6 +105,27 @@ class Mumps(Package): # compiler possible values are -DAdd_, -DAdd__ and/or -DUPPER makefile_conf.append("CDEFS = -DAdd_") + if '+shared' in self.spec: + if sys.platform == 'darwin': + # Building dylibs with mpif90 causes segfaults on 10.8 and 10.10. Use gfortran. (Homebrew) + makefile_conf.extend([ + 'LIBEXT=.dylib', + 'AR=%s -dynamiclib -undefined dynamic_lookup -o ' % os.environ['FC'], + 'RANLIB=echo' + ]) + else: + makefile_conf.extend([ + 'LIBEXT=.so', + 'AR=$(FL) -shared -o', + 'RANLIB=echo' + ]) + else: + makefile_conf.extend([ + 'LIBEXT = .a', + 'AR = ar vr', + 'RANLIB = ranlib' + ]) + makefile_inc_template = join_path(os.path.dirname(self.module.__file__), 'Makefile.inc') @@ -121,7 +142,7 @@ class Mumps(Package): def install(self, spec, prefix): make_libs = [] - # the coice to compile ?examples is to have kind of a sanity + # the choice to compile ?examples is to have kind of a sanity # check on the libraries generated. if '+float' in spec: make_libs.append('sexamples') @@ -135,10 +156,24 @@ class Mumps(Package): self.write_makefile_inc() - # Build fails in parallel, at least on OS-X + # Build fails in parallel make(*make_libs, parallel=False) install_tree('lib', prefix.lib) install_tree('include', prefix.include) if '~mpi' in spec: - install('libseq/libmpiseq.a', prefix.lib) + lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so' + lib_suffix = lib_dsuffix if '+shared' in spec else '.a' + install('libseq/libmpiseq%s' % lib_suffix, prefix.lib) + + # FIXME: extend the tests to mpirun -np 2 (or alike) when build with MPI + # FIXME: use something like numdiff to compare blessed output with the current + with working_dir('examples'): + if '+float' in spec: + os.system('./ssimpletest < input_simpletest_real') + if '+complex' in spec: + os.system('./csimpletest < input_simpletest_real') + if '+double' in spec: + os.system('./dsimpletest < input_simpletest_real') + if '+complex' in spec: + os.system('./zsimpletest < input_simpletest_cmplx') -- cgit v1.2.3-70-g09d2 From 540e57f02686bad7125a951d14784e8fcc896e26 Mon Sep 17 00:00:00 2001 From: Josh Sixsmith Date: Fri, 25 Mar 2016 18:27:02 +1100 Subject: Upload of GDAL, kealib, openjpeg, py-tuiview package builds. --- var/spack/repos/builtin/packages/gdal/package.py | 69 ++++++++++++++++++++++ var/spack/repos/builtin/packages/kealib/package.py | 35 +++++++++++ .../repos/builtin/packages/openjpeg/package.py | 26 ++++++++ .../repos/builtin/packages/py-tuiview/package.py | 19 ++++++ 4 files changed, 149 insertions(+) create mode 100644 var/spack/repos/builtin/packages/gdal/package.py create mode 100644 var/spack/repos/builtin/packages/kealib/package.py create mode 100644 var/spack/repos/builtin/packages/openjpeg/package.py create mode 100644 var/spack/repos/builtin/packages/py-tuiview/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/gdal/package.py b/var/spack/repos/builtin/packages/gdal/package.py new file mode 100644 index 0000000000..4f1f1ec2dd --- /dev/null +++ b/var/spack/repos/builtin/packages/gdal/package.py @@ -0,0 +1,69 @@ +from spack import * + +class Gdal(Package): + """ + GDAL is a translator library for raster and vector geospatial + data formats that is released under an X/MIT style Open Source + license by the Open Source Geospatial Foundation. As a library, + it presents a single raster abstract data model and vector + abstract data model to the calling application for all supported + formats. It also comes with a variety of useful command line + utilities for data translation and processing + """ + + homepage = "http://www.gdal.org/" + url = "http://download.osgeo.org/gdal/2.0.2/gdal-2.0.2.tar.gz" + list_url = "http://download.osgeo.org/gdal/" + list_depth = 2 + + version('2.0.2', '573865f3f59ba7b4f8f4cddf223b52a5') + + extends('python') + + variant('hdf5', default=False, description='Enable HDF5 support') + variant('hdf', default=False, description='Enable HDF4 support') + variant('openjpeg', default=False, description='Enable JPEG2000 support') + variant('geos', default=False, description='Enable GEOS support') + variant('kea', default=False, description='Enable KEA support') + variant('netcdf', default=False, description='Enable netcdf support') + + depends_on('swig') + depends_on("hdf5", when='+hdf5') + depends_on("hdf", when='+hdf') + depends_on("openjpeg", when='+openjpeg') + depends_on("geos", when='+geos') + depends_on("kealib", when='+kea') + depends_on("netcdf", when='+netcdf') + depends_on("libtiff") + depends_on("libpng") + depends_on("zlib") + depends_on("proj") + depends_on("py-numpy") + + parallel = False + + def install(self, spec, prefix): + args = [] + args.append("--prefix=%s" % prefix) + args.append("--with-liblzma=yes") + args.append("--with-zlib=%s" % spec['zlib'].prefix) + args.append("--with-python=%s" % spec['python'].prefix.bin + "/python") + args.append("--without-libtool") + + if '+geos' in spec: + args.append('--with-geos=yes') + if '+hdf' in spec: + args.append('--with-hdf4=%s' % spec['hdf'].prefix) + if '+hdf5' in spec: + args.append('--with-hdf5=%s' % spec['hdf5'].prefix) + if '+openjpeg' in spec: + args.append('--with-openjpeg=%s' % spec['openjpeg'].prefix) + if '+kea' in spec: + args.append('--with-kea=yes') + if '+netcdf' in spec: + args.append('--with-netcdf=%s' % spec['netcdf'].prefix) + + configure(*args) + + make() + make("install") diff --git a/var/spack/repos/builtin/packages/kealib/package.py b/var/spack/repos/builtin/packages/kealib/package.py new file mode 100644 index 0000000000..475d21e1d8 --- /dev/null +++ b/var/spack/repos/builtin/packages/kealib/package.py @@ -0,0 +1,35 @@ +from spack import * + +class Kealib(Package): + """An HDF5 Based Raster File Format + + KEALib provides an implementation of the GDAL data model. + The format supports raster attribute tables, image pyramids, + meta-data and in-built statistics while also handling very + large files and compression throughout. + + Based on the HDF5 standard, it also provides a base from which + other formats can be derived and is a good choice for long + term data archiving. An independent software library (libkea) + provides complete access to the KEA image format and a GDAL + driver allowing KEA images to be used from any GDAL supported software. + + Development work on this project has been funded by Landcare Research. + """ + homepage = "http://kealib.org/" + url = "https://bitbucket.org/chchrsc/kealib/get/kealib-1.4.5.tar.gz" + + version('1.4.5', '112e9c42d980b2d2987a3c15d0833a5d') + + depends_on("hdf5") + + def install(self, spec, prefix): + with working_dir('trunk', create=False): + cmake_args = [] + cmake_args.append("-DCMAKE_INSTALL_PREFIX=%s" % prefix) + cmake_args.append("-DHDF5_INCLUDE_DIR=%s" % spec['hdf5'].prefix.include) + cmake_args.append("-DHDF5_LIB_PATH=%s" % spec['hdf5'].prefix.lib) + cmake('.', *cmake_args) + + make() + make("install") diff --git a/var/spack/repos/builtin/packages/openjpeg/package.py b/var/spack/repos/builtin/packages/openjpeg/package.py new file mode 100644 index 0000000000..afec197d11 --- /dev/null +++ b/var/spack/repos/builtin/packages/openjpeg/package.py @@ -0,0 +1,26 @@ +from spack import * + +class Openjpeg(Package): + """ + OpenJPEG is an open-source JPEG 2000 codec written in C language. + It has been developed in order to promote the use of JPEG 2000, a + still-image compression standard from the Joint Photographic + Experts Group (JPEG). + Since April 2015, it is officially recognized by ISO/IEC and + ITU-T as a JPEG 2000 Reference Software. + """ + homepage = "https://github.com/uclouvain/openjpeg" + url = "https://github.com/uclouvain/openjpeg/archive/version.2.1.tar.gz" + + version('2.1' , '3e1c451c087f8462955426da38aa3b3d') + version('2.0.1', '105876ed43ff7dbb2f90b41b5a43cfa5') + version('2.0' , 'cdf266530fee8af87454f15feb619609') + version('1.5.2', '545f98923430369a6b046ef3632ef95c') + version('1.5.1', 'd774e4b5a0db5f0f171c4fc0aabfa14e') + + + def install(self, spec, prefix): + cmake('.', *std_cmake_args) + + make() + make("install") diff --git a/var/spack/repos/builtin/packages/py-tuiview/package.py b/var/spack/repos/builtin/packages/py-tuiview/package.py new file mode 100644 index 0000000000..984b4196b1 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-tuiview/package.py @@ -0,0 +1,19 @@ +from spack import * + +class PyTuiview(Package): + """ + TuiView is a lightweight raster GIS with powerful raster attribute + table manipulation abilities. + """ + homepage = "https://bitbucket.org/chchrsc/tuiview" + url = "https://bitbucket.org/chchrsc/tuiview/get/tuiview-1.1.7.tar.gz" + + version('1.1.7', '4b3b38a820cc239c8ab4a181ac5d4c30') + + extends("python") + depends_on("py-pyqt") + depends_on("py-numpy") + depends_on("gdal") + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) -- cgit v1.2.3-70-g09d2 From fd67da607e5476b767071dc37af66af6fd492452 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Fri, 25 Mar 2016 08:32:14 +0100 Subject: make netcdf link against Spack's curl --- var/spack/repos/builtin/packages/netcdf/package.py | 7 +++++++ 1 file changed, 7 insertions(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/netcdf/package.py b/var/spack/repos/builtin/packages/netcdf/package.py index 227362399a..b60a2c4e9a 100644 --- a/var/spack/repos/builtin/packages/netcdf/package.py +++ b/var/spack/repos/builtin/packages/netcdf/package.py @@ -43,6 +43,13 @@ class Netcdf(Package): "--enable-dap" ] + # Make sure Netcdf links against Spack's curl + # Otherwise it may pick up system's curl, which could lead to link errors: + # /usr/lib/x86_64-linux-gnu/libcurl.so: undefined reference to `SSL_CTX_use_certificate_chain_file@OPENSSL_1.0.0' + LIBS.append("-lcurl") + CPPFLAGS.append("-I%s" % spec['curl'].prefix.include) + LDFLAGS.append ("-L%s" % spec['curl'].prefix.lib) + if '+mpi' in spec: config_args.append('--enable-parallel4') -- cgit v1.2.3-70-g09d2 From 3e39daeb12aa13a3f3f975ff315143bc3f13a2b4 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Fri, 25 Mar 2016 09:56:24 +0100 Subject: add fPIC to MUMPS when building shared libs --- var/spack/repos/builtin/packages/mumps/package.py | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py index 2801d4194d..b295857ab5 100644 --- a/var/spack/repos/builtin/packages/mumps/package.py +++ b/var/spack/repos/builtin/packages/mumps/package.py @@ -70,6 +70,9 @@ class Mumps(Package): makefile_conf.append("ORDERINGSF = %s" % (' '.join(orderings))) + # when building shared libs need -fPIC, otherwise + # /usr/bin/ld: graph.o: relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC + fpic = '-fPIC' if '+shared' in self.spec else '' # TODO: test this part, it needs a full blas, scalapack and # partitionning environment with 64bit integers if '+idx64' in self.spec: @@ -77,14 +80,14 @@ class Mumps(Package): # the fortran compilation flags most probably are # working only for intel and gnu compilers this is # perhaps something the compiler should provide - ['OPTF = -O -DALLOW_NON_INIT %s' % '-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8', - 'OPTL = -O ', - 'OPTC = -O -DINTSIZE64']) + ['OPTF = %s -O -DALLOW_NON_INIT %s' % (fpic,'-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8'), + 'OPTL = %s -O ' % fpic, + 'OPTC = %s -O -DINTSIZE64' % fpic]) else: makefile_conf.extend( - ['OPTF = -O -DALLOW_NON_INIT', - 'OPTL = -O ', - 'OPTC = -O ']) + ['OPTF = %s -O -DALLOW_NON_INIT' % fpic, + 'OPTL = %s -O ' % fpic, + 'OPTC = %s -O ' % fpic]) if '+mpi' in self.spec: -- cgit v1.2.3-70-g09d2 From 83fea631f1765d4641cde8af2c5c931b22e4ee33 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Tue, 22 Mar 2016 23:04:17 +0100 Subject: extend trilinos --- .../repos/builtin/packages/trilinos/package.py | 32 +++++++++++++++++++--- 1 file changed, 28 insertions(+), 4 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index edc40476e3..22c7ab6d61 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -1,5 +1,5 @@ from spack import * - +import os class Trilinos(Package): """ @@ -10,6 +10,7 @@ class Trilinos(Package): homepage = "https://trilinos.org/" url = "http://trilinos.csbsju.edu/download/files/trilinos-12.2.1-Source.tar.gz" + version('12.6.1', 'adcf2d3aab74cdda98f88fee19cd1442604199b0515ee3da4d80cbe8f37d00e4') version('12.4.2', '7c830f7f0f68b8ad324690603baf404e') version('12.2.1', '6161926ea247863c690e927687f83be9') version('12.0.1', 'bd99741d047471e127b8296b2ec08017') @@ -39,15 +40,38 @@ class Trilinos(Package): options.extend(std_cmake_args) options.extend(['-DTrilinos_ENABLE_ALL_PACKAGES:BOOL=ON', + '-DTrilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=ON', '-DTrilinos_ENABLE_TESTS:BOOL=OFF', '-DTrilinos_ENABLE_EXAMPLES:BOOL=OFF', '-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'), '-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if '+shared' in spec else 'OFF'), - '-DTPL_ENABLE_MPI:STRING=ON', - '-DBLAS_LIBRARY_DIRS:PATH=%s' % spec['blas'].prefix, - '-DLAPACK_LIBRARY_DIRS:PATH=%s' % spec['lapack'].prefix + '-DTPL_ENABLE_MPI:BOOL=ON', + '-DMPI_BASE_DIR:PATH=%s' % spec['mpi'].prefix, + '-DTPL_ENABLE_BLAS=ON', + '-DBLAS_LIBRARY_NAMES=blas', + '-DBLAS_LIBRARY_DIRS=/usr/lib', # % spec['blas'].prefix, + '-DTPL_ENABLE_LAPACK=ON', + '-DLAPACK_LIBRARY_NAMES=lapack', + '-DLAPACK_LIBRARY_DIRS=/usr/lib', # % spec['lapack'].prefix, + '-DTPL_ENABLE_Boost:BOOL=ON', + '-DBOOST_BASE_DIR:PATH=%s' % spec['boost'].prefix, + '-DTrilinos_ENABLE_Fortran=OFF', + '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON', + '-DTrilinos_ENABLE_CXX11:BOOL=ON', + '-DTrilinos_CXX11_FLAGS=-std=c++11' + ]) + + # disable due to compiler / config errors: + options.extend(['-DTrilinos_ENABLE_SEACAS=OFF', + '-DTrilinos_ENABLE_Pike=OFF', + '-DTrilinos_ENABLE_STK=OFF' ]) + if self.compiler.name == "clang": + os.environ['CPPFLAGS']="-Qunused-arguments" + + #os.environ['LDFLAGS']="lgfortran" + with working_dir('spack-build', create=True): cmake('..', *options) make() -- cgit v1.2.3-70-g09d2 From 30ba96e58fe699e92902ce53a87b5e1cfb756d6f Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Tue, 22 Mar 2016 23:56:18 +0100 Subject: same --- .../repos/builtin/packages/trilinos/package.py | 84 +++++++++++++++++++--- 1 file changed, 74 insertions(+), 10 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 22c7ab6d61..7b913031e3 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -2,8 +2,7 @@ from spack import * import os class Trilinos(Package): - """ - The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented + """The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. A unique design feature of Trilinos is its focus on packages. """ @@ -28,10 +27,19 @@ class Trilinos(Package): depends_on('matio') depends_on('glm') depends_on('swig') + depends_on('metis') + depends_on('suite-sparse') + depends_on('tbb') # MPI related dependencies depends_on('mpi') depends_on('netcdf+mpi') + depends_on('parmetis') + depends_on('mumps+metis+parmetis') + depends_on('scalapack') + depends_on('superlu-dist') + depends_on('hypre') + depends_on('hdf5+mpi') depends_on('python') # Needs py-numpy activated @@ -49,23 +57,79 @@ class Trilinos(Package): '-DMPI_BASE_DIR:PATH=%s' % spec['mpi'].prefix, '-DTPL_ENABLE_BLAS=ON', '-DBLAS_LIBRARY_NAMES=blas', - '-DBLAS_LIBRARY_DIRS=/usr/lib', # % spec['blas'].prefix, + '-DBLAS_LIBRARY_DIRS=/usr/lib', # % spec['blas'].prefix, #FIXME '-DTPL_ENABLE_LAPACK=ON', '-DLAPACK_LIBRARY_NAMES=lapack', - '-DLAPACK_LIBRARY_DIRS=/usr/lib', # % spec['lapack'].prefix, + '-DLAPACK_LIBRARY_DIRS=/usr/lib', # % spec['lapack'].prefix, #FIXME '-DTPL_ENABLE_Boost:BOOL=ON', '-DBOOST_BASE_DIR:PATH=%s' % spec['boost'].prefix, - '-DTrilinos_ENABLE_Fortran=OFF', + '-DTrilinos_ENABLE_Fortran=OFF', # FIXME '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON', '-DTrilinos_ENABLE_CXX11:BOOL=ON', - '-DTrilinos_CXX11_FLAGS=-std=c++11' + '-DTrilinos_CXX11_FLAGS=-std=c++11', + '-DTPL_ENABLE_Netcdf:BOOL=ON', + '-DTPL_ENABLE_HYPRE:BOOL=ON', + '-DTPL_ENABLE_HDF5:BOOL=ON', + '-DTPL_ENABLE_TBB:BOOL=ON' ]) + # Amesos, conflicting types of double and complex SLU_D + # see https://trilinos.org/pipermail/trilinos-users/2015-March/004731.html + # and https://trilinos.org/pipermail/trilinos-users/2015-March/004802.html + options.extend([ + '-DTeuchos_ENABLE_COMPLEX:BOOL=OFF', + '-DKokkosTSQR_ENABLE_Complex:BOOL=OFF' + ]) + + # suite-sparse related + options.extend([ + '-DTPL_ENABLE_Cholmod:BOOL=ON', + '-DTPL_ENABLE_UMFPACK:BOOL=ON', + '-DUMFPACK_LIBRARY_NAMES=umfpack;amd;colamd;cholmod;suitesparseconfig' + ]) + + # metis / parmetis + options.extend([ + '-DTPL_ENABLE_METIS:BOOL=ON', + '-DMETIS_LIBRARY_DIRS=%s' % spec['metis'].prefix.lib, + '-DMETIS_LIBRARY_NAMES=metis', + '-DTPL_METIS_INCLUDE_DIRS=%s' % spec['metis'].prefix.include, + '-DTPL_ENABLE_ParMETIS:BOOL=ON', + '-DParMETIS_LIBRARY_DIRS=%s;%s' % (spec['parmetis'].prefix.lib,spec['metis'].prefix.lib), + '-DParMETIS_LIBRARY_NAMES=parmetis;metis', + '-DTPL_ParMETIS_INCLUDE_DIRS=%s' % spec['parmetis'].prefix.include + ]) + + # mumps + options.extend([ + '-DTPL_ENABLE_MUMPS:BOOL=ON"', + '-DMUMPS_LIBRARY_DIRS=%s' % spec['mumps'].prefix.lib, + '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord' # order is important! + ]) + + # scalapack + options.extend([ + '-DTPL_ENABLE_SCALAPACK:BOOL=ON', + '-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64 + ]) + + # superlu_dist + options.extend([ + '-DTPL_ENABLE_SuperLUDist:BOOL=ON', + '-DSuperLUDist_INCLUDE_DIRS=%s' % spec['superlu_dist'].prefix.include + ]) + if spec.satisfies('^superlu-dist@4.0:'): + options.extend([ + '-DHAVE_SUPERLUDIST_LUSTRUCTINIT_2ARG:BOOL=ON' + ]) + + # disable due to compiler / config errors: - options.extend(['-DTrilinos_ENABLE_SEACAS=OFF', - '-DTrilinos_ENABLE_Pike=OFF', - '-DTrilinos_ENABLE_STK=OFF' - ]) + options.extend([ + '-DTrilinos_ENABLE_SEACAS=OFF', + '-DTrilinos_ENABLE_Pike=OFF', + '-DTrilinos_ENABLE_STK=OFF' + ]) if self.compiler.name == "clang": os.environ['CPPFLAGS']="-Qunused-arguments" -- cgit v1.2.3-70-g09d2 From 76006fc346c7880b03356c1cf9d00bab2fdeac45 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 23 Mar 2016 05:30:48 +0100 Subject: fix typo --- var/spack/repos/builtin/packages/trilinos/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 7b913031e3..7d7613d2b5 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -116,7 +116,7 @@ class Trilinos(Package): # superlu_dist options.extend([ '-DTPL_ENABLE_SuperLUDist:BOOL=ON', - '-DSuperLUDist_INCLUDE_DIRS=%s' % spec['superlu_dist'].prefix.include + '-DSuperLUDist_INCLUDE_DIRS=%s' % spec['superlu-dist'].prefix.include ]) if spec.satisfies('^superlu-dist@4.0:'): options.extend([ -- cgit v1.2.3-70-g09d2 From 18db930866b2024b242ea7c825851d7a56b27247 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 23 Mar 2016 07:09:58 +0100 Subject: rearrange --- var/spack/repos/builtin/packages/trilinos/package.py | 18 ++++++++---------- 1 file changed, 8 insertions(+), 10 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 7d7613d2b5..063d179c7e 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -73,14 +73,6 @@ class Trilinos(Package): '-DTPL_ENABLE_TBB:BOOL=ON' ]) - # Amesos, conflicting types of double and complex SLU_D - # see https://trilinos.org/pipermail/trilinos-users/2015-March/004731.html - # and https://trilinos.org/pipermail/trilinos-users/2015-March/004802.html - options.extend([ - '-DTeuchos_ENABLE_COMPLEX:BOOL=OFF', - '-DKokkosTSQR_ENABLE_Complex:BOOL=OFF' - ]) - # suite-sparse related options.extend([ '-DTPL_ENABLE_Cholmod:BOOL=ON', @@ -113,7 +105,14 @@ class Trilinos(Package): '-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64 ]) - # superlu_dist + # superlu_dist: + # Amesos, conflicting types of double and complex SLU_D + # see https://trilinos.org/pipermail/trilinos-users/2015-March/004731.html + # and https://trilinos.org/pipermail/trilinos-users/2015-March/004802.html + options.extend([ + '-DTeuchos_ENABLE_COMPLEX:BOOL=OFF', + '-DKokkosTSQR_ENABLE_Complex:BOOL=OFF' + ]) options.extend([ '-DTPL_ENABLE_SuperLUDist:BOOL=ON', '-DSuperLUDist_INCLUDE_DIRS=%s' % spec['superlu-dist'].prefix.include @@ -123,7 +122,6 @@ class Trilinos(Package): '-DHAVE_SUPERLUDIST_LUSTRUCTINIT_2ARG:BOOL=ON' ]) - # disable due to compiler / config errors: options.extend([ '-DTrilinos_ENABLE_SEACAS=OFF', -- cgit v1.2.3-70-g09d2 From b91a155e8d996c9e51da7f75d4e106469ba488e6 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 23 Mar 2016 07:10:31 +0100 Subject: more specific about dependencies --- var/spack/repos/builtin/packages/trilinos/package.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 063d179c7e..2937ed4c38 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -62,7 +62,7 @@ class Trilinos(Package): '-DLAPACK_LIBRARY_NAMES=lapack', '-DLAPACK_LIBRARY_DIRS=/usr/lib', # % spec['lapack'].prefix, #FIXME '-DTPL_ENABLE_Boost:BOOL=ON', - '-DBOOST_BASE_DIR:PATH=%s' % spec['boost'].prefix, + '-DBoost_BASE_DIR:PATH=%s' % spec['boost'].prefix, '-DTrilinos_ENABLE_Fortran=OFF', # FIXME '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON', '-DTrilinos_ENABLE_CXX11:BOOL=ON', @@ -76,7 +76,9 @@ class Trilinos(Package): # suite-sparse related options.extend([ '-DTPL_ENABLE_Cholmod:BOOL=ON', + '-DCholmod_BASE_DIR:PATH=%s' % spec['suite-sparse'].prefix, '-DTPL_ENABLE_UMFPACK:BOOL=ON', + '-D_UMFPACK_BASE_DIR:PATH=%s' % spec['suite-sparse'].prefix, '-DUMFPACK_LIBRARY_NAMES=umfpack;amd;colamd;cholmod;suitesparseconfig' ]) @@ -94,7 +96,7 @@ class Trilinos(Package): # mumps options.extend([ - '-DTPL_ENABLE_MUMPS:BOOL=ON"', + '-DTPL_ENABLE_MUMPS:BOOL=ON', '-DMUMPS_LIBRARY_DIRS=%s' % spec['mumps'].prefix.lib, '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord' # order is important! ]) @@ -115,6 +117,7 @@ class Trilinos(Package): ]) options.extend([ '-DTPL_ENABLE_SuperLUDist:BOOL=ON', + '-DSuperLUDist_BASE_DIR:PATH=%s' % spec['superlu-dist'].prefix, '-DSuperLUDist_INCLUDE_DIRS=%s' % spec['superlu-dist'].prefix.include ]) if spec.satisfies('^superlu-dist@4.0:'): -- cgit v1.2.3-70-g09d2 From b6a35716ce3e02e1a3661e2433986ad637b65d0c Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 23 Mar 2016 07:33:28 +0100 Subject: same --- var/spack/repos/builtin/packages/trilinos/package.py | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 2937ed4c38..b31cf880bc 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -43,6 +43,8 @@ class Trilinos(Package): depends_on('python') # Needs py-numpy activated + patch('umfpack_from_suitesparse.patch') + def install(self, spec, prefix): options = [] options.extend(std_cmake_args) @@ -76,9 +78,11 @@ class Trilinos(Package): # suite-sparse related options.extend([ '-DTPL_ENABLE_Cholmod:BOOL=ON', - '-DCholmod_BASE_DIR:PATH=%s' % spec['suite-sparse'].prefix, + '-DCholmod_LIBRARY_DIRS=%s' % spec['suite-sparse'].prefix.lib, + '-DCholmod_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include, '-DTPL_ENABLE_UMFPACK:BOOL=ON', - '-D_UMFPACK_BASE_DIR:PATH=%s' % spec['suite-sparse'].prefix, + '-D_UMFPACK_LIBRARY_DIRS:PATH=%s' % spec['suite-sparse'].prefix.lib, + '-D_UMFPACK_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include, '-DUMFPACK_LIBRARY_NAMES=umfpack;amd;colamd;cholmod;suitesparseconfig' ]) @@ -117,7 +121,7 @@ class Trilinos(Package): ]) options.extend([ '-DTPL_ENABLE_SuperLUDist:BOOL=ON', - '-DSuperLUDist_BASE_DIR:PATH=%s' % spec['superlu-dist'].prefix, + '-DSuperLUDist_LIBRARY_DIRS=%s' % spec['superlu-dist'].prefix.lib, '-DSuperLUDist_INCLUDE_DIRS=%s' % spec['superlu-dist'].prefix.include ]) if spec.satisfies('^superlu-dist@4.0:'): -- cgit v1.2.3-70-g09d2 From 45b4895888a2abb3cf11ecf2b26b7940a9f89b5a Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 23 Mar 2016 07:34:22 +0100 Subject: patch --- .../builtin/packages/trilinos/umfpack_from_suitesparse.patch | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 var/spack/repos/builtin/packages/trilinos/umfpack_from_suitesparse.patch (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/umfpack_from_suitesparse.patch b/var/spack/repos/builtin/packages/trilinos/umfpack_from_suitesparse.patch new file mode 100644 index 0000000000..9defc55527 --- /dev/null +++ b/var/spack/repos/builtin/packages/trilinos/umfpack_from_suitesparse.patch @@ -0,0 +1,12 @@ +diff --git a/cmake/TPLs/FindTPLUMFPACK.cmake b/cmake/TPLs/FindTPLUMFPACK.cmake +index 963eb71..998cd02 100644 +--- a/cmake/TPLs/FindTPLUMFPACK.cmake ++++ b/cmake/TPLs/FindTPLUMFPACK.cmake +@@ -55,6 +55,6 @@ + + + TRIBITS_TPL_FIND_INCLUDE_DIRS_AND_LIBRARIES( UMFPACK +- REQUIRED_HEADERS umfpack.h amd.h UFconfig.h ++ REQUIRED_HEADERS umfpack.h amd.h SuiteSparse_config.h + REQUIRED_LIBS_NAMES umfpack amd + ) -- cgit v1.2.3-70-g09d2 From bc3314a57d43963416f709a94967ae8e1758c458 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 23 Mar 2016 08:05:18 +0100 Subject: more and more --- var/spack/repos/builtin/packages/trilinos/package.py | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index b31cf880bc..77ae6f818d 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -64,7 +64,8 @@ class Trilinos(Package): '-DLAPACK_LIBRARY_NAMES=lapack', '-DLAPACK_LIBRARY_DIRS=/usr/lib', # % spec['lapack'].prefix, #FIXME '-DTPL_ENABLE_Boost:BOOL=ON', - '-DBoost_BASE_DIR:PATH=%s' % spec['boost'].prefix, + '-DBoost_INCLUDE_DIRS:PATH=%s' % spec['boost'].prefix.include, + '-DBoost_LIBRARY_DIRS:PATH=%s' % spec['boost'].prefix.lib, '-DTrilinos_ENABLE_Fortran=OFF', # FIXME '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON', '-DTrilinos_ENABLE_CXX11:BOOL=ON', @@ -77,12 +78,13 @@ class Trilinos(Package): # suite-sparse related options.extend([ - '-DTPL_ENABLE_Cholmod:BOOL=ON', - '-DCholmod_LIBRARY_DIRS=%s' % spec['suite-sparse'].prefix.lib, - '-DCholmod_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include, + '-DTPL_ENABLE_Cholmod:BOOL=OFF', # FIXME: Trilinos seems to be looking for static libs only, patch CMake TPL file? + #'-DTPL_ENABLE_Cholmod:BOOL=ON', + #'-DCholmod_LIBRARY_DIRS:PATH=%s' % spec['suite-sparse'].prefix.lib, + #'-DCholmod_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include, '-DTPL_ENABLE_UMFPACK:BOOL=ON', - '-D_UMFPACK_LIBRARY_DIRS:PATH=%s' % spec['suite-sparse'].prefix.lib, - '-D_UMFPACK_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include, + '-DUMFPACK_LIBRARY_DIRS:PATH=%s' % spec['suite-sparse'].prefix.lib, + '-DUMFPACK_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include, '-DUMFPACK_LIBRARY_NAMES=umfpack;amd;colamd;cholmod;suitesparseconfig' ]) -- cgit v1.2.3-70-g09d2 From 2162627f35f98dc7f07cd34a6593f71d74095955 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 23 Mar 2016 08:13:19 +0100 Subject: more --- var/spack/repos/builtin/packages/trilinos/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 77ae6f818d..532db69cc2 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -124,7 +124,7 @@ class Trilinos(Package): options.extend([ '-DTPL_ENABLE_SuperLUDist:BOOL=ON', '-DSuperLUDist_LIBRARY_DIRS=%s' % spec['superlu-dist'].prefix.lib, - '-DSuperLUDist_INCLUDE_DIRS=%s' % spec['superlu-dist'].prefix.include + '-DSuperLUDist_INCLUDE_DIRS=%s/superlu_dist' % spec['superlu-dist'].prefix.include # superlu_dist and superlu have the same header names :-( In order to avoid conflicts, try to keep "dist" version headers in a subfolder ]) if spec.satisfies('^superlu-dist@4.0:'): options.extend([ -- cgit v1.2.3-70-g09d2 From 88a7a23132a379e526220324b8493d3be870f7e6 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 23 Mar 2016 08:46:23 +0100 Subject: even more --- var/spack/repos/builtin/packages/trilinos/package.py | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 532db69cc2..13794ae930 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -36,7 +36,7 @@ class Trilinos(Package): depends_on('netcdf+mpi') depends_on('parmetis') depends_on('mumps+metis+parmetis') - depends_on('scalapack') + # depends_on('scalapack') # see FIXME below depends_on('superlu-dist') depends_on('hypre') depends_on('hdf5+mpi') @@ -49,6 +49,7 @@ class Trilinos(Package): options = [] options.extend(std_cmake_args) + mpi_bin = spec['mpi'].prefix.bin options.extend(['-DTrilinos_ENABLE_ALL_PACKAGES:BOOL=ON', '-DTrilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=ON', '-DTrilinos_ENABLE_TESTS:BOOL=OFF', @@ -73,7 +74,12 @@ class Trilinos(Package): '-DTPL_ENABLE_Netcdf:BOOL=ON', '-DTPL_ENABLE_HYPRE:BOOL=ON', '-DTPL_ENABLE_HDF5:BOOL=ON', - '-DTPL_ENABLE_TBB:BOOL=ON' + '-DTPL_ENABLE_TBB:BOOL=ON', + # Need to use MPI wrappers, otherwise: Undefined symbols for architecture x86_64: "_mpi_abort_","_mpi_allgatherv_", etc from MUMPS + '-DCMAKE_C_COMPILER=%s' % join_path(mpi_bin,'mpicc'), # FIXME: dont hardcode compiler name + '-DCMAKE_CXX_COMPILER=%s' % join_path(mpi_bin,'mpicxx'), + '-DCMAKE_Fortran_COMPILER=%s' % join_path(mpi_bin,'mpicxx'), + '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-lgfortran' ]) # suite-sparse related @@ -109,8 +115,8 @@ class Trilinos(Package): # scalapack options.extend([ - '-DTPL_ENABLE_SCALAPACK:BOOL=ON', - '-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64 + '-DTPL_ENABLE_SCALAPACK:BOOL=OFF', #FIXME: Undefined symbols for architecture x86_64: "_blacs_gridinfo__", referenced from: Amesos_Scalapack::RedistributeA() in Amesos_Scalapack.cpp.o + #'-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64 ]) # superlu_dist: @@ -141,8 +147,6 @@ class Trilinos(Package): if self.compiler.name == "clang": os.environ['CPPFLAGS']="-Qunused-arguments" - #os.environ['LDFLAGS']="lgfortran" - with working_dir('spack-build', create=True): cmake('..', *options) make() -- cgit v1.2.3-70-g09d2 From 7e4e2c988ab4e5163469395ace204d9f332a9675 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 23 Mar 2016 08:48:25 +0100 Subject: minor --- var/spack/repos/builtin/packages/trilinos/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 13794ae930..c915d8eb1a 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -78,7 +78,7 @@ class Trilinos(Package): # Need to use MPI wrappers, otherwise: Undefined symbols for architecture x86_64: "_mpi_abort_","_mpi_allgatherv_", etc from MUMPS '-DCMAKE_C_COMPILER=%s' % join_path(mpi_bin,'mpicc'), # FIXME: dont hardcode compiler name '-DCMAKE_CXX_COMPILER=%s' % join_path(mpi_bin,'mpicxx'), - '-DCMAKE_Fortran_COMPILER=%s' % join_path(mpi_bin,'mpicxx'), + '-DCMAKE_Fortran_COMPILER=%s' % join_path(mpi_bin,'mpif90'), '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-lgfortran' ]) -- cgit v1.2.3-70-g09d2 From 50e4b609c688b573ef882a079e2d45a83966f94c Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 23 Mar 2016 09:11:26 +0100 Subject: minor --- var/spack/repos/builtin/packages/trilinos/package.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index c915d8eb1a..3622548ece 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -52,6 +52,7 @@ class Trilinos(Package): mpi_bin = spec['mpi'].prefix.bin options.extend(['-DTrilinos_ENABLE_ALL_PACKAGES:BOOL=ON', '-DTrilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=ON', + '-DTrilinos_VERBOSE_CONFIGURE:BOOL=OFF', '-DTrilinos_ENABLE_TESTS:BOOL=OFF', '-DTrilinos_ENABLE_EXAMPLES:BOOL=OFF', '-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'), @@ -145,7 +146,9 @@ class Trilinos(Package): ]) if self.compiler.name == "clang": - os.environ['CPPFLAGS']="-Qunused-arguments" + options.extend([ + '-DCMAKE_EXE_LINKER_FLAGS:STRING=-Qunused-arguments' + ]) with working_dir('spack-build', create=True): cmake('..', *options) -- cgit v1.2.3-70-g09d2 From 2fb599ea86c82e3395d8402db116a3a25fed0c73 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 23 Mar 2016 09:16:51 +0100 Subject: minor --- var/spack/repos/builtin/packages/trilinos/package.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 3622548ece..82681e004c 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -55,7 +55,7 @@ class Trilinos(Package): '-DTrilinos_VERBOSE_CONFIGURE:BOOL=OFF', '-DTrilinos_ENABLE_TESTS:BOOL=OFF', '-DTrilinos_ENABLE_EXAMPLES:BOOL=OFF', - '-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'), + '-DCMAKE_BUILD_TYPE:STRING=%s' % ('DEBUG' if '+debug' in spec else 'RELEASE'), '-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if '+shared' in spec else 'OFF'), '-DTPL_ENABLE_MPI:BOOL=ON', '-DMPI_BASE_DIR:PATH=%s' % spec['mpi'].prefix, @@ -83,6 +83,11 @@ class Trilinos(Package): '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-lgfortran' ]) + # for build-debug only: + options.extend([ + '-DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE' + ]) + # suite-sparse related options.extend([ '-DTPL_ENABLE_Cholmod:BOOL=OFF', # FIXME: Trilinos seems to be looking for static libs only, patch CMake TPL file? -- cgit v1.2.3-70-g09d2 From eb5b0767aa20b46932c36203595c124b7463a444 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 23 Mar 2016 09:45:33 +0100 Subject: remove gfortran as we have libnotfound... --- var/spack/repos/builtin/packages/trilinos/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 82681e004c..bb6f095190 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -80,7 +80,7 @@ class Trilinos(Package): '-DCMAKE_C_COMPILER=%s' % join_path(mpi_bin,'mpicc'), # FIXME: dont hardcode compiler name '-DCMAKE_CXX_COMPILER=%s' % join_path(mpi_bin,'mpicxx'), '-DCMAKE_Fortran_COMPILER=%s' % join_path(mpi_bin,'mpif90'), - '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-lgfortran' + # '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-lgfortran' # FIXME ]) # for build-debug only: -- cgit v1.2.3-70-g09d2 From 7897f10126f0f8389326c9e723d73021f654ea6a Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 23 Mar 2016 13:04:43 +0100 Subject: fiddle with fortran --- .../repos/builtin/packages/trilinos/package.py | 21 ++++++++++++++------- 1 file changed, 14 insertions(+), 7 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index bb6f095190..f6f24e967e 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -68,7 +68,7 @@ class Trilinos(Package): '-DTPL_ENABLE_Boost:BOOL=ON', '-DBoost_INCLUDE_DIRS:PATH=%s' % spec['boost'].prefix.include, '-DBoost_LIBRARY_DIRS:PATH=%s' % spec['boost'].prefix.lib, - '-DTrilinos_ENABLE_Fortran=OFF', # FIXME + # '-DTrilinos_ENABLE_Fortran=OFF', # FIXME '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON', '-DTrilinos_ENABLE_CXX11:BOOL=ON', '-DTrilinos_CXX11_FLAGS=-std=c++11', @@ -79,10 +79,17 @@ class Trilinos(Package): # Need to use MPI wrappers, otherwise: Undefined symbols for architecture x86_64: "_mpi_abort_","_mpi_allgatherv_", etc from MUMPS '-DCMAKE_C_COMPILER=%s' % join_path(mpi_bin,'mpicc'), # FIXME: dont hardcode compiler name '-DCMAKE_CXX_COMPILER=%s' % join_path(mpi_bin,'mpicxx'), - '-DCMAKE_Fortran_COMPILER=%s' % join_path(mpi_bin,'mpif90'), - # '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-lgfortran' # FIXME + '-DCMAKE_Fortran_COMPILER=%s' % join_path(mpi_bin,'mpif90') ]) + # Fortran lib + libgfortran = os.path.dirname (os.popen('%s --print-file-name libgfortran.a' % join_path(mpi_bin,'mpif90') ).read()) + #os.environ['LDFLAGS'] = '-L%s -lgfortran' % libgfortran + options.extend([ + '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-lgfortran', + '-DCMAKE_EXE_LINKER_FLAGS:STRING=-L%s -lgfortran' % libgfortran + ]) + # for build-debug only: options.extend([ '-DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE' @@ -150,10 +157,10 @@ class Trilinos(Package): '-DTrilinos_ENABLE_STK=OFF' ]) - if self.compiler.name == "clang": - options.extend([ - '-DCMAKE_EXE_LINKER_FLAGS:STRING=-Qunused-arguments' - ]) + #if self.compiler.name == "clang": + # options.extend([ + # '-DCMAKE_EXE_LINKER_FLAGS:STRING=-Qunused-arguments' + # ]) with working_dir('spack-build', create=True): cmake('..', *options) -- cgit v1.2.3-70-g09d2 From fade526ae4e748a9454fd56c07ef7bc1fca38423 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 23 Mar 2016 16:58:59 +0100 Subject: remove tbb --- var/spack/repos/builtin/packages/trilinos/package.py | 2 -- 1 file changed, 2 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index f6f24e967e..12212360a0 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -29,7 +29,6 @@ class Trilinos(Package): depends_on('swig') depends_on('metis') depends_on('suite-sparse') - depends_on('tbb') # MPI related dependencies depends_on('mpi') @@ -75,7 +74,6 @@ class Trilinos(Package): '-DTPL_ENABLE_Netcdf:BOOL=ON', '-DTPL_ENABLE_HYPRE:BOOL=ON', '-DTPL_ENABLE_HDF5:BOOL=ON', - '-DTPL_ENABLE_TBB:BOOL=ON', # Need to use MPI wrappers, otherwise: Undefined symbols for architecture x86_64: "_mpi_abort_","_mpi_allgatherv_", etc from MUMPS '-DCMAKE_C_COMPILER=%s' % join_path(mpi_bin,'mpicc'), # FIXME: dont hardcode compiler name '-DCMAKE_CXX_COMPILER=%s' % join_path(mpi_bin,'mpicxx'), -- cgit v1.2.3-70-g09d2 From e51fe2934e0189aa5c33c8663819d23e7706f809 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 23 Mar 2016 17:38:36 +0100 Subject: fiddle more --- var/spack/repos/builtin/packages/trilinos/package.py | 11 ++--------- 1 file changed, 2 insertions(+), 9 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 12212360a0..fb14e1f36c 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -67,7 +67,6 @@ class Trilinos(Package): '-DTPL_ENABLE_Boost:BOOL=ON', '-DBoost_INCLUDE_DIRS:PATH=%s' % spec['boost'].prefix.include, '-DBoost_LIBRARY_DIRS:PATH=%s' % spec['boost'].prefix.lib, - # '-DTrilinos_ENABLE_Fortran=OFF', # FIXME '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON', '-DTrilinos_ENABLE_CXX11:BOOL=ON', '-DTrilinos_CXX11_FLAGS=-std=c++11', @@ -82,10 +81,9 @@ class Trilinos(Package): # Fortran lib libgfortran = os.path.dirname (os.popen('%s --print-file-name libgfortran.a' % join_path(mpi_bin,'mpif90') ).read()) - #os.environ['LDFLAGS'] = '-L%s -lgfortran' % libgfortran options.extend([ - '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-lgfortran', - '-DCMAKE_EXE_LINKER_FLAGS:STRING=-L%s -lgfortran' % libgfortran + '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-L%s/ -lgfortran' % libgfortran, + '-DTrilinos_ENABLE_Fortran=OFF' # FIXME: otherwise VerifyFortranC fails as it does not contain -lgfortran , issues with IMPLICIT_LINK_LIBRARIES in CMakeFiles/CMake(C|CXX|Fortran)Compiler.cmake? ]) # for build-debug only: @@ -155,11 +153,6 @@ class Trilinos(Package): '-DTrilinos_ENABLE_STK=OFF' ]) - #if self.compiler.name == "clang": - # options.extend([ - # '-DCMAKE_EXE_LINKER_FLAGS:STRING=-Qunused-arguments' - # ]) - with working_dir('spack-build', create=True): cmake('..', *options) make() -- cgit v1.2.3-70-g09d2 From 3f12a51759fcdd3b11867cb849fc2aa81a4941ef Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 23 Mar 2016 19:35:49 +0100 Subject: keep fiddling --- var/spack/repos/builtin/packages/trilinos/package.py | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index fb14e1f36c..cdc2bf2379 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -1,6 +1,11 @@ from spack import * import os +# Trilinos is complicated to build, as an inspiration a couple of links to other repositories which build it: +# https://github.com/hpcugent/easybuild-easyblocks/blob/master/easybuild/easyblocks/t/trilinos.py#L111 +# https://github.com/koecher/candi/blob/master/deal.II-toolchain/packages/trilinos.package +# https://gitlab.com/configurations/cluster-config/blob/master/trilinos.sh +# https://github.com/Homebrew/homebrew-science/blob/master/trilinos.rb class Trilinos(Package): """The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. @@ -59,11 +64,11 @@ class Trilinos(Package): '-DTPL_ENABLE_MPI:BOOL=ON', '-DMPI_BASE_DIR:PATH=%s' % spec['mpi'].prefix, '-DTPL_ENABLE_BLAS=ON', - '-DBLAS_LIBRARY_NAMES=blas', - '-DBLAS_LIBRARY_DIRS=/usr/lib', # % spec['blas'].prefix, #FIXME + '-DBLAS_LIBRARY_NAMES=blas', # FIXME: for Intel, Clang+GNU, GNU; easybuild add gfortran here... + '-DBLAS_LIBRARY_DIRS=%s' % spec['blas'].prefix.lib, '-DTPL_ENABLE_LAPACK=ON', '-DLAPACK_LIBRARY_NAMES=lapack', - '-DLAPACK_LIBRARY_DIRS=/usr/lib', # % spec['lapack'].prefix, #FIXME + '-DLAPACK_LIBRARY_DIRS=%s' % spec['lapack'].prefix, '-DTPL_ENABLE_Boost:BOOL=ON', '-DBoost_INCLUDE_DIRS:PATH=%s' % spec['boost'].prefix.include, '-DBoost_LIBRARY_DIRS:PATH=%s' % spec['boost'].prefix.lib, @@ -74,9 +79,9 @@ class Trilinos(Package): '-DTPL_ENABLE_HYPRE:BOOL=ON', '-DTPL_ENABLE_HDF5:BOOL=ON', # Need to use MPI wrappers, otherwise: Undefined symbols for architecture x86_64: "_mpi_abort_","_mpi_allgatherv_", etc from MUMPS - '-DCMAKE_C_COMPILER=%s' % join_path(mpi_bin,'mpicc'), # FIXME: dont hardcode compiler name - '-DCMAKE_CXX_COMPILER=%s' % join_path(mpi_bin,'mpicxx'), - '-DCMAKE_Fortran_COMPILER=%s' % join_path(mpi_bin,'mpif90') + #'-DCMAKE_C_COMPILER=%s' % join_path(mpi_bin,'mpicc'), # FIXME: dont hardcode compiler name + #'-DCMAKE_CXX_COMPILER=%s' % join_path(mpi_bin,'mpicxx'), + #'-DCMAKE_Fortran_COMPILER=%s' % join_path(mpi_bin,'mpif90') ]) # Fortran lib -- cgit v1.2.3-70-g09d2 From 8c9f88761384d16c77aa9cbee55cc501712c7b12 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Thu, 24 Mar 2016 12:45:43 +0100 Subject: finally builds --- var/spack/repos/builtin/packages/trilinos/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index cdc2bf2379..b80123838a 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -39,7 +39,7 @@ class Trilinos(Package): depends_on('mpi') depends_on('netcdf+mpi') depends_on('parmetis') - depends_on('mumps+metis+parmetis') + depends_on('mumps+metis+parmetis+shared') # build errors with static libs # depends_on('scalapack') # see FIXME below depends_on('superlu-dist') depends_on('hypre') -- cgit v1.2.3-70-g09d2 From df995c4ef850338823b3a5a5c2ee3b12e05a33b1 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Thu, 24 Mar 2016 12:57:22 +0100 Subject: minor cleanup --- var/spack/repos/builtin/packages/trilinos/package.py | 14 +++++--------- 1 file changed, 5 insertions(+), 9 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index b80123838a..f2e9c37caa 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -77,24 +77,20 @@ class Trilinos(Package): '-DTrilinos_CXX11_FLAGS=-std=c++11', '-DTPL_ENABLE_Netcdf:BOOL=ON', '-DTPL_ENABLE_HYPRE:BOOL=ON', - '-DTPL_ENABLE_HDF5:BOOL=ON', - # Need to use MPI wrappers, otherwise: Undefined symbols for architecture x86_64: "_mpi_abort_","_mpi_allgatherv_", etc from MUMPS - #'-DCMAKE_C_COMPILER=%s' % join_path(mpi_bin,'mpicc'), # FIXME: dont hardcode compiler name - #'-DCMAKE_CXX_COMPILER=%s' % join_path(mpi_bin,'mpicxx'), - #'-DCMAKE_Fortran_COMPILER=%s' % join_path(mpi_bin,'mpif90') + '-DTPL_ENABLE_HDF5:BOOL=ON' ]) # Fortran lib libgfortran = os.path.dirname (os.popen('%s --print-file-name libgfortran.a' % join_path(mpi_bin,'mpif90') ).read()) options.extend([ '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-L%s/ -lgfortran' % libgfortran, - '-DTrilinos_ENABLE_Fortran=OFF' # FIXME: otherwise VerifyFortranC fails as it does not contain -lgfortran , issues with IMPLICIT_LINK_LIBRARIES in CMakeFiles/CMake(C|CXX|Fortran)Compiler.cmake? + '-DTrilinos_ENABLE_Fortran=OFF' # FIXME: otherwise CMake's VerifyFortranC fails as it does not contain -lgfortran ]) # for build-debug only: - options.extend([ - '-DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE' - ]) + # options.extend([ + # '-DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE' + # ]) # suite-sparse related options.extend([ -- cgit v1.2.3-70-g09d2 From 0fc9326a4cc742e7a06cc1bb4192d0dfd008880d Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Thu, 24 Mar 2016 13:23:56 +0100 Subject: add variants --- .../repos/builtin/packages/trilinos/package.py | 111 +++++++++++++-------- 1 file changed, 69 insertions(+), 42 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index f2e9c37caa..2e119581e1 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -22,8 +22,15 @@ class Trilinos(Package): version('11.14.2', 'a43590cf896c677890d75bfe75bc6254') version('11.14.1', '40febc57f76668be8b6a77b7607bb67f') - variant('shared', default=True, description='Enables the build of shared libraries') - variant('debug', default=False, description='Builds a debug version of the libraries') + variant('metis', default=True, description='Compile with METIS') + variant('parmetis', default=True, description='Compile with ParMETIS') + variant('mumps', default=True, description='Compile with support for MUMPS solvers') + variant('superlu-dist', default=True, description='Compile with SuperluDist solvers') + variant('hypre', default=True, description='Compile with Hypre preconditioner') + variant('hdf5', default=True, description='Compile with HDF5') + variant('suite-sparse', default=True, description='Compile with SuiteSparse solvers') + variant('shared', default=True, description='Enables the build of shared libraries') + variant('debug', default=False, description='Builds a debug version of the libraries') # Everything should be compiled with -fpic depends_on('blas') @@ -49,7 +56,23 @@ class Trilinos(Package): patch('umfpack_from_suitesparse.patch') + # check that the combination of variants makes sense + def variants_check(self): + if '+parmetis' in self.spec and '+metis' not in self.spec: + raise RuntimeError('You cannot use the variant parmetis without metis') + + if '+mumps' in self.spec and '+parmetis' not in self.spec: + raise RuntimeError('You cannot use the variant mumps without parmetis') + + if '+superlu-dist' in self.spec and self.spec.satisfies('@:11.4.3'): + # For Trilinos v11 we need to force SuperLUDist=OFF, + # since only the deprecated SuperLUDist v3.3 together with an Amesos patch + # is working. + raise RuntimeError('The superlu-dist variant can only be used with Trilinos @12.0.1:') + def install(self, spec, prefix): + self.variants_check() + options = [] options.extend(std_cmake_args) @@ -93,35 +116,38 @@ class Trilinos(Package): # ]) # suite-sparse related - options.extend([ - '-DTPL_ENABLE_Cholmod:BOOL=OFF', # FIXME: Trilinos seems to be looking for static libs only, patch CMake TPL file? - #'-DTPL_ENABLE_Cholmod:BOOL=ON', - #'-DCholmod_LIBRARY_DIRS:PATH=%s' % spec['suite-sparse'].prefix.lib, - #'-DCholmod_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include, - '-DTPL_ENABLE_UMFPACK:BOOL=ON', - '-DUMFPACK_LIBRARY_DIRS:PATH=%s' % spec['suite-sparse'].prefix.lib, - '-DUMFPACK_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include, - '-DUMFPACK_LIBRARY_NAMES=umfpack;amd;colamd;cholmod;suitesparseconfig' - ]) + if '+suite-sparse' in spec: + options.extend([ + '-DTPL_ENABLE_Cholmod:BOOL=OFF', # FIXME: Trilinos seems to be looking for static libs only, patch CMake TPL file? + #'-DTPL_ENABLE_Cholmod:BOOL=ON', + #'-DCholmod_LIBRARY_DIRS:PATH=%s' % spec['suite-sparse'].prefix.lib, + #'-DCholmod_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include, + '-DTPL_ENABLE_UMFPACK:BOOL=ON', + '-DUMFPACK_LIBRARY_DIRS:PATH=%s' % spec['suite-sparse'].prefix.lib, + '-DUMFPACK_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include, + '-DUMFPACK_LIBRARY_NAMES=umfpack;amd;colamd;cholmod;suitesparseconfig' + ]) # metis / parmetis - options.extend([ - '-DTPL_ENABLE_METIS:BOOL=ON', - '-DMETIS_LIBRARY_DIRS=%s' % spec['metis'].prefix.lib, - '-DMETIS_LIBRARY_NAMES=metis', - '-DTPL_METIS_INCLUDE_DIRS=%s' % spec['metis'].prefix.include, - '-DTPL_ENABLE_ParMETIS:BOOL=ON', - '-DParMETIS_LIBRARY_DIRS=%s;%s' % (spec['parmetis'].prefix.lib,spec['metis'].prefix.lib), - '-DParMETIS_LIBRARY_NAMES=parmetis;metis', - '-DTPL_ParMETIS_INCLUDE_DIRS=%s' % spec['parmetis'].prefix.include - ]) + if '+parmetis' in spec: # metis is required, see variants_check() + options.extend([ + '-DTPL_ENABLE_METIS:BOOL=ON', + '-DMETIS_LIBRARY_DIRS=%s' % spec['metis'].prefix.lib, + '-DMETIS_LIBRARY_NAMES=metis', + '-DTPL_METIS_INCLUDE_DIRS=%s' % spec['metis'].prefix.include, + '-DTPL_ENABLE_ParMETIS:BOOL=ON', + '-DParMETIS_LIBRARY_DIRS=%s;%s' % (spec['parmetis'].prefix.lib,spec['metis'].prefix.lib), + '-DParMETIS_LIBRARY_NAMES=parmetis;metis', + '-DTPL_ParMETIS_INCLUDE_DIRS=%s' % spec['parmetis'].prefix.include + ]) # mumps - options.extend([ - '-DTPL_ENABLE_MUMPS:BOOL=ON', - '-DMUMPS_LIBRARY_DIRS=%s' % spec['mumps'].prefix.lib, - '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord' # order is important! - ]) + if '+mumps' in spec: + options.extend([ + '-DTPL_ENABLE_MUMPS:BOOL=ON', + '-DMUMPS_LIBRARY_DIRS=%s' % spec['mumps'].prefix.lib, + '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord' # order is important! + ]) # scalapack options.extend([ @@ -129,23 +155,24 @@ class Trilinos(Package): #'-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64 ]) - # superlu_dist: - # Amesos, conflicting types of double and complex SLU_D - # see https://trilinos.org/pipermail/trilinos-users/2015-March/004731.html - # and https://trilinos.org/pipermail/trilinos-users/2015-March/004802.html - options.extend([ - '-DTeuchos_ENABLE_COMPLEX:BOOL=OFF', - '-DKokkosTSQR_ENABLE_Complex:BOOL=OFF' - ]) - options.extend([ - '-DTPL_ENABLE_SuperLUDist:BOOL=ON', - '-DSuperLUDist_LIBRARY_DIRS=%s' % spec['superlu-dist'].prefix.lib, - '-DSuperLUDist_INCLUDE_DIRS=%s/superlu_dist' % spec['superlu-dist'].prefix.include # superlu_dist and superlu have the same header names :-( In order to avoid conflicts, try to keep "dist" version headers in a subfolder - ]) - if spec.satisfies('^superlu-dist@4.0:'): + # superlu-dist: + if '+superlu-dist' in spec: + # Amesos, conflicting types of double and complex SLU_D + # see https://trilinos.org/pipermail/trilinos-users/2015-March/004731.html + # and https://trilinos.org/pipermail/trilinos-users/2015-March/004802.html + options.extend([ + '-DTeuchos_ENABLE_COMPLEX:BOOL=OFF', + '-DKokkosTSQR_ENABLE_Complex:BOOL=OFF' + ]) options.extend([ - '-DHAVE_SUPERLUDIST_LUSTRUCTINIT_2ARG:BOOL=ON' + '-DTPL_ENABLE_SuperLUDist:BOOL=ON', + '-DSuperLUDist_LIBRARY_DIRS=%s' % spec['superlu-dist'].prefix.lib, + '-DSuperLUDist_INCLUDE_DIRS=%s/superlu_dist' % spec['superlu-dist'].prefix.include # superlu_dist and superlu have the same header names :-( In order to avoid conflicts, try to keep "dist" version headers in a subfolder ]) + if spec.satisfies('^superlu-dist@4.0:'): + options.extend([ + '-DHAVE_SUPERLUDIST_LUSTRUCTINIT_2ARG:BOOL=ON' + ]) # disable due to compiler / config errors: options.extend([ -- cgit v1.2.3-70-g09d2 From 416fcd081013afa8349d311909d50b21d9685674 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Thu, 24 Mar 2016 13:33:00 +0100 Subject: same --- var/spack/repos/builtin/packages/trilinos/package.py | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 2e119581e1..3beadeb798 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -29,6 +29,7 @@ class Trilinos(Package): variant('hypre', default=True, description='Compile with Hypre preconditioner') variant('hdf5', default=True, description='Compile with HDF5') variant('suite-sparse', default=True, description='Compile with SuiteSparse solvers') + variant('python', default=True, description='Build python wrappers') variant('shared', default=True, description='Enables the build of shared libraries') variant('debug', default=False, description='Builds a debug version of the libraries') @@ -39,20 +40,20 @@ class Trilinos(Package): depends_on('matio') depends_on('glm') depends_on('swig') - depends_on('metis') - depends_on('suite-sparse') + depends_on('metis',when='+metis') + depends_on('suite-sparse',when='+suite-sparse') # MPI related dependencies depends_on('mpi') depends_on('netcdf+mpi') - depends_on('parmetis') - depends_on('mumps+metis+parmetis+shared') # build errors with static libs + depends_on('parmetis',when='+parmetis') + depends_on('mumps+metis+parmetis+shared',when='+mumps') # build errors with static libs # depends_on('scalapack') # see FIXME below - depends_on('superlu-dist') - depends_on('hypre') - depends_on('hdf5+mpi') + depends_on('superlu-dist',when='+superlu-dist') + depends_on('hypre',when='+hypre') + depends_on('hdf5+mpi',when='+hdf5') - depends_on('python') # Needs py-numpy activated + depends_on('python',when='+python') # Needs py-numpy activated patch('umfpack_from_suitesparse.patch') -- cgit v1.2.3-70-g09d2 From c33a63cabc8dcd8c71fc87de60a883cef4a4dae2 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Thu, 24 Mar 2016 13:47:07 +0100 Subject: fix python installation --- var/spack/repos/builtin/packages/trilinos/package.py | 11 +++++++++++ 1 file changed, 11 insertions(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 3beadeb798..886893b639 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -186,3 +186,14 @@ class Trilinos(Package): cmake('..', *options) make() make('install') + + # When trilinos is built with Python, libpytrilinos is included through + # cmake configure files. Namely, Trilinos_LIBRARIES in TrilinosConfig.cmake + # contains pytrilinos. This leads to a run-time error: + # Symbol not found: _PyBool_Type + # and prevents Trilinos to be used in any C++ code, which links executable + # against the libraries listed in Trilinos_LIBRARIES. + # See https://github.com/Homebrew/homebrew-science/issues/2148#issuecomment-103614509 + # A workaround it to remove PyTrilinos from the COMPONENTS_LIST : + if '+python' in self.spec: + filter_file(r'(?:SET\(COMPONENTS_LIST.*)(PyTrilinos;)(?:.*)', '', '%s/cmake/Trilinos/TrilinosConfig.cmake' % prefix.lib) -- cgit v1.2.3-70-g09d2 From d096b155f45d97775affa2bdda640a22823cb73e Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Thu, 24 Mar 2016 19:41:37 +0100 Subject: fix filter_file --- var/spack/repos/builtin/packages/trilinos/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 886893b639..3967d0ef0e 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -196,4 +196,4 @@ class Trilinos(Package): # See https://github.com/Homebrew/homebrew-science/issues/2148#issuecomment-103614509 # A workaround it to remove PyTrilinos from the COMPONENTS_LIST : if '+python' in self.spec: - filter_file(r'(?:SET\(COMPONENTS_LIST.*)(PyTrilinos;)(?:.*)', '', '%s/cmake/Trilinos/TrilinosConfig.cmake' % prefix.lib) + filter_file(r'(SET\(COMPONENTS_LIST.*)(PyTrilinos;)(.*)', (r'\1\3'), '%s/cmake/Trilinos/TrilinosConfig.cmake' % prefix.lib) -- cgit v1.2.3-70-g09d2 From 7f2db8c26793abb1977dbccd2ae8a3a1b5a46568 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Fri, 25 Mar 2016 11:54:51 +0100 Subject: fix w GCC 4.8 on Ubuntu but broke w GCC 5.3/Clang on OSX --- .../repos/builtin/packages/trilinos/package.py | 26 ++++++++++++++++------ 1 file changed, 19 insertions(+), 7 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 3967d0ef0e..1f1601e537 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -48,7 +48,7 @@ class Trilinos(Package): depends_on('netcdf+mpi') depends_on('parmetis',when='+parmetis') depends_on('mumps+metis+parmetis+shared',when='+mumps') # build errors with static libs - # depends_on('scalapack') # see FIXME below + depends_on('scalapack') depends_on('superlu-dist',when='+superlu-dist') depends_on('hypre',when='+hypre') depends_on('hdf5+mpi',when='+hdf5') @@ -108,13 +108,13 @@ class Trilinos(Package): libgfortran = os.path.dirname (os.popen('%s --print-file-name libgfortran.a' % join_path(mpi_bin,'mpif90') ).read()) options.extend([ '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-L%s/ -lgfortran' % libgfortran, - '-DTrilinos_ENABLE_Fortran=OFF' # FIXME: otherwise CMake's VerifyFortranC fails as it does not contain -lgfortran + '-DTrilinos_ENABLE_Fortran=ON' # FIXME: otherwise CMake's VerifyFortranC fails as it does not contain -lgfortran ]) # for build-debug only: - # options.extend([ - # '-DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE' - # ]) + options.extend([ + '-DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE' + ]) # suite-sparse related if '+suite-sparse' in spec: @@ -144,16 +144,22 @@ class Trilinos(Package): # mumps if '+mumps' in spec: + # FIXME: + # since we use mumps with MPI, it will certainly be build against Scalapack. + # Add scalapack lib here as well. + # This likely won't be need if Trilinos would compile with Scalapack options.extend([ '-DTPL_ENABLE_MUMPS:BOOL=ON', '-DMUMPS_LIBRARY_DIRS=%s' % spec['mumps'].prefix.lib, '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord' # order is important! +# '-DMUMPS_LIBRARY_DIRS=%s;%s' % (spec['mumps'].prefix.lib,spec['scalapack'].prefix.lib), +# '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord;scalapack' # order is important! ]) # scalapack options.extend([ - '-DTPL_ENABLE_SCALAPACK:BOOL=OFF', #FIXME: Undefined symbols for architecture x86_64: "_blacs_gridinfo__", referenced from: Amesos_Scalapack::RedistributeA() in Amesos_Scalapack.cpp.o - #'-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64 + '-DTPL_ENABLE_SCALAPACK:BOOL=ON', #FIXME: Undefined symbols for architecture x86_64: "_blacs_gridinfo__", referenced from: Amesos_Scalapack::RedistributeA() in Amesos_Scalapack.cpp.o + '-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64 ]) # superlu-dist: @@ -175,6 +181,12 @@ class Trilinos(Package): '-DHAVE_SUPERLUDIST_LUSTRUCTINIT_2ARG:BOOL=ON' ]) + # python + if '~python' in spec: + options.extend([ + '-DTrilinos_ENABLE_PyTrilinos:BOOL=OFF' + ]) + # disable due to compiler / config errors: options.extend([ '-DTrilinos_ENABLE_SEACAS=OFF', -- cgit v1.2.3-70-g09d2 From 828aeefb1d4e09deb0694c61397a3097bda85ccb Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Fri, 25 Mar 2016 12:01:00 +0100 Subject: minor cleanup --- var/spack/repos/builtin/packages/trilinos/package.py | 12 +++--------- 1 file changed, 3 insertions(+), 9 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 1f1601e537..1dba2b8db3 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -88,7 +88,7 @@ class Trilinos(Package): '-DTPL_ENABLE_MPI:BOOL=ON', '-DMPI_BASE_DIR:PATH=%s' % spec['mpi'].prefix, '-DTPL_ENABLE_BLAS=ON', - '-DBLAS_LIBRARY_NAMES=blas', # FIXME: for Intel, Clang+GNU, GNU; easybuild add gfortran here... + '-DBLAS_LIBRARY_NAMES=blas', # FIXME: don't hardcode names '-DBLAS_LIBRARY_DIRS=%s' % spec['blas'].prefix.lib, '-DTPL_ENABLE_LAPACK=ON', '-DLAPACK_LIBRARY_NAMES=lapack', @@ -108,7 +108,7 @@ class Trilinos(Package): libgfortran = os.path.dirname (os.popen('%s --print-file-name libgfortran.a' % join_path(mpi_bin,'mpif90') ).read()) options.extend([ '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-L%s/ -lgfortran' % libgfortran, - '-DTrilinos_ENABLE_Fortran=ON' # FIXME: otherwise CMake's VerifyFortranC fails as it does not contain -lgfortran + '-DTrilinos_ENABLE_Fortran=ON' ]) # for build-debug only: @@ -144,21 +144,15 @@ class Trilinos(Package): # mumps if '+mumps' in spec: - # FIXME: - # since we use mumps with MPI, it will certainly be build against Scalapack. - # Add scalapack lib here as well. - # This likely won't be need if Trilinos would compile with Scalapack options.extend([ '-DTPL_ENABLE_MUMPS:BOOL=ON', '-DMUMPS_LIBRARY_DIRS=%s' % spec['mumps'].prefix.lib, '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord' # order is important! -# '-DMUMPS_LIBRARY_DIRS=%s;%s' % (spec['mumps'].prefix.lib,spec['scalapack'].prefix.lib), -# '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord;scalapack' # order is important! ]) # scalapack options.extend([ - '-DTPL_ENABLE_SCALAPACK:BOOL=ON', #FIXME: Undefined symbols for architecture x86_64: "_blacs_gridinfo__", referenced from: Amesos_Scalapack::RedistributeA() in Amesos_Scalapack.cpp.o + '-DTPL_ENABLE_SCALAPACK:BOOL=ON', '-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64 ]) -- cgit v1.2.3-70-g09d2 From 21e81e92a9ac88bd498bd65aa9b77a43c27da881 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Fri, 25 Mar 2016 12:05:48 +0100 Subject: try to disable VerifyFortranC tests on Darwin --- var/spack/repos/builtin/packages/trilinos/package.py | 7 +++++++ 1 file changed, 7 insertions(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 1dba2b8db3..0c7d8a7967 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -110,6 +110,13 @@ class Trilinos(Package): '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-L%s/ -lgfortran' % libgfortran, '-DTrilinos_ENABLE_Fortran=ON' ]) + # FIXME: + # VerifyFortranC test of CMake does not contain -lgfortran and thus fails. + # This could be GCC/CMake related, but appears at least on OSX with Clang@7.0.2 and GNU Fortran@5.3.0 + if sys.platform == 'darwin': + options.extend([ + '-DTrilinos_SKIP_FORTRANCINTERFACE_VERIFY_TEST:BOOL=TRUE' + ]) # for build-debug only: options.extend([ -- cgit v1.2.3-70-g09d2 From 26a72619aed8684019ab331889b276b8883b76c8 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Fri, 25 Mar 2016 12:42:26 +0100 Subject: add missing sys --- var/spack/repos/builtin/packages/trilinos/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 0c7d8a7967..e077dfbbfd 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -1,5 +1,5 @@ from spack import * -import os +import os, sys # Trilinos is complicated to build, as an inspiration a couple of links to other repositories which build it: # https://github.com/hpcugent/easybuild-easyblocks/blob/master/easybuild/easyblocks/t/trilinos.py#L111 -- cgit v1.2.3-70-g09d2 From 5172f09b9f966a3f1be438bab972a0267cccc73b Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Fri, 25 Mar 2016 16:47:48 +0100 Subject: builds on OSX again (modulo CC wrappers are solved) --- var/spack/repos/builtin/packages/trilinos/package.py | 19 ++++++++++++------- 1 file changed, 12 insertions(+), 7 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index e077dfbbfd..3003b4ab53 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -113,15 +113,15 @@ class Trilinos(Package): # FIXME: # VerifyFortranC test of CMake does not contain -lgfortran and thus fails. # This could be GCC/CMake related, but appears at least on OSX with Clang@7.0.2 and GNU Fortran@5.3.0 - if sys.platform == 'darwin': - options.extend([ - '-DTrilinos_SKIP_FORTRANCINTERFACE_VERIFY_TEST:BOOL=TRUE' - ]) + #if sys.platform == 'darwin': + # options.extend([ + # '-DTrilinos_SKIP_FORTRANCINTERFACE_VERIFY_TEST:BOOL=TRUE' + # ]) # for build-debug only: - options.extend([ - '-DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE' - ]) + #options.extend([ + # '-DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE' + #]) # suite-sparse related if '+suite-sparse' in spec: @@ -194,6 +194,11 @@ class Trilinos(Package): '-DTrilinos_ENABLE_Pike=OFF', '-DTrilinos_ENABLE_STK=OFF' ]) + if sys.platform == 'darwin': + options.extend([ + '-DTrilinos_ENABLE_FEI=OFF' + ]) + with working_dir('spack-build', create=True): cmake('..', *options) -- cgit v1.2.3-70-g09d2 From eec50b524bdf9e04f9e3536bc389ce633133373b Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Fri, 25 Mar 2016 16:58:14 +0100 Subject: minor cleanup --- .../repos/builtin/packages/trilinos/package.py | 46 ++++++++++++++++------ 1 file changed, 35 insertions(+), 11 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 3003b4ab53..b1caca96ff 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -28,6 +28,7 @@ class Trilinos(Package): variant('superlu-dist', default=True, description='Compile with SuperluDist solvers') variant('hypre', default=True, description='Compile with Hypre preconditioner') variant('hdf5', default=True, description='Compile with HDF5') + variant('scalapack', default=True, description='Compile with Scalapack') variant('suite-sparse', default=True, description='Compile with SuiteSparse solvers') variant('python', default=True, description='Build python wrappers') variant('shared', default=True, description='Enables the build of shared libraries') @@ -110,13 +111,6 @@ class Trilinos(Package): '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-L%s/ -lgfortran' % libgfortran, '-DTrilinos_ENABLE_Fortran=ON' ]) - # FIXME: - # VerifyFortranC test of CMake does not contain -lgfortran and thus fails. - # This could be GCC/CMake related, but appears at least on OSX with Clang@7.0.2 and GNU Fortran@5.3.0 - #if sys.platform == 'darwin': - # options.extend([ - # '-DTrilinos_SKIP_FORTRANCINTERFACE_VERIFY_TEST:BOOL=TRUE' - # ]) # for build-debug only: #options.extend([ @@ -135,6 +129,11 @@ class Trilinos(Package): '-DUMFPACK_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include, '-DUMFPACK_LIBRARY_NAMES=umfpack;amd;colamd;cholmod;suitesparseconfig' ]) + else: + options.extend([ + '-DTPL_ENABLE_Cholmod:BOOL=OFF', + '-DTPL_ENABLE_UMFPACK:BOOL=OFF', + ]) # metis / parmetis if '+parmetis' in spec: # metis is required, see variants_check() @@ -148,6 +147,11 @@ class Trilinos(Package): '-DParMETIS_LIBRARY_NAMES=parmetis;metis', '-DTPL_ParMETIS_INCLUDE_DIRS=%s' % spec['parmetis'].prefix.include ]) + else: + options.extend([ + '-DTPL_ENABLE_METIS:BOOL=OFF', + '-DTPL_ENABLE_ParMETIS:BOOL=OFF', + ]) # mumps if '+mumps' in spec: @@ -156,12 +160,22 @@ class Trilinos(Package): '-DMUMPS_LIBRARY_DIRS=%s' % spec['mumps'].prefix.lib, '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord' # order is important! ]) + else: + options.extend([ + '-DTPL_ENABLE_MUMPS:BOOL=OFF', + ]) # scalapack - options.extend([ - '-DTPL_ENABLE_SCALAPACK:BOOL=ON', - '-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64 - ]) + if '+scalapack' in spec: + options.extend([ + '-DTPL_ENABLE_SCALAPACK:BOOL=ON', + '-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64 + ]) + else: + options.extend([ + '-DTPL_ENABLE_SCALAPACK:BOOL=OFF', + ]) + # superlu-dist: if '+superlu-dist' in spec: @@ -181,12 +195,22 @@ class Trilinos(Package): options.extend([ '-DHAVE_SUPERLUDIST_LUSTRUCTINIT_2ARG:BOOL=ON' ]) + else: + options.extend([ + '-DTPL_ENABLE_SuperLUDist:BOOL=OFF', + ]) + # python if '~python' in spec: options.extend([ '-DTrilinos_ENABLE_PyTrilinos:BOOL=OFF' ]) + else: + options.extend([ + '-DTrilinos_ENABLE_PyTrilinos:BOOL=ON' + ]) + # disable due to compiler / config errors: options.extend([ -- cgit v1.2.3-70-g09d2 From 6699399e5191004ed924b9a8916ec1ae61223000 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Fri, 25 Mar 2016 17:00:42 +0100 Subject: add when to depends_on scalapack --- var/spack/repos/builtin/packages/trilinos/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index b1caca96ff..8b66405137 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -49,7 +49,7 @@ class Trilinos(Package): depends_on('netcdf+mpi') depends_on('parmetis',when='+parmetis') depends_on('mumps+metis+parmetis+shared',when='+mumps') # build errors with static libs - depends_on('scalapack') + depends_on('scalapack',when='+scalapack') depends_on('superlu-dist',when='+superlu-dist') depends_on('hypre',when='+hypre') depends_on('hdf5+mpi',when='+hdf5') -- cgit v1.2.3-70-g09d2 From c7011d21aa95145c7b3978f4220b211e39c9ecf2 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Fri, 25 Mar 2016 22:15:39 +0100 Subject: update dependencies. Builds fine on OSX --- var/spack/repos/builtin/packages/dealii/package.py | 32 +++++++++++----------- 1 file changed, 16 insertions(+), 16 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py index cddf5cd98b..5a50481b9b 100644 --- a/var/spack/repos/builtin/packages/dealii/package.py +++ b/var/spack/repos/builtin/packages/dealii/package.py @@ -12,21 +12,21 @@ class Dealii(Package): depends_on ("lapack") depends_on ("mpi") - #depends_on ("arpack") + depends_on ("arpack-ng") depends_on ("boost") - #depends_on ("doxygen") - depends_on ("hdf5+mpi") + depends_on ("doxygen") + depends_on ("hdf5+mpi~cxx") #FIXME NetCDF declares dependency with ~cxx, why? depends_on ("metis") - #depends_on "muparser" + depends_on ("muparser") depends_on ("netcdf") - #depends_on ("numdiff") - #depends_on ("oce") + #depends_on ("numdiff") #FIXME + depends_on ("oce") depends_on ("p4est") depends_on ("parmetis") depends_on ("petsc") - #depends_on ("slepc") - depends_on ("SuiteSparse") - #depends_on "tbb" + depends_on ("slepc") + depends_on ("suite-sparse") + depends_on ("tbb") depends_on ("trilinos") def install(self, spec, prefix): @@ -42,21 +42,21 @@ class Dealii(Package): '-DCMAKE_BUILD_TYPE=DebugRelease', '-DDEAL_II_WITH_THREADS:BOOL=ON' '-DDEAL_II_WITH_MPI:BOOL=ON', - '-DCMAKE_C_COMPILER=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpicc'), + '-DCMAKE_C_COMPILER=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpicc'), # FIXME: avoid hardcoding mpi wrappers names '-DCMAKE_CXX_COMPILER=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpic++'), '-DCMAKE_Fortran_COMPILER=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif90'), - #'-DARPACK_DIR=%s' % , + '-DARPACK_DIR=%s' % spec['arpack-ng'].prefix, '-DBOOST_DIR=%s' % spec['boost'].prefix, '-DHDF5_DIR=%s' % spec['hdf5'].prefix, '-DMETIS_DIR=%s' % spec['metis'].prefix, - #'-DMUPARSER_DIR=%s ' + '-DMUPARSER_DIR=%s ' % spec['muparser'].prefix, '-DNETCDF_DIR=%s' % spec['netcdf'].prefix, - #'-DOPENCASCADE_DIR= + '-DOPENCASCADE_DIR=%s' % spec['oce'].prefix, '-DP4EST_DIR=%s' % spec['p4est'].prefix, '-DPETSC_DIR=%s' % spec['petsc'].prefix, - #'-DSLEPC_DIR= - '-DUMFPACK_DIR=%s' % spec['SuiteSparse'].prefix, - #'-DTBB_DIR=%s' + '-DSLEPC_DIR=%s' % spec['slepc'].prefix, + '-DUMFPACK_DIR=%s' % spec['suite-sparse'].prefix, + '-DTBB_DIR=%s' % spec['tbb'].prefix, '-DTRILINOS_DIR=%s' % spec['trilinos'].prefix ]) -- cgit v1.2.3-70-g09d2 From 497adc3b42191c000323c55aae5da32fab901265 Mon Sep 17 00:00:00 2001 From: Elizabeth F Date: Fri, 25 Mar 2016 22:45:19 -0400 Subject: Added new version; old versions don't work with Python3. --- var/spack/repos/builtin/packages/py-cython/package.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/py-cython/package.py b/var/spack/repos/builtin/packages/py-cython/package.py index 68eb735ad9..4d728fa8fb 100644 --- a/var/spack/repos/builtin/packages/py-cython/package.py +++ b/var/spack/repos/builtin/packages/py-cython/package.py @@ -3,10 +3,13 @@ from spack import * class PyCython(Package): """The Cython compiler for writing C extensions for the Python language.""" homepage = "https://pypi.python.org/pypi/cython" - url = "https://pypi.python.org/packages/source/C/Cython/cython-0.22.tar.gz" + url = "https://pypi.python.org/packages/source/C/Cython/Cython-0.22.tar.gz" - version('0.21.2', 'd21adb870c75680dc857cd05d41046a4') + version('0.23.4', '157df1f69bcec6b56fd97e0f2e057f6e') + + # These versions contain illegal Python3 code... version('0.22', '1ae25add4ef7b63ee9b4af697300d6b6') + version('0.21.2', 'd21adb870c75680dc857cd05d41046a4') extends('python') -- cgit v1.2.3-70-g09d2 From f603c82e814ebc59ba03b0b83be86f1a4bfcbd94 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Sat, 26 Mar 2016 18:43:55 +0100 Subject: qualify Amesos link errors --- var/spack/repos/builtin/packages/trilinos/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 8b66405137..0ba7a51b8b 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -48,7 +48,7 @@ class Trilinos(Package): depends_on('mpi') depends_on('netcdf+mpi') depends_on('parmetis',when='+parmetis') - depends_on('mumps+metis+parmetis+shared',when='+mumps') # build errors with static libs + depends_on('mumps+metis+parmetis+shared',when='+mumps') # Amesos link errors with static: "__gfortran_adjustl", referenced from: _dmumps_ in libdmumps.a(dmumps_driver.o) "_mpi_abort_", referenced from: _mumps_abort_ in libmumps_common.a(tools_common.o) depends_on('scalapack',when='+scalapack') depends_on('superlu-dist',when='+superlu-dist') depends_on('hypre',when='+hypre') -- cgit v1.2.3-70-g09d2 From 965ce633c311e2bcb765f5e9900f0da6205f9c23 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Sat, 26 Mar 2016 18:51:59 +0100 Subject: cleanup variants --- .../repos/builtin/packages/trilinos/package.py | 40 +++++++--------------- 1 file changed, 13 insertions(+), 27 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 0ba7a51b8b..48bffc65e0 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -22,13 +22,11 @@ class Trilinos(Package): version('11.14.2', 'a43590cf896c677890d75bfe75bc6254') version('11.14.1', '40febc57f76668be8b6a77b7607bb67f') - variant('metis', default=True, description='Compile with METIS') - variant('parmetis', default=True, description='Compile with ParMETIS') + variant('metis', default=True, description='Compile with METIS and ParMETIS') variant('mumps', default=True, description='Compile with support for MUMPS solvers') variant('superlu-dist', default=True, description='Compile with SuperluDist solvers') variant('hypre', default=True, description='Compile with Hypre preconditioner') variant('hdf5', default=True, description='Compile with HDF5') - variant('scalapack', default=True, description='Compile with Scalapack') variant('suite-sparse', default=True, description='Compile with SuiteSparse solvers') variant('python', default=True, description='Build python wrappers') variant('shared', default=True, description='Enables the build of shared libraries') @@ -47,9 +45,9 @@ class Trilinos(Package): # MPI related dependencies depends_on('mpi') depends_on('netcdf+mpi') - depends_on('parmetis',when='+parmetis') - depends_on('mumps+metis+parmetis+shared',when='+mumps') # Amesos link errors with static: "__gfortran_adjustl", referenced from: _dmumps_ in libdmumps.a(dmumps_driver.o) "_mpi_abort_", referenced from: _mumps_abort_ in libmumps_common.a(tools_common.o) - depends_on('scalapack',when='+scalapack') + depends_on('parmetis',when='+metis') + depends_on('mumps+mpi+metis+parmetis+shared',when='+mumps') # Amesos link errors with static: "__gfortran_adjustl", referenced from: _dmumps_ in libdmumps.a(dmumps_driver.o) "_mpi_abort_", referenced from: _mumps_abort_ in libmumps_common.a(tools_common.o) + depends_on('scalapack',when='+mumps') depends_on('superlu-dist',when='+superlu-dist') depends_on('hypre',when='+hypre') depends_on('hdf5+mpi',when='+hdf5') @@ -60,11 +58,8 @@ class Trilinos(Package): # check that the combination of variants makes sense def variants_check(self): - if '+parmetis' in self.spec and '+metis' not in self.spec: - raise RuntimeError('You cannot use the variant parmetis without metis') - - if '+mumps' in self.spec and '+parmetis' not in self.spec: - raise RuntimeError('You cannot use the variant mumps without parmetis') + if '+mumps' in self.spec and '+metis' not in self.spec: + raise RuntimeError('You cannot use the variant mumps without metis') if '+superlu-dist' in self.spec and self.spec.satisfies('@:11.4.3'): # For Trilinos v11 we need to force SuperLUDist=OFF, @@ -136,7 +131,7 @@ class Trilinos(Package): ]) # metis / parmetis - if '+parmetis' in spec: # metis is required, see variants_check() + if '+metis' in spec: options.extend([ '-DTPL_ENABLE_METIS:BOOL=ON', '-DMETIS_LIBRARY_DIRS=%s' % spec['metis'].prefix.lib, @@ -153,30 +148,21 @@ class Trilinos(Package): '-DTPL_ENABLE_ParMETIS:BOOL=OFF', ]) - # mumps + # mumps / scalapack if '+mumps' in spec: options.extend([ '-DTPL_ENABLE_MUMPS:BOOL=ON', '-DMUMPS_LIBRARY_DIRS=%s' % spec['mumps'].prefix.lib, - '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord' # order is important! - ]) - else: - options.extend([ - '-DTPL_ENABLE_MUMPS:BOOL=OFF', - ]) - - # scalapack - if '+scalapack' in spec: - options.extend([ + '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord', # order is important! '-DTPL_ENABLE_SCALAPACK:BOOL=ON', '-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64 ]) else: options.extend([ + '-DTPL_ENABLE_MUMPS:BOOL=OFF', '-DTPL_ENABLE_SCALAPACK:BOOL=OFF', ]) - # superlu-dist: if '+superlu-dist' in spec: # Amesos, conflicting types of double and complex SLU_D @@ -202,13 +188,13 @@ class Trilinos(Package): # python - if '~python' in spec: + if '+python' in spec: options.extend([ - '-DTrilinos_ENABLE_PyTrilinos:BOOL=OFF' + '-DTrilinos_ENABLE_PyTrilinos:BOOL=ON' ]) else: options.extend([ - '-DTrilinos_ENABLE_PyTrilinos:BOOL=ON' + '-DTrilinos_ENABLE_PyTrilinos:BOOL=OFF' ]) -- cgit v1.2.3-70-g09d2 From 9c391bbda1c8379dd60cf21d82779db704183f32 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Sat, 26 Mar 2016 20:52:08 +0100 Subject: minor changes to variants --- var/spack/repos/builtin/packages/dealii/package.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py index 5a50481b9b..19bb3814be 100644 --- a/var/spack/repos/builtin/packages/dealii/package.py +++ b/var/spack/repos/builtin/packages/dealii/package.py @@ -12,7 +12,7 @@ class Dealii(Package): depends_on ("lapack") depends_on ("mpi") - depends_on ("arpack-ng") + depends_on ("arpack-ng+mpi") depends_on ("boost") depends_on ("doxygen") depends_on ("hdf5+mpi~cxx") #FIXME NetCDF declares dependency with ~cxx, why? @@ -23,7 +23,7 @@ class Dealii(Package): depends_on ("oce") depends_on ("p4est") depends_on ("parmetis") - depends_on ("petsc") + depends_on ("petsc+mpi") depends_on ("slepc") depends_on ("suite-sparse") depends_on ("tbb") -- cgit v1.2.3-70-g09d2 From 11ca06b1045283e2c89dc84a91ceb88fcadb6163 Mon Sep 17 00:00:00 2001 From: Elizabeth F Date: Sat, 26 Mar 2016 20:35:34 -0400 Subject: Added new py-cython version --- var/spack/repos/builtin/packages/py-cython/package.py | 1 + 1 file changed, 1 insertion(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/py-cython/package.py b/var/spack/repos/builtin/packages/py-cython/package.py index 4d728fa8fb..072355026e 100644 --- a/var/spack/repos/builtin/packages/py-cython/package.py +++ b/var/spack/repos/builtin/packages/py-cython/package.py @@ -5,6 +5,7 @@ class PyCython(Package): homepage = "https://pypi.python.org/pypi/cython" url = "https://pypi.python.org/packages/source/C/Cython/Cython-0.22.tar.gz" + version('0.23.5', '66b62989a67c55af016c916da36e7514') version('0.23.4', '157df1f69bcec6b56fd97e0f2e057f6e') # These versions contain illegal Python3 code... -- cgit v1.2.3-70-g09d2 From 9b130e1d199bcff10903e981bd7592ed941d0107 Mon Sep 17 00:00:00 2001 From: citibeth Date: Sat, 26 Mar 2016 20:42:35 -0400 Subject: Added googletest package. --- .../repos/builtin/packages/googletest/package.py | 40 ++++++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 var/spack/repos/builtin/packages/googletest/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/googletest/package.py b/var/spack/repos/builtin/packages/googletest/package.py new file mode 100644 index 0000000000..ed27afa10c --- /dev/null +++ b/var/spack/repos/builtin/packages/googletest/package.py @@ -0,0 +1,40 @@ +# FIXME: +# This is a template package file for Spack. We've conveniently +# put "FIXME" labels next to all the things you'll want to change. +# +# Once you've edited all the FIXME's, delete this whole message, +# save this file, and test out your package like this: +# +# spack install googletest +# +# You can always get back here to change things with: +# +# spack edit googletest +# +# See the spack documentation for more information on building +# packages. +# +from spack import * + +class Googletest(Package): + """Google test framework for C++. Also called gtest.""" + homepage = "https://github.com/google/googletest" + url = "https://github.com/google/googletest/tarball/release-1.7.0" + + version('1.7.0', '5eaf03ed925a47b37c8e1d559eb19bc4') + + depends_on("cmake") + + def install(self, spec, prefix): + which('cmake')('.', *std_cmake_args) + + make() + + # Google Test doesn't have a make install + # We have to do our own install here. + install_tree('include', prefix.include) + + mkdirp(prefix.lib) + install('./libgtest.a', '%s' % prefix.lib) + install('./libgtest_main.a', '%s' % prefix.lib) + -- cgit v1.2.3-70-g09d2 From a82a587b3298ffec0c11ddf1c9639c6de228fa6a Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Sun, 27 Mar 2016 06:17:43 +0200 Subject: lower requirement on mumps --- var/spack/repos/builtin/packages/trilinos/package.py | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 48bffc65e0..e8c4bcd7e2 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -46,7 +46,7 @@ class Trilinos(Package): depends_on('mpi') depends_on('netcdf+mpi') depends_on('parmetis',when='+metis') - depends_on('mumps+mpi+metis+parmetis+shared',when='+mumps') # Amesos link errors with static: "__gfortran_adjustl", referenced from: _dmumps_ in libdmumps.a(dmumps_driver.o) "_mpi_abort_", referenced from: _mumps_abort_ in libmumps_common.a(tools_common.o) + depends_on('mumps+mpi+shared',when='+mumps') # Amesos link errors with static: "__gfortran_adjustl", referenced from: _dmumps_ in libdmumps.a(dmumps_driver.o) "_mpi_abort_", referenced from: _mumps_abort_ in libmumps_common.a(tools_common.o) depends_on('scalapack',when='+mumps') depends_on('superlu-dist',when='+superlu-dist') depends_on('hypre',when='+hypre') @@ -58,9 +58,6 @@ class Trilinos(Package): # check that the combination of variants makes sense def variants_check(self): - if '+mumps' in self.spec and '+metis' not in self.spec: - raise RuntimeError('You cannot use the variant mumps without metis') - if '+superlu-dist' in self.spec and self.spec.satisfies('@:11.4.3'): # For Trilinos v11 we need to force SuperLUDist=OFF, # since only the deprecated SuperLUDist v3.3 together with an Amesos patch -- cgit v1.2.3-70-g09d2 From 9cff241ad52ba628a0bdad47cee98bbbf6ba5511 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Sun, 27 Mar 2016 10:39:09 +0200 Subject: fix install name on Darwin --- var/spack/repos/builtin/packages/trilinos/package.py | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index e8c4bcd7e2..72f904d8aa 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -1,5 +1,5 @@ from spack import * -import os, sys +import os, sys, glob # Trilinos is complicated to build, as an inspiration a couple of links to other repositories which build it: # https://github.com/hpcugent/easybuild-easyblocks/blob/master/easybuild/easyblocks/t/trilinos.py#L111 @@ -222,3 +222,10 @@ class Trilinos(Package): # A workaround it to remove PyTrilinos from the COMPONENTS_LIST : if '+python' in self.spec: filter_file(r'(SET\(COMPONENTS_LIST.*)(PyTrilinos;)(.*)', (r'\1\3'), '%s/cmake/Trilinos/TrilinosConfig.cmake' % prefix.lib) + + # The shared libraries are not installed correctly on Darwin; correct this + if (sys.platform == 'darwin') and ('+shared' in spec): + fs = glob.glob(join_path(prefix.lib,"*.dylib")) + install_name_tool = which('install_name_tool') + for f in fs: + install_name_tool('-id',f,f) -- cgit v1.2.3-70-g09d2 From 69ebc8173e1843ea570d78ac27465b0ea32c753d Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Sun, 27 Mar 2016 16:04:13 +0200 Subject: use global tool to fix install_name --- var/spack/repos/builtin/packages/trilinos/package.py | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 72f904d8aa..6608f64ea7 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -225,7 +225,4 @@ class Trilinos(Package): # The shared libraries are not installed correctly on Darwin; correct this if (sys.platform == 'darwin') and ('+shared' in spec): - fs = glob.glob(join_path(prefix.lib,"*.dylib")) - install_name_tool = which('install_name_tool') - for f in fs: - install_name_tool('-id',f,f) + fix_darwin_install_name(prefix.lib) -- cgit v1.2.3-70-g09d2 From cc42391e0fa6eda490c4aeffcbfbae584f077db3 Mon Sep 17 00:00:00 2001 From: citibeth Date: Sun, 27 Mar 2016 11:06:10 -0400 Subject: Added py-netcdf --- var/spack/repos/builtin/packages/py-netcdf/package.py | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-netcdf/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/py-netcdf/package.py b/var/spack/repos/builtin/packages/py-netcdf/package.py new file mode 100644 index 0000000000..7faa15ad25 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-netcdf/package.py @@ -0,0 +1,16 @@ +from spack import * + +class PyNetcdf(Package): + """Python interface to the netCDF Library.""" + homepage = "http://unidata.github.io/netcdf4-python" + url = "https://github.com/Unidata/netcdf4-python/tarball/v1.2.3.1rel" + + version('1.2.3.1', '4fc4320d4f2a77b894ebf8da1c9895af') + + extends('python') + depends_on('py-numpy') + depends_on('py-cython') + depends_on('netcdf') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) -- cgit v1.2.3-70-g09d2 From 439d3b3ddb4e53721b216bd19bec1e8fa16faf89 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Sun, 27 Mar 2016 17:38:25 +0200 Subject: mumps: add install_name / soname --- var/spack/repos/builtin/packages/mumps/package.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py index b295857ab5..26440ab7c8 100644 --- a/var/spack/repos/builtin/packages/mumps/package.py +++ b/var/spack/repos/builtin/packages/mumps/package.py @@ -113,13 +113,13 @@ class Mumps(Package): # Building dylibs with mpif90 causes segfaults on 10.8 and 10.10. Use gfortran. (Homebrew) makefile_conf.extend([ 'LIBEXT=.dylib', - 'AR=%s -dynamiclib -undefined dynamic_lookup -o ' % os.environ['FC'], + 'AR=%s -dynamiclib -Wl,-install_name -Wl,%s/$(notdir $@) -undefined dynamic_lookup -o ' % (os.environ['FC'],prefix.lib), 'RANLIB=echo' ]) else: makefile_conf.extend([ 'LIBEXT=.so', - 'AR=$(FL) -shared -o', + 'AR=$(FL) -shared -Wl,-soname -Wl,%s/$(notdir $@) -o' % prefix.lib, 'RANLIB=echo' ]) else: -- cgit v1.2.3-70-g09d2 From 66bb71534b3ab7eaf7b27743efc0ecf9763e4982 Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Sat, 26 Mar 2016 20:02:08 -0700 Subject: Better blas/lapack and scipy packages: more robust, added `shared` variants. - py-scipy now builds with netlib-lapack, openblas, and atlas. - started a convention for passing lib info from blas/lapack implementations. - Improved netlib-lapack: - Also build static libs when `shared` variant is enabled. - Enable CBLAS build - needed minor patch to build correctly. - Added `shared` variant to OpenBLAS. - Made OpenBLAS build properly shared and static. --- .../builtin/packages/netlib-lapack/package.py | 40 +++++++++++++++-- .../repos/builtin/packages/openblas/package.py | 52 +++++++++++++++++----- .../repos/builtin/packages/py-scipy/package.py | 12 +++-- 3 files changed, 88 insertions(+), 16 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/netlib-lapack/package.py b/var/spack/repos/builtin/packages/netlib-lapack/package.py index c4b7ce3b04..05436332ac 100644 --- a/var/spack/repos/builtin/packages/netlib-lapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-lapack/package.py @@ -31,8 +31,16 @@ class NetlibLapack(Package): depends_on('cmake') depends_on('blas', when='+external-blas') - def install(self, spec, prefix): - cmake_args = ['-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if '+shared' in spec else 'OFF'), + + def patch(self): + # Fix cblas CMakeLists.txt -- has wrong case for subdirectory name. + filter_file('${CMAKE_CURRENT_SOURCE_DIR}/CMAKE/', + '${CMAKE_CURRENT_SOURCE_DIR}/cmake/', 'CBLAS/CMakeLists.txt', string=True) + + + def install_one(self, spec, prefix, shared): + cmake_args = ['-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if shared else 'OFF'), + '-DCBLAS=ON', # always build CBLAS '-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'), '-DLAPACKE:BOOL=%s' % ('ON' if '+lapacke' in spec else 'OFF')] if '+external-blas' in spec: @@ -45,7 +53,33 @@ class NetlibLapack(Package): cmake_args.extend(std_cmake_args) - with working_dir('spack-build', create=True): + build_dir = 'spack-build' + ('-shared' if shared else '-static') + with working_dir(build_dir, create=True): cmake('..', *cmake_args) make() make("install") + + + def install(self, spec, prefix): + # Always build static libraries. + self.install_one(spec, prefix, False) + + # Build shared libraries if requested. + if '+shared' in spec: + self.install_one(spec, prefix, True) + + + def setup_dependent_package(self, module, dspec): + # This is WIP for a prototype interface for virtual packages. + # We can update this as more builds start depending on BLAS/LAPACK. + libdir = find_library_path('libblas.a', self.prefix.lib64, self.prefix.lib) + + self.spec.blas_static_lib = join_path(libdir, 'libblas.a') + self.spec.lapack_static_lib = join_path(libdir, 'liblapack.a') + + if '+shared' in self.spec: + self.spec.blas_shared_lib = join_path(libdir, 'libblas.%s' % dso_suffix) + self.spec.lapack_shared_lib = join_path(libdir, 'liblapack.%s' % dso_suffix) + + + diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py index 1d10f217c4..4ec829a85b 100644 --- a/var/spack/repos/builtin/packages/openblas/package.py +++ b/var/spack/repos/builtin/packages/openblas/package.py @@ -1,5 +1,6 @@ from spack import * import sys +import os class Openblas(Package): """OpenBLAS: An optimized BLAS library""" @@ -10,29 +11,60 @@ class Openblas(Package): version('0.2.16', 'fef46ab92463bdbb1479dcec594ef6dc') version('0.2.15', 'b1190f3d3471685f17cfd1ec1d252ac9') + variant('shared', default=True, description="Build shared libraries as well as static libs.") + # virtual dependency provides('blas') provides('lapack') + def install(self, spec, prefix): - extra=[] + make_defs = ['CC=%s' % spack_cc, + 'FC=%s' % spack_fc] + + make_targets = ['libs', 'netlib'] + + # Build shared if variant is set. + if '+shared' in spec: + make_targets += ['shared'] + else: + make_defs += ['NO_SHARED=1'] + + # fix missing _dggsvd_ and _sggsvd_ if spec.satisfies('@0.2.16'): - extra.extend([ - 'BUILD_LAPACK_DEPRECATED=1' # fix missing _dggsvd_ and _sggsvd_ - ]) + make_defs += ['BUILD_LAPACK_DEPRECATED=1'] + + make_args = make_defs + make_targets + make(*make_args) - make('libs', 'netlib', 'shared', 'CC=cc', 'FC=f77',*extra) - make("tests") - make('install', "PREFIX='%s'" % prefix) + make("tests", *make_defs) + + # no quotes around prefix (spack doesn't use a shell) + make('install', "PREFIX=%s" % prefix, *make_defs) - lib_dsuffix = 'dylib' if sys.platform == 'darwin' else 'so' # Blas virtual package should provide blas.a and libblas.a with working_dir(prefix.lib): symlink('libopenblas.a', 'blas.a') symlink('libopenblas.a', 'libblas.a') - symlink('libopenblas.%s' % lib_dsuffix, 'libblas.%s' % lib_dsuffix) + if '+shared' in spec: + symlink('libopenblas.%s' % dso_suffix, 'libblas.%s' % dso_suffix) # Lapack virtual package should provide liblapack.a with working_dir(prefix.lib): symlink('libopenblas.a', 'liblapack.a') - symlink('libopenblas.%s' % lib_dsuffix, 'liblapack.%s' % lib_dsuffix) + if '+shared' in spec: + symlink('libopenblas.%s' % dso_suffix, 'liblapack.%s' % dso_suffix) + + + def setup_dependent_package(self, module, dspec): + # This is WIP for a prototype interface for virtual packages. + # We can update this as more builds start depending on BLAS/LAPACK. + libdir = find_library_path('libopenblas.a', self.prefix.lib64, self.prefix.lib) + + self.spec.blas_static_lib = join_path(libdir, 'libopenblas.a') + self.spec.lapack_static_lib = self.spec.blas_static_lib + + if '+shared' in self.spec: + self.spec.blas_shared_lib = join_path(libdir, 'libopenblas.%s' % dso_suffix) + self.spec.lapack_shared_lib = self.spec.blas_shared_lib + diff --git a/var/spack/repos/builtin/packages/py-scipy/package.py b/var/spack/repos/builtin/packages/py-scipy/package.py index c2161c90c4..4d47c641ee 100644 --- a/var/spack/repos/builtin/packages/py-scipy/package.py +++ b/var/spack/repos/builtin/packages/py-scipy/package.py @@ -11,9 +11,15 @@ class PyScipy(Package): extends('python') depends_on('py-nose') - depends_on('py-numpy') - depends_on('blas') - depends_on('lapack') + depends_on('py-numpy+blas+lapack') def install(self, spec, prefix): + if 'atlas' in spec: + # libatlas.so actually isn't always installed, but this + # seems to make the build autodetect things correctly. + env['ATLAS'] = join_path(spec['atlas'].prefix.lib, 'libatlas.' + dso_suffix) + else: + env['BLAS'] = spec['blas'].blas_shared_lib + env['LAPACK'] = spec['lapack'].lapack_shared_lib + python('setup.py', 'install', '--prefix=%s' % prefix) -- cgit v1.2.3-70-g09d2 From 20600b8cac9488ff416397de374c2d3dacf4afe4 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Sun, 27 Mar 2016 21:03:18 +0200 Subject: add tests and netcdf-cxx4 --- var/spack/repos/builtin/packages/dealii/package.py | 38 ++++++++++++++++++++-- 1 file changed, 36 insertions(+), 2 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py index 19bb3814be..1d4c800288 100644 --- a/var/spack/repos/builtin/packages/dealii/package.py +++ b/var/spack/repos/builtin/packages/dealii/package.py @@ -1,4 +1,5 @@ from spack import * +import shutil class Dealii(Package): """C++ software library providing well-documented tools to build finite element codes for a broad variety of PDEs.""" @@ -18,7 +19,7 @@ class Dealii(Package): depends_on ("hdf5+mpi~cxx") #FIXME NetCDF declares dependency with ~cxx, why? depends_on ("metis") depends_on ("muparser") - depends_on ("netcdf") + depends_on ("netcdf-cxx4") #depends_on ("numdiff") #FIXME depends_on ("oce") depends_on ("p4est") @@ -50,7 +51,7 @@ class Dealii(Package): '-DHDF5_DIR=%s' % spec['hdf5'].prefix, '-DMETIS_DIR=%s' % spec['metis'].prefix, '-DMUPARSER_DIR=%s ' % spec['muparser'].prefix, - '-DNETCDF_DIR=%s' % spec['netcdf'].prefix, + '-DNETCDF_DIR=%s' % spec['netcdf-cxx4'].prefix, '-DOPENCASCADE_DIR=%s' % spec['oce'].prefix, '-DP4EST_DIR=%s' % spec['p4est'].prefix, '-DPETSC_DIR=%s' % spec['petsc'].prefix, @@ -65,3 +66,36 @@ class Dealii(Package): make() make("test") make("install") + + # run some MPI examples with different solvers from PETSc and Trilinos + env['DEAL_II_DIR'] = prefix + # take bare-bones step-3 + with working_dir('examples/step-3'): + cmake('.') + make('release') + make('run',parallel=False) + + # take step-40 which can use both PETSc and Trilinos + # FIXME: switch step-40 to MPI run + with working_dir('examples/step-40'): + # list the number of cycles to speed up + filter_file(r'(const unsigned int n_cycles = 8;)', ('const unsigned int n_cycles = 2;'), 'step-40.cc') + cmake('.') + make('release') + make('run',parallel=False) + + # change Linear Algebra to Trilinos + filter_file(r'(#define USE_PETSC_LA.*)', (''), 'step-40.cc') + make('release') + make('run',parallel=False) + + with working_dir('examples/step-36'): + cmake('.') + make('release') + make('run',parallel=False) + + with working_dir('examples/step-54'): + cmake('.') + make('release') + # FIXME + # make('run',parallel=False) -- cgit v1.2.3-70-g09d2 From fc73e93b50a708ecfa2395a636bc32161c9d3051 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Sun, 27 Mar 2016 23:47:43 +0200 Subject: rework netcdf --- var/spack/repos/builtin/packages/dealii/package.py | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py index 1d4c800288..baedd155ef 100644 --- a/var/spack/repos/builtin/packages/dealii/package.py +++ b/var/spack/repos/builtin/packages/dealii/package.py @@ -1,5 +1,5 @@ from spack import * -import shutil +import sys class Dealii(Package): """C++ software library providing well-documented tools to build finite element codes for a broad variety of PDEs.""" @@ -39,6 +39,7 @@ class Dealii(Package): if word.startswith('-DCMAKE_BUILD_TYPE'): options.remove(word) + dsuf = 'dylib' if sys.platform == 'darwin' else 'so' options.extend([ '-DCMAKE_BUILD_TYPE=DebugRelease', '-DDEAL_II_WITH_THREADS:BOOL=ON' @@ -51,7 +52,14 @@ class Dealii(Package): '-DHDF5_DIR=%s' % spec['hdf5'].prefix, '-DMETIS_DIR=%s' % spec['metis'].prefix, '-DMUPARSER_DIR=%s ' % spec['muparser'].prefix, - '-DNETCDF_DIR=%s' % spec['netcdf-cxx4'].prefix, + # since Netcdf is spread among two, need to do it by hand: + '-DNETCDF_FOUND=true', + '-DNETCDF_LIBRARIES=%s;%s' % + (join_path(spec['netcdf-cxx4'].prefix.lib,'libnetcdf_c++4.%s' % dsuf), + join_path(spec['netcdf'].prefix.lib,'libnetcdf.%s' % dsuf)), + '-DNETCDF_INCLUDE_DIRS=%s;%s' % + (spec['netcdf-cxx4'].prefix.include, + spec['netcdf'].prefix.include), '-DOPENCASCADE_DIR=%s' % spec['oce'].prefix, '-DP4EST_DIR=%s' % spec['p4est'].prefix, '-DPETSC_DIR=%s' % spec['petsc'].prefix, -- cgit v1.2.3-70-g09d2 From ccd155572fc8ef066b93424e90a74f9bb8fcf435 Mon Sep 17 00:00:00 2001 From: citibeth Date: Sun, 27 Mar 2016 18:18:54 -0400 Subject: Removed redundant package py-libxml2. Use libxml2 instead. --- var/spack/repos/builtin/packages/py-libxml2/package.py | 15 --------------- 1 file changed, 15 deletions(-) delete mode 100644 var/spack/repos/builtin/packages/py-libxml2/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/py-libxml2/package.py b/var/spack/repos/builtin/packages/py-libxml2/package.py deleted file mode 100644 index 59005428e4..0000000000 --- a/var/spack/repos/builtin/packages/py-libxml2/package.py +++ /dev/null @@ -1,15 +0,0 @@ -from spack import * - -class PyLibxml2(Package): - """A Python wrapper around libxml2.""" - homepage = "https://xmlsoft.org/python.html" - url = "ftp://xmlsoft.org/libxml2/python/libxml2-python-2.6.21.tar.gz" - - version('2.6.21', '229dd2b3d110a77defeeaa73af83f7f3') - - extends('python') - depends_on('libxml2') - depends_on('libxslt') - - def install(self, spec, prefix): - python('setup.py', 'install', '--prefix=%s' % prefix) -- cgit v1.2.3-70-g09d2 From 7eca1284c81c3efc5a87b8a174a0974811656b3e Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Sun, 27 Mar 2016 08:59:25 +0200 Subject: metis/parmetis/boost/oce/scalapack: correct install_name on Darwin via a global function. --- lib/spack/llnl/util/filesystem.py | 30 ++++++++++++- var/spack/repos/builtin/packages/boost/package.py | 50 ++++++++++++---------- var/spack/repos/builtin/packages/metis/package.py | 6 ++- .../builtin/packages/netlib-scalapack/package.py | 5 +++ var/spack/repos/builtin/packages/oce/package.py | 6 ++- .../repos/builtin/packages/parmetis/package.py | 6 ++- 6 files changed, 76 insertions(+), 27 deletions(-) (limited to 'var') diff --git a/lib/spack/llnl/util/filesystem.py b/lib/spack/llnl/util/filesystem.py index c4665c284c..46ca03bec4 100644 --- a/lib/spack/llnl/util/filesystem.py +++ b/lib/spack/llnl/util/filesystem.py @@ -27,9 +27,10 @@ __all__ = ['set_install_permissions', 'install', 'install_tree', 'traverse_tree' 'force_remove', 'join_path', 'ancestor', 'can_access', 'filter_file', 'FileFilter', 'change_sed_delimiter', 'is_exe', 'force_symlink', 'set_executable', 'copy_mode', 'unset_executable_mode', - 'remove_dead_links', 'remove_linked_tree'] + 'remove_dead_links', 'remove_linked_tree', 'fix_darwin_install_name'] import os +import glob import sys import re import shutil @@ -38,6 +39,7 @@ import errno import getpass from contextlib import contextmanager, closing from tempfile import NamedTemporaryFile +import subprocess import llnl.util.tty as tty from spack.util.compression import ALLOWED_ARCHIVE_TYPES @@ -392,3 +394,29 @@ def remove_linked_tree(path): os.unlink(path) else: shutil.rmtree(path, True) + +def fix_darwin_install_name(path): + """ + Fix install name of dynamic libraries on Darwin to have full path. + There are two parts of this task: + (i) use install_name('-id',...) to change install name of a single lib; + (ii) use install_name('-change',...) to change the cross linking between libs. + The function assumes that all libraries are in one folder and currently won't + follow subfolders. + + Args: + path: directory in which .dylib files are alocated + + """ + libs = glob.glob(join_path(path,"*.dylib")) + for lib in libs: + # fix install name first: + subprocess.Popen(["install_name_tool", "-id",lib,lib], stdout=subprocess.PIPE).communicate()[0] + long_deps = subprocess.Popen(["otool", "-L",lib], stdout=subprocess.PIPE).communicate()[0].split('\n') + deps = [dep.partition(' ')[0][1::] for dep in long_deps[2:-1]] + # fix all dependencies: + for dep in deps: + for loc in libs: + if dep == os.path.basename(loc): + subprocess.Popen(["install_name_tool", "-change",dep,loc,lib], stdout=subprocess.PIPE).communicate()[0] + break diff --git a/var/spack/repos/builtin/packages/boost/package.py b/var/spack/repos/builtin/packages/boost/package.py index fb1f5daee7..82ce6fbb74 100644 --- a/var/spack/repos/builtin/packages/boost/package.py +++ b/var/spack/repos/builtin/packages/boost/package.py @@ -1,5 +1,6 @@ from spack import * import spack +import sys class Boost(Package): """Boost provides free peer-reviewed portable C++ source @@ -45,34 +46,34 @@ class Boost(Package): version('1.34.1', '2d938467e8a448a2c9763e0a9f8ca7e5') version('1.34.0', 'ed5b9291ffad776f8757a916e1726ad0') - default_install_libs = set(['atomic', - 'chrono', - 'date_time', - 'filesystem', + default_install_libs = set(['atomic', + 'chrono', + 'date_time', + 'filesystem', 'graph', 'iostreams', 'locale', 'log', - 'math', + 'math', 'program_options', - 'random', - 'regex', - 'serialization', - 'signals', - 'system', - 'test', - 'thread', + 'random', + 'regex', + 'serialization', + 'signals', + 'system', + 'test', + 'thread', 'wave']) - # mpi/python are not installed by default because they pull in many - # dependencies and/or because there is a great deal of customization + # mpi/python are not installed by default because they pull in many + # dependencies and/or because there is a great deal of customization # possible (and it would be difficult to choose sensible defaults) default_noinstall_libs = set(['mpi', 'python']) all_libs = default_install_libs | default_noinstall_libs for lib in all_libs: - variant(lib, default=(lib not in default_noinstall_libs), + variant(lib, default=(lib not in default_noinstall_libs), description="Compile with {0} library".format(lib)) variant('debug', default=False, description='Switch to the debug version of Boost') @@ -124,9 +125,9 @@ class Boost(Package): with open('user-config.jam', 'w') as f: compiler_wrapper = join_path(spack.build_env_path, 'c++') - f.write("using {0} : : {1} ;\n".format(boostToolsetId, + f.write("using {0} : : {1} ;\n".format(boostToolsetId, compiler_wrapper)) - + if '+mpi' in spec: f.write('using mpi : %s ;\n' % join_path(spec['mpi'].prefix.bin, 'mpicxx')) @@ -155,7 +156,7 @@ class Boost(Package): linkTypes = ['static'] if '+shared' in spec: linkTypes.append('shared') - + threadingOpts = [] if '+multithreaded' in spec: threadingOpts.append('multi') @@ -163,12 +164,12 @@ class Boost(Package): threadingOpts.append('single') if not threadingOpts: raise RuntimeError("At least one of {singlethreaded, multithreaded} must be enabled") - + options.extend([ 'toolset=%s' % self.determine_toolset(spec), 'link=%s' % ','.join(linkTypes), '--layout=tagged']) - + return threadingOpts def install(self, spec, prefix): @@ -177,14 +178,14 @@ class Boost(Package): if "+{0}".format(lib) in spec: withLibs.append(lib) if not withLibs: - # if no libraries are specified for compilation, then you dont have + # if no libraries are specified for compilation, then you dont have # to configure/build anything, just copy over to the prefix directory. src = join_path(self.stage.source_path, 'boost') mkdirp(join_path(prefix, 'include')) dst = join_path(prefix, 'include', 'boost') install_tree(src, dst) return - + # to make Boost find the user-config.jam env['BOOST_BUILD_PATH'] = './' @@ -207,4 +208,7 @@ class Boost(Package): # Boost.MPI if the threading options are not separated. for threadingOpt in threadingOpts: b2('install', 'threading=%s' % threadingOpt, *b2_options) - + + # The shared libraries are not installed correctly on Darwin; correct this + if (sys.platform == 'darwin') and ('+shared' in spec): + fix_darwin_install_name(prefix.lib) diff --git a/var/spack/repos/builtin/packages/metis/package.py b/var/spack/repos/builtin/packages/metis/package.py index 68b9f6fd30..9301135f9f 100644 --- a/var/spack/repos/builtin/packages/metis/package.py +++ b/var/spack/repos/builtin/packages/metis/package.py @@ -24,7 +24,7 @@ ############################################################################## from spack import * -import glob +import glob,sys class Metis(Package): """ @@ -90,3 +90,7 @@ class Metis(Package): fs = glob.glob(join_path(source_directory,'GKlib',"*.h")) for f in fs: install(f, GKlib_dist) + + # The shared library is not installed correctly on Darwin; correct this + if (sys.platform == 'darwin') and ('+shared' in spec): + fix_darwin_install_name(prefix.lib) diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py index c3e6822cdf..d59f8e41fe 100644 --- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py @@ -41,6 +41,11 @@ class NetlibScalapack(Package): make() make("install") + # The shared libraries are not installed correctly on Darwin; correct this + if (sys.platform == 'darwin') and ('+shared' in spec): + fix_darwin_install_name(prefix.lib) + + def setup_dependent_package(self, module, dependent_spec): spec = self.spec lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so' diff --git a/var/spack/repos/builtin/packages/oce/package.py b/var/spack/repos/builtin/packages/oce/package.py index 06acb96736..4d5081ac9d 100644 --- a/var/spack/repos/builtin/packages/oce/package.py +++ b/var/spack/repos/builtin/packages/oce/package.py @@ -1,5 +1,5 @@ from spack import * -import platform +import platform, sys class Oce(Package): """ @@ -45,3 +45,7 @@ class Oce(Package): cmake('.', *options) make("install/strip") + + # The shared libraries are not installed correctly on Darwin; correct this + if (sys.platform == 'darwin'): + fix_darwin_install_name(prefix.lib) diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py index f5b8b6de91..ff4370aa4b 100644 --- a/var/spack/repos/builtin/packages/parmetis/package.py +++ b/var/spack/repos/builtin/packages/parmetis/package.py @@ -24,7 +24,7 @@ ############################################################################## from spack import * - +import sys class Parmetis(Package): """ @@ -83,3 +83,7 @@ class Parmetis(Package): cmake(source_directory, *options) make() make("install") + + # The shared library is not installed correctly on Darwin; correct this + if (sys.platform == 'darwin') and ('+shared' in spec): + fix_darwin_install_name(prefix.lib) -- cgit v1.2.3-70-g09d2 From 3bd550d6a2ceb279743aae626c6a3a614519d2f5 Mon Sep 17 00:00:00 2001 From: Elizabeth F Date: Sun, 27 Mar 2016 18:27:06 -0400 Subject: GEOS Python extension did not compile with Python3. --- var/spack/repos/builtin/packages/geos/package.py | 24 ++++++++++++++++++++---- 1 file changed, 20 insertions(+), 4 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/geos/package.py b/var/spack/repos/builtin/packages/geos/package.py index 4a2657e32f..030703f286 100644 --- a/var/spack/repos/builtin/packages/geos/package.py +++ b/var/spack/repos/builtin/packages/geos/package.py @@ -1,4 +1,5 @@ from spack import * +import os class Geos(Package): """GEOS (Geometry Engine - Open Source) is a C++ port of the Java @@ -10,6 +11,10 @@ class Geos(Package): homepage = "http://trac.osgeo.org/geos/" url = "http://download.osgeo.org/geos/geos-3.4.2.tar.bz2" + # Verison 3.5.0 supports Autotools and CMake + version('3.5.0', '136842690be7f504fba46b3c539438dd') + + # Versions through 3.4.2 have CMake, but only Autotools is supported version('3.4.2', 'fc5df2d926eb7e67f988a43a92683bae') version('3.4.1', '4c930dec44c45c49cd71f3e0931ded7e') version('3.4.0', 'e41318fc76b5dc764a69d43ac6b18488') @@ -21,11 +26,22 @@ class Geos(Package): version('3.3.4', '1bb9f14d57ef06ffa41cb1d67acb55a1') version('3.3.3', '8454e653d7ecca475153cc88fd1daa26') - extends('python') - depends_on('swig') +# # Python3 is not supported. +# variant('python', default=False, description='Enable Python support') + +# extends('python', when='+python') +# depends_on('python', when='+python') +# depends_on('swig', when='+python') def install(self, spec, prefix): - configure("--prefix=%s" % prefix, - "--enable-python") + args = ["--prefix=%s" % prefix] +# if '+python' in spec: +# os.environ['PYTHON'] = join_path(spec['python'].prefix, 'bin', +# 'python' if spec['python'].version[:1][0] <= 2 else 'python3') +# os.environ['SWIG'] = join_path(spec['swig'].prefix, 'bin', 'swig') +# +# args.append("--enable-python") + + configure(*args) make() make("install") -- cgit v1.2.3-70-g09d2 From 9c894f59354bafd9cd45e874be599dc8535e426e Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Mon, 28 Mar 2016 10:19:25 +0200 Subject: new package: netcdf-cxx --- var/spack/repos/builtin/packages/netcdf-cxx/package.py | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 var/spack/repos/builtin/packages/netcdf-cxx/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/netcdf-cxx/package.py b/var/spack/repos/builtin/packages/netcdf-cxx/package.py new file mode 100644 index 0000000000..5334dfb853 --- /dev/null +++ b/var/spack/repos/builtin/packages/netcdf-cxx/package.py @@ -0,0 +1,15 @@ +from spack import * + +class NetcdfCxx(Package): + """C++ compatibility bindings for NetCDF""" + homepage = "http://www.unidata.ucar.edu/software/netcdf" + url = "http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-cxx-4.2.tar.gz" + + version('4.2', 'd32b20c00f144ae6565d9e98d9f6204c') + + depends_on('netcdf') + + def install(self, spec, prefix): + configure('--prefix=%s' % prefix) + make() + make("install") -- cgit v1.2.3-70-g09d2 From 97cdd7947894b3b631e2a209f0573ed839eb7b8a Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Mon, 28 Mar 2016 10:49:20 +0200 Subject: fix netcdf --- var/spack/repos/builtin/packages/dealii/package.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py index baedd155ef..486aa6e4a4 100644 --- a/var/spack/repos/builtin/packages/dealii/package.py +++ b/var/spack/repos/builtin/packages/dealii/package.py @@ -19,7 +19,7 @@ class Dealii(Package): depends_on ("hdf5+mpi~cxx") #FIXME NetCDF declares dependency with ~cxx, why? depends_on ("metis") depends_on ("muparser") - depends_on ("netcdf-cxx4") + depends_on ("netcdf-cxx") #depends_on ("numdiff") #FIXME depends_on ("oce") depends_on ("p4est") @@ -55,10 +55,10 @@ class Dealii(Package): # since Netcdf is spread among two, need to do it by hand: '-DNETCDF_FOUND=true', '-DNETCDF_LIBRARIES=%s;%s' % - (join_path(spec['netcdf-cxx4'].prefix.lib,'libnetcdf_c++4.%s' % dsuf), + (join_path(spec['netcdf-cxx'].prefix.lib,'libnetcdf_c++.%s' % dsuf), join_path(spec['netcdf'].prefix.lib,'libnetcdf.%s' % dsuf)), '-DNETCDF_INCLUDE_DIRS=%s;%s' % - (spec['netcdf-cxx4'].prefix.include, + (spec['netcdf-cxx'].prefix.include, spec['netcdf'].prefix.include), '-DOPENCASCADE_DIR=%s' % spec['oce'].prefix, '-DP4EST_DIR=%s' % spec['p4est'].prefix, -- cgit v1.2.3-70-g09d2 From e00cab75bd6721ac49bb6199d77ad99df80556a9 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Mon, 28 Mar 2016 12:12:55 +0200 Subject: more elaborated tests/direct solvers --- var/spack/repos/builtin/packages/dealii/package.py | 42 +++++++++++++++++++++- 1 file changed, 41 insertions(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py index 486aa6e4a4..9ac1572b95 100644 --- a/var/spack/repos/builtin/packages/dealii/package.py +++ b/var/spack/repos/builtin/packages/dealii/package.py @@ -77,7 +77,13 @@ class Dealii(Package): # run some MPI examples with different solvers from PETSc and Trilinos env['DEAL_II_DIR'] = prefix + print('=====================================') + print('============ EXAMPLES ===============') + print('=====================================') # take bare-bones step-3 + print('=====================================') + print('============ Step-3 =================') + print('=====================================') with working_dir('examples/step-3'): cmake('.') make('release') @@ -86,22 +92,56 @@ class Dealii(Package): # take step-40 which can use both PETSc and Trilinos # FIXME: switch step-40 to MPI run with working_dir('examples/step-40'): + print('=====================================') + print('========== Step-40 PETSc ============') + print('=====================================') # list the number of cycles to speed up filter_file(r'(const unsigned int n_cycles = 8;)', ('const unsigned int n_cycles = 2;'), 'step-40.cc') cmake('.') make('release') make('run',parallel=False) + print('=====================================') + print('========= Step-40 Trilinos ==========') + print('=====================================') # change Linear Algebra to Trilinos - filter_file(r'(#define USE_PETSC_LA.*)', (''), 'step-40.cc') + filter_file(r'(\/\/ #define FORCE_USE_OF_TRILINOS.*)', ('#define FORCE_USE_OF_TRILINOS'), 'step-40.cc') make('release') make('run',parallel=False) + print('=====================================') + print('=== Step-40 Trilinos SuperluDist ====') + print('=====================================') + # change to direct solvers + filter_file(r'(LA::SolverCG solver\(solver_control\);)', ('TrilinosWrappers::SolverDirect::AdditionalData data(false,"Amesos_Superludist"); TrilinosWrappers::SolverDirect solver(solver_control,data);'), 'step-40.cc') + filter_file(r'(LA::MPI::PreconditionAMG preconditioner;)', (''), 'step-40.cc') + filter_file(r'(LA::MPI::PreconditionAMG::AdditionalData data;)', (''), 'step-40.cc') + filter_file(r'(preconditioner.initialize\(system_matrix, data\);)', (''), 'step-40.cc') + filter_file(r'(solver\.solve \(system_matrix, completely_distributed_solution, system_rhs,)', ('solver.solve (system_matrix, completely_distributed_solution, system_rhs);'), 'step-40.cc') + filter_file(r'(preconditioner\);)', (''), 'step-40.cc') + + make('release') + make('run',paralle=False) + + print('=====================================') + print('====== Step-40 Trilinos MUMPS =======') + print('=====================================') + # switch to Mumps + filter_file(r'(Amesos_Superludist)', ('Amesos_Mumps'), 'step-40.cc') + make('release') + make('run',parallel=False) + + print('=====================================') + print('============ Step-36 ================') + print('=====================================') with working_dir('examples/step-36'): cmake('.') make('release') make('run',parallel=False) + print('=====================================') + print('============ Step-54 ================') + print('=====================================') with working_dir('examples/step-54'): cmake('.') make('release') -- cgit v1.2.3-70-g09d2 From 0da545ecac1c57a04abf814c9fed4f9929726ff5 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Mon, 28 Mar 2016 13:16:08 +0200 Subject: tell amesos that we use mumps 5 --- var/spack/repos/builtin/packages/trilinos/package.py | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 6608f64ea7..90b7bff149 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -6,6 +6,9 @@ import os, sys, glob # https://github.com/koecher/candi/blob/master/deal.II-toolchain/packages/trilinos.package # https://gitlab.com/configurations/cluster-config/blob/master/trilinos.sh # https://github.com/Homebrew/homebrew-science/blob/master/trilinos.rb +# and some relevant documentation/examples: +# https://trilinos.org/docs/dev/packages/amesos2/doc/html/classAmesos2_1_1MUMPS.html +# https://github.com/trilinos/Trilinos/issues/175 class Trilinos(Package): """The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. @@ -46,7 +49,7 @@ class Trilinos(Package): depends_on('mpi') depends_on('netcdf+mpi') depends_on('parmetis',when='+metis') - depends_on('mumps+mpi+shared',when='+mumps') # Amesos link errors with static: "__gfortran_adjustl", referenced from: _dmumps_ in libdmumps.a(dmumps_driver.o) "_mpi_abort_", referenced from: _mumps_abort_ in libmumps_common.a(tools_common.o) + depends_on('mumps@5.0:+mpi+shared',when='+mumps') # Amesos link errors with static: "__gfortran_adjustl", referenced from: _dmumps_ in libdmumps.a(dmumps_driver.o) "_mpi_abort_", referenced from: _mumps_abort_ in libmumps_common.a(tools_common.o) depends_on('scalapack',when='+mumps') depends_on('superlu-dist',when='+superlu-dist') depends_on('hypre',when='+hypre') @@ -67,6 +70,7 @@ class Trilinos(Package): def install(self, spec, prefix): self.variants_check() + cxx_flags = [] options = [] options.extend(std_cmake_args) @@ -91,7 +95,6 @@ class Trilinos(Package): '-DBoost_LIBRARY_DIRS:PATH=%s' % spec['boost'].prefix.lib, '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON', '-DTrilinos_ENABLE_CXX11:BOOL=ON', - '-DTrilinos_CXX11_FLAGS=-std=c++11', '-DTPL_ENABLE_Netcdf:BOOL=ON', '-DTPL_ENABLE_HYPRE:BOOL=ON', '-DTPL_ENABLE_HDF5:BOOL=ON' @@ -154,6 +157,10 @@ class Trilinos(Package): '-DTPL_ENABLE_SCALAPACK:BOOL=ON', '-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64 ]) + # see https://github.com/trilinos/Trilinos/blob/master/packages/amesos/README-MUMPS + cxx_flags.extend([ + '-DMUMPS_5_0' + ]) else: options.extend([ '-DTPL_ENABLE_MUMPS:BOOL=OFF', @@ -194,6 +201,10 @@ class Trilinos(Package): '-DTrilinos_ENABLE_PyTrilinos:BOOL=OFF' ]) + # collect CXX flags: + options.extend([ + '-DCMAKE_CXX_FLAGS:STRING=%s' % (' '.join(cxx_flags)), + ]) # disable due to compiler / config errors: options.extend([ -- cgit v1.2.3-70-g09d2 From 5eefca43e75d2df1c2f859d199f7bb37e7142993 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Mon, 28 Mar 2016 14:35:01 +0200 Subject: petsc: extend variants by mumps, complex and debug --- var/spack/repos/builtin/packages/petsc/package.py | 33 ++++++++++++++--------- 1 file changed, 20 insertions(+), 13 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py index 3dd117eed1..dd3d2aa162 100644 --- a/var/spack/repos/builtin/packages/petsc/package.py +++ b/var/spack/repos/builtin/packages/petsc/package.py @@ -17,14 +17,17 @@ class Petsc(Package): version('3.5.1', 'a557e029711ebf425544e117ffa44d8f') version('3.4.4', '7edbc68aa6d8d6a3295dd5f6c2f6979d') - variant('shared', default=True, description='Enables the build of shared libraries') - variant('mpi', default=True, description='Activates MPI support') - variant('double', default=True, description='Switches between single and double precision') - - variant('metis', default=True, description='Activates support for metis and parmetis') - variant('hdf5', default=True, description='Activates support for HDF5 (only parallel)') - variant('boost', default=True, description='Activates support for Boost') - variant('hypre', default=True, description='Activates support for Hypre') + variant('shared', default=True, description='Enables the build of shared libraries') + variant('mpi', default=True, description='Activates MPI support') + variant('double', default=True, description='Switches between single and double precision') + variant('complex', default=False, description='Build with complex numbers') + variant('debug', default=False, description='Compile in debug mode') + + variant('metis', default=True, description='Activates support for metis and parmetis') + variant('hdf5', default=True, description='Activates support for HDF5 (only parallel)') + variant('boost', default=True, description='Activates support for Boost') + variant('hypre', default=True, description='Activates support for Hypre (only parallel)') + variant('mumps', default=True, description='Activates support for MUMPS (only parallel)') # Virtual dependencies depends_on('blas') @@ -40,7 +43,10 @@ class Petsc(Package): depends_on('hdf5+mpi', when='+hdf5+mpi') depends_on('parmetis', when='+metis+mpi') - depends_on('hypre', when='+hypre+mpi') + depends_on('hypre', when='+hypre+mpi~complex') # Hypre does not support complex numbers + + depends_on('mumps+mpi', when='+mumps+mpi') + depends_on('scalapack', when='+mumps+mpi') def mpi_dependent_options(self): if '~mpi' in self.spec: @@ -55,7 +61,7 @@ class Petsc(Package): # If mpi is disabled (~mpi), it's an error to have any of these enabled. # This generates a list of any such errors. errors = [error_message_fmt.format(library=x) - for x in ('hdf5', 'hypre', 'parmetis') + for x in ('hdf5', 'hypre', 'parmetis','mumps') if ('+'+x) in self.spec] if errors: errors = ['incompatible variants given'] + errors @@ -77,16 +83,17 @@ class Petsc(Package): return compiler_opts def install(self, spec, prefix): - options = ['--with-debugging=0', - '--with-ssl=0'] + options = ['--with-ssl=0'] options.extend(self.mpi_dependent_options()) options.extend([ '--with-precision=%s' % ('double' if '+double' in spec else 'single'), + '--with-scalar-type=%s' % ('complex' if '+complex' in spec else 'real'), '--with-shared-libraries=%s' % ('1' if '+shared' in spec else '0'), + '--with-debugging=%s' % ('1' if '+debug' in spec else '0'), '--with-blas-lapack-dir=%s' % spec['lapack'].prefix ]) # Activates library support if needed - for library in ('metis', 'boost', 'hdf5', 'hypre', 'parmetis'): + for library in ('metis', 'boost', 'hdf5', 'hypre', 'parmetis','mumps','scalapack'): options.append( '--with-{library}={value}'.format(library=library, value=('1' if library in spec else '0')) ) -- cgit v1.2.3-70-g09d2 From dd60cc326c12bfa8434b68afec72f4b68c18a94c Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Mon, 28 Mar 2016 17:52:22 +0200 Subject: adopt modifed superlu and hypre --- var/spack/repos/builtin/packages/trilinos/package.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 90b7bff149..b2dc8df0ea 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -52,7 +52,7 @@ class Trilinos(Package): depends_on('mumps@5.0:+mpi+shared',when='+mumps') # Amesos link errors with static: "__gfortran_adjustl", referenced from: _dmumps_ in libdmumps.a(dmumps_driver.o) "_mpi_abort_", referenced from: _mumps_abort_ in libmumps_common.a(tools_common.o) depends_on('scalapack',when='+mumps') depends_on('superlu-dist',when='+superlu-dist') - depends_on('hypre',when='+hypre') + depends_on('hypre~internal-superlu',when='+hypre') depends_on('hdf5+mpi',when='+hdf5') depends_on('python',when='+python') # Needs py-numpy activated @@ -179,7 +179,7 @@ class Trilinos(Package): options.extend([ '-DTPL_ENABLE_SuperLUDist:BOOL=ON', '-DSuperLUDist_LIBRARY_DIRS=%s' % spec['superlu-dist'].prefix.lib, - '-DSuperLUDist_INCLUDE_DIRS=%s/superlu_dist' % spec['superlu-dist'].prefix.include # superlu_dist and superlu have the same header names :-( In order to avoid conflicts, try to keep "dist" version headers in a subfolder + '-DSuperLUDist_INCLUDE_DIRS=%s' % spec['superlu-dist'].prefix.include ]) if spec.satisfies('^superlu-dist@4.0:'): options.extend([ -- cgit v1.2.3-70-g09d2 From 207215980b05e4916e05ded8b05044b3edbe92c0 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Mon, 28 Mar 2016 17:54:27 +0200 Subject: make hypre and hdf5 be ON/OFF --- var/spack/repos/builtin/packages/trilinos/package.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index b2dc8df0ea..eb3bd1e0ee 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -96,8 +96,8 @@ class Trilinos(Package): '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON', '-DTrilinos_ENABLE_CXX11:BOOL=ON', '-DTPL_ENABLE_Netcdf:BOOL=ON', - '-DTPL_ENABLE_HYPRE:BOOL=ON', - '-DTPL_ENABLE_HDF5:BOOL=ON' + '-DTPL_ENABLE_HYPRE:BOOL=%s' % ('ON' if '+hypre' in spec else 'OFF'),, + '-DTPL_ENABLE_HDF5:BOOL=%s' % ('ON' if '+hdf5' in spec else 'OFF'), ]) # Fortran lib -- cgit v1.2.3-70-g09d2 From 4e87cf9d7492133d30675a64703b91ec6992ca00 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Mon, 28 Mar 2016 18:00:34 +0200 Subject: fix extra comma --- var/spack/repos/builtin/packages/trilinos/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index eb3bd1e0ee..71c0be61c3 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -96,7 +96,7 @@ class Trilinos(Package): '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON', '-DTrilinos_ENABLE_CXX11:BOOL=ON', '-DTPL_ENABLE_Netcdf:BOOL=ON', - '-DTPL_ENABLE_HYPRE:BOOL=%s' % ('ON' if '+hypre' in spec else 'OFF'),, + '-DTPL_ENABLE_HYPRE:BOOL=%s' % ('ON' if '+hypre' in spec else 'OFF'), '-DTPL_ENABLE_HDF5:BOOL=%s' % ('ON' if '+hdf5' in spec else 'OFF'), ]) -- cgit v1.2.3-70-g09d2 From 09e77812b67d92094bea8dae54617e3e02ebaa61 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Mon, 28 Mar 2016 17:49:20 +0200 Subject: fix installation of superlu_dist headers and add it as a dependency to petsc; add a variant to hypre to disable internal superlu --- var/spack/repos/builtin/packages/hypre/package.py | 5 +++++ var/spack/repos/builtin/packages/petsc/package.py | 21 ++++++++++++++++++--- .../repos/builtin/packages/superlu-dist/package.py | 11 ++++++----- 3 files changed, 29 insertions(+), 8 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/hypre/package.py b/var/spack/repos/builtin/packages/hypre/package.py index 8d93d48d1f..0e99553293 100644 --- a/var/spack/repos/builtin/packages/hypre/package.py +++ b/var/spack/repos/builtin/packages/hypre/package.py @@ -14,6 +14,8 @@ class Hypre(Package): # hypre does not know how to build shared libraries on Darwin variant('shared', default=sys.platform!='darwin', description="Build shared library version (disables static library)") + # SuperluDist have conflicting headers with those in Hypre + variant('internal-superlu', default=True, description="Use internal Superlu routines") depends_on("mpi") depends_on("blas") @@ -38,6 +40,9 @@ class Hypre(Package): if '+shared' in self.spec: configure_args.append("--enable-shared") + if '~internal-superlu' in self.spec: + configure_args.append("--without-superlu") + # Hypre's source is staged under ./src so we'll have to manually # cd into it. with working_dir("src"): diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py index dd3d2aa162..e9b7c8a732 100644 --- a/var/spack/repos/builtin/packages/petsc/package.py +++ b/var/spack/repos/builtin/packages/petsc/package.py @@ -28,6 +28,7 @@ class Petsc(Package): variant('boost', default=True, description='Activates support for Boost') variant('hypre', default=True, description='Activates support for Hypre (only parallel)') variant('mumps', default=True, description='Activates support for MUMPS (only parallel)') + variant('superlu-dist', default=True, description='Activates support for SuperluDist (only parallel)') # Virtual dependencies depends_on('blas') @@ -43,8 +44,11 @@ class Petsc(Package): depends_on('hdf5+mpi', when='+hdf5+mpi') depends_on('parmetis', when='+metis+mpi') - depends_on('hypre', when='+hypre+mpi~complex') # Hypre does not support complex numbers - + # Hypre does not support complex numbers. + # Also PETSc prefer to build it without internal superlu, likely due to conflict in headers + # see https://bitbucket.org/petsc/petsc/src/90564b43f6b05485163c147b464b5d6d28cde3ef/config/BuildSystem/config/packages/hypre.py + depends_on('hypre~internal-superlu', when='+hypre+mpi~complex') + depends_on('superlu-dist', when='+superlu-dist+mpi') depends_on('mumps+mpi', when='+mumps+mpi') depends_on('scalapack', when='+mumps+mpi') @@ -61,7 +65,7 @@ class Petsc(Package): # If mpi is disabled (~mpi), it's an error to have any of these enabled. # This generates a list of any such errors. errors = [error_message_fmt.format(library=x) - for x in ('hdf5', 'hypre', 'parmetis','mumps') + for x in ('hdf5', 'hypre', 'parmetis','mumps','superlu-dist') if ('+'+x) in self.spec] if errors: errors = ['incompatible variants given'] + errors @@ -101,6 +105,17 @@ class Petsc(Package): options.append( '--with-{library}-dir={path}'.format(library=library, path=spec[library].prefix) ) + # PETSc does not pick up SuperluDist from the dir as they look for superlu_dist_4.1.a + if 'superlu-dist' in spec: + options.extend([ + '--with-superlu_dist-include=%s' % spec['superlu-dist'].prefix.include, + '--with-superlu_dist-lib=%s' % join_path(spec['superlu-dist'].prefix.lib, 'libsuperlu_dist.a'), + '--with-superlu_dist=1' + ]) + else: + options.append( + '--with-superlu_dist=0' + ) configure('--prefix=%s' % prefix, *options) diff --git a/var/spack/repos/builtin/packages/superlu-dist/package.py b/var/spack/repos/builtin/packages/superlu-dist/package.py index 9a94de8ba5..ddcb7f9225 100644 --- a/var/spack/repos/builtin/packages/superlu-dist/package.py +++ b/var/spack/repos/builtin/packages/superlu-dist/package.py @@ -1,4 +1,5 @@ from spack import * +import glob class SuperluDist(Package): """A general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.""" @@ -52,13 +53,13 @@ class SuperluDist(Package): # system "make" # need to install by hand - headers_location = join_path(self.prefix.include,'superlu_dist') + headers_location = self.prefix.include mkdirp(headers_location) mkdirp(prefix.lib) - # FIXME: fetch all headers in the folder automatically - for header in ['Cnames.h','cublas_utils.h','dcomplex.h','html_mainpage.h','machines.h','old_colamd.h','psymbfact.h','superlu_ddefs.h','superlu_defs.h','superlu_enum_consts.h','superlu_zdefs.h','supermatrix.h','util_dist.h']: - superludist_header = join_path(self.stage.source_path, 'SRC/',header) - install(superludist_header, headers_location) + + headers = glob.glob(join_path(self.stage.source_path, 'SRC','*.h')) + for h in headers: + install(h,headers_location) superludist_lib = join_path(self.stage.source_path, 'lib/libsuperlu_dist.a') install(superludist_lib,self.prefix.lib) -- cgit v1.2.3-70-g09d2 From f9bcce6a683b1d948190b9927254e3ee29d3606c Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Tue, 29 Mar 2016 09:19:24 +0200 Subject: turn off python by default --- var/spack/repos/builtin/packages/trilinos/package.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 71c0be61c3..0ab4addd52 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -31,7 +31,8 @@ class Trilinos(Package): variant('hypre', default=True, description='Compile with Hypre preconditioner') variant('hdf5', default=True, description='Compile with HDF5') variant('suite-sparse', default=True, description='Compile with SuiteSparse solvers') - variant('python', default=True, description='Build python wrappers') + # not everyone has py-numpy activated, keep it disabled by default to avoid configure errors + variant('python', default=False, description='Build python wrappers') variant('shared', default=True, description='Enables the build of shared libraries') variant('debug', default=False, description='Builds a debug version of the libraries') @@ -55,7 +56,7 @@ class Trilinos(Package): depends_on('hypre~internal-superlu',when='+hypre') depends_on('hdf5+mpi',when='+hdf5') - depends_on('python',when='+python') # Needs py-numpy activated + depends_on('python',when='+python') patch('umfpack_from_suitesparse.patch') -- cgit v1.2.3-70-g09d2 From 7753d823cbe1d1983957fb948bf095d624d76b7c Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Tue, 29 Mar 2016 09:27:55 +0200 Subject: add a comment on static mumps --- var/spack/repos/builtin/packages/trilinos/package.py | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 0ab4addd52..6223848c68 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -7,7 +7,6 @@ import os, sys, glob # https://gitlab.com/configurations/cluster-config/blob/master/trilinos.sh # https://github.com/Homebrew/homebrew-science/blob/master/trilinos.rb # and some relevant documentation/examples: -# https://trilinos.org/docs/dev/packages/amesos2/doc/html/classAmesos2_1_1MUMPS.html # https://github.com/trilinos/Trilinos/issues/175 class Trilinos(Package): """The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented @@ -50,7 +49,14 @@ class Trilinos(Package): depends_on('mpi') depends_on('netcdf+mpi') depends_on('parmetis',when='+metis') - depends_on('mumps@5.0:+mpi+shared',when='+mumps') # Amesos link errors with static: "__gfortran_adjustl", referenced from: _dmumps_ in libdmumps.a(dmumps_driver.o) "_mpi_abort_", referenced from: _mumps_abort_ in libmumps_common.a(tools_common.o) + # Trilinos' Tribits config system is limited which makes it + # very tricky to link Amesos with static MUMPS, see + # https://trilinos.org/docs/dev/packages/amesos2/doc/html/classAmesos2_1_1MUMPS.html + # One could work it out by getting linking flags from mpif90 --showme:link (or alike) + # and adding results to -DTrilinos_EXTRA_LINK_FLAGS + # together with Blas and Lapack and ScaLAPACK and Blacs and -lgfortran and + # it may work at the end. But let's avoid all this by simply using shared libs + depends_on('mumps@5.0:+mpi+shared',when='+mumps') depends_on('scalapack',when='+mumps') depends_on('superlu-dist',when='+superlu-dist') depends_on('hypre~internal-superlu',when='+hypre') -- cgit v1.2.3-70-g09d2 From 63c3feb79e7e4022e5565deb9f2749fa9732e7d2 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Tue, 29 Mar 2016 09:41:57 +0200 Subject: minor fixes to hypre and muparser on Linux --- var/spack/repos/builtin/packages/hypre/package.py | 3 +++ var/spack/repos/builtin/packages/muparser/package.py | 2 +- 2 files changed, 4 insertions(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/hypre/package.py b/var/spack/repos/builtin/packages/hypre/package.py index 0e99553293..4b915daa68 100644 --- a/var/spack/repos/builtin/packages/hypre/package.py +++ b/var/spack/repos/builtin/packages/hypre/package.py @@ -42,6 +42,9 @@ class Hypre(Package): if '~internal-superlu' in self.spec: configure_args.append("--without-superlu") + # MLI and FEI do not build without superlu on Linux + configure_args.append("--without-mli") + configure_args.append("--without-fei") # Hypre's source is staged under ./src so we'll have to manually # cd into it. diff --git a/var/spack/repos/builtin/packages/muparser/package.py b/var/spack/repos/builtin/packages/muparser/package.py index a1a9ff90e5..19ca8ce287 100644 --- a/var/spack/repos/builtin/packages/muparser/package.py +++ b/var/spack/repos/builtin/packages/muparser/package.py @@ -14,5 +14,5 @@ class Muparser(Package): configure(*options) - make() + make(parallel=False) make("install") -- cgit v1.2.3-70-g09d2 From ccc1b23bea57a9c8a31ab1f4e9b739b54440466b Mon Sep 17 00:00:00 2001 From: Patrick Gartung Date: Mon, 28 Mar 2016 16:28:29 -0500 Subject: this allows gcc4.9.3 to build on OSX10 --- .../builtin/packages/gcc/darwin/gcc-4.9.patch1 | 42 ++++++++++++++++++++++ .../builtin/packages/gcc/darwin/gcc-4.9.patch2 | 28 +++++++++++++++ var/spack/repos/builtin/packages/gcc/package.py | 12 ++++++- 3 files changed, 81 insertions(+), 1 deletion(-) create mode 100644 var/spack/repos/builtin/packages/gcc/darwin/gcc-4.9.patch1 create mode 100644 var/spack/repos/builtin/packages/gcc/darwin/gcc-4.9.patch2 (limited to 'var') diff --git a/var/spack/repos/builtin/packages/gcc/darwin/gcc-4.9.patch1 b/var/spack/repos/builtin/packages/gcc/darwin/gcc-4.9.patch1 new file mode 100644 index 0000000000..444e292786 --- /dev/null +++ b/var/spack/repos/builtin/packages/gcc/darwin/gcc-4.9.patch1 @@ -0,0 +1,42 @@ +diff --git a/gcc/configure b/gcc/configure +index 9523773..52b0bf7 100755 +--- a/gcc/configure ++++ b/gcc/configure +@@ -24884,7 +24884,7 @@ if test "${gcc_cv_as_ix86_filds+set}" = set; then : + else + gcc_cv_as_ix86_filds=no + if test x$gcc_cv_as != x; then +- $as_echo 'filds mem; fists mem' > conftest.s ++ $as_echo 'filds (%ebp); fists (%ebp)' > conftest.s + if { ac_try='$gcc_cv_as $gcc_cv_as_flags -o conftest.o conftest.s >&5' + { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_try\""; } >&5 + (eval $ac_try) 2>&5 +@@ -24915,7 +24915,7 @@ if test "${gcc_cv_as_ix86_fildq+set}" = set; then : + else + gcc_cv_as_ix86_fildq=no + if test x$gcc_cv_as != x; then +- $as_echo 'fildq mem; fistpq mem' > conftest.s ++ $as_echo 'fildq (%ebp); fistpq (%ebp)' > conftest.s + if { ac_try='$gcc_cv_as $gcc_cv_as_flags -o conftest.o conftest.s >&5' + { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_try\""; } >&5 + (eval $ac_try) 2>&5 +diff --git a/gcc/configure.ac b/gcc/configure.ac +index 68b0ee8..bd53978 100644 +--- a/gcc/configure.ac ++++ b/gcc/configure.ac +@@ -3869,13 +3869,13 @@ foo: nop + + gcc_GAS_CHECK_FEATURE([filds and fists mnemonics], + gcc_cv_as_ix86_filds,,, +- [filds mem; fists mem],, ++ [filds (%ebp); fists (%ebp)],, + [AC_DEFINE(HAVE_AS_IX86_FILDS, 1, + [Define if your assembler uses filds and fists mnemonics.])]) + + gcc_GAS_CHECK_FEATURE([fildq and fistpq mnemonics], + gcc_cv_as_ix86_fildq,,, +- [fildq mem; fistpq mem],, ++ [fildq (%ebp); fistpq (%ebp)],, + [AC_DEFINE(HAVE_AS_IX86_FILDQ, 1, + [Define if your assembler uses fildq and fistq mnemonics.])]) + diff --git a/var/spack/repos/builtin/packages/gcc/darwin/gcc-4.9.patch2 b/var/spack/repos/builtin/packages/gcc/darwin/gcc-4.9.patch2 new file mode 100644 index 0000000000..b065997f45 --- /dev/null +++ b/var/spack/repos/builtin/packages/gcc/darwin/gcc-4.9.patch2 @@ -0,0 +1,28 @@ +From 82f81877458ea372176eabb5de36329431dce99b Mon Sep 17 00:00:00 2001 +From: Iain Sandoe +Date: Sat, 21 Dec 2013 00:30:18 +0000 +Subject: [PATCH] don't try to mark local symbols as no-dead-strip + +--- + gcc/config/darwin.c | 5 +++++ + 1 file changed, 5 insertions(+) + +diff --git a/gcc/config/darwin.c b/gcc/config/darwin.c +index 40804b8..0080299 100644 +--- a/gcc/config/darwin.c ++++ b/gcc/config/darwin.c +@@ -1259,6 +1259,11 @@ darwin_encode_section_info (tree decl, rtx rtl, int first ATTRIBUTE_UNUSED) + void + darwin_mark_decl_preserved (const char *name) + { ++ /* Actually we shouldn't mark any local symbol this way, but for now ++ this only happens with ObjC meta-data. */ ++ if (darwin_label_is_anonymous_local_objc_name (name)) ++ return; ++ + fprintf (asm_out_file, "\t.no_dead_strip "); + assemble_name (asm_out_file, name); + fputc ('\n', asm_out_file); +-- +2.2.1 + diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py index 232d0020df..6043b62279 100644 --- a/var/spack/repos/builtin/packages/gcc/package.py +++ b/var/spack/repos/builtin/packages/gcc/package.py @@ -27,6 +27,7 @@ from spack import * from contextlib import closing from glob import glob import sys +import os class Gcc(Package): """The GNU Compiler Collection includes front ends for C, C++, @@ -63,6 +64,9 @@ class Gcc(Package): # TODO: integrate these libraries. #depends_on("ppl") #depends_on("cloog") + if sys.platform == 'darwin': + patch('darwin/gcc-4.9.patch1', when='@4.9.3') + patch('darwin/gcc-4.9.patch2', when='@4.9.3') def install(self, spec, prefix): # libjava/configure needs a minor fix to install into spack paths. @@ -70,6 +74,7 @@ class Gcc(Package): string=True) enabled_languages = set(('c', 'c++', 'fortran', 'java', 'objc')) + if spec.satisfies("@4.7.1:") and sys.platform != 'darwin': enabled_languages.add('go') @@ -101,12 +106,17 @@ class Gcc(Package): isl_options = ["--with-isl=%s" % spec['isl'].prefix] options.extend(isl_options) + if sys.platform == 'darwin' : + darwin_options = [ "--with-build-config=bootstrap-debug" ] + options.extend(darwin_options) + build_dir = join_path(self.stage.path, 'spack-build') configure = Executable( join_path(self.stage.source_path, 'configure') ) with working_dir(build_dir, create=True): # Rest of install is straightforward. configure(*options) - make() + if sys.platform == 'darwin' : make("bootstrap") + else: make() make("install") self.write_rpath_specs() -- cgit v1.2.3-70-g09d2 From ad402ff85bc4150aa49fb394929b062b40b27604 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Mon, 21 Mar 2016 22:36:31 +0100 Subject: astyle@2.04: add new package --- var/spack/repos/builtin/packages/astyle/package.py | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 var/spack/repos/builtin/packages/astyle/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/astyle/package.py b/var/spack/repos/builtin/packages/astyle/package.py new file mode 100644 index 0000000000..7260fd74a1 --- /dev/null +++ b/var/spack/repos/builtin/packages/astyle/package.py @@ -0,0 +1,17 @@ +from spack import * +import os + +class Astyle(Package): + """A Free, Fast, and Small Automatic Formatter for C, C++, C++/CLI, Objective-C, C#, and Java Source Code.""" + homepage = "http://astyle.sourceforge.net/" + url = "http://downloads.sourceforge.net/project/astyle/astyle/astyle%202.04/astyle_2.04_linux.tar.gz" + + version('2.04', '30b1193a758b0909d06e7ee8dd9627f6') + + def install(self, spec, prefix): + + with working_dir('src'): + make('-f', + join_path(self.stage.source_path,'build','clang','Makefile'), + parallel=False) + install(join_path(self.stage.source_path, 'src','bin','astyle'), self.prefix.bin) -- cgit v1.2.3-70-g09d2 From d96ea5ba0075c63e8cd042337a1d99225b92b2d5 Mon Sep 17 00:00:00 2001 From: Patrick Gartung Date: Tue, 29 Mar 2016 12:20:11 -0500 Subject: add modules package and have setup script find it if built --- share/spack/setup-env.sh | 10 +++++++++ .../repos/builtin/packages/modules/package.py | 25 ++++++++++++++++++++++ 2 files changed, 35 insertions(+) create mode 100644 var/spack/repos/builtin/packages/modules/package.py (limited to 'var') diff --git a/share/spack/setup-env.sh b/share/spack/setup-env.sh index 764af68400..529517ff83 100755 --- a/share/spack/setup-env.sh +++ b/share/spack/setup-env.sh @@ -176,3 +176,13 @@ _spack_pathadd PATH "${_sp_prefix%/}/bin" _sp_sys_type=$(spack-python -c 'print(spack.architecture.sys_type())') _spack_pathadd DK_NODE "${_sp_share_dir%/}/dotkit/$_sp_sys_type" _spack_pathadd MODULEPATH "${_sp_share_dir%/}/modules/$_sp_sys_type" + +# +# Use spack built modules package if available +# for system that does not have it +# + +_modules_install_path=$(command spack location -i modules) +if [ -n "$_modules_install_path" ] ; then + . $_modules_install_path/Modules/init/sh +fi diff --git a/var/spack/repos/builtin/packages/modules/package.py b/var/spack/repos/builtin/packages/modules/package.py new file mode 100644 index 0000000000..b014ee460c --- /dev/null +++ b/var/spack/repos/builtin/packages/modules/package.py @@ -0,0 +1,25 @@ +from spack import * + +class Modules(Package): + """ The Environment Modules package provides for the dynamic modification of a user's environment via modulefiles. """ + + homepage = "http://modules.sf.net" + url = "http://downloads.sourceforge.net/project/modules/Modules/modules-3.2.10/modules-3.2.10.tar.gz" + + version('3.2.10', '8b097fdcb90c514d7540bb55a3cb90fb') + + depends_on("tcl") + + def install(self, spec, prefix): + + options = ['--prefix=%s' % prefix, + '--disable-debug', + '--disable-dependency-tracking', + '--disable-silent-rules', + '--disable-versioning', + '--datarootdir=%s' % prefix.share, + 'CPPFLAGS=-DUSE_INTERP_ERRORLINE'] + + configure(*options) + make() + make("install") -- cgit v1.2.3-70-g09d2 From 4ddba5f7edd97c8c17781368edc5b9a0db74417d Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Tue, 29 Mar 2016 14:47:16 -0500 Subject: Add CUDA and HOOMD-blue packages --- var/spack/repos/builtin/packages/cuda/package.py | 42 ++++++++++++++ .../repos/builtin/packages/hoomd-blue/package.py | 67 ++++++++++++++++++++++ 2 files changed, 109 insertions(+) create mode 100644 var/spack/repos/builtin/packages/cuda/package.py create mode 100644 var/spack/repos/builtin/packages/hoomd-blue/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/cuda/package.py b/var/spack/repos/builtin/packages/cuda/package.py new file mode 100644 index 0000000000..547b43d6d2 --- /dev/null +++ b/var/spack/repos/builtin/packages/cuda/package.py @@ -0,0 +1,42 @@ +from spack import * +from glob import glob +import os + +class Cuda(Package): + """CUDA is a parallel computing platform and programming model invented by + NVIDIA. It enables dramatic increases in computing performance by harnessing + the power of the graphics processing unit (GPU). + + Note: NVIDIA does not provide a download URL for CUDA so you will need to + download it yourself. Go to https://developer.nvidia.com/cuda-downloads + and select your Operating System, Architecture, Distribution, and Version. + For the Installer Type, select runfile and click Download. Spack will search + your current directory for this file. Alternatively, add this file to a + mirror so that Spack can find it. For instructions on how to set up a mirror, + see http://software.llnl.gov/spack/mirrors.html""" + + homepage = "http://www.nvidia.com/object/cuda_home_new.html" + url = "file://%s/cuda_7.5.18_linux.run" % os.getcwd() + + version('7.5.18', '4b3bcecf0dfc35928a0898793cf3e4c6', expand=False) + + def install(self, spec, prefix): + runfile = glob(os.path.join(self.stage.path, 'cuda*.run'))[0] + chmod = which('chmod') + chmod('+x', runfile) + runfile = which(runfile) + + # Note: NVIDIA does not officially support many newer versions of compilers. + # For example, on CentOS 6, you must use GCC 4.4.7 or older. + # The --override flag disables these checks. See: + # http://docs.nvidia.com/cuda/cuda-installation-guide-linux/#system-requirements + # for details. + + runfile( + '--silent', # disable interactive prompts + '--verbose', # create verbose log file + '--override', # ignore compiler checks + '--toolkit', # install CUDA Toolkit + '--toolkitpath=%s' % prefix + ) + diff --git a/var/spack/repos/builtin/packages/hoomd-blue/package.py b/var/spack/repos/builtin/packages/hoomd-blue/package.py new file mode 100644 index 0000000000..97ce9c0cf0 --- /dev/null +++ b/var/spack/repos/builtin/packages/hoomd-blue/package.py @@ -0,0 +1,67 @@ +from spack import * +import os + +class HoomdBlue(Package): + """HOOMD-blue is a general-purpose particle simulation toolkit. It scales + from a single CPU core to thousands of GPUs. + + You define particle initial conditions and interactions in a high-level + python script. Then tell HOOMD-blue how you want to execute the job and it + takes care of the rest. Python job scripts give you unlimited flexibility + to create custom initialization routines, control simulation parameters, + and perform in situ analysis.""" + + homepage = "https://codeblue.umich.edu/hoomd-blue/index.html" + url = "https://bitbucket.org/glotzer/hoomd-blue/get/v1.3.3.tar.bz2" + + version('1.3.3', '1469ef4531dc14b579c0acddbfe6a273') + + variant('mpi', default=False, description='Compile with MPI enabled') + variant('cuda', default=False, description='Compile with CUDA Toolkit') + variant('doc', default=False, description='Generate documentation') + + extends('python') + depends_on('py-numpy') + depends_on('boost+python') + depends_on('cmake') + depends_on('mpi', when='+mpi') + depends_on('cuda', when='+cuda') + depends_on('doxygen', when='+doc') + + def install(self, spec, prefix): + + cmake_args = [ + '-DPYTHON_EXECUTABLE=%s/python' % spec['python'].prefix.bin, + '-DBOOST_ROOT=%s' % spec['boost' ].prefix + ] + + # MPI support + if '+mpi' in spec: + os.environ['MPI_HOME'] = spec['mpi'].prefix + cmake_args.append('-DENABLE_MPI=ON') + else: + cmake_args.append('-DENABLE_MPI=OFF') + + # CUDA support + if '+cuda' in spec: + cmake_args.append('-DENABLE_CUDA=ON') + else: + cmake_args.append('-DENABLE_CUDA=OFF') + + # CUDA-aware MPI library support + if '+cuda' in spec and '+mpi' in spec: + cmake_args.append('-DENABLE_MPI_CUDA=ON') + else: + cmake_args.append('-DENABLE_MPI_CUDA=OFF') + + # Documentation + if '+doc' in spec: + cmake_args.append('-DENABLE_DOXYGEN=ON') + else: + cmake_args.append('-DENABLE_DOXYGEN=OFF') + + cmake_args.extend(std_cmake_args) + cmake('.', *cmake_args) + + make() + make("install") -- cgit v1.2.3-70-g09d2 From abee9c83b440b8341be6df1f07c7c5f1bef9dd89 Mon Sep 17 00:00:00 2001 From: Elizabeth Fischer Date: Tue, 29 Mar 2016 17:26:34 -0400 Subject: Removed googletest FIXME... --- var/spack/repos/builtin/packages/googletest/package.py | 16 ---------------- 1 file changed, 16 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/googletest/package.py b/var/spack/repos/builtin/packages/googletest/package.py index ed27afa10c..663b758747 100644 --- a/var/spack/repos/builtin/packages/googletest/package.py +++ b/var/spack/repos/builtin/packages/googletest/package.py @@ -1,19 +1,3 @@ -# FIXME: -# This is a template package file for Spack. We've conveniently -# put "FIXME" labels next to all the things you'll want to change. -# -# Once you've edited all the FIXME's, delete this whole message, -# save this file, and test out your package like this: -# -# spack install googletest -# -# You can always get back here to change things with: -# -# spack edit googletest -# -# See the spack documentation for more information on building -# packages. -# from spack import * class Googletest(Package): -- cgit v1.2.3-70-g09d2 From a4eff6de3faa3624a529015ea4cf5ebb1af41484 Mon Sep 17 00:00:00 2001 From: "Kelly (KT) Thompson" Date: Tue, 29 Mar 2016 17:10:49 -0600 Subject: + New version of cmake (3.5.1). --- var/spack/repos/builtin/packages/cmake/package.py | 1 + 1 file changed, 1 insertion(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py index 1f93d39769..91a4e3b415 100644 --- a/var/spack/repos/builtin/packages/cmake/package.py +++ b/var/spack/repos/builtin/packages/cmake/package.py @@ -30,6 +30,7 @@ class Cmake(Package): homepage = 'https://www.cmake.org' url = 'https://cmake.org/files/v3.4/cmake-3.4.3.tar.gz' + version('3.5.1', 'ca051f4a66375c89d1a524e726da0296') version('3.5.0', '33c5d09d4c33d4ffcc63578a6ba8777e') version('3.4.3', '4cb3ff35b2472aae70f542116d616e63') version('3.4.0', 'cd3034e0a44256a0917e254167217fc8') -- cgit v1.2.3-70-g09d2 From 98bb151d85fc35389e0b76eaac90448fa688aa6c Mon Sep 17 00:00:00 2001 From: "Gregory L. Lee" Date: Tue, 29 Mar 2016 20:25:56 -0700 Subject: updated geos version --- var/spack/repos/builtin/packages/dbus/package.py | 1 + 1 file changed, 1 insertion(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/dbus/package.py b/var/spack/repos/builtin/packages/dbus/package.py index 294b0de54e..422f5a19eb 100644 --- a/var/spack/repos/builtin/packages/dbus/package.py +++ b/var/spack/repos/builtin/packages/dbus/package.py @@ -13,6 +13,7 @@ class Dbus(Package): homepage = "http://dbus.freedesktop.org/" url = "http://dbus.freedesktop.org/releases/dbus/dbus-1.8.8.tar.gz" + version('1.11.2', '957a07f066f3730d2bb3ea0932f0081b') version('1.9.0', 'ec6895a4d5c0637b01f0d0e7689e2b36') version('1.8.8', 'b9f4a18ee3faa1e07c04aa1d83239c43') version('1.8.6', '6a08ba555d340e9dfe2d623b83c0eea8') -- cgit v1.2.3-70-g09d2 From 5b6eefbf0417668c19e4c898c31cf56764d5bc2b Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 30 Mar 2016 11:30:35 +0200 Subject: add variants and extra dependencies --- var/spack/repos/builtin/packages/dealii/package.py | 176 ++++++++++++++++----- 1 file changed, 140 insertions(+), 36 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py index 9ac1572b95..396601356c 100644 --- a/var/spack/repos/builtin/packages/dealii/package.py +++ b/var/spack/repos/builtin/packages/dealii/package.py @@ -8,27 +8,48 @@ class Dealii(Package): version('8.4.0', 'ac5dbf676096ff61e092ce98c80c2b00') - depends_on ("cmake") + variant('mpi', default=True, description='Compile with MPI') + variant('arpack', default=True, description='Compile with Arpack and PArpack (only with MPI)') + variant('doxygen', default=True, description='Compile with Doxygen documentation') + variant('hdf5', default=True, description='Compile with HDF5 (only with MPI)') + variant('metis', default=True, description='Compile with Metis or ParMetis') + variant('netcdf', default=True, description='Compile with Netcdf (only with MPI)') + variant('oce', default=True, description='Compile with OCE') + variant('p4est', default=True, description='Compile with P4est (only with MPI)') + variant('petsc', default=True, description='Compile with Petsc (only with MPI)') + variant('slepc', default=True, description='Compile with Slepc (only with Petsc and MPI)') + variant('trilinos', default=True, description='Compile with Trilinos (only with MPI)') + + # required dependencies, light version depends_on ("blas") + depends_on ("boost", when='~mpi') + depends_on ("boost+mpi", when='+mpi') + depends_on ("bzip2") + depends_on ("cmake") depends_on ("lapack") - depends_on ("mpi") - - depends_on ("arpack-ng+mpi") - depends_on ("boost") - depends_on ("doxygen") - depends_on ("hdf5+mpi~cxx") #FIXME NetCDF declares dependency with ~cxx, why? - depends_on ("metis") depends_on ("muparser") - depends_on ("netcdf-cxx") - #depends_on ("numdiff") #FIXME - depends_on ("oce") - depends_on ("p4est") - depends_on ("parmetis") - depends_on ("petsc+mpi") - depends_on ("slepc") depends_on ("suite-sparse") depends_on ("tbb") - depends_on ("trilinos") + depends_on ("zlib") + + # optional dependencies + depends_on ("mpi", when="+mpi") + depends_on ("arpack-ng+mpi", when='+arpack+mpi') + depends_on ("doxygen", when='+doxygen') + depends_on ("hdf5+mpi~cxx", when='+hdf5+mpi') #FIXME NetCDF declares dependency with ~cxx, why? + depends_on ("metis", when='+metis') + depends_on ("netcdf+mpi", when="+netcdf+mpi") + depends_on ("netcdf-cxx", when='+netcdf+mpi') + depends_on ("oce", when='+oce') + depends_on ("p4est", when='+p4est+mpi') + depends_on ("parmetis", when='+metis+mpi') + depends_on ("petsc+mpi", when='+petsc+mpi') + depends_on ("slepc", when='+slepc+petsc+mpi') + depends_on ("trilinos", when='+trilinos+mpi') + + # developer dependnecies + #depends_on ("numdiff") #FIXME + #depends_on ("astyle") #FIXME def install(self, spec, prefix): options = [] @@ -42,33 +63,116 @@ class Dealii(Package): dsuf = 'dylib' if sys.platform == 'darwin' else 'so' options.extend([ '-DCMAKE_BUILD_TYPE=DebugRelease', - '-DDEAL_II_WITH_THREADS:BOOL=ON' - '-DDEAL_II_WITH_MPI:BOOL=ON', - '-DCMAKE_C_COMPILER=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpicc'), # FIXME: avoid hardcoding mpi wrappers names - '-DCMAKE_CXX_COMPILER=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpic++'), - '-DCMAKE_Fortran_COMPILER=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif90'), - '-DARPACK_DIR=%s' % spec['arpack-ng'].prefix, + '-DDEAL_II_COMPONENT_EXAMPLES=ON', + '-DDEAL_II_WITH_THREADS:BOOL=ON', '-DBOOST_DIR=%s' % spec['boost'].prefix, - '-DHDF5_DIR=%s' % spec['hdf5'].prefix, - '-DMETIS_DIR=%s' % spec['metis'].prefix, + '-DBZIP2_DIR=%s' % spec['bzip2'].prefix, + # CMake's FindBlas/Lapack may pickup system's blas/lapack instead of Spack's. + # Be more specific to avoid this. + # Note that both lapack and blas are provided in -DLAPACK_XYZ variables + '-DLAPACK_FOUND=true', + '-DLAPACK_INCLUDE_DIRS=%s;%s' % + (spec['lapack'].prefix.include, + spec['blas'].prefix.include), + '-DLAPACK_LIBRARIES=%s;%s' % + (join_path(spec['lapack'].prefix.lib,'liblapack.%s' % dsuf), # FIXME don't hardcode names + join_path(spec['blas'].prefix.lib,'libblas.%s' % dsuf)), # FIXME don't hardcode names '-DMUPARSER_DIR=%s ' % spec['muparser'].prefix, - # since Netcdf is spread among two, need to do it by hand: - '-DNETCDF_FOUND=true', - '-DNETCDF_LIBRARIES=%s;%s' % - (join_path(spec['netcdf-cxx'].prefix.lib,'libnetcdf_c++.%s' % dsuf), - join_path(spec['netcdf'].prefix.lib,'libnetcdf.%s' % dsuf)), - '-DNETCDF_INCLUDE_DIRS=%s;%s' % - (spec['netcdf-cxx'].prefix.include, - spec['netcdf'].prefix.include), - '-DOPENCASCADE_DIR=%s' % spec['oce'].prefix, '-DP4EST_DIR=%s' % spec['p4est'].prefix, - '-DPETSC_DIR=%s' % spec['petsc'].prefix, - '-DSLEPC_DIR=%s' % spec['slepc'].prefix, '-DUMFPACK_DIR=%s' % spec['suite-sparse'].prefix, '-DTBB_DIR=%s' % spec['tbb'].prefix, - '-DTRILINOS_DIR=%s' % spec['trilinos'].prefix + '-DZLIB_DIR=%s' % spec['zlib'].prefix ]) + # MPI + if '+mpi' in spec: + options.extend([ + '-DDEAL_II_WITH_MPI:BOOL=ON', + '-DCMAKE_C_COMPILER=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpicc'), # FIXME: avoid hardcoding mpi wrappers names + '-DCMAKE_CXX_COMPILER=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpic++'), + '-DCMAKE_Fortran_COMPILER=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif90'), + ]) + else: + options.extend([ + '-DDEAL_II_WITH_MPI:BOOL=OFF', + ]) + + # Optional dependencies for which librariy names are the same as CMake variables + for library in ('hdf5', 'p4est','petsc', 'slepc','trilinos','metis','parmetis'): + if library in spec: + options.extend([ + '-D{library}_DIR={value}'.format(library=library.upper(), value=spec[library].prefix), + '-DDEAL_II_WITH_{library}:BOOL=ON'.format(library=library.upper()) + ]) + else: + options.extend([ + '-DDEAL_II_WITH_{library}:BOOL=OFF'.format(library=library.upper()) + ]) + + # doxygen + options.extend([ + '-DDEAL_II_COMPONENT_DOCUMENTATION=%s' % ('ON' if '+doxygen' in spec else 'OFF'), + ]) + + + # arpack + if '+arpack' in spec: + options.extend([ + '-DARPACK_DIR=%s' % spec['arpack-ng'].prefix, + '-DDEAL_II_WITH_ARPACK=ON', + '-DDEAL_II_ARPACK_WITH_PARPACK=ON' + ]) + else: + options.extend([ + '-DDEAL_II_WITH_ARPACK=OFF' + ]) + + # # metis + # if '+metis' in spec: + # + # if 'mpi' in spec: + # options.extend([ + # '-DMETIS_DIR=%s' % spec['parmetis'].prefix, + # ]) + # else: + # options.extend([ + # '-DMETIS_DIR=%s' % spec['metis'].prefix, + # ]) + # options.extend([ + # '-DDEAL_II_WITH_METIS=ON' + # ]) + # else: + # options.extend([ + # '-DDEAL_II_WITH_METIS=OFF' + # ]) + + # since Netcdf is spread among two, need to do it by hand: + if '+netcdf' in spec: + options.extend([ + '-DNETCDF_FOUND=true', + '-DNETCDF_LIBRARIES=%s;%s' % + (join_path(spec['netcdf-cxx'].prefix.lib,'libnetcdf_c++.%s' % dsuf), + join_path(spec['netcdf'].prefix.lib,'libnetcdf.%s' % dsuf)), + '-DNETCDF_INCLUDE_DIRS=%s;%s' % + (spec['netcdf-cxx'].prefix.include, + spec['netcdf'].prefix.include), + ]) + else: + options.extend([ + '-DDEAL_II_WITH_NETCDF=OFF' + ]) + + # Open Cascade + if '+oce' in spec: + options.extend([ + '-DOPENCASCADE_DIR=%s' % spec['oce'].prefix, + '-DDEAL_II_WITH_OPENCASCADE=ON' + ]) + else: + options.extend([ + '-DDEAL_II_WITH_OPENCASCADE=OFF' + ]) + cmake('.', *options) make() -- cgit v1.2.3-70-g09d2 From bafc6cebe1ca37116badc1baf60e88564eb01614 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 30 Mar 2016 12:00:21 +0200 Subject: doxygen off by default --- var/spack/repos/builtin/packages/dealii/package.py | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py index 396601356c..907aa33356 100644 --- a/var/spack/repos/builtin/packages/dealii/package.py +++ b/var/spack/repos/builtin/packages/dealii/package.py @@ -8,17 +8,17 @@ class Dealii(Package): version('8.4.0', 'ac5dbf676096ff61e092ce98c80c2b00') - variant('mpi', default=True, description='Compile with MPI') - variant('arpack', default=True, description='Compile with Arpack and PArpack (only with MPI)') - variant('doxygen', default=True, description='Compile with Doxygen documentation') - variant('hdf5', default=True, description='Compile with HDF5 (only with MPI)') - variant('metis', default=True, description='Compile with Metis or ParMetis') - variant('netcdf', default=True, description='Compile with Netcdf (only with MPI)') - variant('oce', default=True, description='Compile with OCE') - variant('p4est', default=True, description='Compile with P4est (only with MPI)') - variant('petsc', default=True, description='Compile with Petsc (only with MPI)') - variant('slepc', default=True, description='Compile with Slepc (only with Petsc and MPI)') - variant('trilinos', default=True, description='Compile with Trilinos (only with MPI)') + variant('mpi', default=True, description='Compile with MPI') + variant('arpack', default=True, description='Compile with Arpack and PArpack (only with MPI)') + variant('doxygen', default=False, description='Compile with Doxygen documentation') + variant('hdf5', default=True, description='Compile with HDF5 (only with MPI)') + variant('metis', default=True, description='Compile with Metis or ParMetis') + variant('netcdf', default=True, description='Compile with Netcdf (only with MPI)') + variant('oce', default=True, description='Compile with OCE') + variant('p4est', default=True, description='Compile with P4est (only with MPI)') + variant('petsc', default=True, description='Compile with Petsc (only with MPI)') + variant('slepc', default=True, description='Compile with Slepc (only with Petsc and MPI)') + variant('trilinos', default=True, description='Compile with Trilinos (only with MPI)') # required dependencies, light version depends_on ("blas") -- cgit v1.2.3-70-g09d2 From 9e9f5d01ad43e9b00262a12d1fd1225ac368581d Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 30 Mar 2016 11:59:13 +0200 Subject: doxygen: add missing dependencies --- var/spack/repos/builtin/packages/doxygen/package.py | 5 +++++ 1 file changed, 5 insertions(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/doxygen/package.py b/var/spack/repos/builtin/packages/doxygen/package.py index 3d4a4e47a7..3a1deba9e1 100644 --- a/var/spack/repos/builtin/packages/doxygen/package.py +++ b/var/spack/repos/builtin/packages/doxygen/package.py @@ -4,6 +4,7 @@ #------------------------------------------------------------------------------ from spack import * +import sys class Doxygen(Package): """Doxygen is the de facto standard tool for generating documentation @@ -17,6 +18,10 @@ class Doxygen(Package): version('1.8.10', '79767ccd986f12a0f949015efb5f058f') depends_on("cmake@2.8.12:") + # flex does not build on OSX, but it's provided there anyway + depends_on("flex", sys.platform != 'darwin') + depends_on("bison", sys.platform != 'darwin') + def install(self, spec, prefix): cmake('.', *std_cmake_args) -- cgit v1.2.3-70-g09d2 From 2abdd71b414b4f551e927edb7304b4dcc053d09e Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 30 Mar 2016 15:19:29 +0200 Subject: add dev version and conditionals for tests; remove parmetis --- var/spack/repos/builtin/packages/dealii/package.py | 62 +++++++++------------- 1 file changed, 24 insertions(+), 38 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py index 907aa33356..32dfb33c6d 100644 --- a/var/spack/repos/builtin/packages/dealii/package.py +++ b/var/spack/repos/builtin/packages/dealii/package.py @@ -7,12 +7,13 @@ class Dealii(Package): url = "https://github.com/dealii/dealii/releases/download/v8.4.0/dealii-8.4.0.tar.gz" version('8.4.0', 'ac5dbf676096ff61e092ce98c80c2b00') + version('dev', git='https://github.com/dealii/dealii.git') variant('mpi', default=True, description='Compile with MPI') variant('arpack', default=True, description='Compile with Arpack and PArpack (only with MPI)') variant('doxygen', default=False, description='Compile with Doxygen documentation') variant('hdf5', default=True, description='Compile with HDF5 (only with MPI)') - variant('metis', default=True, description='Compile with Metis or ParMetis') + variant('metis', default=True, description='Compile with Metis') variant('netcdf', default=True, description='Compile with Netcdf (only with MPI)') variant('oce', default=True, description='Compile with OCE') variant('p4est', default=True, description='Compile with P4est (only with MPI)') @@ -42,7 +43,6 @@ class Dealii(Package): depends_on ("netcdf-cxx", when='+netcdf+mpi') depends_on ("oce", when='+oce') depends_on ("p4est", when='+p4est+mpi') - depends_on ("parmetis", when='+metis+mpi') depends_on ("petsc+mpi", when='+petsc+mpi') depends_on ("slepc", when='+slepc+petsc+mpi') depends_on ("trilinos", when='+trilinos+mpi') @@ -98,7 +98,7 @@ class Dealii(Package): ]) # Optional dependencies for which librariy names are the same as CMake variables - for library in ('hdf5', 'p4est','petsc', 'slepc','trilinos','metis','parmetis'): + for library in ('hdf5', 'p4est','petsc', 'slepc','trilinos','metis'): if library in spec: options.extend([ '-D{library}_DIR={value}'.format(library=library.upper(), value=spec[library].prefix), @@ -127,25 +127,6 @@ class Dealii(Package): '-DDEAL_II_WITH_ARPACK=OFF' ]) - # # metis - # if '+metis' in spec: - # - # if 'mpi' in spec: - # options.extend([ - # '-DMETIS_DIR=%s' % spec['parmetis'].prefix, - # ]) - # else: - # options.extend([ - # '-DMETIS_DIR=%s' % spec['metis'].prefix, - # ]) - # options.extend([ - # '-DDEAL_II_WITH_METIS=ON' - # ]) - # else: - # options.extend([ - # '-DDEAL_II_WITH_METIS=OFF' - # ]) - # since Netcdf is spread among two, need to do it by hand: if '+netcdf' in spec: options.extend([ @@ -202,16 +183,18 @@ class Dealii(Package): # list the number of cycles to speed up filter_file(r'(const unsigned int n_cycles = 8;)', ('const unsigned int n_cycles = 2;'), 'step-40.cc') cmake('.') - make('release') - make('run',parallel=False) + if '^petsc' in spec: + make('release') + make('run',parallel=False) print('=====================================') print('========= Step-40 Trilinos ==========') print('=====================================') # change Linear Algebra to Trilinos filter_file(r'(\/\/ #define FORCE_USE_OF_TRILINOS.*)', ('#define FORCE_USE_OF_TRILINOS'), 'step-40.cc') - make('release') - make('run',parallel=False) + if '^trilinos+hypre' in spec: + make('release') + make('run',parallel=False) print('=====================================') print('=== Step-40 Trilinos SuperluDist ====') @@ -223,31 +206,34 @@ class Dealii(Package): filter_file(r'(preconditioner.initialize\(system_matrix, data\);)', (''), 'step-40.cc') filter_file(r'(solver\.solve \(system_matrix, completely_distributed_solution, system_rhs,)', ('solver.solve (system_matrix, completely_distributed_solution, system_rhs);'), 'step-40.cc') filter_file(r'(preconditioner\);)', (''), 'step-40.cc') - - make('release') - make('run',paralle=False) + if '^trilinos+superlu-dist' in spec: + make('release') + make('run',paralle=False) print('=====================================') print('====== Step-40 Trilinos MUMPS =======') print('=====================================') # switch to Mumps filter_file(r'(Amesos_Superludist)', ('Amesos_Mumps'), 'step-40.cc') - make('release') - make('run',parallel=False) + if '^trilinos+mumps' in spec: + make('release') + make('run',parallel=False) print('=====================================') print('============ Step-36 ================') print('=====================================') with working_dir('examples/step-36'): - cmake('.') - make('release') - make('run',parallel=False) + if 'slepc' in spec: + cmake('.') + make('release') + make('run',parallel=False) print('=====================================') print('============ Step-54 ================') print('=====================================') with working_dir('examples/step-54'): - cmake('.') - make('release') - # FIXME - # make('run',parallel=False) + if 'oce' in spec: + cmake('.') + make('release') + if sys.platform != 'darwin': #FIXME + make('run',parallel=False) -- cgit v1.2.3-70-g09d2 From 5b1ef64e31a56877f6859820ca7a79dd51f6fe84 Mon Sep 17 00:00:00 2001 From: "Kelly (KT) Thompson" Date: Wed, 30 Mar 2016 09:33:00 -0600 Subject: + Provide basic instructions for providing subversion w/o additional language bindings. --- .../packages/apr-util/apr-util.new/package.py | 44 ------------- .../repos/builtin/packages/apr-util/package.py | 44 +++++++++++++ .../repos/builtin/packages/apr/apr.new/package.py | 51 -------------- var/spack/repos/builtin/packages/apr/package.py | 38 +++++++++++ .../repos/builtin/packages/subversion/package.py | 77 ++++++++++++++++++++++ .../packages/subversion/subversion.new/package.py | 59 ----------------- 6 files changed, 159 insertions(+), 154 deletions(-) delete mode 100644 var/spack/repos/builtin/packages/apr-util/apr-util.new/package.py create mode 100644 var/spack/repos/builtin/packages/apr-util/package.py delete mode 100644 var/spack/repos/builtin/packages/apr/apr.new/package.py create mode 100644 var/spack/repos/builtin/packages/apr/package.py create mode 100644 var/spack/repos/builtin/packages/subversion/package.py delete mode 100644 var/spack/repos/builtin/packages/subversion/subversion.new/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/apr-util/apr-util.new/package.py b/var/spack/repos/builtin/packages/apr-util/apr-util.new/package.py deleted file mode 100644 index 8f19c84d22..0000000000 --- a/var/spack/repos/builtin/packages/apr-util/apr-util.new/package.py +++ /dev/null @@ -1,44 +0,0 @@ -############################################################################## -# Copyright (c) 2013, Lawrence Livermore National Security, LLC. -# Produced at the Lawrence Livermore National Laboratory. -# -# This file is part of Spack. -# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. -# LLNL-CODE-647188 -# -# For details, see https://github.com/llnl/spack -# Please also see the LICENSE file for our notice and the LGPL. -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU General Public License (as published by -# the Free Software Foundation) version 2.1 dated February 1999. -# -# This program is distributed in the hope that it will be useful, but -# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and -# conditions of the GNU General Public License for more details. -# -# You should have received a copy of the GNU Lesser General Public License -# along with this program; if not, write to the Free Software Foundation, -# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA -############################################################################## -from spack import * - -class AprUtil(Package): - """Apache Portable Runtime Utility""" - homepage = 'https://apr.apache.org/' - url = 'http://archive.apache.org/dist/apr/apr-util-1.5.4.tar.gz' - - version('1.5.4', '866825c04da827c6e5f53daff5569f42') - - depends_on('apr') - - def install(self, spec, prefix): - - # configure, build, install: - options = ['--prefix=%s' % prefix] - options.append('--with-apr=%s' % spec['apr'].prefix) - - configure(*options) - make() - make('install') diff --git a/var/spack/repos/builtin/packages/apr-util/package.py b/var/spack/repos/builtin/packages/apr-util/package.py new file mode 100644 index 0000000000..8f19c84d22 --- /dev/null +++ b/var/spack/repos/builtin/packages/apr-util/package.py @@ -0,0 +1,44 @@ +############################################################################## +# Copyright (c) 2013, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License (as published by +# the Free Software Foundation) version 2.1 dated February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program; if not, write to the Free Software Foundation, +# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + +class AprUtil(Package): + """Apache Portable Runtime Utility""" + homepage = 'https://apr.apache.org/' + url = 'http://archive.apache.org/dist/apr/apr-util-1.5.4.tar.gz' + + version('1.5.4', '866825c04da827c6e5f53daff5569f42') + + depends_on('apr') + + def install(self, spec, prefix): + + # configure, build, install: + options = ['--prefix=%s' % prefix] + options.append('--with-apr=%s' % spec['apr'].prefix) + + configure(*options) + make() + make('install') diff --git a/var/spack/repos/builtin/packages/apr/apr.new/package.py b/var/spack/repos/builtin/packages/apr/apr.new/package.py deleted file mode 100644 index 5cbbad350b..0000000000 --- a/var/spack/repos/builtin/packages/apr/apr.new/package.py +++ /dev/null @@ -1,51 +0,0 @@ -############################################################################## -# Copyright (c) 2013, Lawrence Livermore National Security, LLC. -# Produced at the Lawrence Livermore National Laboratory. -# -# This file is part of Spack. -# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. -# LLNL-CODE-647188 -# -# For details, see https://github.com/llnl/spack -# Please also see the LICENSE file for our notice and the LGPL. -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU General Public License (as published by -# the Free Software Foundation) version 2.1 dated February 1999. -# -# This program is distributed in the hope that it will be useful, but -# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and -# conditions of the GNU General Public License for more details. -# -# You should have received a copy of the GNU Lesser General Public License -# along with this program; if not, write to the Free Software Foundation, -# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA -############################################################################## -from spack import * - -class Apr(Package): - """Apache portable runtime.""" - homepage = 'https://apr.apache.org/' - url = 'http://archive.apache.org/dist/apr/apr-1.5.2.tar.gz' - - version('1.5.2', '98492e965963f852ab29f9e61b2ad700') - - #variant('ncurses', default=True, description='Enables the build of the ncurses gui') - #variant('qt', default=False, description='Enables the build of cmake-gui') - #variant('doc', default=False, description='Enables the generation of html and man page documentation') - - #depends_on('ncurses', when='+ncurses') - #depends_on('qt', when='+qt') - #depends_on('python@2.7.11:', when='+doc') - #depends_on('py-sphinx', when='+doc') - - #def url_for_version(self, version): - # """Handle CMake's version-based custom URLs.""" - # return 'https://cmake.org/files/v%s/cmake-%s.tar.gz' % (version.up_to(2), version) - - def install(self, spec, prefix): - options = ['--prefix=%s' % prefix] - configure(*options) - make() - make('install') diff --git a/var/spack/repos/builtin/packages/apr/package.py b/var/spack/repos/builtin/packages/apr/package.py new file mode 100644 index 0000000000..8a440766ec --- /dev/null +++ b/var/spack/repos/builtin/packages/apr/package.py @@ -0,0 +1,38 @@ +############################################################################## +# Copyright (c) 2013, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License (as published by +# the Free Software Foundation) version 2.1 dated February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program; if not, write to the Free Software Foundation, +# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + +class Apr(Package): + """Apache portable runtime.""" + homepage = 'https://apr.apache.org/' + url = 'http://archive.apache.org/dist/apr/apr-1.5.2.tar.gz' + + version('1.5.2', '98492e965963f852ab29f9e61b2ad700') + + def install(self, spec, prefix): + options = ['--prefix=%s' % prefix] + configure(*options) + make() + make('install') diff --git a/var/spack/repos/builtin/packages/subversion/package.py b/var/spack/repos/builtin/packages/subversion/package.py new file mode 100644 index 0000000000..5db1c3eb92 --- /dev/null +++ b/var/spack/repos/builtin/packages/subversion/package.py @@ -0,0 +1,77 @@ +############################################################################## +# Copyright (c) 2013, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License (as published by +# the Free Software Foundation) version 2.1 dated February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program; if not, write to the Free Software Foundation, +# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * +#import os + +class Subversion(Package): + """Apache Subversion - an open source version control system.""" + homepage = 'https://subversion.apache.org/' + url = 'http://archive.apache.org/dist/subversion/subversion-1.8.13.tar.gz' + + version('1.8.13', '8065b3698d799507fb72dd7926ed32b6') + version('1.9.3', 'a92bcfaec4e5038f82c74a7b5bbd2f46') + + depends_on('apr') + depends_on('apr-util') + depends_on('zlib') + depends_on('sqlite') + + # Optional: We need swig if we want the Perl, Python or Ruby + # bindings. + #depends_on('swig') + #depends_on('python') + #depends_on('perl') + #depends_on('ruby') + + def install(self, spec, prefix): + + # configure, build, install: + # Ref: http://www.linuxfromscratch.org/blfs/view/svn/general/subversion.html + options = ['--prefix=%s' % prefix] + options.append('--with-apr=%s' % spec['apr'].prefix) + options.append('--with-apr-util=%s' % spec['apr-util'].prefix) + options.append('--with-zlib=%s' % spec['zlib'].prefix) + options.append('--with-sqlite=%s' % spec['sqlite'].prefix) + #options.append('--with-swig=%s' % spec['swig'].prefix) + + configure(*options) + make() + make('install') + + # python bindings + #make('swig-py', + # 'swig-pydir=/usr/lib/python2.7/site-packages/libsvn', + # 'swig_pydir_extra=/usr/lib/python2.7/site-packages/svn') + #make('install-swig-py', + # 'swig-pydir=/usr/lib/python2.7/site-packages/libsvn', + # 'swig_pydir_extra=/usr/lib/python2.7/site-packages/svn') + + # perl bindings + #make('swig-pl') + #make('install-swig-pl') + + # ruby bindings + #make('swig-rb') + #make('isntall-swig-rb') diff --git a/var/spack/repos/builtin/packages/subversion/subversion.new/package.py b/var/spack/repos/builtin/packages/subversion/subversion.new/package.py deleted file mode 100644 index b1c3380238..0000000000 --- a/var/spack/repos/builtin/packages/subversion/subversion.new/package.py +++ /dev/null @@ -1,59 +0,0 @@ -############################################################################## -# Copyright (c) 2013, Lawrence Livermore National Security, LLC. -# Produced at the Lawrence Livermore National Laboratory. -# -# This file is part of Spack. -# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. -# LLNL-CODE-647188 -# -# For details, see https://github.com/llnl/spack -# Please also see the LICENSE file for our notice and the LGPL. -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU General Public License (as published by -# the Free Software Foundation) version 2.1 dated February 1999. -# -# This program is distributed in the hope that it will be useful, but -# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and -# conditions of the GNU General Public License for more details. -# -# You should have received a copy of the GNU Lesser General Public License -# along with this program; if not, write to the Free Software Foundation, -# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA -############################################################################## -from spack import * -#import os - -class Subversion(Package): - """Apache Subversion - an open source version control system.""" - homepage = 'https://subversion.apache.org/' - url = 'http://archive.apache.org/dist/subversion/subversion-1.8.13.tar.gz' - - version('1.8.13', '8065b3698d799507fb72dd7926ed32b6') - version('1.9.3', 'a92bcfaec4e5038f82c74a7b5bbd2f46') - - depends_on('apr') - depends_on('apr-util') - depends_on('zlib') - depends_on('sqlite') - #depends_on('swig') - - def install(self, spec, prefix): - - # configure, build, install: - # Ref: http://www.linuxfromscratch.org/blfs/view/svn/general/subversion.html - options = ['--prefix=%s' % prefix] - options.append('--with-apr=%s' % spec['apr'].prefix) - options.append('--with-apr-util=%s' % spec['apr-util'].prefix) - options.append('--with-zlib=%s' % spec['zlib'].prefix) - options.append('--with-sqlite=%s' % spec['sqlite'].prefix) - #options.append('--with-swig=%s' % spec['swig'].prefix) - - configure(*options) - make() - make('install') - #make('swig-py') # python bindings - #make('install-swig-py') - #make('swig-pl') # perl bindings - #make('install-swig-pl') -- cgit v1.2.3-70-g09d2 From a7ceacb991b2a3b0caba8da41a39e045912f9e22 Mon Sep 17 00:00:00 2001 From: "Kelly (KT) Thompson" Date: Wed, 30 Mar 2016 09:47:31 -0600 Subject: + Changes to swig are not needed with this PR. --- var/spack/repos/builtin/packages/swig/package.py | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/swig/package.py b/var/spack/repos/builtin/packages/swig/package.py index de6055e965..8d46c4fe46 100644 --- a/var/spack/repos/builtin/packages/swig/package.py +++ b/var/spack/repos/builtin/packages/swig/package.py @@ -36,14 +36,11 @@ class Swig(Package): homepage = "http://www.swig.org" url = "http://prdownloads.sourceforge.net/swig/swig-3.0.2.tar.gz" - version('3.0.8', 'c96a1d5ecb13d38604d7e92148c73c97') - version('3.0.2', '62f9b0d010cef36a13a010dc530d0d41') - version('2.0.12', 'c3fb0b2d710cc82ed0154b91e43085a4') + version('3.0.2', '62f9b0d010cef36a13a010dc530d0d41') depends_on('pcre') def install(self, spec, prefix): configure("--prefix=%s" % prefix) - make() make("install") -- cgit v1.2.3-70-g09d2 From bc309e42d8f4d5c536ea43dc01a8356bf0aba3f2 Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Wed, 30 Mar 2016 11:00:18 -0500 Subject: New package, py-bottleneck. --- var/spack/repos/builtin/packages/py-bottleneck/package.py | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-bottleneck/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/py-bottleneck/package.py b/var/spack/repos/builtin/packages/py-bottleneck/package.py new file mode 100644 index 0000000000..0aa4208b4d --- /dev/null +++ b/var/spack/repos/builtin/packages/py-bottleneck/package.py @@ -0,0 +1,14 @@ +from spack import * + +class PyBottleneck(Package): + """Bottleneck is a collection of fast NumPy array functions written in Cython.""" + homepage = "https://pypi.python.org/pypi/Bottleneck/1.0.0" + url = "https://pypi.python.org/packages/source/B/Bottleneck/Bottleneck-1.0.0.tar.gz" + + version('1.0.0', '380fa6f275bd24f27e7cf0e0d752f5d2') + + extends('python', ignore=r'bin/f2py$') + depends_on('py-numpy') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) -- cgit v1.2.3-70-g09d2 From 5c95977dccef17a3cceb741d39f94aa075a0a9c4 Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Wed, 30 Mar 2016 11:06:04 -0500 Subject: Added version 15.0.1 --- var/spack/repos/builtin/packages/py-virtualenv/package.py | 1 + 1 file changed, 1 insertion(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/py-virtualenv/package.py b/var/spack/repos/builtin/packages/py-virtualenv/package.py index 037a6fc59f..09303d37b4 100644 --- a/var/spack/repos/builtin/packages/py-virtualenv/package.py +++ b/var/spack/repos/builtin/packages/py-virtualenv/package.py @@ -8,6 +8,7 @@ class PyVirtualenv(Package): version('1.11.6', 'f61cdd983d2c4e6aeabb70b1060d6f49') version('13.0.1', '1ffc011bde6667f0e37ecd976f4934db') + version('15.0.1', '28d76a0d9cbd5dc42046dd14e76a6ecc') extends('python') depends_on('py-setuptools') -- cgit v1.2.3-70-g09d2 From 3b19cc303fae89eed11581d7cdfe2ab8e9d469ef Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Wed, 30 Mar 2016 11:08:28 -0500 Subject: Added version 1.10.0. --- var/spack/repos/builtin/packages/py-six/package.py | 1 + 1 file changed, 1 insertion(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/py-six/package.py b/var/spack/repos/builtin/packages/py-six/package.py index 05c5bd00a9..df277100f7 100644 --- a/var/spack/repos/builtin/packages/py-six/package.py +++ b/var/spack/repos/builtin/packages/py-six/package.py @@ -6,6 +6,7 @@ class PySix(Package): url = "https://pypi.python.org/packages/source/s/six/six-1.9.0.tar.gz" version('1.9.0', '476881ef4012262dfc8adc645ee786c4') + version('1.10.0', '34eed507548117b2ab523ab14b2f8b55') extends('python') depends_on('py-setuptools') -- cgit v1.2.3-70-g09d2 From 9153e03e5ce5bdd5161aa4b493854208040fcf3d Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Wed, 30 Mar 2016 11:09:47 -0500 Subject: Added version 20.5. --- var/spack/repos/builtin/packages/py-setuptools/package.py | 1 + 1 file changed, 1 insertion(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/py-setuptools/package.py b/var/spack/repos/builtin/packages/py-setuptools/package.py index 26c048bfd4..c6d9be1add 100644 --- a/var/spack/repos/builtin/packages/py-setuptools/package.py +++ b/var/spack/repos/builtin/packages/py-setuptools/package.py @@ -9,6 +9,7 @@ class PySetuptools(Package): version('16.0', '0ace0b96233516fc5f7c857d086aa3ad') version('18.1', 'f72e87f34fbf07f299f6cb46256a0b06') version('19.2', '78353b1f80375ca5e088f4b4627ffe03') + version('20.5', 'fadc1e1123ddbe31006e5e43e927362b') extends('python') -- cgit v1.2.3-70-g09d2 From 42729d9cceafaf2382455f9e765cbc261dc41578 Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Wed, 30 Mar 2016 11:10:32 -0500 Subject: Added version 2016.3. --- var/spack/repos/builtin/packages/py-pytz/package.py | 1 + 1 file changed, 1 insertion(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/py-pytz/package.py b/var/spack/repos/builtin/packages/py-pytz/package.py index da6311a784..060cf0cde4 100644 --- a/var/spack/repos/builtin/packages/py-pytz/package.py +++ b/var/spack/repos/builtin/packages/py-pytz/package.py @@ -7,6 +7,7 @@ class PyPytz(Package): version('2014.10', 'eb1cb941a20c5b751352c52486aa1dd7') version('2015.4', '417a47b1c432d90333e42084a605d3d8') + version('2016.3', 'abae92c3301b27bd8a9f56b14f52cb29') extends('python') -- cgit v1.2.3-70-g09d2 From 17075736a0ff4f8f677527664e37d55b39cbfe93 Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Wed, 30 Mar 2016 11:16:11 -0500 Subject: Add version 2.5.2. --- var/spack/repos/builtin/packages/py-dateutil/package.py | 1 + 1 file changed, 1 insertion(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/py-dateutil/package.py b/var/spack/repos/builtin/packages/py-dateutil/package.py index 0a17f2f2d2..b67e91ace6 100644 --- a/var/spack/repos/builtin/packages/py-dateutil/package.py +++ b/var/spack/repos/builtin/packages/py-dateutil/package.py @@ -7,6 +7,7 @@ class PyDateutil(Package): version('2.4.0', '75714163bb96bedd07685cdb2071b8bc') version('2.4.2', '4ef68e1c485b09e9f034e10473e5add2') + version('2.5.2', 'eafe168e8f404bf384514f5116eedbb6') extends('python') depends_on('py-setuptools') -- cgit v1.2.3-70-g09d2 From 8948cb100be21034b7e4bc78b7383fa73005a03a Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Wed, 30 Mar 2016 11:16:35 -0500 Subject: Add version 1.3.7. --- var/spack/repos/builtin/packages/py-nose/package.py | 1 + 1 file changed, 1 insertion(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/py-nose/package.py b/var/spack/repos/builtin/packages/py-nose/package.py index 4fee99098e..c2c2b52e03 100644 --- a/var/spack/repos/builtin/packages/py-nose/package.py +++ b/var/spack/repos/builtin/packages/py-nose/package.py @@ -10,6 +10,7 @@ class PyNose(Package): version('1.3.4', '6ed7169887580ddc9a8e16048d38274d') version('1.3.6', '0ca546d81ca8309080fc80cb389e7a16') + version('1.3.7', '4d3ad0ff07b61373d2cefc89c5d0b20b') extends('python', ignore=r'bin/nosetests.*$') depends_on('py-setuptools') -- cgit v1.2.3-70-g09d2 From f3b353f5f95c21641d4bee274393879e3a068c3c Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Wed, 30 Mar 2016 11:17:24 -0500 Subject: Add 'bin/f2py' to ignore so activation works. --- var/spack/repos/builtin/packages/py-matplotlib/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/py-matplotlib/package.py b/var/spack/repos/builtin/packages/py-matplotlib/package.py index 2167735fb8..45e77dd631 100644 --- a/var/spack/repos/builtin/packages/py-matplotlib/package.py +++ b/var/spack/repos/builtin/packages/py-matplotlib/package.py @@ -12,7 +12,7 @@ class PyMatplotlib(Package): variant('gui', default=False, description='Enable GUI') variant('ipython', default=False, description='Enable ipython support') - extends('python', ignore=r'bin/nosetests.*$|bin/pbr$') + extends('python', ignore=r'bin/nosetests.*$|bin/pbr$|bin/f2py$') depends_on('py-pyside', when='+gui') depends_on('py-ipython', when='+ipython') -- cgit v1.2.3-70-g09d2 From e7ae983b41943939a20ca4964824b166833c282b Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Wed, 30 Mar 2016 11:20:27 -0500 Subject: Added version 2.5. Added 'bin/f2py' to ignore so that activation works. --- var/spack/repos/builtin/packages/py-numexpr/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/py-numexpr/package.py b/var/spack/repos/builtin/packages/py-numexpr/package.py index 89f8a525b1..081a79dec6 100644 --- a/var/spack/repos/builtin/packages/py-numexpr/package.py +++ b/var/spack/repos/builtin/packages/py-numexpr/package.py @@ -7,8 +7,9 @@ class PyNumexpr(Package): url = "https://pypi.python.org/packages/source/n/numexpr/numexpr-2.4.6.tar.gz" version('2.4.6', '17ac6fafc9ea1ce3eb970b9abccb4fbd') + version('2.5', '84f66cced45ba3e30dcf77a937763aaa') - extends('python') + extends('python', ignore=r'bin/f2py$') depends_on('py-numpy') def install(self, spec, prefix): -- cgit v1.2.3-70-g09d2 From 78be85c84f89d861086c04e4fcc4fa70c21d0a5f Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Wed, 30 Mar 2016 11:21:17 -0500 Subject: Added version 1.11.0. --- var/spack/repos/builtin/packages/py-numpy/package.py | 1 + 1 file changed, 1 insertion(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/py-numpy/package.py b/var/spack/repos/builtin/packages/py-numpy/package.py index a08e612df6..40988fb44a 100644 --- a/var/spack/repos/builtin/packages/py-numpy/package.py +++ b/var/spack/repos/builtin/packages/py-numpy/package.py @@ -9,6 +9,7 @@ class PyNumpy(Package): homepage = "http://www.numpy.org/" url = "https://pypi.python.org/packages/source/n/numpy/numpy-1.9.1.tar.gz" + version('1.11.0', 'bc56fb9fc2895aa4961802ffbdb31d0b') version('1.10.4', 'aed294de0aa1ac7bd3f9745f4f1968ad') version('1.9.2', 'a1ed53432dbcd256398898d35bc8e645') version('1.9.1', '78842b73560ec378142665e712ae4ad9') -- cgit v1.2.3-70-g09d2 From 8ae84cfabaf22e52b01911c909b2d2342b75f3d9 Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Wed, 30 Mar 2016 11:21:38 -0500 Subject: This commit updates pandas and fixes dependencies. Added version 0.18.0. Added 'bin/f2py' to ignore so that activation works. Removed unneccessary dependencies on - libdrm - libpciaccess - llvm - mesa Added recommended dependencies from the pandas project site. http://pandas.pydata.org/pandas-docs/stable/install.html - py-numexpr - py-bottleneck The py-bottleneck is a new package that is also in this branch. Removed optional dependencies - py-scipy - py-matplotlib While those are most likely desired to be in the same python stack as pandas they are not required by pandas. --- var/spack/repos/builtin/packages/py-pandas/package.py | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/py-pandas/package.py b/var/spack/repos/builtin/packages/py-pandas/package.py index 5b9997faa9..2320b1f92f 100644 --- a/var/spack/repos/builtin/packages/py-pandas/package.py +++ b/var/spack/repos/builtin/packages/py-pandas/package.py @@ -8,18 +8,15 @@ class PyPandas(Package): version('0.16.0', 'bfe311f05dc0c351f8955fbd1e296e73') version('0.16.1', 'fac4f25748f9610a3e00e765474bdea8') + version('0.18.0', 'f143762cd7a59815e348adf4308d2cf6') - extends('python') + extends('python', ignore=r'bin/f2py$') depends_on('py-dateutil') depends_on('py-numpy') - depends_on('py-matplotlib') - depends_on('py-scipy') depends_on('py-setuptools') depends_on('py-pytz') - depends_on('libdrm') - depends_on('libpciaccess') - depends_on('llvm') - depends_on('mesa') + depends_on('py-numexpr') + depends_on('py-bottleneck') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) -- cgit v1.2.3-70-g09d2 From 9519f3d988d4f83cd3edf9bbdd90080559ba9549 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Wed, 30 Mar 2016 11:46:58 -0500 Subject: Fix MPI-CUDA bug --- var/spack/repos/builtin/packages/cuda/package.py | 11 ++++++----- var/spack/repos/builtin/packages/hoomd-blue/package.py | 13 +++++++++---- 2 files changed, 15 insertions(+), 9 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/cuda/package.py b/var/spack/repos/builtin/packages/cuda/package.py index 547b43d6d2..eca371d05a 100644 --- a/var/spack/repos/builtin/packages/cuda/package.py +++ b/var/spack/repos/builtin/packages/cuda/package.py @@ -16,9 +16,12 @@ class Cuda(Package): see http://software.llnl.gov/spack/mirrors.html""" homepage = "http://www.nvidia.com/object/cuda_home_new.html" - url = "file://%s/cuda_7.5.18_linux.run" % os.getcwd() - version('7.5.18', '4b3bcecf0dfc35928a0898793cf3e4c6', expand=False) + version('7.5.18', '4b3bcecf0dfc35928a0898793cf3e4c6', expand=False, + url="file://%s/cuda_7.5.18_linux.run" % os.getcwd()) + version('6.5.14', '90b1b8f77313600cc294d9271741f4da', expand=False, + url="file://%s/cuda_6.5.14_linux_64.run" % os.getcwd()) + def install(self, spec, prefix): runfile = glob(os.path.join(self.stage.path, 'cuda*.run'))[0] @@ -27,15 +30,13 @@ class Cuda(Package): runfile = which(runfile) # Note: NVIDIA does not officially support many newer versions of compilers. - # For example, on CentOS 6, you must use GCC 4.4.7 or older. - # The --override flag disables these checks. See: + # For example, on CentOS 6, you must use GCC 4.4.7 or older. See: # http://docs.nvidia.com/cuda/cuda-installation-guide-linux/#system-requirements # for details. runfile( '--silent', # disable interactive prompts '--verbose', # create verbose log file - '--override', # ignore compiler checks '--toolkit', # install CUDA Toolkit '--toolkitpath=%s' % prefix ) diff --git a/var/spack/repos/builtin/packages/hoomd-blue/package.py b/var/spack/repos/builtin/packages/hoomd-blue/package.py index 97ce9c0cf0..32fdff9426 100644 --- a/var/spack/repos/builtin/packages/hoomd-blue/package.py +++ b/var/spack/repos/builtin/packages/hoomd-blue/package.py @@ -49,10 +49,14 @@ class HoomdBlue(Package): cmake_args.append('-DENABLE_CUDA=OFF') # CUDA-aware MPI library support - if '+cuda' in spec and '+mpi' in spec: - cmake_args.append('-DENABLE_MPI_CUDA=ON') - else: - cmake_args.append('-DENABLE_MPI_CUDA=OFF') + #if '+cuda' in spec and '+mpi' in spec: + # cmake_args.append('-DENABLE_MPI_CUDA=ON') + #else: + # cmake_args.append('-DENABLE_MPI_CUDA=OFF') + + # There may be a bug in the MPI-CUDA code. See: + # https://groups.google.com/forum/#!msg/hoomd-users/2griTESmc5I/E69s_M5fDwAJ + cmake_args.append('-DENABLE_MPI_CUDA=OFF') # Documentation if '+doc' in spec: @@ -64,4 +68,5 @@ class HoomdBlue(Package): cmake('.', *cmake_args) make() + make("test") make("install") -- cgit v1.2.3-70-g09d2 From b909da759d7b6d0443a97c13ba1c97118acd3e7a Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 30 Mar 2016 19:26:03 +0200 Subject: petsc: remove no longer needed -Qunused-arguments hack --- var/spack/repos/builtin/packages/petsc/package.py | 17 ++++------------- 1 file changed, 4 insertions(+), 13 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py index e9b7c8a732..5c1fc6cc92 100644 --- a/var/spack/repos/builtin/packages/petsc/package.py +++ b/var/spack/repos/builtin/packages/petsc/package.py @@ -71,19 +71,10 @@ class Petsc(Package): errors = ['incompatible variants given'] + errors raise RuntimeError('\n'.join(errors)) else: - if self.compiler.name == "clang": - compiler_opts = [ - '--with-mpi=1', - '--with-cc=%s -Qunused-arguments' % join_path(self.spec['mpi'].prefix.bin, 'mpicc'), # Avoid confusing PETSc config by clang: warning: argument unused during compilation - '--with-cxx=%s -Qunused-arguments' % join_path(self.spec['mpi'].prefix.bin, 'mpic++'), - '--with-fc=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif90'), - '--with-f77=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif77'), - ] - else: - compiler_opts = [ - '--with-mpi=1', - '--with-mpi-dir=%s' % self.spec['mpi'].prefix, - ] + compiler_opts = [ + '--with-mpi=1', + '--with-mpi-dir=%s' % self.spec['mpi'].prefix, + ] return compiler_opts def install(self, spec, prefix): -- cgit v1.2.3-70-g09d2 From 01657e6991197c999180c2fec367fc75e59fba15 Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Wed, 30 Mar 2016 11:41:25 -0700 Subject: Make suite-sparse use spack compilers. --- var/spack/repos/builtin/packages/suite-sparse/package.py | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/suite-sparse/package.py b/var/spack/repos/builtin/packages/suite-sparse/package.py index b57f9967c3..c2196dcec4 100644 --- a/var/spack/repos/builtin/packages/suite-sparse/package.py +++ b/var/spack/repos/builtin/packages/suite-sparse/package.py @@ -23,4 +23,14 @@ class SuiteSparse(Package): # FIXME : this actually uses the current workaround # FIXME : (blas / lapack always provide libblas and liblapack as aliases) - make('install', 'INSTALL=%s' % prefix, 'BLAS=-lblas', 'LAPACK=-llapack') + make('install', 'INSTALL=%s' % prefix, + + # inject Spack compiler wrappers + 'AUTOCC=no', + 'CC=cc', + 'CXX=c++', + 'F77=f77', + + # BLAS arguments require path to libraries + 'BLAS=-lblas', + 'LAPACK=-llapack') -- cgit v1.2.3-70-g09d2 From 5506e89aa9f45b94a7b16a24e24e3c081fdf1e38 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 30 Mar 2016 21:41:23 +0200 Subject: rename variant doxygen to doc --- var/spack/repos/builtin/packages/dealii/package.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py index 32dfb33c6d..7aaf33380e 100644 --- a/var/spack/repos/builtin/packages/dealii/package.py +++ b/var/spack/repos/builtin/packages/dealii/package.py @@ -11,7 +11,7 @@ class Dealii(Package): variant('mpi', default=True, description='Compile with MPI') variant('arpack', default=True, description='Compile with Arpack and PArpack (only with MPI)') - variant('doxygen', default=False, description='Compile with Doxygen documentation') + variant('doc', default=False, description='Compile with documentation') variant('hdf5', default=True, description='Compile with HDF5 (only with MPI)') variant('metis', default=True, description='Compile with Metis') variant('netcdf', default=True, description='Compile with Netcdf (only with MPI)') @@ -36,7 +36,7 @@ class Dealii(Package): # optional dependencies depends_on ("mpi", when="+mpi") depends_on ("arpack-ng+mpi", when='+arpack+mpi') - depends_on ("doxygen", when='+doxygen') + depends_on ("doxygen", when='+doc') depends_on ("hdf5+mpi~cxx", when='+hdf5+mpi') #FIXME NetCDF declares dependency with ~cxx, why? depends_on ("metis", when='+metis') depends_on ("netcdf+mpi", when="+netcdf+mpi") @@ -111,7 +111,7 @@ class Dealii(Package): # doxygen options.extend([ - '-DDEAL_II_COMPONENT_DOCUMENTATION=%s' % ('ON' if '+doxygen' in spec else 'OFF'), + '-DDEAL_II_COMPONENT_DOCUMENTATION=%s' % ('ON' if '+doc' in spec else 'OFF'), ]) -- cgit v1.2.3-70-g09d2 From dbb25bfeed7113cbd6be090df52b97fcc10588e1 Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Wed, 30 Mar 2016 16:17:52 -0400 Subject: ninja: fix installation on OS X The cp -t flag is a GNU-ism. Instead, add a trailing slash to bindir to ensure that it is not treated as a file. --- var/spack/repos/builtin/packages/ninja/package.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/ninja/package.py b/var/spack/repos/builtin/packages/ninja/package.py index 9e6bf4e358..0722dd49a6 100644 --- a/var/spack/repos/builtin/packages/ninja/package.py +++ b/var/spack/repos/builtin/packages/ninja/package.py @@ -16,7 +16,7 @@ class Ninja(Package): cp = which('cp') - bindir = os.path.join(prefix, 'bin') + bindir = os.path.join(prefix, 'bin/') mkdir(bindir) - cp('-a', '-t', bindir, 'ninja') - cp('-ra', 'misc', prefix) + cp('-a', 'ninja', bindir) + cp('-a', 'misc', prefix) -- cgit v1.2.3-70-g09d2 From d1a3adfcf09fb489acce9d29b2f9494df5f5d848 Mon Sep 17 00:00:00 2001 From: "Kelly (KT) Thompson" Date: Wed, 30 Mar 2016 14:25:44 -0600 Subject: + Make --disable-perl the default configure option. --- var/spack/repos/builtin/packages/graphviz/package.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/graphviz/package.py b/var/spack/repos/builtin/packages/graphviz/package.py index 84bd696af2..a45cd8743e 100644 --- a/var/spack/repos/builtin/packages/graphviz/package.py +++ b/var/spack/repos/builtin/packages/graphviz/package.py @@ -7,7 +7,11 @@ class Graphviz(Package): version('2.38.0', '5b6a829b2ac94efcd5fa3c223ed6d3ae') - variant('perl', default=True, description='Disable if you have problems with the optional script language bindings') + # By default disable optional Perl language support to prevent build issues + # related to missing Perl packages. If spack begins support for Perl in the + # future, this package can be updated to depend_on('perl') and the + # ncecessary devel packages. + variant('perl', default=False, description='Disable if you have problems with the optional script language bindings') parallel = False @@ -17,7 +21,7 @@ class Graphviz(Package): def install(self, spec, prefix): options = ['--prefix=%s' % prefix] - if '~perl' in spec: + if not '+perl' in spec: options.append('--disable-perl') configure(*options) -- cgit v1.2.3-70-g09d2 From 4ab362ae17da96db2a5fb7bacb3035824817c15d Mon Sep 17 00:00:00 2001 From: "Kelly (KT) Thompson" Date: Wed, 30 Mar 2016 14:27:23 -0600 Subject: + Fix variant description. --- var/spack/repos/builtin/packages/graphviz/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/graphviz/package.py b/var/spack/repos/builtin/packages/graphviz/package.py index a45cd8743e..ecf92620d4 100644 --- a/var/spack/repos/builtin/packages/graphviz/package.py +++ b/var/spack/repos/builtin/packages/graphviz/package.py @@ -11,7 +11,7 @@ class Graphviz(Package): # related to missing Perl packages. If spack begins support for Perl in the # future, this package can be updated to depend_on('perl') and the # ncecessary devel packages. - variant('perl', default=False, description='Disable if you have problems with the optional script language bindings') + variant('perl', default=False, description='Enable if you need the optional Perl language bindings.') parallel = False -- cgit v1.2.3-70-g09d2 From f1a0619821fc4c4aaa0a13b114ecaf8ca35b1ce9 Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Wed, 30 Mar 2016 17:19:29 -0400 Subject: mpich: disable fortran without a fortran compiler --- var/spack/repos/builtin/packages/mpich/package.py | 3 +++ 1 file changed, 3 insertions(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py index b20dc8dd60..2d7955e08d 100644 --- a/var/spack/repos/builtin/packages/mpich/package.py +++ b/var/spack/repos/builtin/packages/mpich/package.py @@ -78,6 +78,9 @@ class Mpich(Package): if not self.compiler.fc: config_args.append("--disable-fc") + if not self.compiler.fc and not self.compiler.f77: + config_args.append("--disable-fortran") + configure(*config_args) make() make("install") -- cgit v1.2.3-70-g09d2 From 2ad5d2ea2a280dd81a254458fcfb465073aef8da Mon Sep 17 00:00:00 2001 From: "Kelly (KT) Thompson" Date: Wed, 30 Mar 2016 15:40:04 -0600 Subject: + For darwin, add a dependency on gettext. This change was recommended in the discussion for PR#601. --- var/spack/repos/builtin/packages/numdiff/package.py | 3 +++ 1 file changed, 3 insertions(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/numdiff/package.py b/var/spack/repos/builtin/packages/numdiff/package.py index a51f6206cf..e72c60fadb 100644 --- a/var/spack/repos/builtin/packages/numdiff/package.py +++ b/var/spack/repos/builtin/packages/numdiff/package.py @@ -23,6 +23,7 @@ # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * +import sys class Numdiff(Package): """Numdiff is a little program that can be used to compare putatively @@ -34,6 +35,8 @@ class Numdiff(Package): version('5.8.1', 'a295eb391f6cb1578209fc6b4f9d994e') + depends_on('gettext', sys.platform=='darwin') + def install(self, spec, prefix): options = ['--prefix=%s' % prefix] configure(*options) -- cgit v1.2.3-70-g09d2 From a364ab0d0f5ac226ba9d5a519f2da8ab7a09a846 Mon Sep 17 00:00:00 2001 From: "Kelly (KT) Thompson" Date: Wed, 30 Mar 2016 17:12:32 -0600 Subject: libpng depends on zlib. --- var/spack/repos/builtin/packages/libpng/package.py | 2 ++ 1 file changed, 2 insertions(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/libpng/package.py b/var/spack/repos/builtin/packages/libpng/package.py index e02b08663e..73c8c62341 100644 --- a/var/spack/repos/builtin/packages/libpng/package.py +++ b/var/spack/repos/builtin/packages/libpng/package.py @@ -9,6 +9,8 @@ class Libpng(Package): version('1.6.15', '829a256f3de9307731d4f52dc071916d') version('1.6.14', '2101b3de1d5f348925990f9aa8405660') + depends_on('zlib') + def install(self, spec, prefix): configure("--prefix=%s" % prefix) make() -- cgit v1.2.3-70-g09d2 From a88c15e1010ccadd2f81de9edac48b140d70f9f1 Mon Sep 17 00:00:00 2001 From: "Kelly (KT) Thompson" Date: Wed, 30 Mar 2016 21:18:04 -0600 Subject: + libdrm depends_on libpciaccess. Use spack provided libpciaccess. --- var/spack/repos/builtin/packages/libdrm/package.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/libdrm/package.py b/var/spack/repos/builtin/packages/libdrm/package.py index 00736b7811..d5d779f796 100644 --- a/var/spack/repos/builtin/packages/libdrm/package.py +++ b/var/spack/repos/builtin/packages/libdrm/package.py @@ -2,7 +2,7 @@ from spack import * class Libdrm(Package): """A userspace library for accessing the DRM, direct - rendering manager, on Linux, BSD and other operating + rendering manager, on Linux, BSD and other operating systems that support the ioctl interface.""" homepage = "http://dri.freedesktop.org/libdrm/" # no real website... @@ -11,6 +11,8 @@ class Libdrm(Package): version('2.4.59', '105ac7af1afcd742d402ca7b4eb168b6') version('2.4.33', '86e4e3debe7087d5404461e0032231c8') + depends_on('libpciaccess') + def install(self, spec, prefix): configure("--prefix=%s" % prefix) -- cgit v1.2.3-70-g09d2 From 44b89474453bf80fd603eb5ea5b629b0d9dff123 Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Wed, 30 Mar 2016 23:33:57 -0700 Subject: arpack-ng needs an extra libtoolize to build. --- var/spack/repos/builtin/packages/arpack-ng/package.py | 7 +++++++ 1 file changed, 7 insertions(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/arpack-ng/package.py b/var/spack/repos/builtin/packages/arpack-ng/package.py index dd86b17a53..6b152f7863 100644 --- a/var/spack/repos/builtin/packages/arpack-ng/package.py +++ b/var/spack/repos/builtin/packages/arpack-ng/package.py @@ -41,10 +41,17 @@ class ArpackNg(Package): depends_on('blas') depends_on('lapack') + depends_on('automake') + depends_on('autoconf') + depends_on('libtool@2.4.2:') + depends_on('mpi', when='+mpi') def install(self, spec, prefix): # Apparently autotools are not bootstrapped + # TODO: switch to use the CMake build in the next version + # rather than bootstrapping. + which('libtoolize')() bootstrap = Executable('./bootstrap') options = ['--prefix=%s' % prefix] -- cgit v1.2.3-70-g09d2 From 397e0d1368d8f6077cb7ea59ee953b993ef3d244 Mon Sep 17 00:00:00 2001 From: Mayeul d'Avezac Date: Thu, 31 Mar 2016 10:12:20 +0100 Subject: Fixes #454 in a simpler way than 34a8f0c Rather than mess with the environment, have espresso install into the right directory (prefix/bin). --- var/spack/repos/builtin/packages/espresso/package.py | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/espresso/package.py b/var/spack/repos/builtin/packages/espresso/package.py index 59f362ab46..167bb38e38 100644 --- a/var/spack/repos/builtin/packages/espresso/package.py +++ b/var/spack/repos/builtin/packages/espresso/package.py @@ -24,7 +24,7 @@ class Espresso(Package): depends_on('fftw~mpi', when='~mpi') depends_on('fftw+mpi', when='+mpi') depends_on('scalapack', when='+scalapack+mpi') # TODO : + mpi needed to avoid false dependencies installation - + def check_variants(self, spec): error = 'you cannot ask for \'+{variant}\' when \'+mpi\' is not active' if '+scalapack' in spec and '~mpi' in spec: @@ -32,14 +32,10 @@ class Espresso(Package): if '+elpa' in spec and ('~mpi' in spec or '~scalapack' in spec): raise RuntimeError(error.format(variant='elpa')) - def setup_environment(self, spack_env, run_env): - # Espresso copies every executable in prefix without creating sub-folders - run_env.prepend_path('PATH', self.prefix) - def install(self, spec, prefix): self.check_variants(spec) - options = ['-prefix=%s' % prefix] + options = ['-prefix=%s' % prefix.bin] if '+mpi' in spec: options.append('--enable-parallel') -- cgit v1.2.3-70-g09d2 From 7430f9142fc3fc590232a21a193321be9de33df7 Mon Sep 17 00:00:00 2001 From: Mayeul d'Avezac Date: Thu, 31 Mar 2016 10:16:40 +0100 Subject: Can install espresso on OS/X Espresso uses unix utility `find dir -name \*.x` to determine the executable to install. On OS/X, it also finds a bunch of debug symbols associated with the exectuble. These files have the same name, but are in a different directory. So the install process is done by hand in the package.py file, for OS/X. --- var/spack/repos/builtin/packages/espresso/package.py | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/espresso/package.py b/var/spack/repos/builtin/packages/espresso/package.py index 167bb38e38..0dad57a9f6 100644 --- a/var/spack/repos/builtin/packages/espresso/package.py +++ b/var/spack/repos/builtin/packages/espresso/package.py @@ -33,6 +33,7 @@ class Espresso(Package): raise RuntimeError(error.format(variant='elpa')) def install(self, spec, prefix): + from glob import glob self.check_variants(spec) options = ['-prefix=%s' % prefix.bin] @@ -61,5 +62,11 @@ class Espresso(Package): configure(*options) make('all') - make('install') + + if spec.architecture.startswith('darwin'): + mkdirp(prefix.bin) + for filename in glob("bin/*.x"): + install(filename, prefix.bin) + else: + make('install') -- cgit v1.2.3-70-g09d2 From 6d0b4a28abf8216ed141dac80a6779f6a51f03f1 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Thu, 31 Mar 2016 09:39:37 +0200 Subject: oce: fix bugs related to NULL pointers and compiler optimisation --- var/spack/repos/builtin/packages/dealii/package.py | 3 +- var/spack/repos/builtin/packages/oce/null.patch | 482 +++++++++++++++++++++ var/spack/repos/builtin/packages/oce/package.py | 22 +- 3 files changed, 502 insertions(+), 5 deletions(-) create mode 100644 var/spack/repos/builtin/packages/oce/null.patch (limited to 'var') diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py index 7aaf33380e..0b76db3827 100644 --- a/var/spack/repos/builtin/packages/dealii/package.py +++ b/var/spack/repos/builtin/packages/dealii/package.py @@ -235,5 +235,4 @@ class Dealii(Package): if 'oce' in spec: cmake('.') make('release') - if sys.platform != 'darwin': #FIXME - make('run',parallel=False) + make('run',parallel=False) diff --git a/var/spack/repos/builtin/packages/oce/null.patch b/var/spack/repos/builtin/packages/oce/null.patch new file mode 100644 index 0000000000..42a3f0e44f --- /dev/null +++ b/var/spack/repos/builtin/packages/oce/null.patch @@ -0,0 +1,482 @@ +From 61cb965b9ffeca419005bc15e635e67589c421dd Mon Sep 17 00:00:00 2001 +From: Martin Siggel +Date: Thu, 28 Jan 2016 19:05:00 +0100 +Subject: [PATCH] Workaround clang optimizations for null references + +OCCT/OCE includes some evil code that uses NULL references, +which are normally not possible. Clang removes code in +branches like if(&myNullRef==NULL) as it assumes this can +never be true. This fix was inspired from the mantis issue +http://tracker.dev.opencascade.org/view.php?id=26042. This +code will be fixed in OCCT 7, but we might require the fix +for earlier releases as well. + +Fixes issue #576 +--- + inc/PLib.hxx | 2 +- + src/BSplCLib/BSplCLib.cxx | 16 ++++++------- + src/BSplCLib/BSplCLib_2.cxx | 6 ++--- + src/BSplCLib/BSplCLib_CurveComputation.gxx | 26 ++++++++++----------- + src/BSplSLib/BSplSLib.cxx | 36 +++++++++++++++--------------- + src/BSplSLib/BSplSLib_BzSyntaxes.cxx | 2 +- + src/PLib/PLib.cxx | 10 ++++----- + 7 files changed, 49 insertions(+), 49 deletions(-) + +diff --git a/inc/PLib.hxx b/inc/PLib.hxx +index 7513234..52b1f84 100644 +--- a/inc/PLib.hxx ++++ b/inc/PLib.hxx +@@ -343,6 +343,6 @@ friend class PLib_DoubleJacobiPolynomial; + + + +- ++#define IS_NULL_REF(ref) ((reinterpret_cast(&ref) & 0xFFFFFF) == 0) + + #endif // _PLib_HeaderFile +diff --git a/src/BSplCLib/BSplCLib.cxx b/src/BSplCLib/BSplCLib.cxx +index 683e4ab..2a2d9ea 100644 +--- a/src/BSplCLib/BSplCLib.cxx ++++ b/src/BSplCLib/BSplCLib.cxx +@@ -298,7 +298,7 @@ void BSplCLib::LocateParameter + Standard_Real& NewU) + { + Standard_Integer first,last; +- if (&Mults) { ++ if (!IS_NULL_REF(Mults)) { + if (Periodic) { + first = Knots.Lower(); + last = Knots.Upper(); +@@ -1434,7 +1434,7 @@ void BSplCLib::BuildKnots(const Standard_Integer Degree, + const Standard_Real * pkn = &Knots(KLower); + pkn -= KLower; + Standard_Real *knot = &LK; +- if (&Mults == NULL) { ++ if (IS_NULL_REF(Mults)) { + switch (Degree) { + case 1 : { + Standard_Integer j = Index ; +@@ -1672,7 +1672,7 @@ Standard_Boolean BSplCLib::PrepareInsertKnots + const Standard_Real Tolerance, + const Standard_Boolean Add) + { +- Standard_Boolean addflat = &AddMults == NULL; ++ Standard_Boolean addflat = IS_NULL_REF(AddMults); + + Standard_Integer first,last; + if (Periodic) { +@@ -1856,7 +1856,7 @@ void BSplCLib::InsertKnots + const Standard_Real Tolerance, + const Standard_Boolean Add) + { +- Standard_Boolean addflat = &AddMults == NULL; ++ Standard_Boolean addflat = IS_NULL_REF(AddMults); + + Standard_Integer i,k,mult,firstmult; + Standard_Integer index,kn,curnk,curk; +@@ -3902,7 +3902,7 @@ void BSplCLib::Resolution( Standard_Real& Poles, + num_poles = FlatKnots.Length() - Deg1; + switch (ArrayDimension) { + case 2 : { +- if (&Weights != NULL) { ++ if (!IS_NULL_REF(Weights)) { + const Standard_Real * WG = &Weights(Weights.Lower()); + min_weights = WG[0]; + +@@ -3970,7 +3970,7 @@ void BSplCLib::Resolution( Standard_Real& Poles, + break; + } + case 3 : { +- if (&Weights != NULL) { ++ if (!IS_NULL_REF(Weights)) { + const Standard_Real * WG = &Weights(Weights.Lower()); + min_weights = WG[0]; + +@@ -4047,7 +4047,7 @@ void BSplCLib::Resolution( Standard_Real& Poles, + break; + } + case 4 : { +- if (&Weights != NULL) { ++ if (!IS_NULL_REF(Weights)) { + const Standard_Real * WG = &Weights(Weights.Lower()); + min_weights = WG[0]; + +@@ -4134,7 +4134,7 @@ void BSplCLib::Resolution( Standard_Real& Poles, + } + default : { + Standard_Integer kk; +- if (&Weights != NULL) { ++ if (!IS_NULL_REF(Weights)) { + const Standard_Real * WG = &Weights(Weights.Lower()); + min_weights = WG[0]; + +diff --git a/src/BSplCLib/BSplCLib_2.cxx b/src/BSplCLib/BSplCLib_2.cxx +index 35c4639..653b7cd 100644 +--- a/src/BSplCLib/BSplCLib_2.cxx ++++ b/src/BSplCLib/BSplCLib_2.cxx +@@ -70,7 +70,7 @@ void BSplCLib::BuildEval(const Standard_Integer Degree, + Standard_Integer i; + Standard_Integer ip = PLower + Index - 1; + Standard_Real w, *pole = &LP; +- if (&Weights == NULL) { ++ if (IS_NULL_REF(Weights)) { + + for (i = 0; i <= Degree; i++) { + ip++; +@@ -115,13 +115,13 @@ static void PrepareEval + + // make the knots + BSplCLib::BuildKnots(Degree,index,Periodic,Knots,Mults,*dc.knots); +- if (&Mults == NULL) ++ if (IS_NULL_REF(Mults)) + index -= Knots.Lower() + Degree; + else + index = BSplCLib::PoleIndex(Degree,index,Periodic,Mults); + + // check truly rational +- rational = (&Weights != NULL); ++ rational = (!IS_NULL_REF(Weights)); + if (rational) { + Standard_Integer WLower = Weights.Lower() + index; + rational = BSplCLib::IsRational(Weights, WLower, WLower + Degree); +diff --git a/src/BSplCLib/BSplCLib_CurveComputation.gxx b/src/BSplCLib/BSplCLib_CurveComputation.gxx +index e71b4e0..9d42643 100644 +--- a/src/BSplCLib/BSplCLib_CurveComputation.gxx ++++ b/src/BSplCLib/BSplCLib_CurveComputation.gxx +@@ -92,7 +92,7 @@ Standard_Boolean BSplCLib::RemoveKnot + TColStd_Array1OfInteger& NewMults, + const Standard_Real Tolerance) + { +- Standard_Boolean rational = &Weights != NULL; ++ Standard_Boolean rational = !IS_NULL_REF(Weights); + Standard_Integer dim; + dim = Dimension_gen; + if (rational) dim++; +@@ -133,7 +133,7 @@ void BSplCLib::InsertKnots + const Standard_Real Epsilon, + const Standard_Boolean Add) + { +- Standard_Boolean rational = &Weights != NULL; ++ Standard_Boolean rational = !IS_NULL_REF(Weights); + Standard_Integer dim; + dim = Dimension_gen; + if (rational) dim++; +@@ -222,7 +222,7 @@ void BSplCLib::IncreaseDegree + TColStd_Array1OfReal& NewKnots, + TColStd_Array1OfInteger& NewMults) + { +- Standard_Boolean rational = &Weights != NULL; ++ Standard_Boolean rational = !IS_NULL_REF(Weights); + Standard_Integer dim; + dim = Dimension_gen; + if (rational) dim++; +@@ -256,7 +256,7 @@ void BSplCLib::Unperiodize + Array1OfPoints& NewPoles, + TColStd_Array1OfReal& NewWeights) + { +- Standard_Boolean rational = &Weights != NULL; ++ Standard_Boolean rational = !IS_NULL_REF(Weights); + Standard_Integer dim; + dim = Dimension_gen; + if (rational) dim++; +@@ -292,7 +292,7 @@ void BSplCLib::Trimming(const Standard_Integer Degree, + Array1OfPoints& NewPoles, + TColStd_Array1OfReal& NewWeights) + { +- Standard_Boolean rational = &Weights != NULL; ++ Standard_Boolean rational = !IS_NULL_REF(Weights); + Standard_Integer dim; + dim = Dimension_gen; + if (rational) dim++; +@@ -339,7 +339,7 @@ void BSplCLib::BuildEval(const Standard_Integer Degree, + Standard_Integer PUpper = Poles.Upper(); + Standard_Integer i; + Standard_Integer ip = PLower + Index - 1; +- if (&Weights == NULL) { ++ if (IS_NULL_REF(Weights)) { + for (i = 0; i <= Degree; i++) { + ip++; + if (ip > PUpper) ip = PLower; +@@ -384,13 +384,13 @@ static void PrepareEval + + // make the knots + BSplCLib::BuildKnots(Degree,index,Periodic,Knots,Mults,*dc.knots); +- if (&Mults == NULL) ++ if (IS_NULL_REF(Mults)) + index -= Knots.Lower() + Degree; + else + index = BSplCLib::PoleIndex(Degree,index,Periodic,Mults); + + // check truly rational +- rational = (&Weights != NULL); ++ rational = (!IS_NULL_REF(Weights)); + if (rational) { + Standard_Integer WLower = Weights.Lower() + index; + rational = BSplCLib::IsRational(Weights, WLower, WLower + Degree); +@@ -741,7 +741,7 @@ void BSplCLib::CacheD0(const Standard_Real Parameter, + Degree * Dimension_gen, + PArray[0], + myPoint[0]) ; +- if (&WeightsArray != NULL) { ++ if (!IS_NULL_REF(WeightsArray)) { + Standard_Real * + WArray = (Standard_Real *) &WeightsArray(WeightsArray.Lower()) ; + PLib::NoDerivativeEvalPolynomial(NewParameter, +@@ -798,7 +798,7 @@ void BSplCLib::CacheD1(const Standard_Real Parameter, + + ModifyCoords (LocalPDerivatives + Dimension_gen, /= SpanLenght); + +- if (&WeightsArray != NULL) { ++ if (!IS_NULL_REF(WeightsArray)) { + Standard_Real * + WArray = (Standard_Real *) &WeightsArray(WeightsArray.Lower()) ; + PLib::EvalPolynomial(NewParameter, +@@ -878,7 +878,7 @@ void BSplCLib::CacheD2(const Standard_Real Parameter, + Index += Dimension_gen; + } + +- if (&WeightsArray != NULL) { ++ if (!IS_NULL_REF(WeightsArray)) { + Standard_Real * + WArray = (Standard_Real *) &WeightsArray(WeightsArray.Lower()) ; + +@@ -971,7 +971,7 @@ void BSplCLib::CacheD3(const Standard_Real Parameter, + Index += Dimension_gen; + } + +- if (&WeightsArray != NULL) { ++ if (!IS_NULL_REF(WeightsArray)) { + Standard_Real * + WArray = (Standard_Real *) &WeightsArray(WeightsArray.Lower()) ; + +@@ -1081,7 +1081,7 @@ void BSplCLib::BuildCache + LocalValue *= SpanDomain / (Standard_Real) ii ; + } + +- if (&Weights != NULL) { ++ if (!IS_NULL_REF(Weights)) { + for (ii = 1 ; ii <= Degree + 1 ; ii++) + CacheWeights(ii) = 0.0e0 ; + CacheWeights(1) = 1.0e0 ; +diff --git a/src/BSplSLib/BSplSLib.cxx b/src/BSplSLib/BSplSLib.cxx +index 5ad633c..07040d5 100644 +--- a/src/BSplSLib/BSplSLib.cxx ++++ b/src/BSplSLib/BSplSLib.cxx +@@ -309,12 +309,12 @@ static Standard_Boolean PrepareEval (const Standard_Real U, + BSplCLib::BuildKnots(UDegree,uindex,UPer,UKnots,UMults,*dc.knots1); + BSplCLib::BuildKnots(VDegree,vindex,VPer,VKnots,VMults,*dc.knots2); + +- if (&UMults == NULL) ++ if (IS_NULL_REF(UMults)) + uindex -= UKLower + UDegree; + else + uindex = BSplCLib::PoleIndex(UDegree,uindex,UPer,UMults); + +- if (&VMults == NULL) ++ if (IS_NULL_REF(VMults)) + vindex -= VKLower + VDegree; + else + vindex = BSplCLib::PoleIndex(VDegree,vindex,VPer,VMults); +@@ -460,12 +460,12 @@ static Standard_Boolean PrepareEval (const Standard_Real U, + BSplCLib::BuildKnots(UDegree,uindex,UPer,UKnots,UMults,*dc.knots2); + BSplCLib::BuildKnots(VDegree,vindex,VPer,VKnots,VMults,*dc.knots1); + +- if (&UMults == NULL) ++ if (IS_NULL_REF(UMults)) + uindex -= UKLower + UDegree; + else + uindex = BSplCLib::PoleIndex(UDegree,uindex,UPer,UMults); + +- if (&VMults == NULL) ++ if (IS_NULL_REF(VMults)) + vindex -= VKLower + VDegree; + else + vindex = BSplCLib::PoleIndex(VDegree,vindex,VPer,VMults); +@@ -1299,7 +1299,7 @@ void BSplSLib::Iso(const Standard_Real Param, + { + Standard_Integer index = 0; + Standard_Real u = Param; +- Standard_Boolean rational = &Weights != NULL; ++ Standard_Boolean rational = !IS_NULL_REF(Weights); + Standard_Integer dim = rational ? 4 : 3; + + // compute local knots +@@ -1307,7 +1307,7 @@ void BSplSLib::Iso(const Standard_Real Param, + NCollection_LocalArray locknots1 (2*Degree); + BSplCLib::LocateParameter(Degree,Knots,Mults,u,Periodic,index,u); + BSplCLib::BuildKnots(Degree,index,Periodic,Knots,Mults,*locknots1); +- if (&Mults == NULL) ++ if (IS_NULL_REF(Mults)) + index -= Knots.Lower() + Degree; + else + index = BSplCLib::PoleIndex(Degree,index,Periodic,Mults); +@@ -1381,7 +1381,7 @@ void BSplSLib::Iso(const Standard_Real Param, + } + + // if the input is not rational but weights are wanted +- if (!rational && (&CWeights != NULL)) { ++ if (!rational && (!IS_NULL_REF(CWeights))) { + + for (i = CWeights.Lower(); i <= CWeights.Upper(); i++) + CWeights(i) = 1.; +@@ -1741,7 +1741,7 @@ void BSplSLib::InsertKnots(const Standard_Boolean UDirection, + const Standard_Real Epsilon, + const Standard_Boolean Add ) + { +- Standard_Boolean rational = &Weights != NULL; ++ Standard_Boolean rational = !IS_NULL_REF(Weights); + Standard_Integer dim = 3; + if (rational) dim++; + +@@ -1787,7 +1787,7 @@ Standard_Boolean BSplSLib::RemoveKnot + TColStd_Array1OfInteger& NewMults, + const Standard_Real Tolerance) + { +- Standard_Boolean rational = &Weights != NULL; ++ Standard_Boolean rational = !IS_NULL_REF(Weights); + Standard_Integer dim = 3; + if (rational) dim++; + +@@ -1834,7 +1834,7 @@ void BSplSLib::IncreaseDegree + TColStd_Array1OfReal& NewKnots, + TColStd_Array1OfInteger& NewMults) + { +- Standard_Boolean rational = &Weights != NULL; ++ Standard_Boolean rational = !IS_NULL_REF(Weights); + Standard_Integer dim = 3; + if (rational) dim++; + +@@ -1876,7 +1876,7 @@ void BSplSLib::Unperiodize + TColgp_Array2OfPnt& NewPoles, + TColStd_Array2OfReal& NewWeights) + { +- Standard_Boolean rational = &Weights != NULL; ++ Standard_Boolean rational = !IS_NULL_REF(Weights); + Standard_Integer dim = 3; + if (rational) dim++; + +@@ -1929,7 +1929,7 @@ void BSplSLib::BuildCache + Standard_Boolean rational,rational_u,rational_v,flag_u_or_v; + Standard_Integer kk,d1,d1p1,d2,d2p1,ii,jj,iii,jjj,Index; + Standard_Real u1,min_degree_domain,max_degree_domain,f,factor[2],u2; +- if (&Weights != NULL) ++ if (!IS_NULL_REF(Weights)) + rational_u = rational_v = Standard_True; + else + rational_u = rational_v = Standard_False; +@@ -2025,7 +2025,7 @@ void BSplSLib::BuildCache + } + factor[0] *= max_degree_domain / (Standard_Real) (iii) ; + } +- if (&Weights != NULL) { ++ if (!IS_NULL_REF(Weights)) { + // + // means that PrepareEval did found out that the surface was + // locally polynomial but since the surface is constructed +@@ -2110,7 +2110,7 @@ void BSplSLib::CacheD0(const Standard_Real UParameter, + (min_degree << 1) + min_degree, + locpoles[0], + myPoint[0]) ; +- if (&WeightsArray != NULL) { ++ if (!IS_NULL_REF(WeightsArray)) { + dimension = min_degree + 1 ; + Standard_Real * + WArray = (Standard_Real *) +@@ -2190,7 +2190,7 @@ void BSplSLib::CacheD1(const Standard_Real UParameter, + // the coefficients + // + // +- if (&WeightsArray != NULL) { ++ if (!IS_NULL_REF(WeightsArray)) { + + local_poles_array [0][0][0] = 0.0e0 ; + local_poles_array [0][0][1] = 0.0e0 ; +@@ -2275,7 +2275,7 @@ void BSplSLib::CacheD1(const Standard_Real UParameter, + locpoles[dimension], + local_poles_array[1][0][0]) ; + +- if (&WeightsArray != NULL) { ++ if (!IS_NULL_REF(WeightsArray)) { + dimension = min_degree + 1 ; + Standard_Real * + WArray = (Standard_Real *) +@@ -2435,7 +2435,7 @@ void BSplSLib::CacheD2(const Standard_Real UParameter, + // the coefficients + // + // +- if (&WeightsArray != NULL) { ++ if (!IS_NULL_REF(WeightsArray)) { + + local_poles_and_weights_array[0][0][0] = 0.0e0 ; + local_poles_and_weights_array[0][0][1] = 0.0e0 ; +@@ -2564,7 +2564,7 @@ void BSplSLib::CacheD2(const Standard_Real UParameter, + locpoles[dimension + dimension], + local_poles_array[2][0][0]) ; + +- if (&WeightsArray != NULL) { ++ if (!IS_NULL_REF(WeightsArray)) { + dimension = min_degree + 1 ; + Standard_Real * + WArray = (Standard_Real *) +diff --git a/src/BSplSLib/BSplSLib_BzSyntaxes.cxx b/src/BSplSLib/BSplSLib_BzSyntaxes.cxx +index 0faf6b6..f2c0f74 100644 +--- a/src/BSplSLib/BSplSLib_BzSyntaxes.cxx ++++ b/src/BSplSLib/BSplSLib_BzSyntaxes.cxx +@@ -68,7 +68,7 @@ void BSplSLib::PolesCoefficients (const TColgp_Array2OfPnt& Poles, + biduflatknots,bidvflatknots, + Poles,Weights, + CPoles,CWeights); +- if (&Weights == NULL) { ++ if (IS_NULL_REF(Weights)) { + + for (ii = 1; ii <= uclas; ii++) { + +diff --git a/src/PLib/PLib.cxx b/src/PLib/PLib.cxx +index 23fa302..7ee231f 100644 +--- a/src/PLib/PLib.cxx ++++ b/src/PLib/PLib.cxx +@@ -2427,7 +2427,7 @@ void PLib::CoefficientsPoles (const Standard_Integer dim, + TColStd_Array1OfReal& Poles, + TColStd_Array1OfReal& Weights) + { +- Standard_Boolean rat = &WCoefs != NULL; ++ Standard_Boolean rat = !IS_NULL_REF(WCoefs); + Standard_Integer loc = Coefs.Lower(); + Standard_Integer lop = Poles.Lower(); + Standard_Integer lowc=0; +@@ -2550,7 +2550,7 @@ void PLib::Trimming(const Standard_Real U1, + Standard_Integer indc, indw=0; + Standard_Integer upc = Coefs.Upper() - dim + 1, upw=0; + Standard_Integer len = Coefs.Length()/dim; +- Standard_Boolean rat = &WCoefs != NULL; ++ Standard_Boolean rat = !IS_NULL_REF(WCoefs); + + if (rat) { + if(len != WCoefs.Length()) +@@ -2607,7 +2607,7 @@ void PLib::CoefficientsPoles (const TColgp_Array2OfPnt& Coefs, + TColgp_Array2OfPnt& Poles, + TColStd_Array2OfReal& Weights) + { +- Standard_Boolean rat = (&WCoefs != NULL); ++ Standard_Boolean rat = (!IS_NULL_REF(WCoefs)); + Standard_Integer LowerRow = Poles.LowerRow(); + Standard_Integer UpperRow = Poles.UpperRow(); + Standard_Integer LowerCol = Poles.LowerCol(); +@@ -2701,7 +2701,7 @@ void PLib::UTrimming(const Standard_Real U1, + TColgp_Array2OfPnt& Coeffs, + TColStd_Array2OfReal& WCoeffs) + { +- Standard_Boolean rat = &WCoeffs != NULL; ++ Standard_Boolean rat = !IS_NULL_REF(WCoeffs); + Standard_Integer lr = Coeffs.LowerRow(); + Standard_Integer ur = Coeffs.UpperRow(); + Standard_Integer lc = Coeffs.LowerCol(); +@@ -2735,7 +2735,7 @@ void PLib::VTrimming(const Standard_Real V1, + TColgp_Array2OfPnt& Coeffs, + TColStd_Array2OfReal& WCoeffs) + { +- Standard_Boolean rat = &WCoeffs != NULL; ++ Standard_Boolean rat = !IS_NULL_REF(WCoeffs); + Standard_Integer lr = Coeffs.LowerRow(); + Standard_Integer ur = Coeffs.UpperRow(); + Standard_Integer lc = Coeffs.LowerCol(); \ No newline at end of file diff --git a/var/spack/repos/builtin/packages/oce/package.py b/var/spack/repos/builtin/packages/oce/package.py index 4d5081ac9d..3fe6638e66 100644 --- a/var/spack/repos/builtin/packages/oce/package.py +++ b/var/spack/repos/builtin/packages/oce/package.py @@ -13,9 +13,20 @@ class Oce(Package): version('0.17' , 'f1a89395c4b0d199bea3db62b85f818d') version('0.16.1', '4d591b240c9293e879f50d86a0cb2bb3') version('0.16' , '7a4b4df5a104d75a537e25e7dd387eca') - version('0.15' , '7ec541a1c350ca8a684f74980e48801c') + + variant('tbb', default=True, description='Build with Intel Threading Building Blocks') depends_on('cmake@2.8:') + depends_on('tbb', when='+tbb') + + # There is a bug in OCE which appears with Clang (version?) or GCC 6.0 + # and has to do with compiler optimization, see + # https://github.com/tpaviot/oce/issues/576 + # http://tracker.dev.opencascade.org/view.php?id=26042 + # https://github.com/tpaviot/oce/issues/605 + # https://github.com/tpaviot/oce/commit/61cb965b9ffeca419005bc15e635e67589c421dd.patch + patch('null.patch',when='@0.16:0.17.1') + def install(self, spec, prefix): options = [] @@ -23,12 +34,12 @@ class Oce(Package): options.extend([ '-DOCE_INSTALL_PREFIX=%s' % prefix, '-DOCE_BUILD_SHARED_LIB:BOOL=ON', - '-DOCE_BUILD_TYPE:STRING=Release', + '-DCMAKE_BUILD_TYPE:STRING=Release', '-DOCE_DATAEXCHANGE:BOOL=ON', '-DOCE_DISABLE_X11:BOOL=ON', '-DOCE_DRAW:BOOL=OFF', '-DOCE_MODEL:BOOL=ON', - '-DOCE_MULTITHREAD_LIBRARY:STRING=NONE', # FIXME: add tbb + '-DOCE_MULTITHREAD_LIBRARY:STRING=%s' % ('TBB' if '+tbb' in spec else 'NONE'), '-DOCE_OCAF:BOOL=ON', '-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=OFF', '-DOCE_VISUALISATION:BOOL=OFF', @@ -46,6 +57,11 @@ class Oce(Package): make("install/strip") + # OCE tests build is brocken at least on Darwin. + # Unit tests are linked against libTKernel.10.dylib isntead of /full/path/libTKernel.10.dylib + # see https://github.com/tpaviot/oce/issues/612 + # make("test") + # The shared libraries are not installed correctly on Darwin; correct this if (sys.platform == 'darwin'): fix_darwin_install_name(prefix.lib) -- cgit v1.2.3-70-g09d2 From 0bcfd095362c5d04b9add7ebc882b74fad68f9dd Mon Sep 17 00:00:00 2001 From: Dhanannjay Deo Date: Fri, 25 Mar 2016 13:25:29 -0400 Subject: add: VTK lastest versions --- var/spack/repos/builtin/packages/vtk/package.py | 4 ++++ 1 file changed, 4 insertions(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/vtk/package.py b/var/spack/repos/builtin/packages/vtk/package.py index 4a27a8fedb..aeb03fe0a3 100644 --- a/var/spack/repos/builtin/packages/vtk/package.py +++ b/var/spack/repos/builtin/packages/vtk/package.py @@ -7,6 +7,10 @@ class Vtk(Package): homepage = "http://www.vtk.org" url = "http://www.vtk.org/files/release/6.1/VTK-6.1.0.tar.gz" + version("7.0.0", "5fe35312db5fb2341139b8e4955c367d", url="http://www.vtk.org/files/release/7.0/VTK-7.0.0.tar.gz") + + version("6.3.0", '0231ca4840408e9dd60af48b314c5b6d', url="http://www.vtk.org/files/release/6.3/VTK-6.3.0.tar.gz") + version('6.1.0', '25e4dfb3bad778722dcaec80cd5dab7d') depends_on("qt") -- cgit v1.2.3-70-g09d2 From 123996aad0c58bab7de6f615159b2fd7b44c7369 Mon Sep 17 00:00:00 2001 From: Dhanannjay Deo Date: Thu, 31 Mar 2016 10:29:47 -0400 Subject: Fix build for vtk6.1.0 --- var/spack/repos/builtin/packages/vtk/package.py | 4 ++++ 1 file changed, 4 insertions(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/vtk/package.py b/var/spack/repos/builtin/packages/vtk/package.py index aeb03fe0a3..b29d52d0f0 100644 --- a/var/spack/repos/builtin/packages/vtk/package.py +++ b/var/spack/repos/builtin/packages/vtk/package.py @@ -39,6 +39,10 @@ class Vtk(Package): if spec['qt'].satisfies('@5'): cmake_args.append("-DVTK_QT_VERSION:STRING=5") + if spec.satisfies("@6.1.0"): + cmake_args.append("-DCMAKE_C_FLAGS=-DGLX_GLXEXT_LEGACY") + cmake_args.append("-DCMAKE_CXX_FLAGS=-DGLX_GLXEXT_LEGACY") + cmake(*cmake_args) make() make("install") -- cgit v1.2.3-70-g09d2 From 3b0311a1e484a4f731d1cc6448dc6804410ecb3c Mon Sep 17 00:00:00 2001 From: Dhanannjay Deo Date: Thu, 31 Mar 2016 10:30:32 -0400 Subject: Add variant opengl2, which is ON by default Needed for visit which depends on vtk@6.1.0~opengl2 --- var/spack/repos/builtin/packages/vtk/package.py | 10 ++++++++++ 1 file changed, 10 insertions(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/vtk/package.py b/var/spack/repos/builtin/packages/vtk/package.py index b29d52d0f0..24382af406 100644 --- a/var/spack/repos/builtin/packages/vtk/package.py +++ b/var/spack/repos/builtin/packages/vtk/package.py @@ -15,7 +15,15 @@ class Vtk(Package): depends_on("qt") + # VTK7 defaults to OpenGL2 rendering backend + variant('opengl2', default=True, description='Build with OpenGL instead of OpenGL2 as rendering backend') + def install(self, spec, prefix): + def feature_to_bool(feature, on='ON', off='OFF'): + if feature in spec: + return on + return off + with working_dir('spack-build', create=True): cmake_args = [ "..", @@ -43,6 +51,8 @@ class Vtk(Package): cmake_args.append("-DCMAKE_C_FLAGS=-DGLX_GLXEXT_LEGACY") cmake_args.append("-DCMAKE_CXX_FLAGS=-DGLX_GLXEXT_LEGACY") + cmake_args.append('-DVTK_RENDERING_BACKEND:STRING=%s' % feature_to_bool('+opengl2', 'OpenGL2', 'OpenGL')) + cmake(*cmake_args) make() make("install") -- cgit v1.2.3-70-g09d2 From a0902ad8d8a8c629eb921b8701332385d622bc12 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Thu, 31 Mar 2016 11:04:29 -0500 Subject: Change variant defaults and add comment --- var/spack/repos/builtin/packages/cuda/package.py | 6 +++++- var/spack/repos/builtin/packages/hoomd-blue/package.py | 7 ++++--- 2 files changed, 9 insertions(+), 4 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/cuda/package.py b/var/spack/repos/builtin/packages/cuda/package.py index eca371d05a..ea083d8651 100644 --- a/var/spack/repos/builtin/packages/cuda/package.py +++ b/var/spack/repos/builtin/packages/cuda/package.py @@ -13,7 +13,11 @@ class Cuda(Package): For the Installer Type, select runfile and click Download. Spack will search your current directory for this file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, - see http://software.llnl.gov/spack/mirrors.html""" + see http://software.llnl.gov/spack/mirrors.html + + Note: This package does not currently install the drivers necessary to run + CUDA. These will need to be installed manually. See: + http://docs.nvidia.com/cuda/cuda-getting-started-guide-for-linux for details.""" homepage = "http://www.nvidia.com/object/cuda_home_new.html" diff --git a/var/spack/repos/builtin/packages/hoomd-blue/package.py b/var/spack/repos/builtin/packages/hoomd-blue/package.py index 32fdff9426..d310b7687a 100644 --- a/var/spack/repos/builtin/packages/hoomd-blue/package.py +++ b/var/spack/repos/builtin/packages/hoomd-blue/package.py @@ -16,9 +16,9 @@ class HoomdBlue(Package): version('1.3.3', '1469ef4531dc14b579c0acddbfe6a273') - variant('mpi', default=False, description='Compile with MPI enabled') - variant('cuda', default=False, description='Compile with CUDA Toolkit') - variant('doc', default=False, description='Generate documentation') + variant('mpi', default=True, description='Compile with MPI enabled') + variant('cuda', default=True, description='Compile with CUDA Toolkit') + variant('doc', default=True, description='Generate documentation') extends('python') depends_on('py-numpy') @@ -56,6 +56,7 @@ class HoomdBlue(Package): # There may be a bug in the MPI-CUDA code. See: # https://groups.google.com/forum/#!msg/hoomd-users/2griTESmc5I/E69s_M5fDwAJ + # This prevented "make test" from passing for me. cmake_args.append('-DENABLE_MPI_CUDA=OFF') # Documentation -- cgit v1.2.3-70-g09d2 From 66038ef729b5fb8d2efadc48c87a868370ca23c5 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Thu, 31 Mar 2016 13:34:56 -0500 Subject: Add url_for_version function and gtk variant --- var/spack/repos/builtin/packages/qt/package.py | 70 ++++++++++++++++---------- 1 file changed, 44 insertions(+), 26 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py index d08e8e81e1..ab09469042 100644 --- a/var/spack/repos/builtin/packages/qt/package.py +++ b/var/spack/repos/builtin/packages/qt/package.py @@ -1,41 +1,31 @@ -import os from spack import * import os class Qt(Package): """Qt is a comprehensive cross-platform C++ application framework.""" - homepage = "http://qt.io" - list_url = 'http://download.qt-project.org/official_releases/qt/' - list_depth = 2 - - version('5.4.2', 'fa1c4d819b401b267eb246a543a63ea5', - url='http://download.qt-project.org/official_releases/qt/5.4/5.4.2/single/qt-everywhere-opensource-src-5.4.2.tar.gz') - - version('5.4.0', 'e8654e4b37dd98039ba20da7a53877e6', - url='http://download.qt-project.org/official_releases/qt/5.4/5.4.0/single/qt-everywhere-opensource-src-5.4.0.tar.gz') - - version('5.3.2', 'febb001129927a70174467ecb508a682', - url='http://download.qt.io/archive/qt/5.3/5.3.2/single/qt-everywhere-opensource-src-5.3.2.tar.gz') - - version('5.2.1', 'a78408c887c04c34ce615da690e0b4c8', - url='http://download.qt.io/archive/qt/5.2/5.2.1/single/qt-everywhere-opensource-src-5.2.1.tar.gz') - - version('4.8.6', '2edbe4d6c2eff33ef91732602f3518eb', - url="http://download.qt-project.org/official_releases/qt/4.8/4.8.6/qt-everywhere-opensource-src-4.8.6.tar.gz") + homepage = 'http://qt.io' + url = 'http://download.qt.io/archive/qt/5.5/5.5.1/single/qt-everywhere-opensource-src-5.5.1.tar.gz' - version('3.3.8b', '9f05b4125cfe477cc52c9742c3c09009', - url="http://download.qt.io/archive/qt/3/qt-x11-free-3.3.8b.tar.gz") + version('5.5.1', '59f0216819152b77536cf660b015d784') + version('5.4.2', 'fa1c4d819b401b267eb246a543a63ea5') + version('5.4.0', 'e8654e4b37dd98039ba20da7a53877e6') + version('5.3.2', 'febb001129927a70174467ecb508a682') + version('5.2.1', 'a78408c887c04c34ce615da690e0b4c8') + version('4.8.6', '2edbe4d6c2eff33ef91732602f3518eb') + version('3.3.8b', '9f05b4125cfe477cc52c9742c3c09009') - variant('mesa', default=False, description='depend on mesa') # Add patch for compile issues with qt3 found with use in the OpenSpeedShop project - variant('krellpatch', default=False, description="build with openspeedshop based patch.") + variant('krellpatch', default=False, description="Build with openspeedshop based patch.") + variant('mesa', default=False, description="Depend on mesa.") + variant('gtk', default=False, description="Build with gtkplus.") + patch('qt3krell.patch', when='@3.3.8b+krellpatch') # Use system openssl for security. #depends_on("openssl") depends_on("glib") - depends_on("gtkplus") + depends_on("gtkplus", when='+gtk') depends_on("libxml2") depends_on("zlib") depends_on("dbus", when='@4:') @@ -56,6 +46,34 @@ class Qt(Package): depends_on("libxcb") + def url_for_version(self, version): + url = "http://download.qt.io/archive/qt/" + + if version >= Version('5'): + url += "%s/%s/single/qt-everywhere-opensource-src-%s.tar.gz" % \ + (version.up_to(2), version, version) + elif version >= Version('4.8'): + url += "%s/%s/qt-everywhere-opensource-src-%s.tar.gz" % \ + (version.up_to(2), version, version) + elif version >= Version('4.6'): + url += "%s/qt-everywhere-opensource-src-%s.tar.gz" % \ + (version.up_to(2), version) + elif version >= Version('4.0'): + url += "%s/qt-x11-opensource-src-%s.tar.gz" % \ + (version.up_to(2), version) + elif version >= Version('3'): + url += "%s/qt-x11-free-%s.tar.gz" % \ + (version.up_to(1), version) + elif version >= Version('2.1'): + url += "%s/qt-x11-%s.tar.gz" % \ + (version.up_to(1), version) + else: + url += "%s/qt-%s.tar.gz" % \ + (version.up_to(1), version) + + return url + + def setup_environment(self, spack_env, env): env.set('QTDIR', self.prefix) @@ -88,7 +106,7 @@ class Qt(Package): '-v', '-opensource', '-opengl', - "-release", + '-release', '-shared', '-confirm-license', '-openssl-linked', @@ -97,7 +115,7 @@ class Qt(Package): '-no-openvg', '-no-pch', # NIS is deprecated in more recent glibc - "-no-nis"] + '-no-nis'] # Don't disable all the database drivers, but should # really get them into spack at some point. -- cgit v1.2.3-70-g09d2