diff options
Diffstat (limited to 'var')
77 files changed, 1276 insertions, 78 deletions
diff --git a/var/spack/repos/builtin/packages/LuaJIT/package.py b/var/spack/repos/builtin/packages/LuaJIT/package.py new file mode 100644 index 0000000000..7b2a269212 --- /dev/null +++ b/var/spack/repos/builtin/packages/LuaJIT/package.py @@ -0,0 +1,15 @@ +import os +from spack import * + +class Luajit(Package): + """Flast flexible JITed lua""" + homepage = "http://www.luajit.org" + url = "http://luajit.org/download/LuaJIT-2.0.4.tar.gz" + + version('2.0.4', 'dd9c38307f2223a504cbfb96e477eca0') + + def install(self, spec, prefix): + # Linking with the C++ compiler is a dirty hack to deal with the fact + # that unwinding symbols are not included by libc, this is necessary + # on some platforms for the final link stage to work + make("install", "PREFIX=" + prefix, "TARGET_LD=" + os.environ['CXX']) diff --git a/var/spack/repos/builtin/packages/adol-c/openmp_exam.patch b/var/spack/repos/builtin/packages/adol-c/openmp_exam.patch new file mode 100644 index 0000000000..8e21c72d92 --- /dev/null +++ b/var/spack/repos/builtin/packages/adol-c/openmp_exam.patch @@ -0,0 +1,13 @@ +diff --git a/ADOL-C/examples/additional_examples/openmp_exam/liborpar.cpp b/ADOL-C/examples/additional_examples/openmp_exam/liborpar.cpp +index fc6fc28..14103d2 100644 +--- a/ADOL-C/examples/additional_examples/openmp_exam/liborpar.cpp ++++ b/ADOL-C/examples/additional_examples/openmp_exam/liborpar.cpp +@@ -27,7 +27,7 @@ using namespace std; + #include <ctime> + #include <cmath> + +-#include "adolc.h" ++#include <adolc/adolc.h> + + #ifdef _OPENMP + #include <omp.h> diff --git a/var/spack/repos/builtin/packages/adol-c/package.py b/var/spack/repos/builtin/packages/adol-c/package.py new file mode 100644 index 0000000000..70933542ca --- /dev/null +++ b/var/spack/repos/builtin/packages/adol-c/package.py @@ -0,0 +1,80 @@ +from spack import * +import sys + +class AdolC(Package): + """A package for the automatic differentiation of first and higher derivatives of vector functions in C and C++ programs by operator overloading.""" + homepage = "https://projects.coin-or.org/ADOL-C" + url = "http://www.coin-or.org/download/source/ADOL-C/ADOL-C-2.6.1.tgz" + + version('head', svn='https://projects.coin-or.org/svn/ADOL-C/trunk/') + version('2.6.1', '1032b28427d6e399af4610e78c0f087b') + + variant('doc', default=True, description='Install documentation') + variant('openmp', default=False, description='Enable OpenMP support') + variant('sparse', default=False, description='Enable sparse drivers') + variant('tests', default=True, description='Build all included examples as a test case') + + patch('openmp_exam.patch') + + def install(self, spec, prefix): + make_args = ['--prefix=%s' % prefix] + + # --with-cflags=FLAGS use CFLAGS=FLAGS (default: -O3 -Wall -ansi) + # --with-cxxflags=FLAGS use CXXFLAGS=FLAGS (default: -O3 -Wall) + + if '+openmp' in spec: + if spec.satisfies('%gcc'): + make_args.extend([ + '--with-openmp-flag=-fopenmp' # FIXME: Is this required? -I <path to omp.h> -L <LLVM OpenMP library path> + ]) + else: + raise InstallError("OpenMP flags for compilers other than GCC are not implemented.") + + if '+sparse' in spec: + make_args.extend([ + '--enable-sparse' + ]) + + # We can simply use the bundled examples to check + # whether Adol-C works as expected + if '+tests' in spec: + make_args.extend([ + '--enable-docexa', # Documeted examples + '--enable-addexa' # Additional examples + ]) + if '+openmp' in spec: + make_args.extend([ + '--enable-parexa' # Parallel examples + ]) + + configure(*make_args) + make() + make("install") + + # Copy the config.h file, as some packages might require it + source_directory = self.stage.source_path + config_h = join_path(source_directory,'ADOL-C','src','config.h') + install(config_h, join_path(prefix.include,'adolc')) + + # Install documentation to {prefix}/share + if '+doc' in spec: + install_tree(join_path('ADOL-C','doc'), + join_path(prefix.share,'doc')) + + # Install examples to {prefix}/share + if '+tests' in spec: + install_tree(join_path('ADOL-C','examples'), + join_path(prefix.share,'examples')) + + # Run some examples that don't require user input + # TODO: Check that bundled examples produce the correct results + with working_dir(join_path(source_directory,'ADOL-C','examples')): + Executable('./tapeless_scalar')() + Executable('./tapeless_vector')() + + with working_dir(join_path(source_directory,'ADOL-C','examples','additional_examples')): + Executable('./checkpointing/checkpointing')() + + if '+openmp' in spec: + with working_dir(join_path(source_directory,'ADOL-C','examples','additional_examples')): + Executable('./checkpointing/checkpointing')() diff --git a/var/spack/repos/builtin/packages/antlr/package.py b/var/spack/repos/builtin/packages/antlr/package.py new file mode 100644 index 0000000000..c7c7e3e850 --- /dev/null +++ b/var/spack/repos/builtin/packages/antlr/package.py @@ -0,0 +1,47 @@ +from spack import * + +class Antlr(Package): + + homepage = "http://www.antlr.org" + url = "https://github.com/antlr/antlr/tarball/v2.7.7" + + # NOTE: This requires that a system Java be available. + # Spack does not yet know how to install Java compilers + + # Notes from http://nco.sourceforge.net/#bld + # The first steps to build (i.e., compile, for the most part) NCO from + # source code are to install the pre-requisites: ANTLR version 2.7.7 + # (like this one not version 3.x or 4.x!) (required for ncap2)... ANTLR + # binaries from major distributions are pre-built with the source patch + # necessary to allow NCO to link to ANTLR... The ANTLR source file + # CharScanner.hpp must include this line: #include <cstring> or else + # ncap2 will not compile (this tarball is already patched). + version('2.7.7', '914865e853fe8e1e61a9f23d045cb4ab', + # Patched version as described above + url='http://dust.ess.uci.edu/tmp/antlr-2.7.7.tar.gz') + # Unpatched version + # url='http://dust.ess.uci.edu/nco/antlr-2.7.7.tar.gz') + + variant('cxx', default=False, description='Enable ANTLR for C++') + variant('java', default=False, description='Enable ANTLR for Java') + variant('python', default=False, description='Enable ANTLR for Python') + variant('csharp', default=False, description='Enable ANTLR for Csharp') + + + def install(self, spec, prefix): + # Check for future enabling of variants + for v in ('+java', '+python', '+csharp'): + if v in spec: + raise Error('Illegal variant %s; for now, Spack only knows how to build antlr or antlr+cxx') + + config_args = [ + '--prefix=%s' % prefix, + '--%s-cxx' % ('enable' if '+cxx' in spec else 'disable'), + '--%s-java' % ('enable' if '+java' in spec else 'disable'), + '--%s-python' % ('enable' if '+python' in spec else 'disable'), + '--%s-csharp' % ('enable' if '+csharp' in spec else 'disable')] + + # which('autoreconf')('-iv') + configure(*config_args) + make() + make("install") diff --git a/var/spack/repos/builtin/packages/astyle/package.py b/var/spack/repos/builtin/packages/astyle/package.py index 7260fd74a1..5274fc018f 100644 --- a/var/spack/repos/builtin/packages/astyle/package.py +++ b/var/spack/repos/builtin/packages/astyle/package.py @@ -14,4 +14,5 @@ class Astyle(Package): make('-f', join_path(self.stage.source_path,'build','clang','Makefile'), parallel=False) + mkdirp(self.prefix.bin) install(join_path(self.stage.source_path, 'src','bin','astyle'), self.prefix.bin) diff --git a/var/spack/repos/builtin/packages/autoconf/package.py b/var/spack/repos/builtin/packages/autoconf/package.py index 6412e810a6..b5e29b8a27 100644 --- a/var/spack/repos/builtin/packages/autoconf/package.py +++ b/var/spack/repos/builtin/packages/autoconf/package.py @@ -8,6 +8,8 @@ class Autoconf(Package): version('2.69', '82d05e03b93e45f5a39b828dc9c6c29b') version('2.62', '6c1f3b3734999035d77da5024aab4fbd') + depends_on("m4") + def install(self, spec, prefix): configure("--prefix=%s" % prefix) diff --git a/var/spack/repos/builtin/packages/bbcp/package.py b/var/spack/repos/builtin/packages/bbcp/package.py new file mode 100644 index 0000000000..e9baa5ccf4 --- /dev/null +++ b/var/spack/repos/builtin/packages/bbcp/package.py @@ -0,0 +1,17 @@ +from spack import * + +class Bbcp(Package): + """Securely and quickly copy data from source to target""" + homepage = "http://www.slac.stanford.edu/~abh/bbcp/" + + version('git', git='http://www.slac.stanford.edu/~abh/bbcp/bbcp.git', branch="master") + + def install(self, spec, prefix): + cd("src") + make() + # BBCP wants to build the executable in a directory whose name depends on the system type + makesname = Executable("../MakeSname") + bbcp_executable_path = "../bin/%s/bbcp" % makesname(output=str).rstrip("\n") + destination_path = "%s/bin/" % prefix + mkdirp(destination_path) + install(bbcp_executable_path, destination_path) diff --git a/var/spack/repos/builtin/packages/binutils/package.py b/var/spack/repos/builtin/packages/binutils/package.py index b8064093d2..158d722046 100644 --- a/var/spack/repos/builtin/packages/binutils/package.py +++ b/var/spack/repos/builtin/packages/binutils/package.py @@ -29,6 +29,7 @@ class Binutils(Package): configure_args = [ '--prefix=%s' % prefix, '--disable-dependency-tracking', + '--disable-werror', '--enable-interwork', '--enable-multilib', '--enable-shared', diff --git a/var/spack/repos/builtin/packages/bison/package.py b/var/spack/repos/builtin/packages/bison/package.py index 7c526fb958..9a2ddcbf96 100644 --- a/var/spack/repos/builtin/packages/bison/package.py +++ b/var/spack/repos/builtin/packages/bison/package.py @@ -10,6 +10,8 @@ class Bison(Package): version('3.0.4', 'a586e11cd4aff49c3ff6d3b6a4c9ccf8') + depends_on("m4") + def install(self, spec, prefix): configure("--prefix=%s" % prefix) diff --git a/var/spack/repos/builtin/packages/cnmem/package.py b/var/spack/repos/builtin/packages/cnmem/package.py new file mode 100644 index 0000000000..0a83e8fc20 --- /dev/null +++ b/var/spack/repos/builtin/packages/cnmem/package.py @@ -0,0 +1,12 @@ +from spack import * + +class Cnmem(Package): + """CNMem mempool for CUDA devices""" + homepage = "https://github.com/NVIDIA/cnmem" + + version('git', git='https://github.com/NVIDIA/cnmem.git', branch="master") + + def install(self, spec, prefix): + cmake('.',*std_cmake_args) + make() + make('install') diff --git a/var/spack/repos/builtin/packages/cryptopp/package.py b/var/spack/repos/builtin/packages/cryptopp/package.py index bc83cb2b65..c2778e14da 100644 --- a/var/spack/repos/builtin/packages/cryptopp/package.py +++ b/var/spack/repos/builtin/packages/cryptopp/package.py @@ -13,6 +13,7 @@ class Cryptopp(Package): version('5.6.3', '3c5b70e2ec98b7a24988734446242d07') version('5.6.2', '7ed022585698df48e65ce9218f6c6a67') + version('5.6.1', '96cbeba0907562b077e26bcffb483828') def install(self, spec, prefix): make() diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py index 6810e86868..df8330384d 100644 --- a/var/spack/repos/builtin/packages/dealii/package.py +++ b/var/spack/repos/builtin/packages/dealii/package.py @@ -12,6 +12,7 @@ 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('doc', default=False, description='Compile with documentation') + variant('gsl' , default=True, description='Compile with GSL') 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)') @@ -39,6 +40,8 @@ class Dealii(Package): depends_on ("mpi", when="+mpi") depends_on ("arpack-ng+mpi", when='+arpack+mpi') depends_on ("doxygen", when='+doc') + depends_on ("gsl", when='@8.5.0:+gsl') + depends_on ("gsl", when='@dev+gsl') depends_on ("hdf5+mpi~cxx", when='+hdf5+mpi') #FIXME NetCDF declares dependency with ~cxx, why? depends_on ("metis@5:", when='+metis') depends_on ("netcdf+mpi", when="+netcdf+mpi") @@ -50,8 +53,8 @@ class Dealii(Package): depends_on ("trilinos", when='+trilinos+mpi') # developer dependnecies - #depends_on ("numdiff") #FIXME - #depends_on ("astyle") #FIXME + depends_on ("numdiff", when='@dev') + depends_on ("astyle@2.04", when='@dev') def install(self, spec, prefix): options = [] @@ -80,7 +83,6 @@ class Dealii(Package): (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, - '-DP4EST_DIR=%s' % spec['p4est'].prefix, '-DUMFPACK_DIR=%s' % spec['suite-sparse'].prefix, '-DTBB_DIR=%s' % spec['tbb'].prefix, '-DZLIB_DIR=%s' % spec['zlib'].prefix @@ -100,7 +102,7 @@ class Dealii(Package): ]) # Optional dependencies for which librariy names are the same as CMake variables - for library in ('hdf5', 'p4est','petsc', 'slepc','trilinos','metis'): + for library in ('gsl','hdf5','p4est','petsc','slepc','trilinos','metis'): if library in spec: options.extend([ '-D{library}_DIR={value}'.format(library=library.upper(), value=spec[library].prefix), diff --git a/var/spack/repos/builtin/packages/eigen/package.py b/var/spack/repos/builtin/packages/eigen/package.py index 1501989812..6b38ab0261 100644 --- a/var/spack/repos/builtin/packages/eigen/package.py +++ b/var/spack/repos/builtin/packages/eigen/package.py @@ -45,6 +45,7 @@ class Eigen(Package): # TODO : dependency on googlehash, superlu, adolc missing + depends_on('cmake') depends_on('metis@5:', when='+metis') depends_on('scotch', when='+scotch') depends_on('fftw', when='+fftw') diff --git a/var/spack/repos/builtin/packages/flex/package.py b/var/spack/repos/builtin/packages/flex/package.py index b065904912..e4795893e0 100644 --- a/var/spack/repos/builtin/packages/flex/package.py +++ b/var/spack/repos/builtin/packages/flex/package.py @@ -6,6 +6,7 @@ class Flex(Package): homepage = "http://flex.sourceforge.net/" url = "http://download.sourceforge.net/flex/flex-2.5.39.tar.gz" + version('2.6.0', '5724bcffed4ebe39e9b55a9be80859ec') version('2.5.39', 'e133e9ead8ec0a58d81166b461244fde') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py index 6043b62279..8f90757232 100644 --- a/var/spack/repos/builtin/packages/gcc/package.py +++ b/var/spack/repos/builtin/packages/gcc/package.py @@ -38,6 +38,7 @@ class Gcc(Package): list_url = 'http://open-source-box.org/gcc/' list_depth = 2 + version('6.1.0', '8fb6cb98b8459f5863328380fbf06bd1') version('5.3.0', 'c9616fd448f980259c31de613e575719') version('5.2.0', 'a51bcfeb3da7dd4c623e27207ed43467') version('4.9.3', '6f831b4d251872736e8e9cc09746f327') diff --git a/var/spack/repos/builtin/packages/gdb/package.py b/var/spack/repos/builtin/packages/gdb/package.py index b346fe80c2..0e9e8fc099 100644 --- a/var/spack/repos/builtin/packages/gdb/package.py +++ b/var/spack/repos/builtin/packages/gdb/package.py @@ -34,6 +34,7 @@ class Gdb(Package): homepage = "https://www.gnu.org/software/gdb" url = "http://ftp.gnu.org/gnu/gdb/gdb-7.10.tar.gz" + version('7.11', 'f585059252836a981ea5db9a5f8ce97f') version('7.10.1', 'b93a2721393e5fa226375b42d567d90b') version('7.10', 'fa6827ad0fd2be1daa418abb11a54d86') version('7.9.1', 'f3b97de919a9dba84490b2e076ec4cb0') diff --git a/var/spack/repos/builtin/packages/glib/package.py b/var/spack/repos/builtin/packages/glib/package.py index 67ead5f941..a3fc3f79eb 100644 --- a/var/spack/repos/builtin/packages/glib/package.py +++ b/var/spack/repos/builtin/packages/glib/package.py @@ -1,4 +1,5 @@ from spack import * +import sys class Glib(Package): """The GLib package contains a low-level libraries useful for @@ -12,6 +13,8 @@ class Glib(Package): depends_on("libffi") depends_on("zlib") + depends_on("pkg-config") + depends_on('gettext', sys.platform=='darwin') def install(self, spec, prefix): configure("--prefix=%s" % prefix) diff --git a/var/spack/repos/builtin/packages/glm/package.py b/var/spack/repos/builtin/packages/glm/package.py index d00c301b4c..ecae89f1e8 100644 --- a/var/spack/repos/builtin/packages/glm/package.py +++ b/var/spack/repos/builtin/packages/glm/package.py @@ -11,6 +11,8 @@ class Glm(Package): url = "https://github.com/g-truc/glm/archive/0.9.7.1.tar.gz" version('0.9.7.1', '61af6639cdf652d1cdd7117190afced8') + + depends_on ("cmake") def install(self, spec, prefix): with working_dir('spack-build', create=True): diff --git a/var/spack/repos/builtin/packages/gmp/package.py b/var/spack/repos/builtin/packages/gmp/package.py index fe13de3b95..85e9c237d6 100644 --- a/var/spack/repos/builtin/packages/gmp/package.py +++ b/var/spack/repos/builtin/packages/gmp/package.py @@ -35,6 +35,8 @@ class Gmp(Package): version('6.0.0a', 'b7ff2d88cae7f8085bd5006096eed470') version('6.0.0' , '6ef5869ae735db9995619135bd856b84') + depends_on("m4") + def install(self, spec, prefix): configure("--prefix=%s" % prefix) make() diff --git a/var/spack/repos/builtin/packages/gmsh/package.py b/var/spack/repos/builtin/packages/gmsh/package.py index 9d759303cb..5f659c56df 100644 --- a/var/spack/repos/builtin/packages/gmsh/package.py +++ b/var/spack/repos/builtin/packages/gmsh/package.py @@ -63,6 +63,11 @@ class Gmsh(Package): build_directory = join_path(self.stage.path, 'spack-build') source_directory = self.stage.source_path + options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib' % prefix) + + # Prevent GMsh from using its own strange directory structure on OSX + options.append('-DENABLE_OS_SPECIFIC_INSTALL=OFF') + if '+shared' in spec: options.extend(['-DENABLE_BUILD_SHARED:BOOL=ON', '-DENABLE_BUILD_DYNAMIC:BOOL=ON']) # Builds dynamic executable and installs shared library diff --git a/var/spack/repos/builtin/packages/hdf5/package.py b/var/spack/repos/builtin/packages/hdf5/package.py index cce609eb29..470969832f 100644 --- a/var/spack/repos/builtin/packages/hdf5/package.py +++ b/var/spack/repos/builtin/packages/hdf5/package.py @@ -38,7 +38,7 @@ class Hdf5(Package): list_depth = 3 version('1.10.0', 'bdc935337ee8282579cd6bc4270ad199') - version('1.8.16', 'b8ed9a36ae142317f88b0c7ef4b9c618') + version('1.8.16', 'b8ed9a36ae142317f88b0c7ef4b9c618', preferred=True) version('1.8.15', '03cccb5b33dbe975fdcd8ae9dc021f24') version('1.8.13', 'c03426e9e77d7766944654280b467289') diff --git a/var/spack/repos/builtin/packages/hwloc/package.py b/var/spack/repos/builtin/packages/hwloc/package.py index ab7205646e..a461a7482c 100644 --- a/var/spack/repos/builtin/packages/hwloc/package.py +++ b/var/spack/repos/builtin/packages/hwloc/package.py @@ -17,6 +17,7 @@ class Hwloc(Package): list_url = "http://www.open-mpi.org/software/hwloc/" list_depth = 3 + version('1.11.3', 'c1d36a9de6028eac1d18ea4782ef958f') version('1.11.2', 'e4ca55c2a5c5656da4a4e37c8fc51b23') version('1.11.1', 'feb4e416a1b25963ed565d8b42252fdc') version('1.9', '1f9f9155682fe8946a97c08896109508') diff --git a/var/spack/repos/builtin/packages/hydra/package.py b/var/spack/repos/builtin/packages/hydra/package.py new file mode 100644 index 0000000000..c1b8868276 --- /dev/null +++ b/var/spack/repos/builtin/packages/hydra/package.py @@ -0,0 +1,21 @@ +from spack import * + +class Hydra(Package): + """Hydra is a process management system for starting parallel jobs. + Hydra is designed to natively work with existing launcher daemons + (such as ssh, rsh, fork), as well as natively integrate with resource + management systems (such as slurm, pbs, sge).""" + + homepage = "http://www.mpich.org" + url = "http://www.mpich.org/static/downloads/3.2/hydra-3.2.tar.gz" + list_url = "http://www.mpich.org/static/downloads/" + list_depth = 2 + + version('3.2', '4d670916695bf7e3a869cc336a881b39') + + + def install(self, spec, prefix): + configure('--prefix=%s' % prefix) + + make() + make("install") diff --git a/var/spack/repos/builtin/packages/ior/package.py b/var/spack/repos/builtin/packages/ior/package.py new file mode 100644 index 0000000000..c46650a674 --- /dev/null +++ b/var/spack/repos/builtin/packages/ior/package.py @@ -0,0 +1,42 @@ +from spack import * +import os + +class Ior(Package): + """The IOR software is used for benchmarking parallel file systems + using POSIX, MPI-IO, or HDF5 interfaces.""" + + homepage = "https://github.com/LLNL/ior" + url = "https://github.com/LLNL/ior/archive/3.0.1.tar.gz" + + version('3.0.1', '71150025e0bb6ea1761150f48b553065') + + variant('hdf5', default=False, description='support IO with HDF5 backend') + variant('ncmpi', default=False, description='support IO with NCMPI backend') + + depends_on('mpi') + depends_on('hdf5+mpi', when='+hdf5') + depends_on('netcdf+mpi', when='+ncmpi') + + + def install(self, spec, prefix): + os.system('./bootstrap') + + config_args = [ + 'MPICC=%s' % spec['mpi'].prefix.bin + '/mpicc', + '--prefix=%s' % prefix, + ] + + if '+hdf5' in spec: + config_args.append('--with-hdf5') + else: + config_args.append('--without-hdf5') + + if '+ncmpi' in spec: + config_args.append('--with-ncmpi') + else: + config_args.append('--without-ncmpi') + + configure(*config_args) + + make() + make('install') diff --git a/var/spack/repos/builtin/packages/jpeg/package.py b/var/spack/repos/builtin/packages/jpeg/package.py index 87820467db..2f15e59ad4 100644 --- a/var/spack/repos/builtin/packages/jpeg/package.py +++ b/var/spack/repos/builtin/packages/jpeg/package.py @@ -1,14 +1,19 @@ from spack import * class Jpeg(Package): - """jpeg library""" + """libjpeg is a widely used free library with functions for handling the + JPEG image data format. It implements a JPEG codec (encoding and decoding) + alongside various utilities for handling JPEG data.""" + homepage = "http://www.ijg.org" - url = "http://www.ijg.org/files/jpegsrc.v9a.tar.gz" + url = "http://www.ijg.org/files/jpegsrc.v9b.tar.gz" + version('9b', '6a9996ce116ec5c52b4870dbcd6d3ddb') version('9a', '3353992aecaee1805ef4109aadd433e7') def install(self, spec, prefix): configure("--prefix=%s" % prefix) make() + make("test") make("install") diff --git a/var/spack/repos/builtin/packages/kripke/package.py b/var/spack/repos/builtin/packages/kripke/package.py new file mode 100644 index 0000000000..7d067ea44d --- /dev/null +++ b/var/spack/repos/builtin/packages/kripke/package.py @@ -0,0 +1,32 @@ +from spack import * + +class Kripke(Package): + """Kripke is a simple, scalable, 3D Sn deterministic particle + transport proxy/mini app. + """ + homepage = "https://codesign.llnl.gov/kripke.php" + url = "https://codesign.llnl.gov/downloads/kripke-openmp-1.1.tar.gz" + + version('1.1', '7fe6f2b26ed983a6ce5495ab701f85bf') + + variant('mpi', default=True, description='Build with MPI.') + variant('openmp', default=True, description='Build with OpenMP enabled.') + + depends_on('mpi', when="+mpi") + + def install(self, spec, prefix): + with working_dir('build', create=True): + def enabled(variant): + return (1 if variant in spec else 0) + + cmake('-DCMAKE_INSTALL_PREFIX:PATH=.', + '-DENABLE_OPENMP=%d' % enabled('+openmp'), + '-DENABLE_MPI=%d' % enabled('+mpi'), + '..', + *std_cmake_args) + make() + + # Kripke does not provide install target, so we have to copy + # things into place. + mkdirp(prefix.bin) + install('kripke', prefix.bin) diff --git a/var/spack/repos/builtin/packages/libtermkey/package.py b/var/spack/repos/builtin/packages/libtermkey/package.py new file mode 100644 index 0000000000..7f25edaf76 --- /dev/null +++ b/var/spack/repos/builtin/packages/libtermkey/package.py @@ -0,0 +1,17 @@ +from spack import * + +class Libtermkey(Package): + """Easy keyboard entry processing for terminal programs""" + homepage = "http://www.leonerd.org.uk/code/libtermkey/" + url = "http://www.leonerd.org.uk/code/libtermkey/libtermkey-0.18.tar.gz" + + version('0.18' , '3be2e3e5a851a49cc5e8567ac108b520') + version('0.17' , '20edb99e0d95ec1690fe90e6a555ae6d') + version('0.16' , '7a24b675aaeb142d30db28e7554987d4') + version('0.15b', '27689756e6c86c56ae454f2ac259bc3d') + version('0.14' , 'e08ce30f440f9715c459060e0e048978') + + + def install(self, spec, prefix): + make() + make("install", "PREFIX=" + prefix) diff --git a/var/spack/repos/builtin/packages/libtool/package.py b/var/spack/repos/builtin/packages/libtool/package.py index 82a54953b2..c804f5ab5d 100644 --- a/var/spack/repos/builtin/packages/libtool/package.py +++ b/var/spack/repos/builtin/packages/libtool/package.py @@ -8,6 +8,8 @@ class Libtool(Package): version('2.4.6' , 'addf44b646ddb4e3919805aa88fa7c5e') version('2.4.2' , 'd2f3b7d4627e69e13514a40e72a24d50') + depends_on('m4') + def install(self, spec, prefix): configure("--prefix=%s" % prefix) diff --git a/var/spack/repos/builtin/packages/libuv/package.py b/var/spack/repos/builtin/packages/libuv/package.py new file mode 100644 index 0000000000..eace94d1a6 --- /dev/null +++ b/var/spack/repos/builtin/packages/libuv/package.py @@ -0,0 +1,21 @@ +from spack import * + +class Libuv(Package): + """Multi-platform library with a focus on asynchronous IO""" + homepage = "http://libuv.org" + url = "https://github.com/libuv/libuv/archive/v1.9.0.tar.gz" + + version('1.9.0', '14737f9c76123a19a290dabb7d1cd04c') + + depends_on('automake') + depends_on('autoconf') + depends_on('libtool') + + def install(self, spec, prefix): + bash = which("bash") + bash('autogen.sh') + configure('--prefix=%s' % prefix) + + make() + make("check") + make("install") diff --git a/var/spack/repos/builtin/packages/libvterm/package.py b/var/spack/repos/builtin/packages/libvterm/package.py new file mode 100644 index 0000000000..3212f6550d --- /dev/null +++ b/var/spack/repos/builtin/packages/libvterm/package.py @@ -0,0 +1,12 @@ +from spack import * + +class Libvterm(Package): + """An abstract library implementation of a terminal emulator""" + homepage = "http://www.leonerd.org.uk/code/libvterm/" + url = "http://www.leonerd.org.uk/code/libvterm/libvterm-0+bzr681.tar.gz" + + version('681', '7a4325a7350b7092245c04e8ee185ac3') + + def install(self, spec, prefix): + make() + make("install", "PREFIX=" + prefix) diff --git a/var/spack/repos/builtin/packages/libxcb/package.py b/var/spack/repos/builtin/packages/libxcb/package.py index d7d94c4546..b2543be5da 100644 --- a/var/spack/repos/builtin/packages/libxcb/package.py +++ b/var/spack/repos/builtin/packages/libxcb/package.py @@ -13,6 +13,7 @@ class Libxcb(Package): version('1.11.1', '118623c15a96b08622603a71d8789bf3') depends_on("python") depends_on("xcb-proto") + depends_on("pkg-config") # depends_on('pthread') # Ubuntu: apt-get install libpthread-stubs0-dev # depends_on('xau') # Ubuntu: apt-get install libxau-dev diff --git a/var/spack/repos/builtin/packages/mfem/package.py b/var/spack/repos/builtin/packages/mfem/package.py new file mode 100644 index 0000000000..510e09c4e1 --- /dev/null +++ b/var/spack/repos/builtin/packages/mfem/package.py @@ -0,0 +1,125 @@ +from spack import * +import glob, string + +class Mfem(Package): + """Free, lightweight, scalable C++ library for finite element methods.""" + + homepage = 'http://www.mfem.org' + url = 'https://github.com/mfem/mfem' + +# version('3.1', git='https://github.com/mfem/mfem.git', +# commit='dbae60fe32e071989b52efaaf59d7d0eb2a3b574') + + version('3.1', '841ea5cf58de6fae4de0f553b0e01ebaab9cd9c67fa821e8a715666ecf18fc57', + url='http://goo.gl/xrScXn', expand=False) + + variant('metis', default=False, description='Activate support for metis') + variant('hypre', default=False, description='Activate support for hypre') + variant('suite-sparse', default=False, + description='Activate support for SuiteSparse') + variant('mpi', default=False, description='Activate support for MPI') + variant('lapack', default=False, description='Activate support for LAPACK') + variant('debug', default=False, description='Build debug version') + + depends_on('blas', when='+lapack') + depends_on('lapack', when='+lapack') + + depends_on('mpi', when='+mpi') + depends_on('metis', when='+mpi') + depends_on('hypre', when='+mpi') + + depends_on('hypre', when='+hypre') + + depends_on('metis@4:', when='+metis') + + depends_on('suite-sparse', when='+suite-sparse') + depends_on('blas', when='+suite-sparse') + depends_on('lapack', when='+suite-sparse') + depends_on('metis@5:', when='+suite-sparse ^suite-sparse@4.5:') + depends_on('cmake', when='^metis@5:') + + def check_variants(self, spec): + if '+mpi' in spec and ('+hypre' not in spec or '+metis' not in spec): + raise InstallError('mfem+mpi must be built with +hypre ' + + 'and +metis!') + if '+suite-sparse' in spec and ('+metis' not in spec or + '+lapack' not in spec): + raise InstallError('mfem+suite-sparse must be built with ' + + '+metis and +lapack!') + if 'metis@5:' in spec and '%clang' in spec and ('^cmake %gcc' not in spec): + raise InstallError('To work around CMake bug with clang, must ' + + 'build mfem with mfem[+variants] %clang ' + + '^cmake %gcc to force CMake to build with gcc') + return + + def install(self, spec, prefix): + self.check_variants(spec) + + options = ['PREFIX=%s' % prefix] + + if '+lapack' in spec: + lapack_lib = '-L{0} -llapack -L{1} -lblas'.format( + spec['lapack'].prefix.lib, spec['blas'].prefix.lib) + options.extend(['MFEM_USE_LAPACK=YES', + 'LAPACK_OPT=-I%s' % spec['lapack'].prefix.include, + 'LAPACK_LIB=%s' % lapack_lib]) + + if '+hypre' in spec: + options.extend(['HYPRE_DIR=%s' % spec['hypre'].prefix, + 'HYPRE_OPT=-I%s' % spec['hypre'].prefix.include, + 'HYPRE_LIB=-L%s' % spec['hypre'].prefix.lib + + ' -lHYPRE']) + + if '+metis' in spec: + metis_lib = '-L%s -lmetis' % spec['metis'].prefix.lib + if spec['metis'].satisfies('@5:'): + metis_str = 'MFEM_USE_METIS_5=YES' + else: + metis_str = 'MFEM_USE_METIS_5=NO' + options.extend([metis_str, + 'METIS_DIR=%s' % spec['metis'].prefix, + 'METIS_OPT=-I%s' % spec['metis'].prefix.include, + 'METIS_LIB=%s' % metis_lib]) + + if '+mpi' in spec: options.extend(['MFEM_USE_MPI=YES']) + + if '+suite-sparse' in spec: + ssp = spec['suite-sparse'].prefix + ss_lib = '-L%s' % ssp.lib + ss_lib += (' -lumfpack -lcholmod -lcolamd -lamd -lcamd' + + ' -lccolamd -lsuitesparseconfig') + + no_librt_archs = ['darwin-i686', 'darwin-x86_64'] + no_rt = any(map(lambda a: spec.satisfies('='+a), no_librt_archs)) + if not no_rt: ss_lib += ' -lrt' + ss_lib += (' ' + metis_lib + ' ' + lapack_lib) + + options.extend(['MFEM_USE_SUITESPARSE=YES', + 'SUITESPARSE_DIR=%s' % ssp, + 'SUITESPARSE_OPT=-I%s' % ssp.include, + 'SUITESPARSE_LIB=%s' % ss_lib]) + + if '+debug' in spec: options.extend(['MFEM_DEBUG=YES']) + + # Dirty hack to cope with URL redirect + tgz_file = string.split(self.url,'/')[-1] + tar = which('tar') + tar('xzvf', tgz_file) + cd(glob.glob('mfem*')[0]) + # End dirty hack to cope with URL redirect + + make('config', *options) + make('all') + + # Run a small test before installation + args = ['-m', join_path('data','star.mesh'), '--no-visualization'] + if '+mpi' in spec: + Executable(join_path(spec['mpi'].prefix.bin, + 'mpirun'))('-np', + '4', + join_path('examples','ex1p'), + *args) + else: + Executable(join_path('examples', 'ex1'))(*args) + + make('install') diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py index b317ec6651..2179086fe5 100644 --- a/var/spack/repos/builtin/packages/mpich/package.py +++ b/var/spack/repos/builtin/packages/mpich/package.py @@ -43,6 +43,8 @@ class Mpich(Package): version('3.0.4', '9c5d5d4fe1e17dd12153f40bc5b6dbc0') variant('verbs', default=False, description='Build support for OpenFabrics verbs.') + variant('pmi', default=True, description='Build with PMI support') + variant('hydra', default=True, description='Build the hydra process manager') provides('mpi@:3.0', when='@3:') provides('mpi@:1.3', when='@1:') @@ -55,12 +57,15 @@ class Mpich(Package): spack_env.set('MPICH_FC', spack_fc) 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') + self.spec.mpicc = join_path(self.prefix.bin, 'mpicc') + self.spec.mpicxx = join_path(self.prefix.bin, 'mpic++') + self.spec.mpifc = join_path(self.prefix.bin, 'mpif90') + self.spec.mpif77 = join_path(self.prefix.bin, 'mpif77') def install(self, spec, prefix): config_args = ["--prefix=" + prefix, + "--with-pmi=" + ("yes" if '+pmi' in spec else 'no'), + "--with-pm=" + ('hydra' if '+hydra' in spec else 'no'), "--enable-shared"] # Variants diff --git a/var/spack/repos/builtin/packages/mrnet/package.py b/var/spack/repos/builtin/packages/mrnet/package.py index a3abb71285..b52233be4a 100644 --- a/var/spack/repos/builtin/packages/mrnet/package.py +++ b/var/spack/repos/builtin/packages/mrnet/package.py @@ -6,6 +6,7 @@ class Mrnet(Package): url = "ftp://ftp.cs.wisc.edu/paradyn/mrnet/mrnet_5.0.1.tar.gz" list_url = "http://ftp.cs.wisc.edu/paradyn/mrnet" + version('5.0.1-2', git='https://github.com/dyninst/mrnet.git', commit='20b1eacfc6d680d9f6472146d2dfaa0f900cc2e9') version('5.0.1', '17f65738cf1b9f9b95647ff85f69ecdd') version('4.1.0', '5a248298b395b329e2371bf25366115c') version('4.0.0', 'd00301c078cba57ef68613be32ceea2f') diff --git a/var/spack/repos/builtin/packages/msgpack-c/package.py b/var/spack/repos/builtin/packages/msgpack-c/package.py new file mode 100644 index 0000000000..a363bc89be --- /dev/null +++ b/var/spack/repos/builtin/packages/msgpack-c/package.py @@ -0,0 +1,14 @@ +from spack import * + +class MsgpackC(Package): + """A small, fast binary interchange format convertible to/from JSON""" + homepage = "http://www.msgpack.org" + url = "https://github.com/msgpack/msgpack-c/archive/cpp-1.4.1.tar.gz" + + version('1.4.1', 'e2fd3a7419b9bc49e5017fdbefab87e0') + + def install(self, spec, prefix): + cmake('.', *std_cmake_args) + + make() + make("install") diff --git a/var/spack/repos/builtin/packages/mvapich2/package.py b/var/spack/repos/builtin/packages/mvapich2/package.py index 3e60b517db..c68a04d251 100644 --- a/var/spack/repos/builtin/packages/mvapich2/package.py +++ b/var/spack/repos/builtin/packages/mvapich2/package.py @@ -147,6 +147,12 @@ class Mvapich2(Package): spack_env.set('MPICH_F90', spack_fc) spack_env.set('MPICH_FC', spack_fc) + def setup_dependent_package(self, module, dep_spec): + self.spec.mpicc = join_path(self.prefix.bin, 'mpicc') + self.spec.mpicxx = join_path(self.prefix.bin, 'mpicxx') + self.spec.mpifc = join_path(self.prefix.bin, 'mpif90') + self.spec.mpif77 = join_path(self.prefix.bin, 'mpif77') + def install(self, spec, prefix): # we'll set different configure flags depending on our environment configure_args = [ diff --git a/var/spack/repos/builtin/packages/nco/package.py b/var/spack/repos/builtin/packages/nco/package.py new file mode 100644 index 0000000000..3a9aeaa656 --- /dev/null +++ b/var/spack/repos/builtin/packages/nco/package.py @@ -0,0 +1,30 @@ +from spack import * +import os + +class Nco(Package): + """The NCO toolkit manipulates and analyzes data stored in + netCDF-accessible formats""" + + homepage = "https://sourceforge.net/projects/nco" + url = "https://github.com/nco/nco/archive/4.5.5.tar.gz" + + version('4.5.5', '9f1f1cb149ad6407c5a03c20122223ce') + + # See "Compilation Requirements" at: + # http://nco.sourceforge.net/#bld + + depends_on('netcdf') + depends_on('antlr@2.7.7+cxx') # (required for ncap2) + depends_on('gsl') # (desirable for ncap2) + depends_on('udunits2') # (allows dimensional unit transformations) + # depends_on('opendap') # (enables network transparency), + + def install(self, spec, prefix): + opts = [ + '--prefix=%s' % prefix, + '--disable-openmp', # TODO: Make this a variant + '--disable-dap', # TODO: Make this a variant + '--disable-esmf'] + configure(*opts) + make() + make("install") diff --git a/var/spack/repos/builtin/packages/netcdf/package.py b/var/spack/repos/builtin/packages/netcdf/package.py index b60a2c4e9a..4aad0f6f3c 100644 --- a/var/spack/repos/builtin/packages/netcdf/package.py +++ b/var/spack/repos/builtin/packages/netcdf/package.py @@ -12,15 +12,19 @@ class Netcdf(Package): version('4.4.0', 'cffda0cbd97fdb3a06e9274f7aef438e') version('4.3.3', '5fbd0e108a54bd82cb5702a73f56d2ae') - variant('mpi', default=True, description='Enables MPI parallelism') - variant('hdf4', default=False, description="Enable HDF4 support") + variant('mpi', default=True, description='Enables MPI parallelism') + variant('hdf4', default=False, description='Enable HDF4 support') - # Dependencies: - depends_on("curl") # required for DAP support + depends_on("m4") depends_on("hdf", when='+hdf4') - depends_on("hdf5+mpi~cxx", when='+mpi') # required for NetCDF-4 support - depends_on("hdf5~mpi", when='~mpi') # required for NetCDF-4 support - depends_on("zlib") # required for NetCDF-4 support + + # Required for DAP support + depends_on("curl") + + # Required for NetCDF-4 support + depends_on("zlib") + depends_on("hdf5+mpi", when='+mpi') + depends_on("hdf5~mpi", when='~mpi') def install(self, spec, prefix): # Environment variables @@ -48,7 +52,7 @@ class Netcdf(Package): # /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) + LDFLAGS.append( "-L%s" % spec['curl'].prefix.lib) if '+mpi' in spec: config_args.append('--enable-parallel4') diff --git a/var/spack/repos/builtin/packages/openblas/make.patch b/var/spack/repos/builtin/packages/openblas/make.patch new file mode 100644 index 0000000000..851214211a --- /dev/null +++ b/var/spack/repos/builtin/packages/openblas/make.patch @@ -0,0 +1,35 @@ +diff --git a/Makefile.system b/Makefile.system +index b89f60e..2dbdad0 100644 +--- a/Makefile.system ++++ b/Makefile.system +@@ -139,6 +139,10 @@ NO_PARALLEL_MAKE=0 + endif + GETARCH_FLAGS += -DNO_PARALLEL_MAKE=$(NO_PARALLEL_MAKE) + ++ifdef MAKE_NO_J ++GETARCH_FLAGS += -DMAKE_NO_J=$(MAKE_NO_J) ++endif ++ + ifdef MAKE_NB_JOBS + GETARCH_FLAGS += -DMAKE_NB_JOBS=$(MAKE_NB_JOBS) + endif +diff --git a/getarch.c b/getarch.c +index f9c49e6..dffad70 100644 +--- a/getarch.c ++++ b/getarch.c +@@ -1012,6 +1012,7 @@ int main(int argc, char *argv[]){ + #endif + #endif + ++#ifndef MAKE_NO_J + #ifdef MAKE_NB_JOBS + printf("MAKE += -j %d\n", MAKE_NB_JOBS); + #elif NO_PARALLEL_MAKE==1 +@@ -1021,6 +1022,7 @@ int main(int argc, char *argv[]){ + printf("MAKE += -j %d\n", get_num_cores()); + #endif + #endif ++#endif + + break; + diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py index 4522130ccc..99649da9ca 100644 --- a/var/spack/repos/builtin/packages/openblas/package.py +++ b/var/spack/repos/builtin/packages/openblas/package.py @@ -1,6 +1,7 @@ from spack import * import sys import os +import shutil class Openblas(Package): """OpenBLAS: An optimized BLAS library""" @@ -13,18 +14,21 @@ class Openblas(Package): variant('shared', default=True, description="Build shared libraries as well as static libs.") variant('openmp', default=True, description="Enable OpenMP support.") + variant('fpic', default=True, description="Build position independent code") # virtual dependency provides('blas') provides('lapack') + patch('make.patch') def install(self, spec, prefix): # Openblas is picky about compilers. Configure fails with # FC=/abs/path/to/f77, whereas FC=f77 works fine. # To circumvent this, provide basename only: make_defs = ['CC=%s' % os.path.basename(spack_cc), - 'FC=%s' % os.path.basename(spack_f77)] + 'FC=%s' % os.path.basename(spack_f77), + 'MAKE_NO_J=1'] make_targets = ['libs', 'netlib'] @@ -32,6 +36,8 @@ class Openblas(Package): if '+shared' in spec: make_targets += ['shared'] else: + if '+fpic' in spec: + make_defs.extend(['CFLAGS=-fPIC', 'FFLAGS=-fPIC']) make_defs += ['NO_SHARED=1'] # fix missing _dggsvd_ and _sggsvd_ @@ -64,6 +70,10 @@ class Openblas(Package): if '+shared' in spec: symlink('libopenblas.%s' % dso_suffix, 'liblapack.%s' % dso_suffix) + # Openblas may pass its own test but still fail to compile Lapack + # symbols. To make sure we get working Blas and Lapack, do a small test. + self.check_install(spec) + def setup_dependent_package(self, module, dspec): # This is WIP for a prototype interface for virtual packages. @@ -76,3 +86,60 @@ class Openblas(Package): 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 + + def check_install(self, spec): + "Build and run a small program to test that we have Lapack symbols" + print "Checking Openblas installation..." + checkdir = "spack-check" + with working_dir(checkdir, create=True): + source = r""" +#include <cblas.h> +#include <stdio.h> +int main(void) { +int i=0; +double A[6] = {1.0, 2.0, 1.0, -3.0, 4.0, -1.0}; +double B[6] = {1.0, 2.0, 1.0, -3.0, 4.0, -1.0}; +double C[9] = {.5, .5, .5, .5, .5, .5, .5, .5, .5}; +cblas_dgemm(CblasColMajor, CblasNoTrans, CblasTrans, + 3, 3, 2, 1, A, 3, B, 3, 2, C, 3); +for (i = 0; i < 9; i++) + printf("%f\n", C[i]); +return 0; +} +""" + expected = """\ +11.000000 +-9.000000 +5.000000 +-9.000000 +21.000000 +-1.000000 +5.000000 +-1.000000 +3.000000 +""" + with open("check.c", 'w') as f: + f.write(source) + cc = which('cc') + # TODO: Automate these path and library settings + cc('-c', "-I%s" % join_path(spec.prefix, "include"), "check.c") + cc('-o', "check", "check.o", + "-L%s" % join_path(spec.prefix, "lib"), "-llapack", "-lblas", "-lpthread") + try: + check = Executable('./check') + output = check(return_output=True) + except: + output = "" + success = output == expected + if not success: + print "Produced output does not match expected output." + print "Expected output:" + print '-'*80 + print expected + print '-'*80 + print "Produced output:" + print '-'*80 + print output + print '-'*80 + raise RuntimeError("Openblas install check failed") + shutil.rmtree(checkdir) diff --git a/var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.c b/var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.c new file mode 100644 index 0000000000..634e99d20b --- /dev/null +++ b/var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.c @@ -0,0 +1,13 @@ +#include <cblas.h> +#include <stdio.h> +int main(void) { +int i=0; +double A[6] = {1.0, 2.0, 1.0, -3.0, 4.0, -1.0}; +double B[6] = {1.0, 2.0, 1.0, -3.0, 4.0, -1.0}; +double C[9] = {.5, .5, .5, .5, .5, .5, .5, .5, .5}; +cblas_dgemm(CblasColMajor, CblasNoTrans, CblasTrans, + 3, 3, 2, 1, A, 3, B, 3, 2, C, 3); +for (i = 0; i < 9; i++) + printf("%f\n", C[i]); +return 0; +} diff --git a/var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.output b/var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.output new file mode 100644 index 0000000000..b8316d7477 --- /dev/null +++ b/var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.output @@ -0,0 +1,9 @@ +11.000000 +-9.000000 +5.000000 +-9.000000 +21.000000 +-1.000000 +5.000000 +-1.000000 +3.000000 diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py index 9a127f1812..d0dd2d657f 100644 --- a/var/spack/repos/builtin/packages/openmpi/package.py +++ b/var/spack/repos/builtin/packages/openmpi/package.py @@ -1,7 +1,5 @@ -import os - from spack import * - +import os class Openmpi(Package): """Open MPI is a project combining technologies and resources from @@ -28,6 +26,7 @@ class Openmpi(Package): patch('configure.patch', when="@1.10.0:1.10.1") variant('psm', default=False, description='Build support for the PSM library.') + variant('pmi', default=True, description='Build support for PMI-based launchers') variant('verbs', default=False, description='Build support for OpenFabrics verbs.') # TODO : variant support for other schedulers is missing @@ -38,6 +37,7 @@ class Openmpi(Package): depends_on('hwloc') + 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) @@ -48,6 +48,12 @@ class Openmpi(Package): spack_env.set('OMPI_FC', spack_fc) spack_env.set('OMPI_F77', spack_f77) + def setup_dependent_package(self, module, dep_spec): + self.spec.mpicc = join_path(self.prefix.bin, 'mpicc') + self.spec.mpicxx = join_path(self.prefix.bin, 'mpic++') + self.spec.mpifc = join_path(self.prefix.bin, 'mpif90') + self.spec.mpif77 = join_path(self.prefix.bin, 'mpif77') + def install(self, spec, prefix): config_args = ["--prefix=%s" % prefix, @@ -62,6 +68,9 @@ class Openmpi(Package): if '+psm' in spec: config_args.append("--with-psm") + if '+pmi' in spec: + config_args.append("--with-pmi") #TODO: let user specify directory when possible + if '+verbs' in spec: # Up through version 1.6, this option was previously named --with-openib if spec.satisfies('@:1.6'): diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py index 70afaf4038..d0c95731a2 100644 --- a/var/spack/repos/builtin/packages/openssl/package.py +++ b/var/spack/repos/builtin/packages/openssl/package.py @@ -3,6 +3,7 @@ import llnl.util.tty as tty from spack import * + class Openssl(Package): """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, and Open Source @@ -14,10 +15,12 @@ class Openssl(Package): version('1.0.1h', '8d6d684a9430d5cc98a62a5d8fbda8cf') version('1.0.1r', '1abd905e079542ccae948af37e393d28') + version('1.0.1t', '9837746fcf8a6727d46d22ca35953da1') version('1.0.2d', '38dd619b2e77cbac69b99f52a053d25a') version('1.0.2e', '5262bfa25b60ed9de9f28d5d52d77fc5') version('1.0.2f', 'b3bf73f507172be9292ea2a8c28b659d') version('1.0.2g', 'f3c710c045cdee5fd114feb69feba7aa') + version('1.0.2h', '9392e65072ce4b614c1392eefc1f23d0') depends_on("zlib") parallel = False @@ -30,26 +33,14 @@ class Openssl(Package): # Same idea, but just to avoid issuing the same message multiple times warnings_given_to_user = getattr(Openssl, '_warnings_given', {}) if openssl_url is None: - latest = 'http://www.openssl.org/source/openssl-{version}.tar.gz' - older = 'http://www.openssl.org/source/old/{version_number}/openssl-{version_full}.tar.gz' - # Try to use the url where the latest tarballs are stored. If the url does not exist (404), then - # return the url for older format - 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 self.spec.satisfies('@external'): + # The version @external is reserved to system openssl. In that case return a fake url and exit + openssl_url = '@external (reserved version for system openssl)' 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)) + tty.msg('Using openssl@external : the version @external is reserved for system openssl') warnings_given_to_user[version] = True else: - openssl_url = latest_url - # Store the computed URL + openssl_url = self.check_for_outdated_release(version, warnings_given_to_user) # Store the computed URL openssl_urls[version] = openssl_url # Store the updated dictionary of URLS Openssl._openssl_url = openssl_urls @@ -58,6 +49,28 @@ class Openssl(Package): return openssl_url + def check_for_outdated_release(self, version, warnings_given_to_user): + latest = 'ftp://ftp.openssl.org/source/openssl-{version}.tar.gz' + older = 'http://www.openssl.org/source/old/{version_number}/openssl-{version_full}.tar.gz' + # Try to use the url where the latest tarballs are stored. If the url does not exist (404), then + # return the url for older format + version_number = '.'.join([str(x) for x in version[:-1]]) + try: + openssl_url = latest.format(version=version) + urllib.urlopen(openssl_url) + except IOError: + openssl_url = older.format(version_number=version_number, version_full=version) + # 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 + + return openssl_url + def install(self, spec, prefix): # OpenSSL uses a variable APPS in its Makefile. If it happens to be set # in the environment, then this will override what is set in the diff --git a/var/spack/repos/builtin/packages/p4est/package.py b/var/spack/repos/builtin/packages/p4est/package.py index 1e2969fe64..adf75babb9 100644 --- a/var/spack/repos/builtin/packages/p4est/package.py +++ b/var/spack/repos/builtin/packages/p4est/package.py @@ -7,10 +7,17 @@ class P4est(Package): version('1.1', '37ba7f4410958cfb38a2140339dbf64f') - # disable by default to make it work on frontend of clusters - variant('tests', default=False, description='Run small tests') + variant('tests', default=True, description='Run small tests') + # build dependencies + depends_on('automake') + depends_on('autoconf') + depends_on('libtool@2.4.2:') + + # other dependencies + depends_on('lua') # Needed for the submodule sc depends_on('mpi') + depends_on('zlib') def install(self, spec, prefix): options = ['--enable-mpi', @@ -19,16 +26,20 @@ class P4est(Package): '--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'), + 'CC=%s' % self.spec['mpi'].mpicc, + 'CXX=%s' % self.spec['mpi'].mpicxx, + 'FC=%s' % self.spec['mpi'].mpifc, + 'F77=%s' % self.spec['mpi'].mpif77 ] configure('--prefix=%s' % prefix, *options) make() + # Make tests optional as sometimes mpiexec can't be run with an error: + # mpiexec has detected an attempt to run as root. + # Running at root is *strongly* discouraged as any mistake (e.g., in + # defining TMPDIR) or bug can result in catastrophic damage to the OS + # file system, leaving your system in an unusable state. if '+tests' in self.spec: - make("check") - + make("check") make("install") diff --git a/var/spack/repos/builtin/packages/paradiseo/enable_eoserial.patch b/var/spack/repos/builtin/packages/paradiseo/enable_eoserial.patch new file mode 100644 index 0000000000..8b3ccfeb84 --- /dev/null +++ b/var/spack/repos/builtin/packages/paradiseo/enable_eoserial.patch @@ -0,0 +1,14 @@ +diff --git a/eo/src/CMakeLists.txt b/eo/src/CMakeLists.txt +index b2b445a..d45ddc7 100644 +--- a/eo/src/CMakeLists.txt ++++ b/eo/src/CMakeLists.txt +@@ -47,7 +47,7 @@ install(DIRECTORY do es ga gp other utils + add_subdirectory(es) + add_subdirectory(ga) + add_subdirectory(utils) +-#add_subdirectory(serial) ++add_subdirectory(serial) # Required when including <paradiseo/eo/utils/eoTimer.h> , which is need by <paradiseo/eo/mpi/eoMpi.h> + + if(ENABLE_PYEO) + add_subdirectory(pyeo) +
\ No newline at end of file diff --git a/var/spack/repos/builtin/packages/paradiseo/fix_osx_detection.patch b/var/spack/repos/builtin/packages/paradiseo/fix_osx_detection.patch new file mode 100644 index 0000000000..27b240f673 --- /dev/null +++ b/var/spack/repos/builtin/packages/paradiseo/fix_osx_detection.patch @@ -0,0 +1,13 @@ +diff --git a/cmake/Config.cmake b/cmake/Config.cmake +index 02593ba..d198ca9 100644 +--- a/cmake/Config.cmake ++++ b/cmake/Config.cmake +@@ -6,7 +6,7 @@ if(${CMAKE_SYSTEM_NAME} MATCHES "Darwin") + + # detect OS X version. (use '/usr/bin/sw_vers -productVersion' to extract V from '10.V.x'.) + execute_process (COMMAND /usr/bin/sw_vers -productVersion OUTPUT_VARIABLE MACOSX_VERSION_RAW) +- string(REGEX REPLACE "10\\.([0-9]).*" "\\1" MACOSX_VERSION "${MACOSX_VERSION_RAW}") ++ string(REGEX REPLACE "10\\.([0-9]+).*" "\\1" MACOSX_VERSION "${MACOSX_VERSION_RAW}") + if(${MACOSX_VERSION} LESS 5) + message(FATAL_ERROR "Unsupported version of OS X : ${MACOSX_VERSION_RAW}") + return() diff --git a/var/spack/repos/builtin/packages/paradiseo/fix_tests.patch b/var/spack/repos/builtin/packages/paradiseo/fix_tests.patch new file mode 100644 index 0000000000..607c5d5262 --- /dev/null +++ b/var/spack/repos/builtin/packages/paradiseo/fix_tests.patch @@ -0,0 +1,13 @@ +diff --git a/moeo/test/t-moeo2DMinHypervolumeArchive.cpp b/moeo/test/t-moeo2DMinHypervolumeArchive.cpp +index 994a9a4..c4ba77b 100644 +--- a/moeo/test/t-moeo2DMinHypervolumeArchive.cpp ++++ b/moeo/test/t-moeo2DMinHypervolumeArchive.cpp +@@ -41,7 +41,7 @@ + #include <moeo> + #include <cassert> + +-#include<archive/moeo2DMinHyperVolumeArchive.h> ++#include<archive/moeo2DMinHypervolumeArchive.h> + + //----------------------------------------------------------------------------- + diff --git a/var/spack/repos/builtin/packages/paradiseo/fix_tutorials.patch b/var/spack/repos/builtin/packages/paradiseo/fix_tutorials.patch new file mode 100644 index 0000000000..14cb5fed74 --- /dev/null +++ b/var/spack/repos/builtin/packages/paradiseo/fix_tutorials.patch @@ -0,0 +1,13 @@ +diff --git a/eo/tutorial/Lesson3/exercise3.1.cpp b/eo/tutorial/Lesson3/exercise3.1.cpp +index dc37479..d178941 100644 +--- a/eo/tutorial/Lesson3/exercise3.1.cpp ++++ b/eo/tutorial/Lesson3/exercise3.1.cpp +@@ -289,7 +289,7 @@ void main_function(int argc, char **argv) + checkpoint.add(fdcStat); + + // The Stdout monitor will print parameters to the screen ... +- eoStdoutMonitor monitor(false); ++ eoStdoutMonitor monitor; + + // when called by the checkpoint (i.e. at every generation) + checkpoint.add(monitor); diff --git a/var/spack/repos/builtin/packages/paradiseo/package.py b/var/spack/repos/builtin/packages/paradiseo/package.py new file mode 100644 index 0000000000..34766099da --- /dev/null +++ b/var/spack/repos/builtin/packages/paradiseo/package.py @@ -0,0 +1,66 @@ +from spack import * +import sys + +class Paradiseo(Package): + """A C++ white-box object-oriented framework dedicated to the reusable design of metaheuristics.""" + homepage = "http://paradiseo.gforge.inria.fr/" + + # Installing from the development version is a better option at this + # point than using the very old supplied packages + version('head', git='https://gforge.inria.fr/git/paradiseo/paradiseo.git') + # This is a version that the package formula author has tested successfully. + # However, the clone is very large (~1Gb git history). The history in the + # head version has been trimmed significantly. + version('dev-safe', git='https://gforge.inria.fr/git/paradiseo/paradiseo.git', + commit='dbb8fbe9a786efd4d1c26408ac1883442e7643a6') + + variant('mpi', default=True, description='Compile with parallel and distributed metaheuristics module') + variant('smp', default=True, description='Compile with symmetric multi-processing module ') + variant('edo', default=True, description='Compile with (Experimental) EDO module') + #variant('tests', default=False, description='Compile with build tests') + #variant('doc', default=False, description='Compile with documentation') + variant('debug', default=False, description='Builds a debug version of the libraries') + variant('openmp', default=False, description='Enable OpenMP support') + variant('gnuplot', default=False, description='Enable GnuPlot support') + + # Required dependencies + depends_on ("cmake") + + # Optional dependencies + depends_on ("mpi", when="+mpi") + depends_on ("doxygen", when='+doc') + depends_on ("gnuplot", when='+gnuplot') + depends_on ("eigen", when='+edo') + depends_on ("boost~mpi", when='+edo~mpi') + depends_on ("boost+mpi", when='+edo+mpi') + + # Patches + patch('enable_eoserial.patch') + patch('fix_osx_detection.patch') + patch('fix_tests.patch') + patch('fix_tutorials.patch') + + def install(self, spec, prefix): + options = [] + options.extend(std_cmake_args) + + options.extend([ + '-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'), + '-DINSTALL_TYPE:STRING=MIN', + '-DMPI:BOOL=%s' % ('TRUE' if '+mpi' in spec else 'FALSE'), + '-DSMP:BOOL=%s' % ('TRUE' if '+smp' in spec else 'FALSE'), # Note: This requires a C++11 compatible compiler + '-DEDO:BOOL=%s' % ('TRUE' if '+edo' in spec else 'FALSE'), + '-DENABLE_CMAKE_TESTING:BOOL=%s' % ('TRUE' if '+tests' in spec else 'FALSE'), + '-DENABLE_OPENMP:BOOL=%s' % ('TRUE' if '+openmp' in spec else 'FALSE'), + '-DENABLE_GNUPLOT:BOOL=%s' % ('TRUE' if '+gnuplot' in spec else 'FALSE') + ]) + + with working_dir('spack-build', create=True): + # Configure + cmake('..', *options) + + # Build, test and install + make("VERBOSE=1") + if '+tests' in spec: + make("test") + make("install") diff --git a/var/spack/repos/builtin/packages/py-SQLAlchemy/package.py b/var/spack/repos/builtin/packages/py-SQLAlchemy/package.py new file mode 100644 index 0000000000..9aecc95c63 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-SQLAlchemy/package.py @@ -0,0 +1,14 @@ +from spack import * + +class PySqlalchemy(Package): + """The Python SQL Toolkit and Object Relational Mapper""" + + homepage = 'http://www.sqlalchemy.org/' + url = "https://pypi.python.org/packages/source/S/SQLAlchemy/SQLAlchemy-1.0.12.tar.gz" + + version('1.0.12', '6d19ef29883bbebdcac6613cf391cac4') + + extends('python') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-bottleneck/package.py b/var/spack/repos/builtin/packages/py-bottleneck/package.py index 0aa4208b4d..d43308543b 100644 --- a/var/spack/repos/builtin/packages/py-bottleneck/package.py +++ b/var/spack/repos/builtin/packages/py-bottleneck/package.py @@ -7,7 +7,7 @@ class PyBottleneck(Package): version('1.0.0', '380fa6f275bd24f27e7cf0e0d752f5d2') - extends('python', ignore=r'bin/f2py$') + extends('python') depends_on('py-numpy') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/py-csvkit/package.py b/var/spack/repos/builtin/packages/py-csvkit/package.py new file mode 100644 index 0000000000..def30457be --- /dev/null +++ b/var/spack/repos/builtin/packages/py-csvkit/package.py @@ -0,0 +1,22 @@ +from spack import * + +class PyCsvkit(Package): + """A library of utilities for working with CSV, the king of tabular file + formats""" + + homepage = 'http://csvkit.rtfd.org/' + url = "https://pypi.python.org/packages/source/c/csvkit/csvkit-0.9.1.tar.gz" + + version('0.9.1', '48d78920019d18846933ee969502fff6') + + extends('python') + + depends_on('py-dateutil') + depends_on('py-dbf') + depends_on('py-xlrd') + depends_on('py-SQLAlchemy') + depends_on('py-six') + depends_on('py-openpyxl') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-dbf/package.py b/var/spack/repos/builtin/packages/py-dbf/package.py new file mode 100644 index 0000000000..698b221903 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-dbf/package.py @@ -0,0 +1,15 @@ +from spack import * + +class PyDbf(Package): + """Pure python package for reading/writing dBase, FoxPro, and Visual FoxPro + .dbf files (including memos)""" + + homepage = 'https://pypi.python.org/pypi/dbf' + url = "https://pypi.python.org/packages/source/d/dbf/dbf-0.96.005.tar.gz" + + version('0.96.005', 'bce1a1ed8b454a30606e7e18dd2f8277') + + extends('python') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-jdcal/package.py b/var/spack/repos/builtin/packages/py-jdcal/package.py new file mode 100644 index 0000000000..54169b2c21 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-jdcal/package.py @@ -0,0 +1,14 @@ +from spack import * + +class PyJdcal(Package): + """Julian dates from proleptic Gregorian and Julian calendars""" + + homepage = 'http://github.com/phn/jdcal' + url = "https://pypi.python.org/packages/source/j/jdcal/jdcal-1.2.tar.gz" + + version('1.2', 'ab8d5ba300fd1eb01514f363d19b1eb9') + + extends('python') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-matplotlib/package.py b/var/spack/repos/builtin/packages/py-matplotlib/package.py index 19194c942e..1a190cc5f3 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.*$|bin/pbr$|bin/f2py$') + extends('python', ignore=r'bin/nosetests.*$|bin/pbr$') depends_on('py-pyside', when='+gui') depends_on('py-ipython', when='+ipython') diff --git a/var/spack/repos/builtin/packages/py-numexpr/package.py b/var/spack/repos/builtin/packages/py-numexpr/package.py index 081a79dec6..0076aa456b 100644 --- a/var/spack/repos/builtin/packages/py-numexpr/package.py +++ b/var/spack/repos/builtin/packages/py-numexpr/package.py @@ -9,7 +9,7 @@ class PyNumexpr(Package): version('2.4.6', '17ac6fafc9ea1ce3eb970b9abccb4fbd') version('2.5', '84f66cced45ba3e30dcf77a937763aaa') - extends('python', ignore=r'bin/f2py$') + extends('python') depends_on('py-numpy') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/py-openpyxl/package.py b/var/spack/repos/builtin/packages/py-openpyxl/package.py new file mode 100644 index 0000000000..87ff9f3521 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-openpyxl/package.py @@ -0,0 +1,17 @@ +from spack import * + +class PyOpenpyxl(Package): + """A Python library to read/write Excel 2007 xlsx/xlsm files""" + + homepage = 'http://openpyxl.readthedocs.org/' + url = "https://pypi.python.org/packages/source/o/openpyxl/openpyxl-2.4.0-a1.tar.gz" + + version('2.4.0-a1', 'e5ca6d23ceccb15115d45cdf26e736fc') + + extends('python') + + depends_on('py-jdcal') + depends_on('py-setuptools') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-pandas/package.py b/var/spack/repos/builtin/packages/py-pandas/package.py index 2320b1f92f..59d515eb5e 100644 --- a/var/spack/repos/builtin/packages/py-pandas/package.py +++ b/var/spack/repos/builtin/packages/py-pandas/package.py @@ -10,7 +10,7 @@ class PyPandas(Package): version('0.16.1', 'fac4f25748f9610a3e00e765474bdea8') version('0.18.0', 'f143762cd7a59815e348adf4308d2cf6') - extends('python', ignore=r'bin/f2py$') + extends('python') depends_on('py-dateutil') depends_on('py-numpy') depends_on('py-setuptools') diff --git a/var/spack/repos/builtin/packages/py-scikit-image/package.py b/var/spack/repos/builtin/packages/py-scikit-image/package.py index 22ce1f8374..d13339060e 100644 --- a/var/spack/repos/builtin/packages/py-scikit-image/package.py +++ b/var/spack/repos/builtin/packages/py-scikit-image/package.py @@ -7,7 +7,7 @@ class PyScikitImage(Package): version('0.12.3', '04ea833383e0b6ad5f65da21292c25e1') - extends('python', ignore=r'bin/.*\.py$|bin/f2py$') + extends('python', ignore=r'bin/.*\.py$') depends_on('py-dask') depends_on('py-pillow') diff --git a/var/spack/repos/builtin/packages/py-xlrd/package.py b/var/spack/repos/builtin/packages/py-xlrd/package.py new file mode 100644 index 0000000000..8f25c06aad --- /dev/null +++ b/var/spack/repos/builtin/packages/py-xlrd/package.py @@ -0,0 +1,15 @@ +from spack import * + +class PyXlrd(Package): + """Library for developers to extract data from Microsoft Excel (tm) + spreadsheet files""" + + homepage = 'http://www.python-excel.org/' + url = "https://pypi.python.org/packages/source/x/xlrd/xlrd-0.9.4.tar.gz" + + version('0.9.4', '911839f534d29fe04525ef8cd88fe865') + + extends('python') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index f5237c3b57..f7e1d94567 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -151,6 +151,8 @@ class Python(Package): patterns.append(r'setuptools\.pth') patterns.append(r'bin/easy_install[^/]*$') patterns.append(r'setuptools.*egg$') + if ext_pkg.name != 'py-numpy': + patterns.append(r'bin/f2py$') return match_predicate(ignore_arg, patterns) diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py index 93688fb777..1e1d6302f3 100644 --- a/var/spack/repos/builtin/packages/qt/package.py +++ b/var/spack/repos/builtin/packages/qt/package.py @@ -101,7 +101,7 @@ class Qt(Package): @property def common_config_args(self): - return [ + config_args = [ '-prefix', self.prefix, '-v', '-opensource', @@ -115,7 +115,16 @@ class Qt(Package): '-no-openvg', '-no-pch', # NIS is deprecated in more recent glibc - '-no-nis'] + '-no-nis' + ] + + if '+gtk' in self.spec: + config_args.append('-gtkstyle') + else: + config_args.append('-no-gtkstyle') + + return config_args + # Don't disable all the database drivers, but should # really get them into spack at some point. @@ -128,8 +137,7 @@ class Qt(Package): '-thread', '-shared', '-release', - '-fast' - ) + '-fast') @when('@4') def configure(self): diff --git a/var/spack/repos/builtin/packages/qthreads/ldflags.patch b/var/spack/repos/builtin/packages/qthreads/ldflags.patch new file mode 100644 index 0000000000..0c15eab386 --- /dev/null +++ b/var/spack/repos/builtin/packages/qthreads/ldflags.patch @@ -0,0 +1,11 @@ +--- a/configure ++++ b/configure +@@ -40456,7 +40456,7 @@ + hwloc_saved_LDFLAGS="$LDFLAGS" + if test "x$with_hwloc" != x; then + CPPFLAGS="-I$with_hwloc/include $CPPFLAGS" +- LDFLAGS="-L$with_hwloc/lib $CPPFLAGS" ++ LDFLAGS="-L$with_hwloc/lib $LDFLAGS" + fi + + diff --git a/var/spack/repos/builtin/packages/qthreads/package.py b/var/spack/repos/builtin/packages/qthreads/package.py index dacdb71524..5da9340927 100644 --- a/var/spack/repos/builtin/packages/qthreads/package.py +++ b/var/spack/repos/builtin/packages/qthreads/package.py @@ -16,7 +16,12 @@ class Qthreads(Package): version('1.10', '5af8c8bbe88c2a6d45361643780d1671') + patch("ldflags.patch") + patch("restrict.patch") + patch("trap.patch") + def install(self, spec, prefix): - configure("--prefix=%s" % prefix) + configure("--prefix=%s" % prefix, + "--enable-guard-pages") make() make("install") diff --git a/var/spack/repos/builtin/packages/qthreads/restrict.patch b/var/spack/repos/builtin/packages/qthreads/restrict.patch new file mode 100644 index 0000000000..4c95714f6b --- /dev/null +++ b/var/spack/repos/builtin/packages/qthreads/restrict.patch @@ -0,0 +1,12 @@ +--- a/include/qthread/common.h.in ++++ b/include/qthread/common.h.in +@@ -84,7 +84,9 @@ + /* Define to the equivalent of the C99 'restrict' keyword, or to + nothing if this is not supported. Do not define if restrict is + supported directly. */ ++#ifndef restrict + #undef restrict ++#endif + /* Work around a bug in Sun C++: it does not support _Restrict or + __restrict__, even though the corresponding Sun C compiler ends up with + "#define restrict _Restrict" or "#define restrict __restrict__" in the diff --git a/var/spack/repos/builtin/packages/qthreads/trap.patch b/var/spack/repos/builtin/packages/qthreads/trap.patch new file mode 100644 index 0000000000..7aa94d82d5 --- /dev/null +++ b/var/spack/repos/builtin/packages/qthreads/trap.patch @@ -0,0 +1,11 @@ +--- a/include/qthread/qthread.hpp ++++ b/include/qthread/qthread.hpp +@@ -236,7 +236,7 @@ + return qthread_incr64((uint64_t *)operand, incr); + + default: +- *(int *)(0) = 0; ++ __builtin_trap(); + } + return T(0); // never hit - keep compiler happy + } diff --git a/var/spack/repos/builtin/packages/raja/package.py b/var/spack/repos/builtin/packages/raja/package.py new file mode 100644 index 0000000000..f807ab71af --- /dev/null +++ b/var/spack/repos/builtin/packages/raja/package.py @@ -0,0 +1,12 @@ +from spack import * + +class Raja(Package): + """RAJA Parallel Framework.""" + homepage = "http://software.llnl.gov/RAJA/" + + version('git', git='https://github.com/LLNL/RAJA.git', branch="master") + + def install(self, spec, prefix): + cmake('.',*std_cmake_args) + make() + make('install') diff --git a/var/spack/repos/builtin/packages/scons/package.py b/var/spack/repos/builtin/packages/scons/package.py new file mode 100644 index 0000000000..594aeced88 --- /dev/null +++ b/var/spack/repos/builtin/packages/scons/package.py @@ -0,0 +1,13 @@ +from spack import * + +class Scons(Package): + """SCons is a software construction tool""" + homepage = "http://scons.org" + url = "http://downloads.sourceforge.net/project/scons/scons/2.5.0/scons-2.5.0.tar.gz" + + version('2.5.0', '9e00fa0df8f5ca5c5f5975b40e0ed354') + + extends('python') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/serf/package.py b/var/spack/repos/builtin/packages/serf/package.py new file mode 100644 index 0000000000..a5c9057b99 --- /dev/null +++ b/var/spack/repos/builtin/packages/serf/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 Serf(Package): + """Apache Serf - a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library""" + homepage = 'https://serf.apache.org/' + url = 'https://archive.apache.org/dist/serf/serf-1.3.8.tar.bz2' + + version('1.3.8', '1d45425ca324336ce2f4ae7d7b4cfbc5567c5446') + + depends_on('apr') + depends_on('apr-util') + depends_on('scons') + depends_on('expat') + depends_on('openssl') + + def install(self, spec, prefix): + scons = which("scons") + + options = ['PREFIX=%s' % prefix] + options.append('APR=%s' % spec['apr'].prefix) + options.append('APU=%s' % spec['apr-util'].prefix) + options.append('OPENSSL=%s' % spec['openssl'].prefix) + options.append('LINKFLAGS=-L%s/lib' % spec['expat'].prefix) + options.append('CPPFLAGS=-I%s/include' % spec['expat'].prefix) + + scons(*options) + scons('install') diff --git a/var/spack/repos/builtin/packages/subversion/package.py b/var/spack/repos/builtin/packages/subversion/package.py index 5db1c3eb92..04cde94aad 100644 --- a/var/spack/repos/builtin/packages/subversion/package.py +++ b/var/spack/repos/builtin/packages/subversion/package.py @@ -37,6 +37,7 @@ class Subversion(Package): depends_on('apr-util') depends_on('zlib') depends_on('sqlite') + depends_on('serf') # Optional: We need swig if we want the Perl, Python or Ruby # bindings. @@ -54,6 +55,7 @@ class Subversion(Package): 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-serf=%s' % spec['serf'].prefix) #options.append('--with-swig=%s' % spec['swig'].prefix) configure(*options) diff --git a/var/spack/repos/builtin/packages/superlu-dist/package.py b/var/spack/repos/builtin/packages/superlu-dist/package.py index 5cf5e129b4..3420d9b90a 100644 --- a/var/spack/repos/builtin/packages/superlu-dist/package.py +++ b/var/spack/repos/builtin/packages/superlu-dist/package.py @@ -6,7 +6,9 @@ class SuperluDist(Package): 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('5.0.0', '2b53baf1b0ddbd9fcf724992577f0670') + # default to version 4.3 since petsc and trilinos are not tested with 5.0. + version('4.3', 'ee66c84e37b4f7cc557771ccc3dc43ae', preferred=True) version('4.2', 'ae9fafae161f775fbac6eba11e530a65') version('4.1', '4edee38cc29f687bd0c8eb361096a455') version('4.0', 'c0b98b611df227ae050bc1635c6940e0') diff --git a/var/spack/repos/builtin/packages/the_silver_searcher/package.py b/var/spack/repos/builtin/packages/the_silver_searcher/package.py index e4020b6766..30f06354bf 100644 --- a/var/spack/repos/builtin/packages/the_silver_searcher/package.py +++ b/var/spack/repos/builtin/packages/the_silver_searcher/package.py @@ -9,6 +9,7 @@ class TheSilverSearcher(Package): depends_on('pcre') depends_on('xz') + depends_on('pkg-config') def install(self, spec, prefix): configure("--prefix=%s" % prefix) diff --git a/var/spack/repos/builtin/packages/turbomole/package.py b/var/spack/repos/builtin/packages/turbomole/package.py new file mode 100644 index 0000000000..acc95e3b10 --- /dev/null +++ b/var/spack/repos/builtin/packages/turbomole/package.py @@ -0,0 +1,124 @@ +from spack import * +import os +import subprocess + +class Turbomole(Package): + """TURBOMOLE: Program Package for ab initio Electronic Structure + Calculations. NB: Requires a license to download.""" + + # NOTE: Turbomole requires purchase of a license to download. Go to the + # NOTE: Turbomole home page, http://www.turbomole-gmbh.com, for details. + # NOTE: Spack will search the current directory for this file. It is + # NOTE: probably best to add this file to a Spack mirror so that it can be + # NOTE: found from anywhere. For information on setting up a Spack mirror + # NOTE: see http://software.llnl.gov/spack/mirrors.html + + homepage = "http://www.turbomole-gmbh.com/" + + version('7.0.2', '92b97e1e52e8dcf02a4d9ac0147c09d6', + url="file://%s/turbolinux702.tar.gz" % os.getcwd()) + + variant('mpi', default=False, description='Set up MPI environment') + variant('smp', default=False, description='Set up SMP environment') + + # Turbomole's install is odd. There are three variants + # - serial + # - parallel, MPI + # - parallel, SMP + # + # Only one of these can be active at a time. MPI and SMP are set as + # variants so there could be up to 3 installs per version. Switching + # between them would be accomplished with `module swap` commands. + + def do_fetch(self, mirror_only=True): + if '+mpi' in self.spec and '+smp' in self.spec: + raise InstallError('Can not have both SMP and MPI enabled in the same build.') + super(Turbomole, self).do_fetch(mirror_only) + + def get_tm_arch(self): + # For python-2.7 we could use `tm_arch = subprocess.check_output()` + # Use the following for compatibility with python 2.6 + if 'TURBOMOLE' in os.getcwd(): + tm_arch = subprocess.Popen(['sh', 'scripts/sysname'], + stdout=subprocess.PIPE).communicate()[0] + return tm_arch.rstrip('\n') + else: + return + + def install(self, spec, prefix): + if spec.satisfies('@:7.0.2'): + calculate_version = 'calculate_2.4_linux64' + molecontrol_version = 'MoleControl_2.5' + + tm_arch=self.get_tm_arch() + + tar = which('tar') + dst = join_path(prefix, 'TURBOMOLE') + + tar('-x', '-z', '-f', 'thermocalc.tar.gz') + with working_dir('thermocalc'): + cmd = 'sh install <<<y' + subprocess.call(cmd, shell=True) + + install_tree('basen', join_path(dst, 'basen')) + install_tree('cabasen', join_path(dst, 'cabasen')) + install_tree(calculate_version, join_path(dst, calculate_version)) + install_tree('cbasen', join_path(dst, 'cbasen')) + install_tree('DOC', join_path(dst, 'DOC')) + install_tree('jbasen', join_path(dst, 'jbasen')) + install_tree('jkbasen', join_path(dst, 'jkbasen')) + install_tree(molecontrol_version, join_path(dst, molecontrol_version)) + install_tree('parameter', join_path(dst, 'parameter')) + install_tree('perlmodules', join_path(dst, 'perlmodules')) + install_tree('scripts', join_path(dst, 'scripts')) + install_tree('smprun_scripts', join_path(dst, 'smprun_scripts')) + install_tree('structures', join_path(dst, 'structures')) + install_tree('thermocalc', join_path(dst, 'thermocalc')) + install_tree('TURBOTEST', join_path(dst, 'TURBOTEST')) + install_tree('xbasen', join_path(dst, 'xbasen')) + + install('Config_turbo_env', dst) + install('Config_turbo_env.tcsh', dst) + install('README', dst) + install('README_LICENSES', dst) + install('TURBOMOLE_702_LinuxPC', dst) + + if '+mpi' in spec: + install_tree('bin/%s_mpi' % tm_arch, join_path(dst, 'bin', '%s_mpi' % tm_arch)) + install_tree('libso/%s_mpi' % tm_arch, join_path(dst, 'libso', '%s_mpi' % tm_arch)) + install_tree('mpirun_scripts/%s_mpi' % tm_arch, join_path(dst, 'mpirun_scripts', '%s_mpi' % tm_arch)) + elif '+smp' in spec: + install_tree('bin/%s_smp' % tm_arch, join_path(dst, 'bin', '%s_smp' % tm_arch)) + install_tree('libso/%s_smp' % tm_arch, join_path(dst, 'libso', '%s_smp' % tm_arch)) + install_tree('mpirun_scripts/%s_smp' % tm_arch, join_path(dst, 'mpirun_scripts', '%s_smp' % tm_arch)) + else: + install_tree('bin/%s' % tm_arch, join_path(dst, 'bin', tm_arch)) + if '+mpi' in spec or '+smp' in spec: + install('mpirun_scripts/ccsdf12', join_path(dst, 'mpirun_scripts')) + install('mpirun_scripts/dscf', join_path(dst, 'mpirun_scripts')) + install('mpirun_scripts/grad', join_path(dst, 'mpirun_scripts')) + install('mpirun_scripts/mpgrad', join_path(dst, 'mpirun_scripts')) + install('mpirun_scripts/pnoccsd', join_path(dst, 'mpirun_scripts')) + install('mpirun_scripts/rdgrad', join_path(dst, 'mpirun_scripts')) + install('mpirun_scripts/ricc2', join_path(dst, 'mpirun_scripts')) + install('mpirun_scripts/ridft', join_path(dst, 'mpirun_scripts')) + + def setup_environment(self, spack_env, run_env): + if self.spec.satisfies('@:7.0.2'): + molecontrol_version = 'MoleControl_2.5' + + tm_arch=self.get_tm_arch() + + run_env.set('TURBODIR', join_path(self.prefix, 'TURBOMOLE')) + run_env.set('MOLE_CONTROL', join_path(self.prefix, 'TURBOMOLE', molecontrol_version)) + + run_env.prepend_path('PATH', join_path(self.prefix, 'TURBOMOLE', 'thermocalc')) + run_env.prepend_path('PATH', join_path(self.prefix, 'TURBOMOLE', 'scripts')) + if '+mpi' in self.spec: + run_env.set('PARA_ARCH', 'MPI') + run_env.prepend_path('PATH', join_path(self.prefix, 'TURBOMOLE', 'bin', '%s_mpi' % tm_arch)) + elif '+smp' in self.spec: + run_env.set('PARA_ARCH', 'SMP') + run_env.prepend_path('PATH', join_path(self.prefix, 'TURBOMOLE', 'bin', '%s_smp' % tm_arch)) + else: + run_env.prepend_path('PATH', join_path(self.prefix, 'TURBOMOLE', 'bin', tm_arch)) diff --git a/var/spack/repos/builtin/packages/unibilium/package.py b/var/spack/repos/builtin/packages/unibilium/package.py new file mode 100644 index 0000000000..ef5de56f79 --- /dev/null +++ b/var/spack/repos/builtin/packages/unibilium/package.py @@ -0,0 +1,12 @@ +from spack import * + +class Unibilium(Package): + """A terminfo parsing library""" + homepage = "https://github.com/mauke/unibilium" + url = "https://github.com/mauke/unibilium/archive/v1.2.0.tar.gz" + + version('1.2.0', '9b1c97839a880a373da6c097443b43c4') + + def install(self, spec, prefix): + make("PREFIX="+prefix) + make("install", "PREFIX="+prefix) diff --git a/var/spack/repos/builtin/packages/xerces-c/package.py b/var/spack/repos/builtin/packages/xerces-c/package.py index e36fb936e0..bd02ddcd4b 100644 --- a/var/spack/repos/builtin/packages/xerces-c/package.py +++ b/var/spack/repos/builtin/packages/xerces-c/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 xerces-c -# -# You can always get back here to change things with: -# -# spack edit xerces-c -# -# See the spack documentation for more information on building -# packages. -# from spack import * class XercesC(Package): diff --git a/var/spack/repos/builtin/packages/zoltan/package.py b/var/spack/repos/builtin/packages/zoltan/package.py index e20ae81adb..738dfb508b 100644 --- a/var/spack/repos/builtin/packages/zoltan/package.py +++ b/var/spack/repos/builtin/packages/zoltan/package.py @@ -1,3 +1,4 @@ +import re, os, glob from spack import * class Zoltan(Package): @@ -12,8 +13,13 @@ class Zoltan(Package): base_url = "http://www.cs.sandia.gov/~kddevin/Zoltan_Distributions" version('3.83', '1ff1bc93f91e12f2c533ddb01f2c095f') + version('3.8', '9d8fba8a990896881b85351d4327c4a9') + version('3.6', '9cce794f7241ecd8dbea36c3d7a880f9') version('3.3', '5eb8f00bda634b25ceefa0122bd18d65') + variant('debug', default=False, description='Builds a debug version of the library') + variant('shared', default=True, description='Builds a shared version of the library') + variant('fortran', default=True, description='Enable Fortran support') variant('mpi', default=False, description='Enable MPI support') @@ -24,28 +30,49 @@ class Zoltan(Package): '--enable-f90interface' if '+fortan' in spec else '--disable-f90interface', '--enable-mpi' if '+mpi' in spec else '--disable-mpi', ] + config_cflags = [ + '-O0' if '+debug' in spec else '-O3', + '-g' if '+debug' in spec else '-g0', + ] + + if '+shared' in spec: + config_args.append('--with-ar=$(CXX) -shared $(LDFLAGS) -o') + config_args.append('RANLIB=echo') + config_cflags.append('-fPIC') if '+mpi' in spec: - config_args.append('--with-mpi=%s' % spec['mpi'].prefix) - config_args.append('--with-mpi-compilers=%s' % spec['mpi'].prefix.bin) config_args.append('CC=%s/mpicc' % spec['mpi'].prefix.bin) config_args.append('CXX=%s/mpicxx' % spec['mpi'].prefix.bin) + config_args.append('--with-mpi=%s' % spec['mpi'].prefix) + config_args.append('--with-mpi-compilers=%s' % spec['mpi'].prefix.bin) # NOTE: Early versions of Zoltan come packaged with a few embedded # library packages (e.g. ParMETIS, Scotch), which messes with Spack's # ability to descend directly into the package's source directory. - if spec.satisfies('@:3.3'): + if spec.satisfies('@:3.6'): cd('Zoltan_v%s' % self.version) mkdirp('build') cd('build') config_zoltan = Executable('../configure') - config_zoltan('--prefix=%s' % pwd(), *config_args) + config_zoltan( + '--prefix=%s' % pwd(), + '--with-cflags=%s' % ' '.join(config_cflags), + '--with-cxxflags=%s' % ' '.join(config_cflags), + *config_args) make() make('install') + # NOTE: Unfortunately, Zoltan doesn't provide any configuration options for + # the extension of the output library files, so this script must change these + # extensions as a post-processing step. + if '+shared' in spec: + for libpath in glob.glob('lib/*.a'): + libdir, libname = (os.path.dirname(libpath), os.path.basename(libpath)) + move(libpath, os.path.join(libdir, re.sub(r'\.a$', '.so', libname))) + mkdirp(prefix) move('include', prefix) move('lib', prefix) |