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