From 84bc1d6654760e7a58d15cff15b98baf51adb483 Mon Sep 17 00:00:00 2001 From: Tiziano Müller Date: Tue, 20 Nov 2018 18:23:01 +0100 Subject: CP2K related fixes and update (#9308) * openblas: enable parallel builds * cp2k: enable parallel builds * cp2k: fix building on multilib/Suse distros use the actual directory path where files where installed to instead of the default prefix+'/lib' * cp2k: ensure we have a non-header-only libxsmm * openblas: disable max num CPU detection on virtualized build * cp2k: install data and set compiled-in DATA_DIR * cp2k: make libxc an optional dependency (enabled by default) * cp2k: link libint statically * cp2k: declare statically linked library deps as type=build * cp2k: add support for PGI compiler * cp2k: rename smm=none to smm=blas for clarification * cp2k: blacklist unsupported compilers * cp2k: mark wannier90 a build-time dep since statically linked * cp2k: make pexsi and elpa optional * cp2k: add support for v6.1 * libxc: add version 4.2.3 * cp2k: use pkg-config to link properly to libxsmm * cp2k: fix OpenMP support by making it explicit Previously, CP2K accepted threaded ELPA or BLAS, leading to #(CPU) processes being spawned even though no explicit OpenMP was requested. Now the `popt` variant should truly be thread free while the `psmp` variant uses threads also internally. * cp2k: source tarballs moved to GitHub --- var/spack/repos/builtin/packages/cp2k/package.py | 244 ++++++++++++++------- var/spack/repos/builtin/packages/libxc/package.py | 16 +- .../repos/builtin/packages/libxsmm/package.py | 10 +- .../repos/builtin/packages/openblas/package.py | 26 ++- 4 files changed, 205 insertions(+), 91 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/cp2k/package.py b/var/spack/repos/builtin/packages/cp2k/package.py index e810c84eb3..ef8fe50bc6 100644 --- a/var/spack/repos/builtin/packages/cp2k/package.py +++ b/var/spack/repos/builtin/packages/cp2k/package.py @@ -15,48 +15,91 @@ class Cp2k(Package): periodic, material, crystal, and biological systems """ homepage = 'https://www.cp2k.org' - url = 'https://sourceforge.net/projects/cp2k/files/cp2k-3.0.tar.bz2' - list_url = 'https://sourceforge.net/projects/cp2k/files/' + url = 'https://github.com/cp2k/cp2k/releases/download/v3.0.0/cp2k-3.0.tar.bz2' + list_url = 'https://github.com/cp2k/cp2k/releases' + version('6.1', '573a4de5a0ee2aaabb213e04543cb10f') version('5.1', 'f25cf301aec471d7059179de4dac3ee7') version('4.1', 'b0534b530592de15ac89828b1541185e') version('3.0', 'c05bc47335f68597a310b1ed75601d35') variant('mpi', default=True, description='Enable MPI support') - variant('smm', default='libxsmm', values=('libxsmm', 'libsmm', 'none'), + variant('blas', default='openblas', values=('openblas', 'mkl', 'accelerate'), + description='Enable the use of OpenBlas/MKL/Accelerate') + variant('openmp', default=False, description='Enable OpenMP support') + variant('smm', default='libxsmm', values=('libxsmm', 'libsmm', 'blas'), description='Library for small matrix multiplications') variant('plumed', default=False, description='Enable PLUMED support') + variant('libxc', default=True, + description='Support additional functionals via libxc') + variant('pexsi', default=False, + description=('Enable the alternative PEXSI method' + 'for density matrix evaluation')) + variant('elpa', default=False, + description='Enable optimised diagonalisation routines from ELPA') depends_on('python', type='build') - depends_on('lapack') - depends_on('blas') - depends_on('fftw@3:') - depends_on('libint@1.1.4:1.2', when='@3.0:5.999') - depends_on('libxsmm', when='smm=libxsmm') - depends_on('libxc@2.2.2:') + depends_on('fftw@3:', when='~openmp') + depends_on('fftw@3:+openmp', when='+openmp') + + # see #1712 for the reason to enumerate BLAS libraries here + depends_on('openblas threads=none', when='blas=openblas ~openmp') + depends_on('openblas threads=openmp', when='blas=openblas +openmp') + depends_on('lapack', when='blas=openblas ~openmp') + + depends_on('intel-mkl', when="blas=mkl ~openmp") + depends_on('intel-mkl threads=openmp', when='blas=mkl +openmp') + + conflicts('blas=accelerate', '+openmp') # there is no Accelerate with OpenMP support + + depends_on('libxsmm@1.10:~header-only', when='smm=libxsmm') + # use pkg-config (support added in libxsmm-1.10) to link to libxsmm + depends_on('pkgconfig', type='build', when='smm=libxsmm') + + # libint & libxc are always statically linked + depends_on('libint@1.1.4:1.2', when='@3.0:6.999', type='build') + depends_on('libxc@2.2.2:', when='+libxc@:5.5999', type='build') + depends_on('libxc@4.0.3:', when='+libxc@6.0:', type='build') depends_on('mpi@2:', when='+mpi') depends_on('scalapack', when='+mpi') - depends_on('elpa@2011.12:2016.13', when='+mpi') - depends_on('pexsi+fortran@0.9.0:0.9.999', when='+mpi@:4.999') - depends_on('pexsi+fortran@0.10.0:', when='+mpi@5.0:') + depends_on('elpa@2011.12:2016.13+openmp', when='+openmp+elpa@:5.999') + depends_on('elpa@2011.12:2017.11+openmp', when='+openmp+elpa@6.0:') + depends_on('elpa@2011.12:2016.13~openmp', when='~openmp+elpa@:5.999') + depends_on('elpa@2011.12:2017.11~openmp', when='~openmp+elpa@6.0:') depends_on('plumed+shared+mpi', when='+plumed+mpi') depends_on('plumed+shared~mpi', when='+plumed~mpi') + # while we link statically against PEXSI, its own deps may be linked in + # dynamically, therefore can't set this as pure build-type dependency. + depends_on('pexsi+fortran@0.9.0:0.9.999', when='+pexsi@:4.999') + depends_on('pexsi+fortran@0.10.0:', when='+pexsi@5.0:') + + # PEXSI and ELPA need MPI in CP2K + conflicts('~mpi', '+pexsi') + conflicts('~mpi', '+elpa') + # Apparently cp2k@4.1 needs an "experimental" version of libwannier.a # which is only available contacting the developer directly. See INSTALL # in the stage of cp2k@4.1 - depends_on('wannier90', when='@3.0+mpi') + depends_on('wannier90', when='@3.0+mpi', type='build') # TODO : add dependency on CUDA - parallel = False + # CP2K needs compiler specific compilation flags, e.g. optflags + conflicts('%clang') + conflicts('%cray') + conflicts('%nag') + conflicts('%xl') def install(self, spec, prefix): # Construct a proper filename for the architecture file cp2k_architecture = '{0.architecture}-{0.compiler.name}'.format(spec) - cp2k_version = 'sopt' if '~mpi' in spec else 'popt' + cp2k_version = ('{prefix}{suffix}' + .format(prefix='p' if '+mpi' in spec else 's', + suffix='smp' if '+openmp' in spec else 'opt')) + makefile_basename = '.'.join([cp2k_architecture, cp2k_version]) makefile = join_path('arch', makefile_basename) @@ -70,25 +113,30 @@ class Cp2k(Package): '-funroll-loops', '-ffast-math', '-ftree-vectorize', - ], 'intel': [ + ], + 'intel': [ '-O2', '-pc64', '-unroll', - ] + ], + 'pgi': [ + '-fast', + ], } dflags = ['-DNDEBUG'] - libxc = spec['libxc:fortran,static'] + if '+openmp' in spec: + fftw = spec['fftw:openmp'] + else: + fftw = spec['fftw'] cppflags = [ '-D__FFTW3', '-D__LIBINT', '-D__LIBINT_MAX_AM=6', '-D__LIBDERIV_MAX_AM1=5', - '-D__LIBXC', - spec['fftw'].headers.cpp_flags, - libxc.headers.cpp_flags + fftw.headers.cpp_flags, ] if '^mpi@3:' in spec: @@ -102,25 +150,40 @@ class Cp2k(Package): cflags = copy.deepcopy(optflags[self.spec.compiler.name]) cxxflags = copy.deepcopy(optflags[self.spec.compiler.name]) fcflags = copy.deepcopy(optflags[self.spec.compiler.name]) + ldflags = [] + libs = [] if '%intel' in spec: cflags.append('-fp-model precise') cxxflags.append('-fp-model precise') fcflags.extend(['-fp-model source', '-heap-arrays 64']) + if '+openmp' in spec: + fcflags.append('-openmp') + ldflags.append('-openmp') elif '%gcc' in spec: fcflags.extend(['-ffree-form', '-ffree-line-length-none']) + if '+openmp' in spec: + fcflags.append('-fopenmp') + ldflags.append('-fopenmp') + elif '%pgi' in spec: + fcflags.extend(['-Mfreeform', '-Mextend']) + if '+openmp' in spec: + fcflags.append('-mp') + ldflags.append('-mp') - fftw = spec['fftw'].libs - ldflags = [fftw.search_flags] + ldflags.append(fftw.libs.search_flags) if 'superlu-dist@4.3' in spec: - ldflags = ['-Wl,--allow-multiple-definition'] + ldflags + ldflags.insert(0, '-Wl,--allow-multiple-definition') - libs = [ - join_path(spec['libint'].prefix.lib, 'libint.so'), - join_path(spec['libint'].prefix.lib, 'libderiv.so'), - join_path(spec['libint'].prefix.lib, 'libr12.so') - ] + # libint-1.x.y has to be linked statically to work around + # inconsistencies in its Fortran interface definition + # (short-int vs int) which otherwise causes segfaults at runtime + # due to wrong offsets into the shared library symbols. + libs.extend([ + join_path(spec['libint'].libs.directories[0], 'libderiv.a'), + join_path(spec['libint'].libs.directories[0], 'libint.a'), + ]) if '+plumed' in self.spec: # Include Plumed.inc in the Makefile @@ -155,6 +218,7 @@ class Cp2k(Package): fc = self.compiler.fc if '~mpi' in spec else self.spec['mpi'].mpifc mkf.write('FC = {0}\n'.format(fc)) mkf.write('LD = {0}\n'.format(fc)) + # Intel if '%intel' in self.spec: cppflags.extend([ @@ -168,79 +232,90 @@ class Cp2k(Package): '-free', '-fpp' ]) + + # FFTW, LAPACK, BLAS + lapack = spec['lapack'].libs + blas = spec['blas'].libs + ldflags.append((lapack + blas).search_flags) + libs.extend([str(x) for x in (fftw.libs, lapack, blas)]) + # MPI if '+mpi' in self.spec: cppflags.extend([ '-D__parallel', - '-D__LIBPEXSI', '-D__SCALAPACK' ]) - elpa = spec['elpa'] - if spec.satisfies('@:4.999'): - if elpa.satisfies('@:2014.5.999'): - cppflags.append('-D__ELPA') - elif elpa.satisfies('@2014.6:2015.10.999'): - cppflags.append('-D__ELPA2') - else: - cppflags.append('-D__ELPA3') - else: - cppflags.append('-D__ELPA={0}{1:02d}'.format( - elpa.version[0], int(elpa.version[1]))) - fcflags.append('-I' + join_path( - elpa.prefix, 'include', - 'elpa-{0}'.format(str(elpa.version)), 'elpa' - )) + scalapack = spec['scalapack'].libs + ldflags.append(scalapack.search_flags) + + libs.extend(scalapack) + libs.extend(self.spec['mpi:cxx'].libs) + libs.extend(self.compiler.stdcxx_libs) if 'wannier90' in spec: cppflags.append('-D__WANNIER90') + wannier = join_path( + spec['wannier90'].libs.directories[0], 'libwannier.a' + ) + libs.append(wannier) - fcflags.extend([ - # spec['elpa:fortran'].headers.cpp_flags - '-I' + join_path( - elpa.prefix, - 'include', - 'elpa-{0}'.format(str(elpa.version)), - 'modules' - ), - # spec[pexsi:fortran].headers.cpp_flags - '-I' + join_path(spec['pexsi'].prefix, 'fortran') - ]) - scalapack = spec['scalapack'].libs - ldflags.append(scalapack.search_flags) + if '+libxc' in spec: + libxc = spec['libxc:fortran,static'] + cppflags += [ + '-D__LIBXC', + libxc.headers.cpp_flags + ] + + ldflags.append(libxc.libs.search_flags) + libs.append(str(libxc.libs)) + + if '+pexsi' in self.spec: + cppflags.append('-D__LIBPEXSI') + fcflags.append('-I' + join_path( + spec['pexsi'].prefix, 'fortran')) libs.extend([ - join_path(elpa.prefix.lib, - 'libelpa.{0}'.format(dso_suffix)), - join_path(spec['pexsi'].prefix.lib, 'libpexsi.a'), - join_path(spec['superlu-dist'].prefix.lib, + join_path(spec['pexsi'].libs.directories[0], + 'libpexsi.a'), + join_path(spec['superlu-dist'].libs.directories[0], 'libsuperlu_dist.a'), join_path( - spec['parmetis'].prefix.lib, + spec['parmetis'].libs.directories[0], 'libparmetis.{0}'.format(dso_suffix) ), join_path( - spec['metis'].prefix.lib, + spec['metis'].libs.directories[0], 'libmetis.{0}'.format(dso_suffix) ), ]) - if 'wannier90' in spec: - wannier = join_path( - spec['wannier90'].prefix.lib, 'libwannier.a' - ) - libs.append(wannier) - - libs.extend(scalapack) - libs.extend(self.spec['mpi:cxx'].libs) - libs.extend(self.compiler.stdcxx_libs) - # LAPACK / BLAS - lapack = spec['lapack'].libs - blas = spec['blas'].libs - ldflags.append((lapack + blas).search_flags) - - ldflags.append(libxc.libs.search_flags) + if '+elpa' in self.spec: + elpa = spec['elpa'] + elpa_suffix = '_openmp' if '+openmp' in elpa else '' + elpa_base_path = join_path( + elpa.prefix, + 'include', + 'elpa{suffix}-{version!s}'.format( + suffix=elpa_suffix, version=elpa.version)) + + fcflags.append('-I' + join_path(elpa_base_path, 'modules')) + libs.append(join_path(elpa.libs.directories[0], + ('libelpa{elpa_suffix}.{dso_suffix}' + .format(elpa_suffix=elpa_suffix, + dso_suffix=dso_suffix)))) - libs.extend([str(x) for x in (fftw, lapack, blas, libxc.libs)]) + if spec.satisfies('@:4.999'): + if elpa.satisfies('@:2014.5.999'): + cppflags.append('-D__ELPA') + elif elpa.satisfies('@2014.6:2015.10.999'): + cppflags.append('-D__ELPA2') + else: + cppflags.append('-D__ELPA3') + else: + cppflags.append('-D__ELPA={0}{1:02d}' + .format(elpa.version[0], + int(elpa.version[1]))) + fcflags.append('-I' + join_path(elpa_base_path, 'elpa')) if 'smm=libsmm' in spec: lib_dir = join_path('lib', cp2k_architecture, cp2k_version) @@ -261,11 +336,10 @@ class Cp2k(Package): elif 'smm=libxsmm' in spec: cppflags.extend([ '-D__LIBXSMM', - spec['libxsmm'].headers.cpp_flags, + '$(shell pkg-config --cflags-only-other libxsmmf)', ]) - libxsmm = spec['libxsmm'].libs - ldflags.append(libxsmm.search_flags) - libs.append(str(libxsmm)) + fcflags.append('$(shell pkg-config --cflags-only-I libxsmmf)') + libs.append('$(shell pkg-config --libs libxsmmf)') dflags.extend(cppflags) cflags.extend(cppflags) @@ -284,6 +358,7 @@ class Cp2k(Package): ' '.join(ldflags) + ' -nofor_main') ) mkf.write('LIBS = {0}\n\n'.format(' '.join(libs))) + mkf.write('DATA_DIR = {0}\n\n'.format(self.prefix.share.data)) with working_dir('makefiles'): # Apparently the Makefile bases its paths on PWD @@ -295,3 +370,4 @@ class Cp2k(Package): env['PWD'] = pwd_backup exe_dir = join_path('exe', cp2k_architecture) install_tree(exe_dir, self.prefix.bin) + install_tree('data', self.prefix.share.data) diff --git a/var/spack/repos/builtin/packages/libxc/package.py b/var/spack/repos/builtin/packages/libxc/package.py index bdb5fcabd2..3eb3902e45 100644 --- a/var/spack/repos/builtin/packages/libxc/package.py +++ b/var/spack/repos/builtin/packages/libxc/package.py @@ -13,10 +13,21 @@ class Libxc(AutotoolsPackage): homepage = "http://www.tddft.org/programs/octopus/wiki/index.php/Libxc" url = "http://www.tddft.org/programs/octopus/down.php?file=libxc/libxc-2.2.2.tar.gz" + version('4.2.3', '6176ac7edf234425d973903f82199350') version('3.0.0', '8227fa3053f8fc215bd9d7b0d36de03c') version('2.2.2', 'd9f90a0d6e36df6c1312b6422280f2ec') version('2.2.1', '38dc3a067524baf4f8521d5bb1cd0b8f') + def url_for_version(self, version): + if version < Version('3.0.0'): + return ("http://www.tddft.org/programs/octopus/" + "down.php?file=libxc/libxc-{0}.tar.gz" + .format(version)) + + return ("http://www.tddft.org/programs/octopus/" + "down.php?file=libxc/{0}/libxc-{0}.tar.gz" + .format(version)) + @property def libs(self): """Libxc can be queried for the following parameters: @@ -38,7 +49,10 @@ class Libxc(AutotoolsPackage): # Libxc has a fortran90 interface: give clients the # possibility to query for it if 'fortran' in query_parameters: - libraries = ['libxcf90'] + libraries + if self.version < Version('4.0.0'): + libraries = ['libxcf90'] + libraries + else: # starting from version 4 there is also a stable f03 iface + libraries = ['libxcf90', 'libxcf03'] + libraries return find_libraries( libraries, root=self.prefix, shared=shared, recursive=True diff --git a/var/spack/repos/builtin/packages/libxsmm/package.py b/var/spack/repos/builtin/packages/libxsmm/package.py index 848351ce1c..176fd61b37 100644 --- a/var/spack/repos/builtin/packages/libxsmm/package.py +++ b/var/spack/repos/builtin/packages/libxsmm/package.py @@ -4,6 +4,7 @@ # SPDX-License-Identifier: (Apache-2.0 OR MIT) from spack import * +import os from glob import glob @@ -72,7 +73,7 @@ class Libxsmm(MakefilePackage): def build(self, spec, prefix): # include symbols by default - make_args = ['SYM=1'] + make_args = ['SYM=1', 'PREFIX=%s' % prefix] if '+header-only' in spec: make_args += ['header-only'] @@ -89,6 +90,13 @@ class Libxsmm(MakefilePackage): def install(self, spec, prefix): install_tree('include', prefix.include) + + # move pkg-config files to their right place + mkdirp('lib/pkgconfig') + for pcfile in glob('lib/*.pc'): + os.rename(pcfile, os.path.join('lib/pkgconfig', + os.path.basename(pcfile))) + if '+header-only' in spec: install_tree('src', prefix.src) else: diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py index dfe1506d1c..0d3cf91db7 100644 --- a/var/spack/repos/builtin/packages/openblas/package.py +++ b/var/spack/repos/builtin/packages/openblas/package.py @@ -58,7 +58,8 @@ class Openblas(MakefilePackage): provides('blas') provides('lapack') - patch('make.patch', when='@0.2.16:') + # OpenBLAS >=3.0 has an official way to disable internal parallel builds + patch('make.patch', when='@0.2.16:0.2.20') # This patch is in a pull request to OpenBLAS that has not been handled # https://github.com/xianyi/OpenBLAS/pull/915 # UPD: the patch has been merged starting version 0.2.20 @@ -87,10 +88,19 @@ class Openblas(MakefilePackage): sha256='714aea33692304a50bd0ccde42590c176c82ded4a8ac7f06e573dc8071929c33', when='@0.3.3') - parallel = False + # Fix parallel build issues on filesystems + # with missing sub-second timestamp resolution + patch('https://github.com/xianyi/OpenBLAS/commit/79ea839b635d1fd84b6ce8a47e086f01d64198e6.patch', + sha256='f1b066a4481a50678caeb7656bf3e6764f45619686ac465f257c8017a2dc1ff0', + when='@0.3.0:0.3.3') conflicts('%intel@16', when='@0.2.15:0.2.19') + @property + def parallel(self): + # unclear whether setting `-j N` externally was supported before 0.3 + return self.spec.version >= Version('0.3.0') + @run_before('edit') def check_compilers(self): # As of 06/2016 there is no mechanism to specify that packages which @@ -124,13 +134,19 @@ class Openblas(MakefilePackage): make_defs = [ 'CC={0}'.format(spack_cc), 'FC={0}'.format(spack_fc), - 'MAKE_NO_J=1' ] + # force OpenBLAS to use externally defined parallel build + if self.spec.version < Version('0.3'): + make_defs.append('MAKE_NO_J=1') # flag defined by our make.patch + else: + make_defs.append('MAKE_NB_JOBS=0') # flag provided by OpenBLAS + if self.spec.variants['virtual_machine'].value: make_defs += [ 'DYNAMIC_ARCH=1', - 'NO_AVX2=1' + 'NO_AVX2=1', + 'NUM_THREADS=64', # OpenBLAS stores present no of CPUs as max ] if self.spec.variants['cpu_target'].value: @@ -192,7 +208,7 @@ class Openblas(MakefilePackage): @run_after('build') @on_package_attributes(run_tests=True) def check_build(self): - make('tests', *self.make_defs) + make('tests', *self.make_defs, parallel=False) @property def install_targets(self): -- cgit v1.2.3-70-g09d2