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Abinit: Added package(s) (#1995)

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* First version of Abinit package

* Ignore *.swp files

* Add libxc, etsf_io packages

* AtomPaw package

* Make Abinit depend on mpi@2: and external version of libxc, netcdf, hdf5, etsf_io

* etsf_io: install Fortran modules in prefix.include

* Remove etsf_io from abinit requirements

* Add libxc2.2.1 (required by Abinit and atompaw)

* Cleanup

* Run make check

* Cleanup

* Use ld_flags instead of hard-coded libs, fix pep8, add copyright

* Put scalapack before lapackblas
This commit is contained in:
gmatteo 2016-10-12 00:22:46 +02:00 committed by Todd Gamblin
parent 37d125b890
commit 949766d92e
5 changed files with 307 additions and 0 deletions
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.gitignore vendored
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@ -15,6 +15,7 @@
/share/spack/modules
/share/spack/lmod
/TAGS
*.swp
/htmlcov
.coverage
#*

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var/spack/repos/builtin/packages/abinit/package.py Normal file
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##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
#
# Author: Matteo Giantomassi <matteo.giantomassiNOSPAM AT uclouvain.be>
# Date: October 11, 2016
from spack import *
class Abinit(Package):
"""ABINIT is a package whose main program allows one to find the total
energy, charge density and electronic structure of systems made of
electrons and nuclei (molecules and periodic solids) within
Density Functional Theory (DFT), using pseudopotentials and a planewave
or wavelet basis. ABINIT also includes options to optimize the geometry
according to the DFT forces and stresses, or to perform molecular dynamics
simulations using these forces, or to generate dynamical matrices,
Born effective charges, and dielectric tensors, based on Density-Functional
Perturbation Theory, and many more properties. Excited states can be
computed within the Many-Body Perturbation Theory (the GW approximation and
the Bethe-Salpeter equation), and Time-Dependent Density Functional Theory
(for molecules). In addition to the main ABINIT code, different utility
programs are provided.
"""
homepage = "http://www.abinit.org"
url = "http://ftp.abinit.org/abinit-8.0.8b.tar.gz"
# Versions before 8.0.8b are not supported.
version("8.0.8b", "abc9e303bfa7f9f43f95598f87d84d5d")
variant('mpi', default=True,
description='Builds with MPI support. Requires MPI2+')
variant('openmp', default=False,
description='Enables OpenMP threads. Use threaded FFTW3')
variant('scalapack', default=False,
description='Enables scalapack support. Requires MPI')
# variant('elpa', default=False,
# description='Uses elpa instead of scalapack. Requires MPI')
# TODO: To be tested.
# It was working before the last `git pull` but now all tests crash.
# For the time being, the default is netcdf3 and the internal fallbacks
variant('hdf5', default=False,
description='Enables HDF5+Netcdf4 with MPI. WARNING: experimental')
# Add dependencies
# currently one cannot forward options to virtual packages, see #1712.
# depends_on("blas", when="~openmp")
# depends_on("blas+openmp", when="+openmp")
depends_on('blas')
depends_on("lapack")
# Require MPI2+
depends_on("mpi@2:", when="+mpi")
depends_on("scalapack", when="+scalapack+mpi")
# depends_on("elpa", when="+elpa+mpi~openmp")
# depends_on("elpa+openmp", when="+elpa+mpi+openmp")
depends_on("fftw+float", when="~openmp")
depends_on("fftw+float+openmp", when="+openmp")
depends_on("netcdf-fortran", when="+hdf5")
depends_on("hdf5+mpi", when='+mpi+hdf5') # required for NetCDF-4 support
# pin libxc version
depends_on("libxc@2.2.1")
def validate(self, spec):
"""
Checks if incompatible variants have been activated at the same time
:param spec: spec of the package
:raises RuntimeError: in case of inconsistencies
"""
error = 'you cannot ask for \'+{variant}\' when \'+mpi\' is not active'
if '+scalapack' in spec and '~mpi' in spec:
raise RuntimeError(error.format(variant='scalapack'))
if '+elpa' in spec and ('~mpi' in spec or '~scalapack' in spec):
raise RuntimeError(error.format(variant='elpa'))
def install(self, spec, prefix):
self.validate(spec)
options = ['--prefix=%s' % prefix]
oapp = options.append
if '+mpi' in spec:
# MPI version:
# let the configure script auto-detect MPI support from mpi_prefix
oapp("--with-mpi-prefix=%s" % spec["mpi"].prefix)
oapp("--enable-mpi=yes")
oapp("--enable-mpi-io=yes")
# Activate OpenMP in Abinit Fortran code.
if '+openmp' in spec:
oapp('--enable-openmp=yes')
# BLAS/LAPACK
if '+scalapack' in spec:
oapp("--with-linalg-flavor=custom+scalapack")
linalg = (spec['scalapack'].scalapack_libs +
spec['lapack'].lapack_libs + spec['blas'].blas_libs)
# elif '+elpa' in spec:
else:
oapp("--with-linalg-flavor=custom")
linalg = spec['lapack'].lapack_libs + spec['blas'].blas_libs
oapp("--with-linalg-libs=%s" % linalg.ld_flags)
# FFTW3: use sequential or threaded version if +openmp
fftflavor, fftlibs = "fftw3", "-lfftw3 -lfftw3f"
if '+openmp' in spec:
fftflavor = "fftw3-threads"
fftlibs = "-lfftw3_omp -lfftw3 -lfftw3f"
options.extend([
"--with-fft-flavor=%s" % fftflavor,
"--with-fft-incs=-I%s" % spec["fftw"].prefix.include,
"--with-fft-libs=-L%s %s" % (spec["fftw"].prefix.lib, fftlibs),
])
oapp("--with-dft-flavor=atompaw+libxc")
# LibXC library
options.extend([
"with_libxc_incs=-I%s" % spec["libxc"].prefix.include,
"with_libxc_libs=-L%s -lxcf90 -lxc" % spec["libxc"].prefix.lib,
])
# Netcdf4/HDF5
if "+hdf5" in spec:
oapp("--with-trio-flavor=netcdf")
hdf_libs = "-L%s -lhdf5_hl -lhdf5" % spec["hdf5"].prefix.lib
options.extend([
"--with-netcdf-incs=-I%s" % (
spec["netcdf-fortran"].prefix.include),
"--with-netcdf-libs=-L%s -lnetcdff -lnetcdf %s" % (
spec["netcdf-fortran"].prefix.lib, hdf_libs),
])
else:
# Use internal fallbacks (netcdf3)
oapp("--with-trio-flavor=netcdf-fallback")
configure(*options)
make()
# make("check")
# make("tests_in")
make("install")

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##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class Atompaw(Package):
"""A Projector Augmented Wave (PAW) code for generating
atom-centered functions.
Official website: http://pwpaw.wfu.edu
User's guide: ~/doc/atompaw-usersguide.pdf
"""
homepage = "http://users.wfu.edu/natalie/papers/pwpaw/man.html"
url = "http://users.wfu.edu/natalie/papers/pwpaw/atompaw-4.0.0.13.tar.gz"
version('4.0.0.13', 'af4a042380356f6780183c4b325aad1d')
version('3.1.0.3', 'c996a277e11707887177f47bbb229aa6')
depends_on("lapack")
depends_on("blas")
# pin libxc version
depends_on("libxc@2.2.1")
def install(self, spec, prefix):
options = ['--prefix=%s' % prefix]
linalg = spec['lapack'].lapack_libs + spec['blas'].blas_libs
options.extend([
"--with-linalg-libs=%s" % linalg.ld_flags,
"--enable-libxc",
"--with-libxc-incs=-I%s" % spec["libxc"].prefix.include,
"--with-libxc-libs=-L%s -lxcf90 -lxc" % spec["libxc"].prefix.lib,
])
configure(*options)
make(parallel=False) # parallel build fails
make("check")
make("install")

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##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class EtsfIo(Package):
"""ETSF_IO is a library implementing the Nanoquanta/ETSF file
format specifications.
ETSF_IO enables an architecture-independent exchange of crystallographic
data, electronic wavefunctions, densities and potentials, as well as
spectroscopic data. It is meant to be used by quantum-physical and
quantum-chemical applications relying upon Density Functional Theory (DFT).
"""
homepage = "http://www.etsf.eu/resources/software/libraries_and_tools"
url = "https://launchpad.net/etsf-io/1.0/1.0.4/+download/etsf_io-1.0.4.tar.gz"
version('1.0.4', '32d0f7143278bd925b334c69fa425da1')
depends_on("netcdf-fortran")
depends_on("hdf5+mpi~cxx", when='+mpi') # required for NetCDF-4 support
def install(self, spec, prefix):
options = ['--prefix=%s' % prefix]
oapp = options.append
# Specify installation directory for Fortran module files
# Default is [INCLUDEDIR/FC_TYPE]
oapp("--with-moduledir=%s" % prefix.include)
# Netcdf4/HDF
hdf_libs = "-L%s -lhdf5_hl -lhdf5" % spec["hdf5"].prefix.lib
options.extend([
"--with-netcdf-incs=-I%s" % spec["netcdf-fortran"].prefix.include,
"--with-netcdf-libs=-L%s -lnetcdff -lnetcdf %s" % (
spec["netcdf-fortran"].prefix.lib, hdf_libs),
])
configure(*options)
make()
make("check")
make("install")

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var/spack/repos/builtin/packages/libxc/package.py
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@ -34,6 +34,7 @@ class Libxc(Package):
version('3.0.0', '8227fa3053f8fc215bd9d7b0d36de03c')
version('2.2.2', 'd9f90a0d6e36df6c1312b6422280f2ec')
version('2.2.1', '38dc3a067524baf4f8521d5bb1cd0b8f')
def install(self, spec, prefix):
# Optimizations for the Intel compiler, suggested by CP2K