cp2k is now a MakefilePackage (#10570)
* cp2k: archive the Makefile after a successful installation * cp2k: all checksums are now sha256 * libint: all checksums are now sha256 + added versions 2.4.X * libxc: all checksums are now sha256 + added version 4.3.2 * cp2k: os.path.join instead of join_path + simplified openmp flags * cp2k: turned into a MakefilePackage * cp2k: refactored edit method so that Makefile writing happens last
This commit is contained in:
Massimiliano Culpo
GitHub
parent
051c66335f
commit
b3dd95bd62
@ -4,12 +4,13 @@
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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import os
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import os.path
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import copy
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from spack import *
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import spack.util.environment
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class Cp2k(Package):
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class Cp2k(MakefilePackage):
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"""CP2K is a quantum chemistry and solid state physics software package
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that can perform atomistic simulations of solid state, liquid, molecular,
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periodic, material, crystal, and biological systems
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@ -18,10 +19,10 @@ class Cp2k(Package):
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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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version('6.1', sha256='af803558e0a6b9e9d9ce8a3ab955ba32bacd179922455424e061c82c9fefa34b')
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version('5.1', sha256='e23613b593354fa82e0b8410e17d94c607a0b8c6d9b5d843528403ab09904412')
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version('4.1', sha256='4a3e4a101d8a35ebd80a9e9ecb02697fb8256364f1eccdbe4e5a85d31fe21343')
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version('3.0', sha256='1acfacef643141045b7cbade7006f9b7538476d861eeecd9658c9e468dc61151')
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variant('mpi', default=True, description='Enable MPI support')
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variant('blas', default='openblas', values=('openblas', 'mkl', 'accelerate'),
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@ -93,114 +94,240 @@ class Cp2k(Package):
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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 = ('{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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@property
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def makefile_architecture(self):
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return '{0.architecture}-{0.compiler.name}'.format(self.spec)
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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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@property
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def makefile_version(self):
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return '{prefix}{suffix}'.format(
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prefix='p' if '+mpi' in self.spec else 's',
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suffix='smp' if '+openmp' in self.spec else 'opt'
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)
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# Write the custom makefile
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with open(makefile, 'w') as mkf:
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# Optimization flags
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optflags = {
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'gcc': [
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'-O2',
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'-mtune=native',
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'-funroll-loops',
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'-ffast-math',
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'-ftree-vectorize',
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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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'pgi': [
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'-fast',
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],
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}
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@property
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def makefile(self):
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makefile_basename = '.'.join([
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self.makefile_architecture, self.makefile_version
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])
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return os.path.join('arch', makefile_basename)
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dflags = ['-DNDEBUG']
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@property
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def archive_files(self):
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return [os.path.join(self.stage.source_path, self.makefile)]
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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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def edit(self, spec, prefix):
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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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fftw.headers.cpp_flags,
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]
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fftw = spec['fftw:openmp' if '+openmp' in spec else 'fftw']
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if '^mpi@3:' in spec:
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cppflags.append('-D__MPI_VERSION=3')
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elif '^mpi@2:' in spec:
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cppflags.append('-D__MPI_VERSION=2')
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optimization_flags = {
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'gcc': [
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'-O2',
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'-mtune=native',
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'-funroll-loops',
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'-ffast-math',
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'-ftree-vectorize',
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],
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'intel': ['-O2', '-pc64', '-unroll'],
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'pgi': ['-fast'],
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}
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if '^intel-mkl' in spec:
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cppflags.append('-D__FFTSG')
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dflags = ['-DNDEBUG']
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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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fftw.headers.cpp_flags,
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]
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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 '^mpi@3:' in spec:
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cppflags.append('-D__MPI_VERSION=3')
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elif '^mpi@2:' in spec:
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cppflags.append('-D__MPI_VERSION=2')
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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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if '^intel-mkl' in spec:
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cppflags.append('-D__FFTSG')
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ldflags.append(fftw.libs.search_flags)
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cflags = optimization_flags[self.spec.compiler.name][:]
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cxxflags = optimization_flags[self.spec.compiler.name][:]
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fcflags = optimization_flags[self.spec.compiler.name][:]
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ldflags = []
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libs = []
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if 'superlu-dist@4.3' in spec:
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ldflags.insert(0, '-Wl,--allow-multiple-definition')
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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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elif '%gcc' in spec:
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fcflags.extend(['-ffree-form', '-ffree-line-length-none'])
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elif '%pgi' in spec:
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fcflags.extend(['-Mfreeform', '-Mextend'])
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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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if '+openmp' in spec:
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fcflags.append(self.compiler.openmp_flag)
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ldflags.append(self.compiler.openmp_flag)
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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.insert(0, '-Wl,--allow-multiple-definition')
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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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os.path.join(spec['libint'].libs.directories[0], 'libderiv.a'),
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os.path.join(spec['libint'].libs.directories[0], 'libint.a'),
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])
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if '+plumed' in self.spec:
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dflags.extend(['-D__PLUMED2'])
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cppflags.extend(['-D__PLUMED2'])
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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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os.path.join(self.spec['plumed'].prefix.lib,
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'libplumed.{0}'.format(dso_suffix))
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])
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fc = self.compiler.fc if '~mpi' in spec else self.spec['mpi'].mpifc
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# Intel
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if '%intel' in self.spec:
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cppflags.extend([
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'-D__INTEL',
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'-D__HAS_ISO_C_BINDING',
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'-D__USE_CP2K_TRACE',
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'-D__MKL'
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])
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fcflags.extend([
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'-diag-disable 8290,8291,10010,10212,11060',
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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__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 = os.path.join(
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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' + os.path.join(
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spec['pexsi'].prefix, 'fortran'))
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libs.extend([
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os.path.join(spec['pexsi'].libs.directories[0],
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'libpexsi.a'),
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os.path.join(spec['superlu-dist'].libs.directories[0],
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'libsuperlu_dist.a'),
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os.path.join(
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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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os.path.join(
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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 = os.path.join(
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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' + os.path.join(elpa_base_path, 'modules'))
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libs.append(os.path.join(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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elif elpa.satisfies('@2014.6:2015.10.999'):
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cppflags.append('-D__ELPA2')
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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}'
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.format(elpa.version[0],
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int(elpa.version[1])))
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fcflags.append('-I' + os.path.join(elpa_base_path, 'elpa'))
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if 'smm=libsmm' in spec:
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lib_dir = os.path.join(
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'lib', self.makefile_architecture, self.makefile_version
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)
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mkdirp(lib_dir)
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try:
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copy(env['LIBSMM_PATH'], os.path.join(lib_dir, 'libsmm.a'))
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except KeyError:
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raise KeyError('Point environment variable LIBSMM_PATH to '
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'the absolute path of the libsmm.a file')
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except IOError:
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raise IOError('The file LIBSMM_PATH pointed to does not '
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'exist. Note that it must be absolute path.')
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cppflags.extend([
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'-D__HAS_smm_dnn',
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'-D__HAS_smm_vec',
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])
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libs.append('-lsmm')
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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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'$(shell pkg-config --cflags-only-other libxsmmf)',
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])
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fcflags.append('$(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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cxxflags.extend(cppflags)
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fcflags.extend(cppflags)
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with open(self.makefile, 'w') as mkf:
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if '+plumed' in self.spec:
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# Include Plumed.inc in the Makefile
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mkf.write('include {0}\n'.format(
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join_path(self.spec['plumed'].prefix.lib,
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'plumed',
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'src',
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'lib',
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'Plumed.inc')
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self.spec['plumed'].package.plumed_inc
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))
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# Add required macro
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dflags.extend(['-D__PLUMED2'])
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cppflags.extend(['-D__PLUMED2'])
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libs.extend([
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join_path(self.spec['plumed'].prefix.lib,
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'libplumed.{0}'.format(dso_suffix))
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])
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mkf.write('CC = {0.compiler.cc}\n'.format(self))
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if '%intel' in self.spec:
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@ -215,137 +342,9 @@ def install(self, spec, prefix):
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else:
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mkf.write('CPP = # {0.compiler.cc} -E\n\n'.format(self))
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mkf.write('AR = ar -r\n\n')
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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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'-D__INTEL',
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'-D__HAS_ISO_C_BINDING',
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'-D__USE_CP2K_TRACE',
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'-D__MKL'
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])
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fcflags.extend([
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'-diag-disable 8290,8291,10010,10212,11060',
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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__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:
|
||||
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))))
|
||||
|
||||
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)
|
||||
mkdirp(lib_dir)
|
||||
try:
|
||||
copy(env['LIBSMM_PATH'], join_path(lib_dir, 'libsmm.a'))
|
||||
except KeyError:
|
||||
raise KeyError('Point environment variable LIBSMM_PATH to '
|
||||
'the absolute path of the libsmm.a file')
|
||||
except IOError:
|
||||
raise IOError('The file LIBSMM_PATH pointed to does not '
|
||||
'exist. Note that it must be absolute path.')
|
||||
cppflags.extend([
|
||||
'-D__HAS_smm_dnn',
|
||||
'-D__HAS_smm_vec',
|
||||
])
|
||||
libs.append('-lsmm')
|
||||
elif 'smm=libxsmm' in spec:
|
||||
cppflags.extend([
|
||||
'-D__LIBXSMM',
|
||||
'$(shell pkg-config --cflags-only-other libxsmmf)',
|
||||
])
|
||||
fcflags.append('$(shell pkg-config --cflags-only-I libxsmmf)')
|
||||
libs.append('$(shell pkg-config --libs libxsmmf)')
|
||||
|
||||
dflags.extend(cppflags)
|
||||
cflags.extend(cppflags)
|
||||
cxxflags.extend(cppflags)
|
||||
fcflags.extend(cppflags)
|
||||
|
||||
# Write compiler flags to file
|
||||
mkf.write('DFLAGS = {0}\n\n'.format(' '.join(dflags)))
|
||||
mkf.write('CPPFLAGS = {0}\n\n'.format(' '.join(cppflags)))
|
||||
@ -360,14 +359,24 @@ def install(self, spec, prefix):
|
||||
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
|
||||
# so we need to set PWD = os.getcwd()
|
||||
pwd_backup = env['PWD']
|
||||
env['PWD'] = os.getcwd()
|
||||
make('ARCH={0}'.format(cp2k_architecture),
|
||||
'VERSION={0}'.format(cp2k_version))
|
||||
env['PWD'] = pwd_backup
|
||||
exe_dir = join_path('exe', cp2k_architecture)
|
||||
@property
|
||||
def build_directory(self):
|
||||
return os.path.join(self.stage.source_path, 'makefiles')
|
||||
|
||||
@property
|
||||
def build_targets(self):
|
||||
return [
|
||||
'ARCH={0}'.format(self.makefile_architecture),
|
||||
'VERSION={0}'.format(self.makefile_version)
|
||||
]
|
||||
|
||||
def build(self, spec, prefix):
|
||||
# Apparently the Makefile bases its paths on PWD
|
||||
# so we need to set PWD = self.build_directory
|
||||
with spack.util.environment.set_env(PWD=self.build_directory):
|
||||
super(Cp2k, self).build(spec, prefix)
|
||||
|
||||
def install(self, spec, prefix):
|
||||
exe_dir = os.path.join('exe', self.makefile_architecture)
|
||||
install_tree(exe_dir, self.prefix.bin)
|
||||
install_tree('data', self.prefix.share.data)
|
||||
|
||||
@ -14,10 +14,13 @@ class Libint(AutotoolsPackage):
|
||||
homepage = "https://github.com/evaleev/libint"
|
||||
url = "https://github.com/evaleev/libint/archive/v2.1.0.tar.gz"
|
||||
|
||||
version('2.2.0', 'da37dab862fb0b97a7ed7d007695ef47')
|
||||
version('2.1.0', 'd0dcb985fe32ddebc78fe571ce37e2d6')
|
||||
version('1.1.6', '990f67b55f49ecc18f32c58da9240684')
|
||||
version('1.1.5', '379b7d0718ff398715d6898807adf628')
|
||||
version('2.4.2', sha256='86dff38065e69a3a51d15cfdc638f766044cb87e5c6682d960c14f9847e2eac3')
|
||||
version('2.4.1', sha256='0513be124563fdbbc7cd3c7043e221df1bda236a037027ba9343429a27db8ce4')
|
||||
version('2.4.0', sha256='52eb16f065406099dcfaceb12f9a7f7e329c9cfcf6ed9bfacb0cff7431dd6019')
|
||||
version('2.2.0', sha256='f737d485f33ac819d7f28c6ce303b1f3a2296bfd2c14f7c1323f8c5d370bb0e3')
|
||||
version('2.1.0', sha256='43c453a1663aa1c55294df89ff9ece3aefc8d1bbba5ea31dbfe71b2d812e24c8')
|
||||
version('1.1.6', sha256='f201b0c621df678cfe8bdf3990796b8976ff194aba357ae398f2f29b0e2985a6')
|
||||
version('1.1.5', sha256='ec8cd4a4ba1e1a98230165210c293632372f0e573acd878ed62e5ec6f8b6174b')
|
||||
|
||||
# Build dependencies
|
||||
depends_on('autoconf@2.52:', type='build')
|
||||
|
||||
@ -13,10 +13,11 @@ 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')
|
||||
version('4.3.2', sha256='bc159aea2537521998c7fb1199789e1be71e04c4b7758d58282622e347603a6f')
|
||||
version('4.2.3', sha256='02e49e9ba7d21d18df17e9e57eae861e6ce05e65e966e1e832475aa09e344256')
|
||||
version('3.0.0', sha256='5542b99042c09b2925f2e3700d769cda4fb411b476d446c833ea28c6bfa8792a')
|
||||
version('2.2.2', sha256='6ca1d0bb5fdc341d59960707bc67f23ad54de8a6018e19e02eee2b16ea7cc642')
|
||||
version('2.2.1', sha256='ade61c1fa4ed238edd56408fd8ee6c2e305a3d5753e160017e2a71817c98fd00')
|
||||
|
||||
def url_for_version(self, version):
|
||||
if version < Version('3.0.0'):
|
||||
|
||||
@ -4,8 +4,7 @@
|
||||
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
|
||||
|
||||
import collections
|
||||
|
||||
from spack import *
|
||||
import os.path
|
||||
|
||||
|
||||
class Plumed(AutotoolsPackage):
|
||||
@ -80,7 +79,7 @@ def apply_patch(self, other):
|
||||
|
||||
# Get available patches
|
||||
plumed_patch = Executable(
|
||||
join_path(self.spec.prefix.bin, 'plumed-patch')
|
||||
os.path.join(self.spec.prefix.bin, 'plumed-patch')
|
||||
)
|
||||
|
||||
out = plumed_patch('-q', '-l', output=str)
|
||||
@ -103,6 +102,12 @@ def setup_dependent_package(self, module, dependent_spec):
|
||||
# Make plumed visible from dependent packages
|
||||
module.plumed = dependent_spec['plumed'].command
|
||||
|
||||
@property
|
||||
def plumed_inc(self):
|
||||
return os.path.join(
|
||||
self.prefix.lib, 'plumed', 'src', 'lib', 'Plumed.inc'
|
||||
)
|
||||
|
||||
@run_before('autoreconf')
|
||||
def filter_gslcblas(self):
|
||||
# This part is needed to avoid linking with gsl cblas
|
||||
|
||||
Loading…
Reference in New Issue
Block a user