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cp2k: update to 4.1 + update of dependencies (#3561)

Browse source 
* libint: updated version, ported to AutotoolsPackage

* elpa: updated version, ported to AutotoolsPackage

* wannier90: updated version, ported to MakefilePackage

* pexsi: updated version, ported to MakefilePackage

* cp2k: updated version, removed wannier 90 from dependencies if cp2k@4.1

* plumed: updated version

Modifications:

* modules has been turned into a single variant, as different versions
  have different modules available
* added dictionaries for patches

* netlib-scalapack: ported to CMakePackage
This commit is contained in:
Massimiliano Culpo 2017-03-30 16:46:05 +02:00 committed by Adam J. Stewart
parent 73f78cb8c4
commit f9c0348891
8 changed files with 160 additions and 122 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

25
var/spack/repos/builtin/packages/cp2k/package.py
View file

@ -37,6 +37,7 @@ class Cp2k(Package):
homepage = 'https://www.cp2k.org'
url = 'https://sourceforge.net/projects/cp2k/files/cp2k-3.0.tar.bz2'
version('4.1', 'b0534b530592de15ac89828b1541185e')
version('3.0', 'c05bc47335f68597a310b1ed75601d35')
variant('mpi', default=True, description='Enable MPI support')
@ -47,14 +48,18 @@ class Cp2k(Package):
depends_on('lapack')
depends_on('blas')
depends_on('fftw')
depends_on('libint@:1.2', when='@3.0')
depends_on('libint@:1.2', when='@3.0,4.1')
depends_on('mpi', when='+mpi')
depends_on('scalapack', when='+mpi')
depends_on('plumed+shared+mpi', when='+plumed+mpi')
depends_on('plumed+shared~mpi', when='+plumed~mpi')
depends_on('pexsi', when='+mpi')
depends_on('wannier90', when='+mpi')
depends_on('pexsi+fortran', when='+mpi')
# 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('elpa', when='+mpi')
# TODO : add dependency on libsmm, libxsmm
@ -94,6 +99,8 @@ def install(self, spec, prefix):
fcflags.append(spec['fftw'].cppflags)
fftw = find_libraries('libfftw3', root=spec['fftw'].prefix.lib)
ldflags = [fftw.search_flags]
if 'superlu-dist@4.3' in spec:
ldflags = ['-Wl,--allow-multiple-definition'] + ldflags
libs = [
join_path(spec['libint'].prefix.lib, 'libint.so'),
join_path(spec['libint'].prefix.lib, 'libderiv.so'),
@ -147,10 +154,12 @@ def install(self, spec, prefix):
cppflags.extend([
'-D__parallel',
'-D__LIBPEXSI',
'-D__WANNIER90',
'-D__ELPA3',
'-D__SCALAPACK'
])
if 'wannier90' in spec:
cppflags.append('-D__WANNIER90')
fcflags.extend([
# spec['elpa:fortran'].cppflags
'-I' + join_path(
@ -167,7 +176,6 @@ def install(self, spec, prefix):
libs.extend([
join_path(spec['elpa'].prefix.lib,
'libelpa.{0}'.format(dso_suffix)),
join_path(spec['wannier90'].prefix.lib, 'libwannier.a'),
join_path(spec['pexsi'].prefix.lib, 'libpexsi.a'),
join_path(spec['superlu-dist'].prefix.lib,
'libsuperlu_dist.a'),
@ -180,6 +188,13 @@ def install(self, spec, prefix):
'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'].mpicxx_shared_libs)
libs.extend(self.compiler.stdcxx_libs)

63
var/spack/repos/builtin/packages/elpa/package.py
View file

@ -26,24 +26,15 @@
from spack import *
class Elpa(Package):
"""
Eigenvalue solvers for Petaflop-Applications (ELPA)
"""
class Elpa(AutotoolsPackage):
"""Eigenvalue solvers for Petaflop-Applications (ELPA)"""
homepage = 'http://elpa.mpcdf.mpg.de/'
url = 'http://elpa.mpcdf.mpg.de/elpa-2015.11.001.tar.gz'
version(
'2016.05.003',
'88a9f3f3bfb63e16509dd1be089dcf2c',
url='http://elpa.mpcdf.mpg.de/html/Releases/2016.05.003/elpa-2016.05.003.tar.gz'
)
version(
'2015.11.001',
'de0f35b7ee7c971fd0dca35c900b87e6',
url='http://elpa.mpcdf.mpg.de/elpa-2015.11.001.tar.gz'
)
version('2016.05.004', 'c0dd3a53055536fc3a2a221e78d8b376')
version('2016.05.003', '88a9f3f3bfb63e16509dd1be089dcf2c')
version('2015.11.001', 'de0f35b7ee7c971fd0dca35c900b87e6')
variant('openmp', default=False, description='Activates OpenMP support')
@ -52,30 +43,26 @@ class Elpa(Package):
depends_on('lapack')
depends_on('scalapack')
def install(self, spec, prefix):
def url_for_version(self, version):
t = 'http://elpa.mpcdf.mpg.de/html/Releases/{0}/elpa-{0}.tar.gz'
if version < Version('2016.05.003'):
t = 'http://elpa.mpcdf.mpg.de/elpa-{0}.tar.gz'
return t.format(str(version))
options = [
'CC={0}'.format(self.spec['mpi'].mpicc),
'FC={0}'.format(self.spec['mpi'].mpifc),
'CXX={0}'.format(self.spec['mpi'].mpicxx),
'FCFLAGS={0}'.format(
spec['lapack'].libs.joined()
),
'LDFLAGS={0}'.format(
spec['lapack'].libs.joined()
),
'SCALAPACK_FCFLAGS={0}'.format(
spec['scalapack'].libs.joined()
),
'SCALAPACK_LDFLAGS={0}'.format(
spec['scalapack'].libs.joined()
),
'--prefix={0}'.format(self.prefix)
]
def setup_environment(self, spack_env, run_env):
if '+openmp' in spec:
spec = self.spec
spack_env.set('CC', spec['mpi'].mpicc)
spack_env.set('FC', spec['mpi'].mpifc)
spack_env.set('CXX', spec['mpi'].mpicxx)
spack_env.set('LDFLAGS', spec['lapack'].libs.search_flags)
spack_env.set('LIBS', spec['lapack'].libs.link_flags)
spack_env.set('SCALAPACK_LDFLAGS', spec['scalapack'].libs.joined())
def configure_args(self):
options = []
if '+openmp' in self.spec:
options.append("--enable-openmp")
configure(*options)
make()
make("install")
return options

34
var/spack/repos/builtin/packages/libint/package.py
View file

@ -25,25 +25,27 @@
from spack import *
class Libint(Package):
class Libint(AutotoolsPackage):
"""Libint is a high-performance library for computing
Gaussian integrals in quantum mechanics."""
Gaussian integrals in quantum mechanics.
"""
homepage = "https://github.com/evaleev/libint"
url = "https://github.com/evaleev/libint/archive/v2.1.0.tar.gz"
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')
# Build dependencies
depends_on('autoconf@2.52:', type='build')
depends_on('automake', type='build')
depends_on('libtool', type='build')
depends_on('automake', type='build')
depends_on('libtool', type='build')
# Libint 2 dependencies
depends_on('boost', when='@2:')
depends_on('gmp', when='@2:')
depends_on('gmp', when='@2:')
def url_for_version(self, version):
base_url = "https://github.com/evaleev/libint/archive"
@ -54,16 +56,14 @@ def url_for_version(self, version):
else:
return "{0}/v{1}.tar.gz".format(base_url, version)
def install(self, spec, prefix):
# Generate configure
def autoreconf(self, spec, prefix):
libtoolize()
aclocal('-I', 'lib/autoconf')
autoconf()
config_args = [
'--prefix={0}'.format(prefix),
'--enable-shared'
]
def configure_args(self):
config_args = ['--enable-shared']
# Optimizations for the Intel compiler, suggested by CP2K
optflags = '-O2'
@ -93,12 +93,4 @@ def install(self, spec, prefix):
'--with-libint-max-am=5',
'--with-libderiv-max-am1=4'
])
configure(*config_args)
make()
# Testing suite was added in libint 2
if self.version >= Version('2.0.0'):
make('check')
make('install')
return config_args

21
var/spack/repos/builtin/packages/netlib-scalapack/package.py
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@ -26,7 +26,7 @@
import sys
class NetlibScalapack(Package):
class NetlibScalapack(CMakePackage):
"""ScaLAPACK is a library of high-performance linear algebra routines for
parallel distributed memory machines
"""
@ -60,12 +60,16 @@ class NetlibScalapack(Package):
@property
def scalapack_libs(self):
# Note that the default will be to search
# for 'libnetlib-scalapack.<suffix>'
shared = True if '+shared' in self.spec else False
return find_libraries(
'libscalapack', root=self.prefix, shared=shared, recurse=True
)
def install(self, spec, prefix):
def cmake_args(self):
spec = self.spec
options = [
"-DBUILD_SHARED_LIBS:BOOL=%s" % ('ON' if '+shared' in spec else
'OFF'),
@ -89,13 +93,10 @@ def install(self, spec, prefix):
"-DCMAKE_Fortran_FLAGS=-fPIC"
])
options.extend(std_cmake_args)
with working_dir('spack-build', create=True):
cmake('..', *options)
make()
make("install")
return options
@run_after('install')
def fix_darwin_install(self):
# The shared libraries are not installed correctly on Darwin:
if (sys.platform == 'darwin') and ('+shared' in spec):
fix_darwin_install_name(prefix.lib)
if (sys.platform == 'darwin') and ('+shared' in self.spec):
fix_darwin_install_name(self.spec.prefix.lib)

2
var/spack/repos/builtin/packages/pexsi/make.inc
View file

@ -63,7 +63,7 @@ CXXFLAGS = ${COMPILE_FLAG} ${CPPFLAG} ${PROFILE_FLAG} ${INCLUDES}
CCDEFS = ${COMPILE_DEF}
CPPDEFS = ${COMPILE_DEF}
LOADOPTS = ${PROFILE_FLAG} ${LIBS}
FLOADOPTS = ${PROFILE_FLAG} ${LIBS} ${CPP_LIB}
FLOADOPTS = @FLDFLAGS ${PROFILE_FLAG} ${LIBS} ${CPP_LIB}
# Generate auto-dependencies
%.d: %.c

37
var/spack/repos/builtin/packages/pexsi/package.py
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@ -30,7 +30,7 @@
from spack import *
class Pexsi(Package):
class Pexsi(MakefilePackage):
"""The PEXSI library is written in C++, and uses message passing interface
(MPI) to parallelize the computation on distributed memory computing
systems and achieve scalability on more than 10,000 processors.
@ -46,14 +46,20 @@ class Pexsi(Package):
homepage = 'https://math.berkeley.edu/~linlin/pexsi/index.html'
url = 'https://math.berkeley.edu/~linlin/pexsi/download/pexsi_v0.9.0.tar.gz'
version('0.9.2', '0ce491a3a922d271c4edf9b20aa93076')
version('0.9.0', '0c1a2de891ba1445dfc184b2fa270ed8')
depends_on('parmetis')
depends_on('superlu-dist@3.3', when='@0.9.0')
depends_on('superlu-dist@4.3', when='@0.9.2')
variant(
'fortran', default=False, description='Builds the Fortran interface'
)
parallel = False
def install(self, spec, prefix):
def edit(self, spec, prefix):
substitutions = {
'@MPICC': self.spec['mpi'].mpicc,
@ -70,9 +76,13 @@ def install(self, spec, prefix):
'@LAPACK_LIBS': self.spec['lapack'].libs.joined(),
'@BLAS_LIBS': self.spec['blas'].libs.joined(),
# FIXME : what to do with compiler provided libraries ?
'@STDCXX_LIB': ' '.join(self.compiler.stdcxx_libs)
'@STDCXX_LIB': ' '.join(self.compiler.stdcxx_libs),
'@FLDFLAGS': ''
}
if '@0.9.2' in self.spec:
substitutions['@FLDFLAGS'] = '-Wl,--allow-multiple-definition'
template = join_path(
os.path.dirname(inspect.getmodule(self).__file__),
'make.inc'
@ -85,20 +95,29 @@ def install(self, spec, prefix):
for key, value in substitutions.items():
filter_file(key, value, makefile)
make()
def build(self, spec, prefix):
super(Pexsi, self).build(spec, prefix)
if '+fortran' in self.spec:
make('-C', 'fortran')
def install(self, spec, prefix):
# 'make install' does not exist, despite what documentation says
mkdirp(self.prefix.lib)
install(
join_path(self.stage.source_path, 'src', 'libpexsi_linux.a'),
join_path(self.prefix.lib, 'libpexsi.a')
)
install_tree(
join_path(self.stage.source_path, 'include'),
self.prefix.include
)
# fortran "interface"
make('-C', 'fortran')
install_tree(
join_path(self.stage.source_path, 'fortran'),
join_path(self.prefix, 'fortran')
)
if '+fortran' in self.spec:
install_tree(
join_path(self.stage.source_path, 'fortran'),
join_path(self.prefix, 'fortran')
)

54
var/spack/repos/builtin/packages/plumed/package.py
View file

@ -43,17 +43,16 @@ class Plumed(AutotoolsPackage):
homepage = 'http://www.plumed.org/'
url = 'https://github.com/plumed/plumed2/archive/v2.2.3.tar.gz'
version('2.3.0', 'a9b5728f115dca8f0519111f1f5a6fa5')
version('2.2.4', 'afb00da25a3fbd47acf377e53342059d')
version('2.2.3', 'a6e3863e40aac07eb8cf739cbd14ecf8')
# Variants. PLUMED by default builds a number of optional modules.
# The ones listed here are not built by default for various reasons,
# such as stability, lack of testing, or lack of demand.
variant('crystallization', default=False,
description='Build support for optional crystallization module.')
variant('imd', default=False,
description='Build support for optional imd module.')
variant('manyrestraints', default=False,
description='Build support for optional manyrestraints module.')
# FIXME: This needs to be an optional
variant('optional_modules', default='all',
description='String that is used to build optional modules')
variant('shared', default=True, description='Builds shared libraries')
variant('mpi', default=True, description='Activates MPI support')
variant('gsl', default=True, description='Activates GSL support')
@ -73,6 +72,28 @@ class Plumed(AutotoolsPackage):
# Dictionary mapping PLUMED versions to the patches it provides
# interactively
plumed_patches = {
'2.3.0': {
'amber-14': '1',
'gromacs-2016.1': '2',
'gromacs-4.5.7': '3',
'gromacs-5.0.7': '4',
'gromacs-5.1.4': '5',
'lammps-6Apr13': '6',
'namd-2.8': '7',
'namd-2.9': '8',
'espresso-5.0.2': '9'
},
'2.2.4': {
'amber-14': '1',
'gromacs-4.5.7': '2',
'gromacs-4.6.7': '3',
'gromacs-5.0.7': '4',
'gromacs-5.1.2': '5',
'lammps-6Apr13': '6',
'namd-2.8': '7',
'namd-2.9': '8',
'espresso-5.0.2': '9'
},
'2.2.3': {
'amber-14': '1',
'gromacs-4.5.7': '2',
@ -132,7 +153,7 @@ def configure_args(self):
# If the MPI dependency is provided by the intel-mpi package then
# the following additional argument is required to allow it to
# build.
if spec.satisfies('^intel-mpi'):
if 'intel-mpi' in spec:
configure_opts.extend([
'STATIC_LIBS=-mt_mpi'
])
@ -144,19 +165,16 @@ def configure_args(self):
])
# Construct list of optional modules
module_opts = []
module_opts.extend([
'+crystallization' if (
'+crystallization' in spec) else '-crystallization',
'+imd' if '+imd' in spec else '-imd',
'+manyrestraints' if (
'+manyrestraints' in spec) else '-manyrestraints'
])
# If we have specified any optional modules then add the argument to
# enable or disable them.
if module_opts:
configure_opts.extend([
'--enable-modules={0}'.format("".join(module_opts))])
optional_modules = self.spec.variants['optional_modules'].value
if optional_modules:
# From 'configure --help' @2.3:
# all/none/reset or : separated list such as
# +crystallization:-bias default: reset
configure_opts.append(
'--enable-modules={0}'.format(optional_modules)
)
return configure_opts

46
var/spack/repos/builtin/packages/wannier90/package.py
View file

@ -29,7 +29,7 @@
from spack import *
class Wannier90(Package):
class Wannier90(MakefilePackage):
"""Wannier90 calculates maximally-localised Wannier functions (MLWFs).
Wannier90 is released under the GNU General Public License.
@ -37,6 +37,7 @@ class Wannier90(Package):
homepage = 'http://wannier.org'
url = 'http://wannier.org/code/wannier90-2.0.1.tar.gz'
version('2.1.0', '07a81c002b41d6d0f97857e55c57d769')
version('2.0.1', '4edd742506eaba93317249d33261fb22')
depends_on('mpi')
@ -45,7 +46,23 @@ class Wannier90(Package):
parallel = False
def install(self, spec, prefix):
build_targets = [
'wannier', 'post', 'lib', 'w90chk2chk', 'w90vdw', 'w90pov'
]
@property
def makefile_name(self):
# Older versions use 'make.sys'
filename = 'make.sys'
# While newer search for 'make.inc'
if self.spec.satisfies('@2.1.0:'):
filename = 'make.inc'
abspath = join_path(self.stage.source_path, filename)
return abspath
def edit(self, spec, prefix):
lapack = self.spec['lapack'].libs
blas = self.spec['blas'].libs
@ -54,57 +71,46 @@ def install(self, spec, prefix):
'@MPIF90': self.spec['mpi'].mpifc,
'@LIBS': (lapack + blas).joined()
}
#######
# TODO : this part is replicated in PEXSI
# TODO : and may be a common pattern for Editable Makefiles
# TODO : see #1186
template = join_path(
os.path.dirname(inspect.getmodule(self).__file__),
'make.sys'
)
makefile = join_path(
self.stage.source_path,
'make.sys'
)
shutil.copy(template, makefile)
shutil.copy(template, self.makefile_name)
for key, value in substitutions.items():
filter_file(key, value, makefile)
######
filter_file(key, value, self.makefile_name)
def install(self, spec, prefix):
make('wannier')
mkdirp(self.prefix.bin)
mkdirp(self.prefix.lib)
install(
join_path(self.stage.source_path, 'wannier90.x'),
join_path(self.prefix.bin, 'wannier90.x')
)
make('post')
install(
join_path(self.stage.source_path, 'postw90.x'),
join_path(self.prefix.bin, 'postw90.x')
)
make('lib')
mkdirp(self.prefix.lib)
install(
join_path(self.stage.source_path, 'libwannier.a'),
join_path(self.prefix.lib, 'libwannier.a')
)
make('w90chk2chk')
install(
join_path(self.stage.source_path, 'w90chk2chk.x'),
join_path(self.prefix.bin, 'w90chk2chk.x')
)
make('w90vdw')
install(
join_path(self.stage.source_path, 'utility', 'w90vdw', 'w90vdw.x'),
join_path(self.prefix.bin, 'w90vdw.x')
)
make('w90pov')
install(
join_path(self.stage.source_path, 'utility', 'w90pov', 'w90pov'),
join_path(self.prefix.bin, 'w90pov')