diff options
Diffstat (limited to 'var')
31 files changed, 1196 insertions, 300 deletions
diff --git a/var/spack/repos/builtin/packages/R/package.py b/var/spack/repos/builtin/packages/R/package.py index 2471dff09b..7c4aa3520c 100644 --- a/var/spack/repos/builtin/packages/R/package.py +++ b/var/spack/repos/builtin/packages/R/package.py @@ -1,4 +1,14 @@ +import functools +import glob +import inspect +import os +import re +from contextlib import closing + +import spack +from llnl.util.lang import match_predicate from spack import * +from spack.util.environment import * class R(Package): @@ -9,6 +19,8 @@ class R(Package): """ homepage = "https://www.r-project.org" url = "http://cran.cnr.berkeley.edu/src/base/R-3/R-3.1.2.tar.gz" + + extendable = True version('3.2.3', '1ba3dac113efab69e706902810cc2970') version('3.2.2', '57cef5c2e210a5454da1979562a10e5b') @@ -38,12 +50,57 @@ class R(Package): depends_on('tk') def install(self, spec, prefix): + rlibdir = join_path(prefix, 'rlib') options = ['--prefix=%s' % prefix, + '--libdir=%s' % rlibdir, '--enable-R-shlib', - '--enable-BLAS-shlib'] + '--enable-BLAS-shlib', + '--enable-R-framework=no'] if '+external-lapack' in spec: options.extend(['--with-blas', '--with-lapack']) configure(*options) make() make('install') + + # ======================================================================== + # Set up environment to make install easy for R extensions. + # ======================================================================== + + @property + def r_lib_dir(self): + return os.path.join('rlib', 'R', 'library') + + def setup_dependent_environment(self, spack_env, run_env, extension_spec): + # Set R_LIBS to include the library dir for the + # extension and any other R extensions it depends on. + r_libs_path = [] + for d in extension_spec.traverse(): + if d.package.extends(self.spec): + r_libs_path.append(os.path.join(d.prefix, self.r_lib_dir)) + + r_libs_path = ':'.join(r_libs_path) + spack_env.set('R_LIBS', r_libs_path) + + # For run time environment set only the path for extension_spec and prepend it to R_LIBS + if extension_spec.package.extends(self.spec): + run_env.prepend_path('R_LIBS', os.path.join(extension_spec.prefix, self.r_lib_dir)) + + + def setup_dependent_package(self, module, ext_spec): + """ + Called before R modules' install() methods. + + In most cases, extensions will only need to have one line:: + + R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file) + """ + # R extension builds can have a global R executable function + module.R = Executable(join_path(self.spec.prefix.bin, 'R')) + + # Add variable for library directry + module.r_lib_dir = os.path.join(ext_spec.prefix, self.r_lib_dir) + + # Make the site packages directory for extensions, if it does not exist already. + if ext_spec.package.is_extension: + mkdirp(module.r_lib_dir) 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/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/cbtf-argonavis/package.py b/var/spack/repos/builtin/packages/cbtf-argonavis/package.py index 7b07933911..90789a98f2 100644 --- a/var/spack/repos/builtin/packages/cbtf-argonavis/package.py +++ b/var/spack/repos/builtin/packages/cbtf-argonavis/package.py @@ -1,5 +1,5 @@ ################################################################################ -# Copyright (c) 2015 Krell Institute. All Rights Reserved. +# Copyright (c) 2015-2016 Krell Institute. All Rights Reserved. # # 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 @@ -24,43 +24,83 @@ class CbtfArgonavis(Package): homepage = "http://sourceforge.net/p/cbtf/wiki/Home/" # Mirror access template example - #url = "file:/g/g24/jeg/cbtf-argonavis-1.5.tar.gz" - #version('1.5', '1f7f6512f55409ed2135cfceabe26b82') + #url = "file:/home/jeg/OpenSpeedShop_ROOT/SOURCES/cbtf-argonavis-1.6.tar.gz" + #version('1.6', '0fafa0008478405c2c2319450f174ed4') - version('1.6', branch='master', git='http://git.code.sf.net/p/cbtf-argonavis/cbtf-argonavis') + version('1.6', branch='master', git='https://github.com/OpenSpeedShop/cbtf-argonavis.git') - depends_on("cmake@3.0.2:") + depends_on("cmake@3.0.2") + depends_on("boost@1.50.0:") depends_on("papi") + depends_on("mrnet@5.0.1:+lwthreads+krellpatch") depends_on("cbtf") depends_on("cbtf-krell") - depends_on("cuda") + depends_on("cuda@6.0.37") + #depends_on("cuda") parallel = False + def adjustBuildTypeParams_cmakeOptions(self, spec, cmakeOptions): + # Sets build type parameters into cmakeOptions the options that will enable the cbtf-krell built type settings + + compile_flags="-O2 -g" + BuildTypeOptions = [] + + # Set CMAKE_BUILD_TYPE to what cbtf-krell wants it to be, not the stdcmakeargs + for word in cmakeOptions[:]: + if word.startswith('-DCMAKE_BUILD_TYPE'): + cmakeOptions.remove(word) + if word.startswith('-DCMAKE_CXX_FLAGS'): + cmakeOptions.remove(word) + if word.startswith('-DCMAKE_C_FLAGS'): + cmakeOptions.remove(word) + if word.startswith('-DCMAKE_VERBOSE_MAKEFILE'): + cmakeOptions.remove(word) + BuildTypeOptions.extend([ + '-DCMAKE_VERBOSE_MAKEFILE=ON', + '-DCMAKE_BUILD_TYPE=None', + '-DCMAKE_CXX_FLAGS=%s' % compile_flags, + '-DCMAKE_C_FLAGS=%s' % compile_flags + ]) + + cmakeOptions.extend(BuildTypeOptions) + + def install(self, spec, prefix): # Look for package installation information in the cbtf and cbtf-krell prefixes cmake_prefix_path = join_path(spec['cbtf'].prefix) + ':' + join_path(spec['cbtf-krell'].prefix) - # FIXME, hard coded for testing purposes, we will alter when the external package feature is available - cuda_prefix_path = "/usr/local/cudatoolkit-6.0" - cupti_prefix_path = "/usr/local/cudatoolkit-6.0/extras/CUPTI" - - with working_dir('CUDA'): with working_dir('build', create=True): - cmake('..', - '-DCMAKE_INSTALL_PREFIX=%s' % prefix, - '-DCMAKE_LIBRARY_PATH=%s' % prefix.lib64, - '-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path, - '-DCUDA_INSTALL_PATH=%s' % cuda_prefix_path, - '-DCUDA_ROOT=%s' % cuda_prefix_path, - '-DCUPTI_ROOT=%s' % cupti_prefix_path, - '-DCUDA_DIR=%s' % cuda_prefix_path, - '-DPAPI_ROOT=%s' % spec['papi'].prefix, - '-DCBTF_PREFIX=%s' % spec['cbtf'].prefix, - *std_cmake_args) - make("clean") - make() - make("install") + cmakeOptions = [] + cmakeOptions.extend(['-DCMAKE_INSTALL_PREFIX=%s' % prefix, + '-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path, + '-DCUDA_DIR=%s' % spec['cuda'].prefix, + '-DCUDA_INSTALL_PATH=%s' % spec['cuda'].prefix, + '-DCUDA_TOOLKIT_ROOT_DIR=%s' % spec['cuda'].prefix, + '-DCUPTI_DIR=%s' % join_path(spec['cuda'].prefix + '/extras/CUPTI'), + '-DCUPTI_ROOT=%s' % join_path(spec['cuda'].prefix + '/extras/CUPTI'), + '-DPAPI_ROOT=%s' % spec['papi'].prefix, + '-DCBTF_DIR=%s' % spec['cbtf'].prefix, + '-DCBTF_KRELL_DIR=%s' % spec['cbtf-krell'].prefix, + '-DBOOST_ROOT=%s' % spec['boost'].prefix, + '-DBoost_DIR=%s' % spec['boost'].prefix, + '-DBOOST_LIBRARYDIR=%s' % spec['boost'].prefix.lib, + '-DMRNET_DIR=%s' % spec['mrnet'].prefix, + '-DBoost_NO_SYSTEM_PATHS=ON' + ]) + + # Add in the standard cmake arguments + cmakeOptions.extend(std_cmake_args) + + # Adjust the standard cmake arguments to what we want the build type, etc to be + self.adjustBuildTypeParams_cmakeOptions(spec, cmakeOptions) + + # Invoke cmake + cmake('..', *cmakeOptions) + + make("clean") + make() + make("install") diff --git a/var/spack/repos/builtin/packages/cbtf-krell/package.py b/var/spack/repos/builtin/packages/cbtf-krell/package.py index 9458ac113c..e6050cb4a9 100644 --- a/var/spack/repos/builtin/packages/cbtf-krell/package.py +++ b/var/spack/repos/builtin/packages/cbtf-krell/package.py @@ -1,5 +1,5 @@ ################################################################################ -# Copyright (c) 2015 Krell Institute. All Rights Reserved. +# Copyright (c) 2015-2016 Krell Institute. All Rights Reserved. # # 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 @@ -26,21 +26,30 @@ class CbtfKrell(Package): homepage = "http://sourceforge.net/p/cbtf/wiki/Home/" # optional mirror access template - #url = "file:/g/g24/jeg/cbtf-krell-1.5.tar.gz" - #version('1.5', 'b13f6df6a93c44149d977773dd776d2f') + #url = "file:/home/jeg/cbtf-krell-1.6.tar.gz" + #version('1.6', 'edeb61cd488f16e7b124f77db9ce762d') - version('1.6', branch='master', git='http://git.code.sf.net/p/cbtf-krell/cbtf-krell') + version('1.6', branch='master', git='https://github.com/OpenSpeedShop/cbtf-krell.git') + # MPI variants + variant('openmpi', default=False, description="Build mpi experiment collector for openmpi MPI when this variant is enabled.") + variant('mpt', default=False, description="Build mpi experiment collector for SGI MPT MPI when this variant is enabled.") + variant('mvapich2', default=False, description="Build mpi experiment collector for mvapich2 MPI when this variant is enabled.") + variant('mvapich', default=False, description="Build mpi experiment collector for mvapich MPI when this variant is enabled.") + variant('mpich2', default=False, description="Build mpi experiment collector for mpich2 MPI when this variant is enabled.") + variant('mpich', default=False, description="Build mpi experiment collector for mpich MPI when this variant is enabled.") # Dependencies for cbtf-krell + depends_on("cmake@3.0.2") # For binutils service depends_on("binutils@2.24+krellpatch") # collectionTool - depends_on("boost@1.50.0") - depends_on("dyninst@8.2.1") - depends_on("mrnet@4.1.0:+lwthreads") + depends_on("boost@1.50.0:") + depends_on("dyninst@8.2.1:") + depends_on("mrnet@5.0.1:+lwthreads+krellpatch") + depends_on("xerces-c@3.1.1:") depends_on("cbtf") @@ -51,66 +60,207 @@ class CbtfKrell(Package): # MPI Installations # These have not worked either for build or execution, commenting out for now - #depends_on("openmpi") - #depends_on("mvapich2@2.0") - #depends_on("mpich") + depends_on("openmpi", when='+openmpi') + depends_on("mpich", when='+mpich') + depends_on("mpich2", when='+mpich2') + depends_on("mvapich2", when='+mvapich2') + depends_on("mvapich", when='+mvapich') + depends_on("mpt", when='+mpt') parallel = False + def adjustBuildTypeParams_cmakeOptions(self, spec, cmakeOptions): + # Sets build type parameters into cmakeOptions the options that will enable the cbtf-krell built type settings + + compile_flags="-O2 -g" + BuildTypeOptions = [] + # Set CMAKE_BUILD_TYPE to what cbtf-krell wants it to be, not the stdcmakeargs + for word in cmakeOptions[:]: + if word.startswith('-DCMAKE_BUILD_TYPE'): + cmakeOptions.remove(word) + if word.startswith('-DCMAKE_CXX_FLAGS'): + cmakeOptions.remove(word) + if word.startswith('-DCMAKE_C_FLAGS'): + cmakeOptions.remove(word) + if word.startswith('-DCMAKE_VERBOSE_MAKEFILE'): + cmakeOptions.remove(word) + BuildTypeOptions.extend([ + '-DCMAKE_VERBOSE_MAKEFILE=ON', + '-DCMAKE_BUILD_TYPE=None', + '-DCMAKE_CXX_FLAGS=%s' % compile_flags, + '-DCMAKE_C_FLAGS=%s' % compile_flags + ]) + + cmakeOptions.extend(BuildTypeOptions) + + + + def set_mpi_cmakeOptions(self, spec, cmakeOptions): + # Appends to cmakeOptions the options that will enable the appropriate MPI implementations + + MPIOptions = [] + + # openmpi + if '+openmpi' in spec: + MPIOptions.extend([ + '-DOPENMPI_DIR=%s' % spec['openmpi'].prefix + ]) + # mpich + if '+mpich' in spec: + MPIOptions.extend([ + '-DMPICH_DIR=%s' % spec['mpich'].prefix + ]) + # mpich2 + if '+mpich2' in spec: + MPIOptions.extend([ + '-DMPICH2_DIR=%s' % spec['mpich2'].prefix + ]) + # mvapich + if '+mvapich' in spec: + MPIOptions.extend([ + '-DMVAPICH_DIR=%s' % spec['mvapich'].prefix + ]) + # mvapich2 + if '+mvapich2' in spec: + MPIOptions.extend([ + '-DMVAPICH2_DIR=%s' % spec['mvapich2'].prefix + ]) + # mpt + if '+mpt' in spec: + MPIOptions.extend([ + '-DMPT_DIR=%s' % spec['mpt'].prefix + ]) + + cmakeOptions.extend(MPIOptions) + def install(self, spec, prefix): # Add in paths for finding package config files that tell us where to find these packages - cmake_prefix_path = join_path(spec['cbtf'].prefix) + ':' + join_path(spec['dyninst'].prefix) - - # FIXME - hard code path until external package support is available - # Need to change this path and/or add additional paths for MPI experiment support on different platforms - #openmpi_prefix_path = "/opt/openmpi-1.8.2" - #mvapich_prefix_path = "/usr/local/tools/mvapich-gnu" - - # Other possibilities, they will need a -DMVAPICH_DIR=, etc clause in the cmake command to be recognized - # mvapich_prefix_path = "<mvapich install path>" - # mvapich2_prefix_path = "<mvapich2 install path>" - # mpich2_prefix_path = "<mpich2 install path>" - # mpich_prefix_path = "<mpich install path>" - # mpt_prefix_path = "<mpt install path>" - - # Add in paths for cuda if requested via the cuda variant - # FIXME - hard code path until external package support is available - #if '+cuda' in spec: - # cuda_prefix_path = "/usr/local/cuda-6.0" - # cupti_prefix_path = "/usr/local/cuda-6.0/extras/CUPTI" - #else: - # cuda_prefix_path = "" - # cupti_prefix_path = "" - - #'-DMVAPICH2_DIR=%s' % spec['mvapich2'].prefix, - #'-DOPENMPI_DIR=%s' % spec['openmpi'].prefix, - #'-DMPICH_DIR=%s' % spec['mpich'].prefix, - #'-DCMAKE_LIBRARY_PATH=%s' % prefix.lib64, - #'-DOPENMPI_DIR=%s' % openmpi_prefix_path, - #'-DMVAPICH_DIR=%s' % mvapich_prefix_path, - #'-DLIB_SUFFIX=64', - #'-DCUDA_DIR=%s' % cuda_prefix_path, - #'-DCUPTI_DIR=%s' % cupti_prefix_path, + #cmake_prefix_path = join_path(spec['cbtf'].prefix) + ':' + join_path(spec['dyninst'].prefix) + #'-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path # Build cbtf-krell with cmake with working_dir('build_cbtf_krell', create=True): - cmake('..', - '-DCMAKE_BUILD_TYPE=Debug', - '-DCMAKE_INSTALL_PREFIX=%s' % prefix, - '-DCBTF_DIR=%s' % spec['cbtf'].prefix, - '-DBINUTILS_DIR=%s' % spec['binutils'].prefix, - '-DLIBMONITOR_DIR=%s' % spec['libmonitor'].prefix, - '-DLIBUNWIND_DIR=%s' % spec['libunwind'].prefix, - '-DPAPI_DIR=%s' % spec['papi'].prefix, - '-DBOOST_DIR=%s' % spec['boost'].prefix, - '-DMRNET_DIR=%s' % spec['mrnet'].prefix, - '-DDYNINST_DIR=%s' % spec['dyninst'].prefix, - '-DXERCESC_DIR=%s' % spec['xerces-c'].prefix, - '-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path, - *std_cmake_args) + cmakeOptions = [] + cmakeOptions.extend(['-DCMAKE_INSTALL_PREFIX=%s' % prefix, + '-DCBTF_DIR=%s' % spec['cbtf'].prefix, + '-DBINUTILS_DIR=%s' % spec['binutils'].prefix, + '-DLIBMONITOR_DIR=%s' % spec['libmonitor'].prefix, + '-DLIBUNWIND_DIR=%s' % spec['libunwind'].prefix, + '-DPAPI_DIR=%s' % spec['papi'].prefix, + '-DBOOST_DIR=%s' % spec['boost'].prefix, + '-DMRNET_DIR=%s' % spec['mrnet'].prefix, + '-DDYNINST_DIR=%s' % spec['dyninst'].prefix, + '-DXERCESC_DIR=%s' % spec['xerces-c'].prefix + ]) + + + # Add any MPI implementations coming from variant settings + self.set_mpi_cmakeOptions(spec, cmakeOptions) + + # Add in the standard cmake arguments + cmakeOptions.extend(std_cmake_args) + + # Adjust the standard cmake arguments to what we want the build type, etc to be + self.adjustBuildTypeParams_cmakeOptions(spec, cmakeOptions) + + # Invoke cmake + cmake('..', *cmakeOptions) make("clean") make() make("install") + + + #if '+cray' in spec: + #if 'cray' in self.spec.architecture: + # if '+runtime' in spec: + # with working_dir('build_cbtf_cray_runtime', create=True): + # python_vers='%d.%d' % spec['python'].version[:2] + # cmake .. \ + # -DCMAKE_BUILD_TYPE=Debug \ + # -DTARGET_OS="cray" \ + # -DRUNTIME_ONLY="true" \ + # -DCMAKE_INSTALL_PREFIX=${CBTF_KRELL_PREFIX} \ + # -DCMAKE_PREFIX_PATH=${CBTF_ROOT} \ + # -DCBTF_DIR=${CBTF_ROOT} \ + # -DBOOST_ROOT=${BOOST_INSTALL_PREFIX} \ + # -DXERCESC_DIR=${XERCESC_INSTALL_PREFIX} \ + # -DBINUTILS_DIR=${KRELL_ROOT} \ + # -DLIBMONITOR_DIR=${KRELL_ROOT_COMPUTE} \ + # -DLIBUNWIND_DIR=${KRELL_ROOT_COMPUTE} \ + # -DPAPI_DIR=${PAPI_ROOT} \ + # -DDYNINST_DIR=${DYNINST_CN_ROOT} \ + # -DMRNET_DIR=${MRNET_INSTALL_PREFIX} \ + # -DMPICH2_DIR=/opt/cray/mpt/7.0.1/gni/mpich2-gnu/48 + # else: + # with working_dir('build_cbtf_cray_frontend', create=True): + # python_vers='%d.%d' % spec['python'].version[:2] + # cmake .. \ + # -DCMAKE_BUILD_TYPE=Debug \ + # -DCMAKE_INSTALL_PREFIX=${CBTF_KRELL_PREFIX} \ + # -DCMAKE_PREFIX_PATH=${CBTF_ROOT} \ + # -DCBTF_DIR=${CBTF_ROOT} \ + # -DRUNTIME_TARGET_OS="cray" \ + # -DCBTF_KRELL_CN_RUNTIME_DIR=${CBTF_KRELL_CN_RUNTIME_ROOT} \ + # -DCBTF_CN_RUNTIME_DIR=${CBTF_CN_RUNTIME_ROOT} \ + # -DLIBMONITOR_CN_RUNTIME_DIR=${LIBMONITOR_CN_ROOT} \ + # -DLIBUNWIND_CN_RUNTIME_DIR=${LIBUNWIND_CN_ROOT} \ + # -DPAPI_CN_RUNTIME_DIR=${PAPI_CN_ROOT} \ + # -DXERCESC_CN_RUNTIME_DIR=/${XERCESC_CN_ROOT} \ + # -DMRNET_CN_RUNTIME_DIR=${MRNET_CN_ROOT} \ + # -DBOOST_CN_RUNTIME_DIR=${BOOST_CN_ROOT} \ + # -DDYNINST_CN_RUNTIME_DIR=${DYNINST_CN_ROOT} \ + # -DBOOST_ROOT=/${KRELL_ROOT} \ + # -DXERCESC_DIR=/${KRELL_ROOT} \ + # -DBINUTILS_DIR=/${KRELL_ROOT} \ + # -DLIBMONITOR_DIR=${KRELL_ROOT} \ + # -DLIBUNWIND_DIR=${KRELL_ROOT} \ + # -DPAPI_DIR=${PAPI_ROOT} \ + # -DDYNINST_DIR=${KRELL_ROOT} \ + # -DMRNET_DIR=${KRELL_ROOT} \ + # -DMPICH2_DIR=/opt/cray/mpt/7.0.1/gni/mpich2-gnu/48 + # fi +# +# make("clean") +# make() +# make("install") +# +# elif '+mic' in spec: +# if '+runtime' in spec: +# with working_dir('build_cbtf_mic_runtime', create=True): +# python_vers='%d.%d' % spec['python'].version[:2] +# cmake .. \ +# +# else: +# with working_dir('build_cbtf_cray_frontend', create=True): +# python_vers='%d.%d' % spec['python'].version[:2] +# cmake .. \ +# fi +# +# else: +# # Build cbtf-krell with cmake +# with working_dir('build_cbtf_krell', create=True): +# cmake('..', +# '-DCMAKE_BUILD_TYPE=Debug', +# '-DCMAKE_INSTALL_PREFIX=%s' % prefix, +# '-DCBTF_DIR=%s' % spec['cbtf'].prefix, +# '-DBINUTILS_DIR=%s' % spec['binutils'].prefix, +# '-DLIBMONITOR_DIR=%s' % spec['libmonitor'].prefix, +# '-DLIBUNWIND_DIR=%s' % spec['libunwind'].prefix, +# '-DPAPI_DIR=%s' % spec['papi'].prefix, +# '-DBOOST_DIR=%s' % spec['boost'].prefix, +# '-DMRNET_DIR=%s' % spec['mrnet'].prefix, +# '-DDYNINST_DIR=%s' % spec['dyninst'].prefix, +# '-DXERCESC_DIR=%s' % spec['xerces-c'].prefix, +# '-DOPENMPI_DIR=%s' % openmpi_prefix_path, +# '-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path, +# *std_cmake_args) +# +# make("clean") +# make() +# make("install") +# +# fi +# diff --git a/var/spack/repos/builtin/packages/cbtf-lanl/package.py b/var/spack/repos/builtin/packages/cbtf-lanl/package.py index 2da9e8a1f7..5ca88601f3 100644 --- a/var/spack/repos/builtin/packages/cbtf-lanl/package.py +++ b/var/spack/repos/builtin/packages/cbtf-lanl/package.py @@ -1,5 +1,5 @@ ################################################################################ -# Copyright (c) 2015 Krell Institute. All Rights Reserved. +# Copyright (c) 2015-2016 Krell Institute. All Rights Reserved. # # 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 @@ -29,32 +29,65 @@ class CbtfLanl(Package): version('1.6', branch='master', git='http://git.code.sf.net/p/cbtf-lanl/cbtf-lanl') - + depends_on("cmake@3.0.2") # Dependencies for cbtf-krell - depends_on("boost@1.50") - depends_on("mrnet@4.1.0:+lwthreads") + depends_on("mrnet@5.0.1:+lwthreads+krellpatch") depends_on("xerces-c@3.1.1:") depends_on("cbtf") depends_on("cbtf-krell") parallel = False + def adjustBuildTypeParams_cmakeOptions(self, spec, cmakeOptions): + # Sets build type parameters into cmakeOptions the options that will enable the cbtf-krell built type settings + + compile_flags="-O2 -g" + BuildTypeOptions = [] + # Set CMAKE_BUILD_TYPE to what cbtf-krell wants it to be, not the stdcmakeargs + for word in cmakeOptions[:]: + if word.startswith('-DCMAKE_BUILD_TYPE'): + cmakeOptions.remove(word) + if word.startswith('-DCMAKE_CXX_FLAGS'): + cmakeOptions.remove(word) + if word.startswith('-DCMAKE_C_FLAGS'): + cmakeOptions.remove(word) + if word.startswith('-DCMAKE_VERBOSE_MAKEFILE'): + cmakeOptions.remove(word) + BuildTypeOptions.extend([ + '-DCMAKE_VERBOSE_MAKEFILE=ON', + '-DCMAKE_BUILD_TYPE=None', + '-DCMAKE_CXX_FLAGS=%s' % compile_flags, + '-DCMAKE_C_FLAGS=%s' % compile_flags + ]) + + cmakeOptions.extend(BuildTypeOptions) + def install(self, spec, prefix): # Add in paths for finding package config files that tell us where to find these packages cmake_prefix_path = join_path(spec['cbtf'].prefix) + ':' + join_path(spec['cbtf-krell'].prefix) with working_dir('build', create=True): - cmake('..', - '-DCBTF_DIR=%s' % spec['cbtf'].prefix, - '-DCBTF_KRELL_DIR=%s' % spec['cbtf-krell'].prefix, - '-DMRNET_DIR=%s' % spec['mrnet'].prefix, - '-DXERCESC_DIR=%s' % spec['xerces-c'].prefix, - '-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path, - '-DCMAKE_MODULE_PATH=%s' % join_path(prefix.share,'KrellInstitute','cmake'), - *std_cmake_args) - - make("clean") - make() - make("install") + cmakeOptions = [] + cmakeOptions.extend(['-DCMAKE_INSTALL_PREFIX=%s' % prefix, + '-DCBTF_DIR=%s' % spec['cbtf'].prefix, + '-DCBTF_KRELL_DIR=%s' % spec['cbtf-krell'].prefix, + '-DMRNET_DIR=%s' % spec['mrnet'].prefix, + '-DXERCESC_DIR=%s' % spec['xerces-c'].prefix, + '-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path, + '-DCMAKE_MODULE_PATH=%s' % join_path(prefix.share,'KrellInstitute','cmake') + ]) + + # Add in the standard cmake arguments + cmakeOptions.extend(std_cmake_args) + + # Adjust the standard cmake arguments to what we want the build type, etc to be + self.adjustBuildTypeParams_cmakeOptions(spec, cmakeOptions) + + # Invoke cmake + cmake('..', *cmakeOptions) + + make("clean") + make() + make("install") diff --git a/var/spack/repos/builtin/packages/cbtf/package.py b/var/spack/repos/builtin/packages/cbtf/package.py index 52e6a07020..7ce1cd382b 100644 --- a/var/spack/repos/builtin/packages/cbtf/package.py +++ b/var/spack/repos/builtin/packages/cbtf/package.py @@ -1,5 +1,5 @@ ################################################################################ -# Copyright (c) 2015 Krell Institute. All Rights Reserved. +# Copyright (c) 2015-2016 Krell Institute. All Rights Reserved. # # 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 @@ -25,21 +25,44 @@ class Cbtf(Package): homepage = "http://sourceforge.net/p/cbtf/wiki/Home" # Mirror access template example - #url = "file:/g/g24/jeg/cbtf-1.5.tar.gz" - #version('1.6', '1ca88a8834759c4c74452cb97fe7b70a') + #url = "file:/home/jeg/cbtf-1.6.tar.gz" + #version('1.6', 'c1ef4e5aa4e470dffb042abdba0b9987') # Use when the git repository is available - version('1.6', branch='master', git='http://git.code.sf.net/p/cbtf/cbtf') + version('1.6', branch='master', git='https://github.com/OpenSpeedShop/cbtf.git') - depends_on("cmake") - #depends_on("boost@1.42.0:") - depends_on("boost@1.50.0") - depends_on("mrnet@4.1.0+lwthreads") + variant('runtime', default=False, description="build only the runtime libraries and collectors.") + + depends_on("cmake@3.0.2") + depends_on("boost@1.50.0:") + depends_on("mrnet@5.0.1:+lwthreads+krellpatch") depends_on("xerces-c@3.1.1:") - depends_on("libxml2") + # Work around for spack libxml2 package bug, take off python when fixed + depends_on("libxml2+python") parallel = False + def adjustBuildTypeParams_cmakeOptions(self, spec, cmakeOptions): + # Sets build type parameters into cmakeOptions the options that will enable the cbtf-krell built type settings + + compile_flags="-O2 -g" + BuildTypeOptions = [] + # Set CMAKE_BUILD_TYPE to what cbtf-krell wants it to be, not the stdcmakeargs + for word in cmakeOptions[:]: + if word.startswith('-DCMAKE_BUILD_TYPE'): + cmakeOptions.remove(word) + if word.startswith('-DCMAKE_CXX_FLAGS'): + cmakeOptions.remove(word) + if word.startswith('-DCMAKE_C_FLAGS'): + cmakeOptions.remove(word) + BuildTypeOptions.extend([ + '-DCMAKE_BUILD_TYPE=None', + '-DCMAKE_CXX_FLAGS=%s' % compile_flags, + '-DCMAKE_C_FLAGS=%s' % compile_flags + ]) + + cmakeOptions.extend(BuildTypeOptions) + def install(self, spec, prefix): with working_dir('build', create=True): @@ -48,14 +71,45 @@ class Cbtf(Package): # or BOOST_INCLUDEDIR). Useful when specifying BOOST_ROOT. # Defaults to OFF. - cmake('..', - '--debug-output', - '-DBoost_NO_SYSTEM_PATHS=TRUE', - '-DXERCESC_DIR=%s' % spec['xerces-c'].prefix, - '-DBOOST_ROOT=%s' % spec['boost'].prefix, - '-DMRNET_DIR=%s' % spec['mrnet'].prefix, - '-DCMAKE_MODULE_PATH=%s' % join_path(prefix.share,'KrellInstitute','cmake'), - *std_cmake_args) + if '+runtime' in spec: + # Install message tag include file for use in Intel MIC cbtf-krell build + # FIXME + cmakeOptions = [] + cmakeOptions.extend(['-DCMAKE_INSTALL_PREFIX=%s' % prefix, + '-DBoost_NO_SYSTEM_PATHS=TRUE', + '-DXERCESC_DIR=%s' % spec['xerces-c'].prefix, + '-DBOOST_ROOT=%s' % spec['boost'].prefix, + '-DMRNET_DIR=%s' % spec['mrnet'].prefix, + '-DCMAKE_MODULE_PATH=%s' % join_path(prefix.share,'KrellInstitute','cmake') + ]) + + # Add in the standard cmake arguments + cmakeOptions.extend(std_cmake_args) + + # Adjust the standard cmake arguments to what we want the build type, etc to be + self.adjustBuildTypeParams_cmakeOptions(spec, cmakeOptions) + + # Invoke cmake + cmake('..', *cmakeOptions) + + else: + cmakeOptions = [] + cmakeOptions.extend(['-DCMAKE_INSTALL_PREFIX=%s' % prefix, + '-DBoost_NO_SYSTEM_PATHS=TRUE', + '-DXERCESC_DIR=%s' % spec['xerces-c'].prefix, + '-DBOOST_ROOT=%s' % spec['boost'].prefix, + '-DMRNET_DIR=%s' % spec['mrnet'].prefix, + '-DCMAKE_MODULE_PATH=%s' % join_path(prefix.share,'KrellInstitute','cmake') + ]) + + # Add in the standard cmake arguments + cmakeOptions.extend(std_cmake_args) + + # Adjust the standard cmake arguments to what we want the build type, etc to be + self.adjustBuildTypeParams_cmakeOptions(spec, cmakeOptions) + + # Invoke cmake + cmake('..', *cmakeOptions) make("clean") make() diff --git a/var/spack/repos/builtin/packages/fftw/package.py b/var/spack/repos/builtin/packages/fftw/package.py index bc129aaf1a..4ffc787594 100644 --- a/var/spack/repos/builtin/packages/fftw/package.py +++ b/var/spack/repos/builtin/packages/fftw/package.py @@ -42,7 +42,7 @@ class Fftw(Package): variant('float', default=True, description='Produces a single precision version of the library') variant('long_double', default=True, description='Produces a long double precision version of the library') variant('quad', default=False, description='Produces a quad precision version of the library (works only with GCC and libquadmath)') - + variant('openmp', default=False, description="Enable OpenMP support.") variant('mpi', default=False, description='Activate MPI support') depends_on('mpi', when='+mpi') @@ -52,8 +52,15 @@ class Fftw(Package): def install(self, spec, prefix): options = ['--prefix=%s' % prefix, '--enable-shared', - '--enable-threads', - '--enable-openmp'] + '--enable-threads'] + # Add support for OpenMP + if '+openmp' in spec: + # Note: Apple's Clang does not support OpenMP. + if spec.satisfies('%clang'): + ver = str(self.compiler.version) + if ver.endswith('-apple'): + raise InstallError("Apple's clang does not support OpenMP") + options.append('--enable-openmp') if not self.compiler.f77 or not self.compiler.fc: options.append("--disable-fortran") if '+mpi' in spec: 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/gmsh/package.py b/var/spack/repos/builtin/packages/gmsh/package.py index eb2981bba2..5f659c56df 100644 --- a/var/spack/repos/builtin/packages/gmsh/package.py +++ b/var/spack/repos/builtin/packages/gmsh/package.py @@ -62,7 +62,9 @@ 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') diff --git a/var/spack/repos/builtin/packages/hdf5/package.py b/var/spack/repos/builtin/packages/hdf5/package.py index 470969832f..cae46d3301 100644 --- a/var/spack/repos/builtin/packages/hdf5/package.py +++ b/var/spack/repos/builtin/packages/hdf5/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * +import shutil class Hdf5(Package): @@ -114,14 +115,16 @@ class Hdf5(Package): # this is not actually a problem. extra_args.extend([ "--enable-parallel", - "CC=%s" % spec['mpi'].prefix.bin + "/mpicc", + "CC=%s" % join_path(spec['mpi'].prefix.bin, "mpicc"), ]) if '+cxx' in spec: - extra_args.append("CXX=%s" % spec['mpi'].prefix.bin + "/mpic++") + extra_args.append("CXX=%s" % join_path(spec['mpi'].prefix.bin, + "mpic++")) if '+fortran' in spec: - extra_args.append("FC=%s" % spec['mpi'].prefix.bin + "/mpifort") + extra_args.append("FC=%s" % join_path(spec['mpi'].prefix.bin, + "mpifort")) if '+szip' in spec: extra_args.append("--with-szlib=%s" % spec['szip'].prefix) @@ -138,6 +141,58 @@ class Hdf5(Package): *extra_args) make() make("install") + self.check_install(spec) + + def check_install(self, spec): + "Build and run a small program to test the installed HDF5 library" + print "Checking HDF5 installation..." + checkdir = "spack-check" + with working_dir(checkdir, create=True): + source = r""" +#include <hdf5.h> +#include <assert.h> +#include <stdio.h> +int main(int argc, char **argv) { + unsigned majnum, minnum, relnum; + herr_t herr = H5get_libversion(&majnum, &minnum, &relnum); + assert(!herr); + printf("HDF5 version %d.%d.%d %u.%u.%u\n", H5_VERS_MAJOR, H5_VERS_MINOR, + H5_VERS_RELEASE, majnum, minnum, relnum); + return 0; +} +""" + expected = """\ +HDF5 version {version} {version} +""".format(version=str(spec.version)) + with open("check.c", 'w') as f: + f.write(source) + if '+mpi' in spec: + cc = which(join_path(spec['mpi'].prefix.bin, "mpicc")) + else: + 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"), "-lhdf5", + "-lz") + 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("HDF5 install check failed") + shutil.rmtree(checkdir) def url_for_version(self, version): v = str(version) diff --git a/var/spack/repos/builtin/packages/kripke/package.py b/var/spack/repos/builtin/packages/kripke/package.py index 345b8af4d0..7d067ea44d 100644 --- a/var/spack/repos/builtin/packages/kripke/package.py +++ b/var/spack/repos/builtin/packages/kripke/package.py @@ -9,15 +9,19 @@ class Kripke(Package): version('1.1', '7fe6f2b26ed983a6ce5495ab701f85bf') - variant('mpi', default=True, description='Enable MPI support') + 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=1', - '-DENABLE_MPI=1', + '-DENABLE_OPENMP=%d' % enabled('+openmp'), + '-DENABLE_MPI=%d' % enabled('+mpi'), '..', *std_cmake_args) make() 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/nccmp/package.py b/var/spack/repos/builtin/packages/nccmp/package.py new file mode 100644 index 0000000000..72e86831c6 --- /dev/null +++ b/var/spack/repos/builtin/packages/nccmp/package.py @@ -0,0 +1,23 @@ +from spack import * + +class Nccmp(Package): + """Compare NetCDF Files""" + homepage = "http://nccmp.sourceforge.net/" + url = "http://downloads.sourceforge.net/project/nccmp/nccmp-1.8.2.0.tar.gz" + + version('1.8.2.0', '81e6286d4413825aec4327e61a28a580') + + depends_on('netcdf') + + def install(self, spec, prefix): + # Configure says: F90 and F90FLAGS are replaced by FC and + # FCFLAGS respectively in this configure, please unset + # F90/F90FLAGS and set FC/FCFLAGS instead and rerun configure + # again. + env.pop('F90', None) + env.pop('F90FLAGS', None) + + configure('--prefix=%s' % prefix) + make() + make("check") + make("install") 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/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py index 99649da9ca..d147533491 100644 --- a/var/spack/repos/builtin/packages/openblas/package.py +++ b/var/spack/repos/builtin/packages/openblas/package.py @@ -8,13 +8,14 @@ class Openblas(Package): homepage = "http://www.openblas.net" url = "http://github.com/xianyi/OpenBLAS/archive/v0.2.15.tar.gz" + version('0.2.18', '805e7f660877d588ea7e3792cda2ee65') version('0.2.17', '664a12807f2a2a7cda4781e3ab2ae0e1') version('0.2.16', 'fef46ab92463bdbb1479dcec594ef6dc') version('0.2.15', 'b1190f3d3471685f17cfd1ec1d252ac9') - 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") + variant('shared', default=True, description="Build shared libraries as well as static libs.") + variant('openmp', default=False, description="Enable OpenMP support.") + variant('fpic', default=True, description="Build position independent code") # virtual dependency provides('blas') @@ -45,8 +46,13 @@ class Openblas(Package): make_defs += ['BUILD_LAPACK_DEPRECATED=1'] # Add support for OpenMP - # Note: Make sure your compiler supports OpenMP if '+openmp' in spec: + # Note: Apple's most recent Clang 7.3.0 still does not support OpenMP. + # What is worse, Openblas (as of 0.2.18) hardcoded that OpenMP cannot + # be used with any (!) compiler named clang, bummer. + if spec.satisfies('%clang'): + raise InstallError('OpenBLAS does not support OpenMP with clang!') + make_defs += ['USE_OPENMP=1'] make_args = make_defs + make_targets @@ -88,48 +94,33 @@ class Openblas(Package): 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" + # TODO: Pull this out to the framework function which recieves a pair of xyz.c and xyz.output 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 = "" + source_file = join_path(os.path.dirname(self.module.__file__), + 'test_cblas_dgemm.c') + output_file = join_path(os.path.dirname(self.module.__file__), + 'test_cblas_dgemm.output') + + with open(output_file, 'r') as f: + expected = f.read() + + cc = which('cc') + cc('-c', "-I%s" % join_path(spec.prefix, "include"), source_file) + link_flags = ["-L%s" % join_path(spec.prefix, "lib"), + "-llapack", + "-lblas", + "-lpthread" + ] + if '+openmp' in spec: + link_flags.extend([self.compiler.openmp_flag]) + cc('-o', "check", "test_cblas_dgemm.o", + *link_flags) + + 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." @@ -142,4 +133,3 @@ return 0; 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 index 634e99d20b..3813a23b69 100644 --- a/var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.c +++ b/var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.c @@ -1,13 +1,49 @@ #include <cblas.h> #include <stdio.h> + +double m[] = { + 3, 1, 3, + 1, 5, 9, + 2, 6, 5 +}; + +double x[] = { + -1, 3, -3 +}; + +#ifdef __cplusplus +extern "C" { +#endif + + void dgesv_(int *n, int *nrhs, double *a, int *lda, + int *ipivot, double *b, int *ldb, int *info); + +#ifdef __cplusplus +} +#endif + 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; + int i; + // blas: + 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]); + + // lapack: + int ipiv[3]; + int j; + int info; + int n = 1; + int nrhs = 1; + int lda = 3; + int ldb = 3; + dgesv_(&n,&nrhs, &m[0], &lda, ipiv, &x[0], &ldb, &info); + for (i=0; i<3; ++i) + printf("%5.1f %3d\n", x[i], ipiv[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 index b8316d7477..9c235e314f 100644 --- a/var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.output +++ b/var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.output @@ -7,3 +7,6 @@ 5.000000 -1.000000 3.000000 + -0.3 1 + 3.0 1499101120 + -3.0 32767 diff --git a/var/spack/repos/builtin/packages/openspeedshop/package.py b/var/spack/repos/builtin/packages/openspeedshop/package.py index 8c71bcb7c3..bcd77351aa 100644 --- a/var/spack/repos/builtin/packages/openspeedshop/package.py +++ b/var/spack/repos/builtin/packages/openspeedshop/package.py @@ -1,5 +1,5 @@ ################################################################################ -# Copyright (c) 2015 Krell Institute. All Rights Reserved. +# Copyright (c) 2015-2016 Krell Institute. All Rights Reserved. # # 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 @@ -28,20 +28,15 @@ class Openspeedshop(Package): as open source code primarily under LGPL. """ - homepage = "http://www.openspeedshop.org" - url = "http://sourceforge.net/projects/openss/files/openss/openspeedshop-2.2/openspeedshop-2.2.tar.gz/download" + url = "https://github.com/OpenSpeedShop" version('2.2', '16cb051179c2038de4e8a845edf1d573') + # Use when the git repository is available + version('2.2', branch='master', git='https://github.com/OpenSpeedShop/openspeedshop.git') - #homepage = "http://www.openspeedshop.org" - #url = "http://sourceforge.net/projects/openss/files/openss/openspeedshop-2.1/openspeedshop-2.1.tar.gz/download" - #version('2.1', 'bdaa57c1a0db9d0c3e0303fd8496c507') - - # optional mirror template - #url = "file:/g/g24/jeg/openspeedshop-2.1.tar.gz" - #version('2.1', '64ee17166519838c7b94a1adc138e94f') - - + # Optional mirror template + #url = "file:/home/jeg/OpenSpeedShop_ROOT/SOURCES/openspeedshop-2.2.tar.gz" + #version('2.2', '643337740dc6c2faca60f42d3620b0e1') parallel = False @@ -51,11 +46,17 @@ class Openspeedshop(Package): variant('frontend', default=False, description="build only the front-end tool using the runtime_dir to point to the target build.") variant('cuda', default=False, description="build with cuda packages included.") variant('ptgf', default=False, description="build with the PTGF based gui package enabled.") - variant('intelmic', default=False, description="build for the Intel MIC platform.") - variant('cray', default=False, description="build for Cray platforms.") - variant('bluegene', default=False, description="build for Cray platforms.") variant('rtfe', default=False, description="build for generic cluster platforms that have different processors on the fe and be nodes.") + # MPI variants + variant('openmpi', default=False, description="Build mpi experiment collector for openmpi MPI when this variant is enabled.") + variant('mpt', default=False, description="Build mpi experiment collector for SGI MPT MPI when this variant is enabled.") + variant('mvapich2', default=False, description="Build mpi experiment collector for mvapich2 MPI when this variant is enabled.") + variant('mvapich', default=False, description="Build mpi experiment collector for mvapich MPI when this variant is enabled.") + variant('mpich2', default=False, description="Build mpi experiment collector for mpich2 MPI when this variant is enabled.") + variant('mpich', default=False, description="Build mpi experiment collector for mpich MPI when this variant is enabled.") + + depends_on("cmake@3.0.2") # Dependencies for openspeedshop that are common to all the variants of the OpenSpeedShop build depends_on("bison") depends_on("flex") @@ -63,8 +64,8 @@ class Openspeedshop(Package): depends_on("libelf") depends_on("libdwarf") depends_on("sqlite") - depends_on("boost@1.50.0") - depends_on("dyninst@8.2.1") + depends_on("boost@1.50.0:") + depends_on("dyninst@9.1.0") depends_on("python") depends_on("qt@3.3.8b+krellpatch") @@ -72,15 +73,78 @@ class Openspeedshop(Package): depends_on("libunwind", when='+offline') depends_on("papi", when='+offline') depends_on("libmonitor+krellpatch", when='+offline') - #depends_on("openmpi+krelloptions", when='+offline') - #depends_on("openmpi", when='+offline') - #depends_on("mpich", when='+offline') + depends_on("openmpi", when='+offline+openmpi') + depends_on("mpich", when='+offline+mpich') + depends_on("mpich2", when='+offline+mpich2') + depends_on("mvapich2", when='+offline+mvapich2') + depends_on("mvapich", when='+offline+mvapich') + depends_on("mpt", when='+offline+mpt') # Dependencies only for the openspeedshop cbtf package. depends_on("cbtf", when='+cbtf') depends_on("cbtf-krell", when='+cbtf') - depends_on("cbtf-argonavis", when='+cbtf') - depends_on("mrnet@4.1.0:+lwthreads", when='+cbtf') + depends_on("cbtf-argonavis", when='+cbtf+cuda') + depends_on("mrnet@5.0.1:+lwthreads+krellpatch", when='+cbtf') + + def adjustBuildTypeParams_cmakeOptions(self, spec, cmakeOptions): + # Sets build type parameters into cmakeOptions the options that will enable the cbtf-krell built type settings + + compile_flags="-O2 -g" + BuildTypeOptions = [] + # Set CMAKE_BUILD_TYPE to what cbtf-krell wants it to be, not the stdcmakeargs + for word in cmakeOptions[:]: + if word.startswith('-DCMAKE_BUILD_TYPE'): + cmakeOptions.remove(word) + if word.startswith('-DCMAKE_CXX_FLAGS'): + cmakeOptions.remove(word) + if word.startswith('-DCMAKE_C_FLAGS'): + cmakeOptions.remove(word) + BuildTypeOptions.extend([ + '-DCMAKE_BUILD_TYPE=None', + '-DCMAKE_CXX_FLAGS=%s' % compile_flags, + '-DCMAKE_C_FLAGS=%s' % compile_flags + ]) + + cmakeOptions.extend(BuildTypeOptions) + + def set_mpi_cmakeOptions(self, spec, cmakeOptions): + # Appends to cmakeOptions the options that will enable the appropriate MPI implementations + + MPIOptions = [] + + # openmpi + if '+openmpi' in spec: + MPIOptions.extend([ + '-DOPENMPI_DIR=%s' % spec['openmpi'].prefix + ]) + # mpich + if '+mpich' in spec: + MPIOptions.extend([ + '-DMPICH_DIR=%s' % spec['mpich'].prefix + ]) + # mpich2 + if '+mpich2' in spec: + MPIOptions.extend([ + '-DMPICH2_DIR=%s' % spec['mpich2'].prefix + ]) + # mvapich + if '+mvapich' in spec: + MPIOptions.extend([ + '-DMVAPICH_DIR=%s' % spec['mvapich'].prefix + ]) + # mvapich2 + if '+mvapich2' in spec: + MPIOptions.extend([ + '-DMVAPICH2_DIR=%s' % spec['mvapich2'].prefix + ]) + # mpt + if '+mpt' in spec: + MPIOptions.extend([ + '-DMPT_DIR=%s' % spec['mpt'].prefix + ]) + + cmakeOptions.extend(MPIOptions) + def install(self, spec, prefix): @@ -100,51 +164,118 @@ class Openspeedshop(Package): instrumentor_setting = "offline" if '+runtime' in spec: with working_dir('build_runtime', create=True): - cmake('..', - '-DCMAKE_INSTALL_PREFIX=%s' % prefix, - '-DCMAKE_LIBRARY_PATH=%s' % prefix.lib64, - '-DINSTRUMENTOR=%s' % instrumentor_setting, - '-DLIBMONITOR_DIR=%s' % spec['libmonitor'].prefix, - '-DLIBUNWIND_DIR=%s' % spec['libunwind'].prefix, - '-DPAPI_DIR=%s' % spec['papi'].prefix, - *std_cmake_args) + + cmakeOptions = [] + cmakeOptions.extend(['-DCMAKE_INSTALL_PREFIX=%s' % prefix, + '-DCMAKE_LIBRARY_PATH=%s' % prefix.lib64, + '-DINSTRUMENTOR=%s' % instrumentor_setting, + '-DLIBMONITOR_DIR=%s' % spec['libmonitor'].prefix, + '-DLIBUNWIND_DIR=%s' % spec['libunwind'].prefix, + '-DPAPI_DIR=%s' % spec['papi'].prefix + ]) + + # Add any MPI implementations coming from variant settings + self.set_mpi_cmakeOptions(spec, cmakeOptions) + cmakeOptions.extend(std_cmake_args) + + # Adjust the build options to the favored ones for this build + self.adjustBuildTypeParams_cmakeOptions(spec, cmakeOptions) + + cmake('..', *cmakeOptions) + make("clean") make() make("install") else: cmake_prefix_path = join_path(spec['dyninst'].prefix) with working_dir('build', create=True): + #python_vers=join_path(spec['python'].version[:2]) #'-DOPENMPI_DIR=%s' % openmpi_prefix_path, #'-DMVAPICH_DIR=%s' % mvapich_prefix_path, + #'-DMPICH_DIR=%s' % spec['mpich'].prefix, + #'-DMPICH2_DIR=%s' % spec['mpich2'].prefix, + #'-DBoost_NO_SYSTEM_PATHS=TRUE', + #'-DBOOST_ROOT=%s' % spec['boost'].prefix, + #'-DOPENMPI_DIR=%s' % spec['openmpi'].prefix, + python_vers='%d.%d' % spec['python'].version[:2] - cmake('..', - '-DCMAKE_INSTALL_PREFIX=%s' % prefix, - '-DCMAKE_LIBRARY_PATH=%s' % prefix.lib64, - '-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path, - '-DINSTRUMENTOR=%s' % instrumentor_setting, - '-DBINUTILS_DIR=%s' % spec['binutils'].prefix, - '-DLIBELF_DIR=%s' % spec['libelf'].prefix, - '-DLIBDWARF_DIR=%s' % spec['libdwarf'].prefix, - '-DLIBMONITOR_DIR=%s' % spec['libmonitor'].prefix, - '-DLIBUNWIND_DIR=%s' % spec['libunwind'].prefix, - '-DPAPI_DIR=%s' % spec['papi'].prefix, - '-DSQLITE3_DIR=%s' % spec['sqlite'].prefix, - '-DQTLIB_DIR=%s' % spec['qt'].prefix, - '-DPYTHON_EXECUTABLE=%s' % join_path(spec['python'].prefix + '/bin/python'), - '-DPYTHON_INCLUDE_DIR=%s' % join_path(spec['python'].prefix.include) + '/python' + python_vers, - '-DPYTHON_LIBRARY=%s' % join_path(spec['python'].prefix.lib) + '/libpython' + python_vers + '.so', - '-DBoost_NO_SYSTEM_PATHS=TRUE', - '-DBOOST_ROOT=%s' % spec['boost'].prefix, - '-DDYNINST_DIR=%s' % spec['dyninst'].prefix, - *std_cmake_args) + + cmakeOptions = [] + cmakeOptions.extend(['-DCMAKE_INSTALL_PREFIX=%s' % prefix, + '-DCMAKE_LIBRARY_PATH=%s' % prefix.lib64, + '-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path, + '-DINSTRUMENTOR=%s' % instrumentor_setting, + '-DBINUTILS_DIR=%s' % spec['binutils'].prefix, + '-DLIBELF_DIR=%s' % spec['libelf'].prefix, + '-DLIBDWARF_DIR=%s' % spec['libdwarf'].prefix, + '-DLIBMONITOR_DIR=%s' % spec['libmonitor'].prefix, + '-DLIBUNWIND_DIR=%s' % spec['libunwind'].prefix, + '-DPAPI_DIR=%s' % spec['papi'].prefix, + '-DSQLITE3_DIR=%s' % spec['sqlite'].prefix, + '-DQTLIB_DIR=%s' % spec['qt'].prefix, + '-DPYTHON_EXECUTABLE=%s' % join_path(spec['python'].prefix + '/bin/python'), + '-DPYTHON_INCLUDE_DIR=%s' % join_path(spec['python'].prefix.include) + '/python' + python_vers, + '-DPYTHON_LIBRARY=%s' % join_path(spec['python'].prefix.lib) + '/libpython' + python_vers + '.so', + '-DBoost_NO_SYSTEM_PATHS=TRUE', + '-DBOOST_ROOT=%s' % spec['boost'].prefix, + '-DDYNINST_DIR=%s' % spec['dyninst'].prefix + ]) + + # Add any MPI implementations coming from variant settings + self.set_mpi_cmakeOptions(spec, cmakeOptions) + cmakeOptions.extend(std_cmake_args) + + # Adjust the build options to the favored ones for this build + self.adjustBuildTypeParams_cmakeOptions(spec, cmakeOptions) + + cmake('..', *cmakeOptions) + make("clean") make() make("install") elif '+cbtf' in spec: instrumentor_setting = "cbtf" + resolve_symbols = "symtabapi" cmake_prefix_path = join_path(spec['cbtf'].prefix) + ':' + join_path(spec['cbtf-krell'].prefix) + ':' + join_path(spec['dyninst'].prefix) + #runtime_platform_cray = "cray" + #if '+cray' in spec: + # if '+runtime' in spec: + # #-DCBTF_KRELL_CN_RUNTIME_DIR=${CBTF_KRELL_CN_INSTALL_DIR} \ + # with working_dir('build_cbtf_cray_runtime', create=True): + # python_vers='%d.%d' % spec['python'].version[:2] + # cmake('..', + # '-DCMAKE_INSTALL_PREFIX=%s' % prefix, + # '-DCMAKE_LIBRARY_PATH=%s' % prefix.lib64, + # '-DRUNTIME_PLATFORM=%s' % runtime_platform_cray, + # '-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path, + # '-DRESOLVE_SYMBOLS=%s' % resolve_symbols, + # '-DINSTRUMENTOR=%s' % instrumentor_setting, + # '-DCBTF_DIR=%s' % spec['cbtf'].prefix, + # '-DCBTF_KRELL_DIR=%s' % spec['cbtf-krell'].prefix, + # '-DCBTF_KRELL_CN_RUNTIME_DIR=%s' % spec['cbtf-krell'].prefix, + # '-DBINUTILS_DIR=%s' % spec['binutils'].prefix, + # '-DLIBELF_DIR=%s' % spec['libelf'].prefix, + # '-DLIBDWARF_DIR=%s' % spec['libdwarf'].prefix, + # '-DLIBUNWIND_DIR=%s' % spec['libunwind'].prefix, + # '-DPAPI_DIR=%s' % spec['papi'].prefix, + # '-DDYNINST_DIR=%s' % spec['dyninst'].prefix, + # '-DXERCESC_DIR=%s' % spec['xerces-c'].prefix, + # '-DMRNET_DIR=%s' % spec['mrnet'].prefix, + # '-DBoost_NO_SYSTEM_PATHS=TRUE', + # '-DBOOST_ROOT=%s' % spec['boost'].prefix, + # *std_cmake_args) + + # make("clean") + # make() + # make("install") + + + #elif '+mic' in spec: + # comment out else and shift over the default case below until arch detection is in + #else: + if '+runtime' in spec: with working_dir('build_cbtf_runtime', create=True): python_vers='%d.%d' % spec['python'].version[:2] @@ -203,14 +334,63 @@ class Openspeedshop(Package): # tbd - #if '+intelmic' in spec: - # with working_dir('build_intelmic_compute', create=True): - # tbd - # with working_dir('build_intelmic_frontend', create=True): - # tbd - #if '+cray' in spec: - # with working_dir('build_cray_compute', create=True): - # tbd - # with working_dir('build_cray_frontend', create=True): - # tbd + #if '+cbtf' in spec: + # if cray build type detected: + # if '+runtime' in spec: + # with working_dir('build_cray_cbtf_compute', create=True): + # tbd + # else: + # with working_dir('build_cray_cbtf_frontend', create=True): + # tbd + # with working_dir('build_cray_osscbtf_frontend', create=True): + # tbd + # fi + # elif '+intelmic' in spec: + # if '+runtime' in spec: + # with working_dir('build_intelmic_cbtf_compute', create=True): + # tbd + # else: + # with working_dir('build_intelmic_cbtf_frontend', create=True): + # tbd + # with working_dir('build_intelmic_osscbtf_frontend', create=True): + # fi + # else + # with working_dir('build_cluster_cbtf', create=True): + # tbd + # with working_dir('build_cluster osscbtf', create=True): + # tbd + # fi + #elif '+offline' in spec: + # if cray build type detected: + # if '+runtime' in spec: + # with working_dir('build_cray_ossoff_compute', create=True): + # tbd + # else: + # with working_dir('build_cray_ossoff_frontend', create=True): + # tbd + # fi + # elif '+intelmic' in spec: + # if '+runtime' in spec: + # with working_dir('build_intelmic_ossoff_compute', create=True): + # tbd + # else: + # with working_dir('build_intelmic_ossoff_frontend', create=True): + # tbd + # fi + # elif bgq build type detected: + # if '+runtime' in spec: + # with working_dir('build_bgq_ossoff_compute', create=True): + # tbd + # else: + # with working_dir('build_bgq_ossoff_frontend', create=True): + # tbd + # fi + # else + # with working_dir('build_cluster ossoff', create=True): + # tbd + # fi + #fi + + + diff --git a/var/spack/repos/builtin/packages/parallel-netcdf/package.py b/var/spack/repos/builtin/packages/parallel-netcdf/package.py index e6f8cf026b..1bbd24781e 100644 --- a/var/spack/repos/builtin/packages/parallel-netcdf/package.py +++ b/var/spack/repos/builtin/packages/parallel-netcdf/package.py @@ -11,11 +11,25 @@ class ParallelNetcdf(Package): version('1.7.0', '267eab7b6f9dc78c4d0e6def2def3aea4bc7c9f0') version('1.6.1', '62a094eb952f9d1e15f07d56e535052604f1ac34') + variant('cxx', default=True, description='Build the C++ Interface') + variant('fortran', default=True, description='Build the Fortran Interface') + variant('fpic', default=True, description='Produce position-independent code (for use with shared libraries)') + depends_on("m4") depends_on("mpi") + # See: https://trac.mcs.anl.gov/projects/parallel-netcdf/browser/trunk/INSTALL def install(self, spec, prefix): - configure("--prefix=%s" % prefix, - "--with-mpi=%s" % spec['mpi'].prefix) + args = list() + if '+fpic' in spec: + args.extend(['CFLAGS=-fPIC', 'CXXFLAGS=-fPIC', 'FFLAGS=-fPIC']) + if '~cxx' in spec: + args.append('--disable-cxx') + if '~fortran' in spec: + args.append('--disable-fortran') + + args.extend(["--prefix=%s" % prefix, + "--with-mpi=%s" % spec['mpi'].prefix]) + configure(*args) make() make("install") diff --git a/var/spack/repos/builtin/packages/py-argcomplete/package.py b/var/spack/repos/builtin/packages/py-argcomplete/package.py new file mode 100644 index 0000000000..c94ef7238b --- /dev/null +++ b/var/spack/repos/builtin/packages/py-argcomplete/package.py @@ -0,0 +1,14 @@ +from spack import * + +class PyArgcomplete(Package): + """Bash tab completion for argparse.""" + + homepage = "https://pypi.python.org/pypi/argcomplete" + url = "https://pypi.python.org/packages/source/a/argcomplete/argcomplete-1.1.1.tar.gz" + + version('1.1.1', '89a3839096c9f991ad33828e72d21abf') + + extends('python') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/r-BiocGenerics/package.py b/var/spack/repos/builtin/packages/r-BiocGenerics/package.py new file mode 100644 index 0000000000..2d92c1c4d8 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-BiocGenerics/package.py @@ -0,0 +1,14 @@ +from spack import * + +class RBiocgenerics(Package): + """S4 generic functions needed by many Bioconductor packages.""" + + homepage = 'https://www.bioconductor.org/packages/release/bioc/html/BiocGenerics.html' + url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/BiocGenerics_0.16.1.tar.gz" + + version('0.16.1', 'c2148ffd86fc6f1f819c7f68eb2c744f', expand=False) + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file) diff --git a/var/spack/repos/builtin/packages/r-abind/package.py b/var/spack/repos/builtin/packages/r-abind/package.py new file mode 100644 index 0000000000..d06c7e9240 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-abind/package.py @@ -0,0 +1,18 @@ +from spack import * + +class RAbind(Package): + """Combine multidimensional arrays into a single array. This is a + generalization of 'cbind' and 'rbind'. Works with vectors, matrices, and + higher-dimensional arrays. Also provides functions 'adrop', 'asub', and + 'afill' for manipulating, extracting and replacing data in arrays.""" + + homepage = "https://cran.r-project.org/" + url = "https://cran.r-project.org/src/contrib/abind_1.4-3.tar.gz" + + version('1.4-3', '10fcf80c677b991bf263d38be35a1fc5', expand=False) + + extends('R') + + def install(self, spec, prefix): + + R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file) diff --git a/var/spack/repos/builtin/packages/r-filehash/package.py b/var/spack/repos/builtin/packages/r-filehash/package.py new file mode 100644 index 0000000000..4911c636b4 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-filehash/package.py @@ -0,0 +1,22 @@ +from spack import * + +class RFilehash(Package): + """Implements a simple key-value style database where character string keys + are associated with data values that are stored on the disk. A simple + interface is provided for inserting, retrieving, and deleting data from the + database. Utilities are provided that allow 'filehash' databases to be + treated much like environments and lists are already used in R. These + utilities are provided to encourage interactive and exploratory analysis on + large datasets. Three different file formats for representing the database + are currently available and new formats can easily be incorporated by third + parties for use in the 'filehash' framework.""" + + homepage = 'https://cran.r-project.org/' + url = "https://cran.r-project.org/src/contrib/filehash_2.3.tar.gz" + + version('2.3', '01fffafe09b148ccadc9814c103bdc2f', expand=False) + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file) diff --git a/var/spack/repos/builtin/packages/r-magic/package.py b/var/spack/repos/builtin/packages/r-magic/package.py new file mode 100644 index 0000000000..e900cdb216 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-magic/package.py @@ -0,0 +1,19 @@ +from spack import * + +class RMagic(Package): + """A collection of efficient, vectorized algorithms for the creation and + investigation of magic squares and hypercubes, including a variety of + functions for the manipulation and analysis of arbitrarily dimensioned + arrays.""" + + homepage = "https://cran.r-project.org/" + url = "https://cran.r-project.org/src/contrib/magic_1.5-6.tar.gz" + + version('1.5-6', 'a68e5ced253b2196af842e1fc84fd029', expand=False) + + extends('R') + + depends_on('r-abind') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file) diff --git a/var/spack/repos/builtin/packages/scotch/Makefile.esmumps b/var/spack/repos/builtin/packages/scotch/Makefile.esmumps new file mode 100644 index 0000000000..4bfc760197 --- /dev/null +++ b/var/spack/repos/builtin/packages/scotch/Makefile.esmumps @@ -0,0 +1,5 @@ +esmumps : scotch + (cd esmumps ; $(MAKE) scotch && $(MAKE) install) + +ptesmumps : ptscotch + (cd esmumps ; $(MAKE) ptscotch && $(MAKE) ptinstall) diff --git a/var/spack/repos/builtin/packages/scotch/package.py b/var/spack/repos/builtin/packages/scotch/package.py index 8229ed8686..8fad74b24f 100644 --- a/var/spack/repos/builtin/packages/scotch/package.py +++ b/var/spack/repos/builtin/packages/scotch/package.py @@ -1,88 +1,125 @@ from spack import * -import os +import os, re class Scotch(Package): """Scotch is a software package for graph and mesh/hypergraph partitioning, graph clustering, and sparse matrix ordering.""" + homepage = "http://www.labri.fr/perso/pelegrin/scotch/" - url = "http://gforge.inria.fr/frs/download.php/file/34099/scotch_6.0.3.tar.gz" + url = "http://gforge.inria.fr/frs/download.php/latestfile/298/scotch_6.0.3.tar.gz" + base_url = "http://gforge.inria.fr/frs/download.php/latestfile/298" list_url = "http://gforge.inria.fr/frs/?group_id=248" version('6.0.3', '10b0cc0f184de2de99859eafaca83cfc') + version('6.0.0', 'c50d6187462ba801f9a82133ee666e8e') + version('5.1.10b', 'f587201d6cf5cf63527182fbfba70753') variant('mpi', default=False, description='Activate the compilation of PT-Scotch') variant('compression', default=True, description='Activate the posibility to use compressed files') variant('esmumps', default=False, description='Activate the compilation of the lib esmumps needed by mumps') variant('shared', default=True, description='Build shared libraries') - depends_on('mpi', when='+mpi') - depends_on('zlib', when='+compression') depends_on('flex') depends_on('bison') + depends_on('mpi', when='+mpi') + depends_on('zlib', when='+compression') - def compiler_specifics(self, makefile_inc, defines): - if self.compiler.name == 'gcc': - defines.append('-Drestrict=__restrict') - elif self.compiler.name == 'intel': - defines.append('-restrict') + # NOTE: Versions of Scotch up to version 6.0.0 don't include support for + # building with 'esmumps' in their default packages. In order to enable + # support for this feature, we must grab the 'esmumps' enabled archives + # from the Scotch hosting site. These alternative archives include a strict + # superset of the behavior in their default counterparts, so we choose to + # always grab these versions for older Scotch versions for simplicity. + @when('@:6.0.0') + def url_for_version(self, version): + return '%s/scotch_%s_esmumps.tar.gz' % (Scotch.base_url, version) + + @when('@6.0.1:') + def url_for_version(self, version): + return super(Scotch, self).url_for_version(version) + + # NOTE: Several of the 'esmumps' enabled Scotch releases up to version 6.0.0 + # have broken build scripts that don't properly build 'esmumps' as a separate + # target, so we need a patch procedure to remove 'esmumps' from existing targets + # and to add it as a standalone target. + @when('@:6.0.0') + def patch(self): + makefile_path = os.path.join('src', 'Makefile') + with open(makefile_path, 'r') as makefile: + esmumps_enabled = any(re.search(r'^esmumps(\s*):(.*)$', line) for line in makefile.readlines()) - makefile_inc.append('CCS = $(CC)') + if not esmumps_enabled: + mff = FileFilter(makefile_path) + mff.filter(r'^.*((esmumps)|(ptesmumps)).*(install).*$', '') - if '+mpi' in self.spec: + makefile_esmumps_path = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'Makefile.esmumps') + with open(makefile_path, 'a') as makefile: + makefile.write('\ninclude %s\n' % makefile_esmumps_path) + + @when('@6.0.1:') + def patch(self): + pass + + # NOTE: Configuration of Scotch is achieved by writing a 'Makefile.inc' file + # that contains all of the configuration variables and their desired values + # for the installation. This function writes this file based on the given + # installation variants. + def configure(self): + makefile_inc = [] + cflags = [ + '-O3', + '-DCOMMON_RANDOM_FIXED_SEED', + '-DSCOTCH_DETERMINISTIC', + '-DSCOTCH_RENAME', + '-DIDXSIZE64' + ] + + ## Library Build Type ## + + if '+shared' in self.spec: makefile_inc.extend([ - 'CCP = %s' % os.path.join(self.spec['mpi'].prefix.bin, 'mpicc'), - 'CCD = $(CCP)' - ]) + 'LIB = .so', + 'CLIBFLAGS = -shared -fPIC', + 'RANLIB = echo', + 'AR = $(CC)', + 'ARFLAGS = -shared $(LDFLAGS) -o' + ]) + cflags.append('-fPIC') else: makefile_inc.extend([ - 'CCP = mpicc', # It is set but not used - 'CCD = $(CCS)' - ]) + 'LIB = .a', + 'CLIBFLAGS = ', + 'RANLIB = ranlib', + 'AR = ar', + 'ARFLAGS = -ruv ' + ]) + ## Compiler-Specific Options ## + if self.compiler.name == 'gcc': + cflags.append('-Drestrict=__restrict') + elif self.compiler.name == 'intel': + cflags.append('-restrict') - def library_build_type(self, makefile_inc, defines): - makefile_inc.extend([ - 'LIB = .a', - 'CLIBFLAGS = ', - 'RANLIB = ranlib', - 'AR = ar', - 'ARFLAGS = -ruv ' - ]) + makefile_inc.append('CCS = $(CC)') + makefile_inc.append('CCP = %s' % + (self.spec['mpi'].mpicc if '+mpi' in self.spec else 'mpicc')) + makefile_inc.append('CCD = $(CCS)') - @when('+shared') - def library_build_type(self, makefile_inc, defines): - makefile_inc.extend([ - 'LIB = .so', - 'CLIBFLAGS = -shared -fPIC', - 'RANLIB = echo', - 'AR = $(CC)', - 'ARFLAGS = -shared $(LDFLAGS) -o' - ]) + ## Extra Features ## - def extra_features(self, makefile_inc, defines): ldflags = [] - + if '+compression' in self.spec: - defines.append('-DCOMMON_FILE_COMPRESS_GZ') + cflags.append('-DCOMMON_FILE_COMPRESS_GZ') ldflags.append('-L%s -lz' % (self.spec['zlib'].prefix.lib)) - defines.append('-DCOMMON_PTHREAD') + cflags.append('-DCOMMON_PTHREAD') ldflags.append('-lm -lrt -pthread') - - makefile_inc.append('LDFLAGS = %s' % ' '.join(ldflags)) - def patch(self): - makefile_inc = [] - defines = [ - '-DCOMMON_RANDOM_FIXED_SEED', - '-DSCOTCH_DETERMINISTIC', - '-DSCOTCH_RENAME', - '-DIDXSIZE64' ] + makefile_inc.append('LDFLAGS = %s' % ' '.join(ldflags)) - self.library_build_type(makefile_inc, defines) - self.compiler_specifics(makefile_inc, defines) - self.extra_features(makefile_inc, defines) + ## General Features ## makefile_inc.extend([ 'EXE =', @@ -93,18 +130,19 @@ class Scotch(Package): 'MKDIR = mkdir', 'MV = mv', 'CP = cp', - 'CFLAGS = -O3 %s' % (' '.join(defines)), + 'CFLAGS = %s' % ' '.join(cflags), 'LEX = %s -Pscotchyy -olex.yy.c' % os.path.join(self.spec['flex'].prefix.bin , 'flex'), 'YACC = %s -pscotchyy -y -b y' % os.path.join(self.spec['bison'].prefix.bin, 'bison'), - 'prefix = %s' % self.prefix, - '' + 'prefix = %s' % self.prefix ]) with working_dir('src'): with open('Makefile.inc', 'w') as fh: fh.write('\n'.join(makefile_inc)) - + def install(self, spec, prefix): + self.configure() + targets = ['scotch'] if '+mpi' in self.spec: targets.append('ptscotch') @@ -115,12 +153,10 @@ class Scotch(Package): targets.append('ptesmumps') with working_dir('src'): - for app in targets: - make(app, parallel=(not app=='ptesmumps')) + for target in targets: + make(target, parallel=(target!='ptesmumps')) - install_tree('bin', prefix.bin) install_tree('lib', prefix.lib) install_tree('include', prefix.include) install_tree('man/man1', prefix.share_man1) - diff --git a/var/spack/repos/builtin/packages/silo/package.py b/var/spack/repos/builtin/packages/silo/package.py index b7894e4d2b..7e68663c6e 100644 --- a/var/spack/repos/builtin/packages/silo/package.py +++ b/var/spack/repos/builtin/packages/silo/package.py @@ -1,5 +1,6 @@ from spack import * + class Silo(Package): """Silo is a library for reading and writing a wide variety of scientific data to binary, disk files.""" @@ -12,6 +13,7 @@ class Silo(Package): version('4.8', 'b1cbc0e7ec435eb656dc4b53a23663c9') variant('fortran', default=True, description='Enable Fortran support') + variant('shared', default=True, description='Build shared libraries') variant('silex', default=False, description='Builds Silex, a GUI for viewing Silo files') depends_on('hdf5') @@ -21,6 +23,7 @@ class Silo(Package): config_args = [ '--enable-fortran' if '+fortran' in spec else '--disable-fortran', '--enable-silex' if '+silex' in spec else '--disable-silex', + '--enable-shared' if '+shared' in spec else '--disable-shared', ] if '+silex' in spec: @@ -30,6 +33,7 @@ class Silo(Package): '--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), + '--enable-install-lite-headers', *config_args) make() diff --git a/var/spack/repos/builtin/packages/visit/package.py b/var/spack/repos/builtin/packages/visit/package.py new file mode 100644 index 0000000000..14e3b6a0c1 --- /dev/null +++ b/var/spack/repos/builtin/packages/visit/package.py @@ -0,0 +1,31 @@ +from spack import * + + +class Visit(Package): + """VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool.""" + homepage = "https://wci.llnl.gov/simulation/computer-codes/visit/" + url = "http://portal.nersc.gov/project/visit/releases/2.10.1/visit2.10.1.tar.gz" + + version('2.10.1', '3cbca162fdb0249f17c4456605c4211e') + version('2.10.2', '253de0837a9d69fb689befc98ea4d068') + + depends_on("vtk@6.1.0~opengl2") + depends_on("qt@4.8.6") + depends_on("python") + depends_on("silo+shared") + + def install(self, spec, prefix): + with working_dir('spack-build', create=True): + + feature_args = std_cmake_args[:] + feature_args.extend(["-DVTK_MAJOR_VERSION=6", + "-DVTK_MINOR_VERSION=1", + "-DVISIT_LOC_QMAKE_EXE:FILEPATH=%s/qmake-qt4" % spec['qt'].prefix.bin, + "-DPYTHON_EXECUTABLE:FILEPATH=%s/python" % spec['python'].prefix.bin, + "-DVISIT_SILO_DIR:PATH=%s" % spec['silo'].prefix, + "-DVISIT_HDF5_DIR:PATH=%s" % spec['hdf5'].prefix]) + + cmake('../src', *feature_args) + + make() + make("install") |