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cp2k is now a MakefilePackage (#10570)

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* 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 2019-02-14 07:11:20 +01:00 committed by GitHub
parent 051c66335f
commit b3dd95bd62
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GPG Key ID: 4AEE18F83AFDEB23
4 changed files with 261 additions and 243 deletions
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189
var/spack/repos/builtin/packages/cp2k/package.py
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@ -4,12 +4,13 @@
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import os
import os.path
import copy
from spack import *
import spack.util.environment
class Cp2k(Package):
class Cp2k(MakefilePackage):
"""CP2K is a quantum chemistry and solid state physics software package
that can perform atomistic simulations of solid state, liquid, molecular,
periodic, material, crystal, and biological systems
@ -18,10 +19,10 @@ class Cp2k(Package):
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')
version('6.1', sha256='af803558e0a6b9e9d9ce8a3ab955ba32bacd179922455424e061c82c9fefa34b')
version('5.1', sha256='e23613b593354fa82e0b8410e17d94c607a0b8c6d9b5d843528403ab09904412')
version('4.1', sha256='4a3e4a101d8a35ebd80a9e9ecb02697fb8256364f1eccdbe4e5a85d31fe21343')
version('3.0', sha256='1acfacef643141045b7cbade7006f9b7538476d861eeecd9658c9e468dc61151')
variant('mpi', default=True, description='Enable MPI support')
variant('blas', default='openblas', values=('openblas', 'mkl', 'accelerate'),
@ -93,20 +94,33 @@ class Cp2k(Package):
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 = ('{prefix}{suffix}'
.format(prefix='p' if '+mpi' in spec else 's',
suffix='smp' if '+openmp' in spec else 'opt'))
@property
def makefile_architecture(self):
return '{0.architecture}-{0.compiler.name}'.format(self.spec)
makefile_basename = '.'.join([cp2k_architecture, cp2k_version])
makefile = join_path('arch', makefile_basename)
@property
def makefile_version(self):
return '{prefix}{suffix}'.format(
prefix='p' if '+mpi' in self.spec else 's',
suffix='smp' if '+openmp' in self.spec else 'opt'
)
# Write the custom makefile
with open(makefile, 'w') as mkf:
# Optimization flags
optflags = {
@property
def makefile(self):
makefile_basename = '.'.join([
self.makefile_architecture, self.makefile_version
])
return os.path.join('arch', makefile_basename)
@property
def archive_files(self):
return [os.path.join(self.stage.source_path, self.makefile)]
def edit(self, spec, prefix):
fftw = spec['fftw:openmp' if '+openmp' in spec else 'fftw']
optimization_flags = {
'gcc': [
'-O2',
'-mtune=native',
@ -114,23 +128,11 @@ def install(self, spec, prefix):
'-ffast-math',
'-ftree-vectorize',
],
'intel': [
'-O2',
'-pc64',
'-unroll',
],
'pgi': [
'-fast',
],
'intel': ['-O2', '-pc64', '-unroll'],
'pgi': ['-fast'],
}
dflags = ['-DNDEBUG']
if '+openmp' in spec:
fftw = spec['fftw:openmp']
else:
fftw = spec['fftw']
cppflags = [
'-D__FFTW3',
'-D__LIBINT',
@ -147,9 +149,9 @@ def install(self, spec, prefix):
if '^intel-mkl' in spec:
cppflags.append('-D__FFTSG')
cflags = copy.deepcopy(optflags[self.spec.compiler.name])
cxxflags = copy.deepcopy(optflags[self.spec.compiler.name])
fcflags = copy.deepcopy(optflags[self.spec.compiler.name])
cflags = optimization_flags[self.spec.compiler.name][:]
cxxflags = optimization_flags[self.spec.compiler.name][:]
fcflags = optimization_flags[self.spec.compiler.name][:]
ldflags = []
libs = []
@ -157,19 +159,14 @@ def install(self, spec, prefix):
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')
fcflags.append(self.compiler.openmp_flag)
ldflags.append(self.compiler.openmp_flag)
ldflags.append(fftw.libs.search_flags)
@ -181,43 +178,19 @@ def install(self, spec, prefix):
# (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'),
os.path.join(spec['libint'].libs.directories[0], 'libderiv.a'),
os.path.join(spec['libint'].libs.directories[0], 'libint.a'),
])
if '+plumed' in self.spec:
# Include Plumed.inc in the Makefile
mkf.write('include {0}\n'.format(
join_path(self.spec['plumed'].prefix.lib,
'plumed',
'src',
'lib',
'Plumed.inc')
))
# Add required macro
dflags.extend(['-D__PLUMED2'])
cppflags.extend(['-D__PLUMED2'])
libs.extend([
join_path(self.spec['plumed'].prefix.lib,
os.path.join(self.spec['plumed'].prefix.lib,
'libplumed.{0}'.format(dso_suffix))
])
mkf.write('CC = {0.compiler.cc}\n'.format(self))
if '%intel' in self.spec:
# CPP is a commented command in Intel arch of CP2K
# This is the hack through which cp2k developers avoid doing :
#
# ${CPP} <file>.F > <file>.f90
#
# and use `-fpp` instead
mkf.write('CPP = # {0.compiler.cc} -P\n\n'.format(self))
mkf.write('AR = xiar -r\n\n')
else:
mkf.write('CPP = # {0.compiler.cc} -E\n\n'.format(self))
mkf.write('AR = ar -r\n\n')
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:
@ -255,7 +228,7 @@ def install(self, spec, prefix):
if 'wannier90' in spec:
cppflags.append('-D__WANNIER90')
wannier = join_path(
wannier = os.path.join(
spec['wannier90'].libs.directories[0], 'libwannier.a'
)
libs.append(wannier)
@ -272,18 +245,18 @@ def install(self, spec, prefix):
if '+pexsi' in self.spec:
cppflags.append('-D__LIBPEXSI')
fcflags.append('-I' + join_path(
fcflags.append('-I' + os.path.join(
spec['pexsi'].prefix, 'fortran'))
libs.extend([
join_path(spec['pexsi'].libs.directories[0],
os.path.join(spec['pexsi'].libs.directories[0],
'libpexsi.a'),
join_path(spec['superlu-dist'].libs.directories[0],
os.path.join(spec['superlu-dist'].libs.directories[0],
'libsuperlu_dist.a'),
join_path(
os.path.join(
spec['parmetis'].libs.directories[0],
'libparmetis.{0}'.format(dso_suffix)
),
join_path(
os.path.join(
spec['metis'].libs.directories[0],
'libmetis.{0}'.format(dso_suffix)
),
@ -292,14 +265,14 @@ def install(self, spec, prefix):
if '+elpa' in self.spec:
elpa = spec['elpa']
elpa_suffix = '_openmp' if '+openmp' in elpa else ''
elpa_base_path = join_path(
elpa_base_path = os.path.join(
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],
fcflags.append('-I' + os.path.join(elpa_base_path, 'modules'))
libs.append(os.path.join(elpa.libs.directories[0],
('libelpa{elpa_suffix}.{dso_suffix}'
.format(elpa_suffix=elpa_suffix,
dso_suffix=dso_suffix))))
@ -315,13 +288,15 @@ def install(self, spec, prefix):
cppflags.append('-D__ELPA={0}{1:02d}'
.format(elpa.version[0],
int(elpa.version[1])))
fcflags.append('-I' + join_path(elpa_base_path, 'elpa'))
fcflags.append('-I' + os.path.join(elpa_base_path, 'elpa'))
if 'smm=libsmm' in spec:
lib_dir = join_path('lib', cp2k_architecture, cp2k_version)
lib_dir = os.path.join(
'lib', self.makefile_architecture, self.makefile_version
)
mkdirp(lib_dir)
try:
copy(env['LIBSMM_PATH'], join_path(lib_dir, 'libsmm.a'))
copy(env['LIBSMM_PATH'], os.path.join(lib_dir, 'libsmm.a'))
except KeyError:
raise KeyError('Point environment variable LIBSMM_PATH to '
'the absolute path of the libsmm.a file')
@ -333,6 +308,7 @@ def install(self, spec, prefix):
'-D__HAS_smm_vec',
])
libs.append('-lsmm')
elif 'smm=libxsmm' in spec:
cppflags.extend([
'-D__LIBXSMM',
@ -346,6 +322,29 @@ def install(self, spec, prefix):
cxxflags.extend(cppflags)
fcflags.extend(cppflags)
with open(self.makefile, 'w') as mkf:
if '+plumed' in self.spec:
# Include Plumed.inc in the Makefile
mkf.write('include {0}\n'.format(
self.spec['plumed'].package.plumed_inc
))
mkf.write('CC = {0.compiler.cc}\n'.format(self))
if '%intel' in self.spec:
# CPP is a commented command in Intel arch of CP2K
# This is the hack through which cp2k developers avoid doing :
#
# ${CPP} <file>.F > <file>.f90
#
# and use `-fpp` instead
mkf.write('CPP = # {0.compiler.cc} -P\n\n'.format(self))
mkf.write('AR = xiar -r\n\n')
else:
mkf.write('CPP = # {0.compiler.cc} -E\n\n'.format(self))
mkf.write('AR = ar -r\n\n')
mkf.write('FC = {0}\n'.format(fc))
mkf.write('LD = {0}\n'.format(fc))
# 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'):
@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 = 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)
# 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)

11
var/spack/repos/builtin/packages/libint/package.py
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@ -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')

9
var/spack/repos/builtin/packages/libxc/package.py
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@ -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'):

11
var/spack/repos/builtin/packages/plumed/package.py
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@ -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