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:
Tiziano Müller 2018-11-20 18:23:01 +01:00 committed by Gregory Lee
parent 13b95b8ae6
commit 84bc1d6654
4 changed files with 211 additions and 97 deletions

View File

@ -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 @@ def install(self, spec, prefix):
'-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 @@ def install(self, spec, prefix):
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 @@ def install(self, spec, prefix):
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([
@ -168,15 +232,78 @@ def install(self, spec, prefix):
'-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'
])
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)
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(spec['pexsi'].libs.directories[0],
'libpexsi.a'),
join_path(spec['superlu-dist'].libs.directories[0],
'libsuperlu_dist.a'),
join_path(
spec['parmetis'].libs.directories[0],
'libparmetis.{0}'.format(dso_suffix)
),
join_path(
spec['metis'].libs.directories[0],
'libmetis.{0}'.format(dso_suffix)
),
])
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')
@ -185,62 +312,10 @@ def install(self, spec, prefix):
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'
))
if 'wannier90' in spec:
cppflags.append('-D__WANNIER90')
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)
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,
'libsuperlu_dist.a'),
join_path(
spec['parmetis'].prefix.lib,
'libparmetis.{0}'.format(dso_suffix)
),
join_path(
spec['metis'].prefix.lib,
'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)
libs.extend([str(x) for x in (fftw, lapack, blas, libxc.libs)])
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 @@ def install(self, spec, prefix):
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 @@ def install(self, spec, prefix):
' '.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 @@ def install(self, spec, prefix):
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)

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@ -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 @@ 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

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@ -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:

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@ -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):