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
This commit is contained in:
parent
13b95b8ae6
commit
84bc1d6654
@ -15,48 +15,91 @@ class Cp2k(Package):
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periodic, material, crystal, and biological systems
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"""
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homepage = 'https://www.cp2k.org'
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url = 'https://sourceforge.net/projects/cp2k/files/cp2k-3.0.tar.bz2'
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list_url = 'https://sourceforge.net/projects/cp2k/files/'
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url = 'https://github.com/cp2k/cp2k/releases/download/v3.0.0/cp2k-3.0.tar.bz2'
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list_url = 'https://github.com/cp2k/cp2k/releases'
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version('6.1', '573a4de5a0ee2aaabb213e04543cb10f')
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version('5.1', 'f25cf301aec471d7059179de4dac3ee7')
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version('4.1', 'b0534b530592de15ac89828b1541185e')
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version('3.0', 'c05bc47335f68597a310b1ed75601d35')
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variant('mpi', default=True, description='Enable MPI support')
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variant('smm', default='libxsmm', values=('libxsmm', 'libsmm', 'none'),
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variant('blas', default='openblas', values=('openblas', 'mkl', 'accelerate'),
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description='Enable the use of OpenBlas/MKL/Accelerate')
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variant('openmp', default=False, description='Enable OpenMP support')
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variant('smm', default='libxsmm', values=('libxsmm', 'libsmm', 'blas'),
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description='Library for small matrix multiplications')
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variant('plumed', default=False, description='Enable PLUMED support')
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variant('libxc', default=True,
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description='Support additional functionals via libxc')
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variant('pexsi', default=False,
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description=('Enable the alternative PEXSI method'
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'for density matrix evaluation'))
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variant('elpa', default=False,
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description='Enable optimised diagonalisation routines from ELPA')
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depends_on('python', type='build')
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depends_on('lapack')
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depends_on('blas')
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depends_on('fftw@3:')
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depends_on('libint@1.1.4:1.2', when='@3.0:5.999')
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depends_on('libxsmm', when='smm=libxsmm')
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depends_on('libxc@2.2.2:')
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depends_on('fftw@3:', when='~openmp')
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depends_on('fftw@3:+openmp', when='+openmp')
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# see #1712 for the reason to enumerate BLAS libraries here
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depends_on('openblas threads=none', when='blas=openblas ~openmp')
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depends_on('openblas threads=openmp', when='blas=openblas +openmp')
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depends_on('lapack', when='blas=openblas ~openmp')
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depends_on('intel-mkl', when="blas=mkl ~openmp")
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depends_on('intel-mkl threads=openmp', when='blas=mkl +openmp')
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conflicts('blas=accelerate', '+openmp') # there is no Accelerate with OpenMP support
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depends_on('libxsmm@1.10:~header-only', when='smm=libxsmm')
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# use pkg-config (support added in libxsmm-1.10) to link to libxsmm
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depends_on('pkgconfig', type='build', when='smm=libxsmm')
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# libint & libxc are always statically linked
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depends_on('libint@1.1.4:1.2', when='@3.0:6.999', type='build')
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depends_on('libxc@2.2.2:', when='+libxc@:5.5999', type='build')
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depends_on('libxc@4.0.3:', when='+libxc@6.0:', type='build')
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depends_on('mpi@2:', when='+mpi')
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depends_on('scalapack', when='+mpi')
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depends_on('elpa@2011.12:2016.13', when='+mpi')
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depends_on('pexsi+fortran@0.9.0:0.9.999', when='+mpi@:4.999')
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depends_on('pexsi+fortran@0.10.0:', when='+mpi@5.0:')
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depends_on('elpa@2011.12:2016.13+openmp', when='+openmp+elpa@:5.999')
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depends_on('elpa@2011.12:2017.11+openmp', when='+openmp+elpa@6.0:')
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depends_on('elpa@2011.12:2016.13~openmp', when='~openmp+elpa@:5.999')
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depends_on('elpa@2011.12:2017.11~openmp', when='~openmp+elpa@6.0:')
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depends_on('plumed+shared+mpi', when='+plumed+mpi')
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depends_on('plumed+shared~mpi', when='+plumed~mpi')
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# while we link statically against PEXSI, its own deps may be linked in
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# dynamically, therefore can't set this as pure build-type dependency.
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depends_on('pexsi+fortran@0.9.0:0.9.999', when='+pexsi@:4.999')
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depends_on('pexsi+fortran@0.10.0:', when='+pexsi@5.0:')
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# PEXSI and ELPA need MPI in CP2K
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conflicts('~mpi', '+pexsi')
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conflicts('~mpi', '+elpa')
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# Apparently cp2k@4.1 needs an "experimental" version of libwannier.a
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# which is only available contacting the developer directly. See INSTALL
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# in the stage of cp2k@4.1
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depends_on('wannier90', when='@3.0+mpi')
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depends_on('wannier90', when='@3.0+mpi', type='build')
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# TODO : add dependency on CUDA
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parallel = False
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# CP2K needs compiler specific compilation flags, e.g. optflags
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conflicts('%clang')
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conflicts('%cray')
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conflicts('%nag')
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conflicts('%xl')
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def install(self, spec, prefix):
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# Construct a proper filename for the architecture file
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cp2k_architecture = '{0.architecture}-{0.compiler.name}'.format(spec)
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cp2k_version = 'sopt' if '~mpi' in spec else 'popt'
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cp2k_version = ('{prefix}{suffix}'
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.format(prefix='p' if '+mpi' in spec else 's',
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suffix='smp' if '+openmp' in spec else 'opt'))
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makefile_basename = '.'.join([cp2k_architecture, cp2k_version])
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makefile = join_path('arch', makefile_basename)
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@ -70,25 +113,30 @@ def install(self, spec, prefix):
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'-funroll-loops',
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'-ffast-math',
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'-ftree-vectorize',
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], 'intel': [
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],
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'intel': [
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'-O2',
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'-pc64',
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'-unroll',
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]
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],
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'pgi': [
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'-fast',
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],
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}
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dflags = ['-DNDEBUG']
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libxc = spec['libxc:fortran,static']
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if '+openmp' in spec:
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fftw = spec['fftw:openmp']
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else:
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fftw = spec['fftw']
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cppflags = [
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'-D__FFTW3',
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'-D__LIBINT',
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'-D__LIBINT_MAX_AM=6',
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'-D__LIBDERIV_MAX_AM1=5',
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'-D__LIBXC',
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spec['fftw'].headers.cpp_flags,
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libxc.headers.cpp_flags
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fftw.headers.cpp_flags,
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]
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if '^mpi@3:' in spec:
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@ -102,25 +150,40 @@ def install(self, spec, prefix):
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cflags = copy.deepcopy(optflags[self.spec.compiler.name])
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cxxflags = copy.deepcopy(optflags[self.spec.compiler.name])
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fcflags = copy.deepcopy(optflags[self.spec.compiler.name])
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ldflags = []
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libs = []
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if '%intel' in spec:
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cflags.append('-fp-model precise')
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cxxflags.append('-fp-model precise')
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fcflags.extend(['-fp-model source', '-heap-arrays 64'])
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if '+openmp' in spec:
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fcflags.append('-openmp')
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ldflags.append('-openmp')
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elif '%gcc' in spec:
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fcflags.extend(['-ffree-form', '-ffree-line-length-none'])
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if '+openmp' in spec:
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fcflags.append('-fopenmp')
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ldflags.append('-fopenmp')
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elif '%pgi' in spec:
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fcflags.extend(['-Mfreeform', '-Mextend'])
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if '+openmp' in spec:
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fcflags.append('-mp')
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ldflags.append('-mp')
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fftw = spec['fftw'].libs
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ldflags = [fftw.search_flags]
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ldflags.append(fftw.libs.search_flags)
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if 'superlu-dist@4.3' in spec:
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ldflags = ['-Wl,--allow-multiple-definition'] + ldflags
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ldflags.insert(0, '-Wl,--allow-multiple-definition')
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libs = [
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join_path(spec['libint'].prefix.lib, 'libint.so'),
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join_path(spec['libint'].prefix.lib, 'libderiv.so'),
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join_path(spec['libint'].prefix.lib, 'libr12.so')
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]
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# libint-1.x.y has to be linked statically to work around
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# inconsistencies in its Fortran interface definition
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# (short-int vs int) which otherwise causes segfaults at runtime
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# due to wrong offsets into the shared library symbols.
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libs.extend([
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join_path(spec['libint'].libs.directories[0], 'libderiv.a'),
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join_path(spec['libint'].libs.directories[0], 'libint.a'),
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])
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if '+plumed' in self.spec:
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# Include Plumed.inc in the Makefile
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@ -155,6 +218,7 @@ def install(self, spec, prefix):
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fc = self.compiler.fc if '~mpi' in spec else self.spec['mpi'].mpifc
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mkf.write('FC = {0}\n'.format(fc))
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mkf.write('LD = {0}\n'.format(fc))
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# Intel
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if '%intel' in self.spec:
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cppflags.extend([
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@ -168,15 +232,78 @@ def install(self, spec, prefix):
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'-free',
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'-fpp'
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])
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# FFTW, LAPACK, BLAS
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lapack = spec['lapack'].libs
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blas = spec['blas'].libs
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ldflags.append((lapack + blas).search_flags)
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libs.extend([str(x) for x in (fftw.libs, lapack, blas)])
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# MPI
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if '+mpi' in self.spec:
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cppflags.extend([
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'-D__parallel',
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'-D__LIBPEXSI',
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'-D__SCALAPACK'
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])
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scalapack = spec['scalapack'].libs
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ldflags.append(scalapack.search_flags)
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libs.extend(scalapack)
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libs.extend(self.spec['mpi:cxx'].libs)
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libs.extend(self.compiler.stdcxx_libs)
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if 'wannier90' in spec:
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cppflags.append('-D__WANNIER90')
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wannier = join_path(
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spec['wannier90'].libs.directories[0], 'libwannier.a'
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)
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libs.append(wannier)
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if '+libxc' in spec:
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libxc = spec['libxc:fortran,static']
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cppflags += [
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'-D__LIBXC',
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libxc.headers.cpp_flags
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]
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ldflags.append(libxc.libs.search_flags)
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libs.append(str(libxc.libs))
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if '+pexsi' in self.spec:
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cppflags.append('-D__LIBPEXSI')
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fcflags.append('-I' + join_path(
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spec['pexsi'].prefix, 'fortran'))
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libs.extend([
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join_path(spec['pexsi'].libs.directories[0],
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'libpexsi.a'),
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join_path(spec['superlu-dist'].libs.directories[0],
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'libsuperlu_dist.a'),
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join_path(
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spec['parmetis'].libs.directories[0],
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'libparmetis.{0}'.format(dso_suffix)
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),
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join_path(
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spec['metis'].libs.directories[0],
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'libmetis.{0}'.format(dso_suffix)
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),
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])
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if '+elpa' in self.spec:
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elpa = spec['elpa']
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elpa_suffix = '_openmp' if '+openmp' in elpa else ''
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elpa_base_path = join_path(
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elpa.prefix,
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'include',
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'elpa{suffix}-{version!s}'.format(
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suffix=elpa_suffix, version=elpa.version))
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fcflags.append('-I' + join_path(elpa_base_path, 'modules'))
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libs.append(join_path(elpa.libs.directories[0],
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('libelpa{elpa_suffix}.{dso_suffix}'
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.format(elpa_suffix=elpa_suffix,
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dso_suffix=dso_suffix))))
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if spec.satisfies('@:4.999'):
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if elpa.satisfies('@:2014.5.999'):
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cppflags.append('-D__ELPA')
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@ -185,62 +312,10 @@ def install(self, spec, prefix):
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else:
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cppflags.append('-D__ELPA3')
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else:
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cppflags.append('-D__ELPA={0}{1:02d}'.format(
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elpa.version[0], int(elpa.version[1])))
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fcflags.append('-I' + join_path(
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elpa.prefix, 'include',
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'elpa-{0}'.format(str(elpa.version)), 'elpa'
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))
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if 'wannier90' in spec:
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cppflags.append('-D__WANNIER90')
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fcflags.extend([
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# spec['elpa:fortran'].headers.cpp_flags
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'-I' + join_path(
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elpa.prefix,
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'include',
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'elpa-{0}'.format(str(elpa.version)),
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'modules'
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),
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# spec[pexsi:fortran].headers.cpp_flags
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'-I' + join_path(spec['pexsi'].prefix, 'fortran')
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])
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scalapack = spec['scalapack'].libs
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ldflags.append(scalapack.search_flags)
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libs.extend([
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join_path(elpa.prefix.lib,
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'libelpa.{0}'.format(dso_suffix)),
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join_path(spec['pexsi'].prefix.lib, 'libpexsi.a'),
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join_path(spec['superlu-dist'].prefix.lib,
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'libsuperlu_dist.a'),
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join_path(
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spec['parmetis'].prefix.lib,
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'libparmetis.{0}'.format(dso_suffix)
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),
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join_path(
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spec['metis'].prefix.lib,
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'libmetis.{0}'.format(dso_suffix)
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),
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])
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if 'wannier90' in spec:
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wannier = join_path(
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spec['wannier90'].prefix.lib, 'libwannier.a'
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)
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libs.append(wannier)
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libs.extend(scalapack)
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libs.extend(self.spec['mpi:cxx'].libs)
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libs.extend(self.compiler.stdcxx_libs)
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# LAPACK / BLAS
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lapack = spec['lapack'].libs
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blas = spec['blas'].libs
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ldflags.append((lapack + blas).search_flags)
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ldflags.append(libxc.libs.search_flags)
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libs.extend([str(x) for x in (fftw, lapack, blas, libxc.libs)])
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cppflags.append('-D__ELPA={0}{1:02d}'
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.format(elpa.version[0],
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int(elpa.version[1])))
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fcflags.append('-I' + join_path(elpa_base_path, 'elpa'))
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if 'smm=libsmm' in spec:
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lib_dir = join_path('lib', cp2k_architecture, cp2k_version)
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@ -261,11 +336,10 @@ def install(self, spec, prefix):
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elif 'smm=libxsmm' in spec:
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cppflags.extend([
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'-D__LIBXSMM',
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spec['libxsmm'].headers.cpp_flags,
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'$(shell pkg-config --cflags-only-other libxsmmf)',
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])
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libxsmm = spec['libxsmm'].libs
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ldflags.append(libxsmm.search_flags)
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libs.append(str(libxsmm))
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fcflags.append('$(shell pkg-config --cflags-only-I libxsmmf)')
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libs.append('$(shell pkg-config --libs libxsmmf)')
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dflags.extend(cppflags)
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cflags.extend(cppflags)
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@ -284,6 +358,7 @@ def install(self, spec, prefix):
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' '.join(ldflags) + ' -nofor_main')
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)
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mkf.write('LIBS = {0}\n\n'.format(' '.join(libs)))
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mkf.write('DATA_DIR = {0}\n\n'.format(self.prefix.share.data))
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with working_dir('makefiles'):
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# Apparently the Makefile bases its paths on PWD
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@ -295,3 +370,4 @@ def install(self, spec, prefix):
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env['PWD'] = pwd_backup
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exe_dir = join_path('exe', cp2k_architecture)
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install_tree(exe_dir, self.prefix.bin)
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install_tree('data', self.prefix.share.data)
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|
@ -13,10 +13,21 @@ class Libxc(AutotoolsPackage):
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homepage = "http://www.tddft.org/programs/octopus/wiki/index.php/Libxc"
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url = "http://www.tddft.org/programs/octopus/down.php?file=libxc/libxc-2.2.2.tar.gz"
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version('4.2.3', '6176ac7edf234425d973903f82199350')
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version('3.0.0', '8227fa3053f8fc215bd9d7b0d36de03c')
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version('2.2.2', 'd9f90a0d6e36df6c1312b6422280f2ec')
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version('2.2.1', '38dc3a067524baf4f8521d5bb1cd0b8f')
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def url_for_version(self, version):
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if version < Version('3.0.0'):
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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 @@ def libs(self):
|
||||
# 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
|
||||
|
@ -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 @@ def edit(self, spec, prefix):
|
||||
|
||||
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 @@ def build(self, spec, prefix):
|
||||
|
||||
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:
|
||||
|
@ -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 @@ def make_defs(self):
|
||||
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 @@ def build_targets(self):
|
||||
@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):
|
||||
|
Loading…
Reference in New Issue
Block a user