Abinit: Added package(s) (#1995)
* 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
Todd Gamblin
parent
37d125b890
commit
949766d92e
5 changed files with 307 additions and 0 deletions
1
.gitignore
vendored
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.gitignore
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@ -15,6 +15,7 @@
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/share/spack/modules
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/share/spack/modules
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/share/spack/lmod
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/share/spack/lmod
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/TAGS
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/TAGS
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*.swp
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/htmlcov
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/htmlcov
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.coverage
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.coverage
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#*
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#*
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175
var/spack/repos/builtin/packages/abinit/package.py
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var/spack/repos/builtin/packages/abinit/package.py
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##############################################################################
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# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/llnl/spack
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# Please also see the LICENSE file for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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#
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# Author: Matteo Giantomassi <matteo.giantomassiNOSPAM AT uclouvain.be>
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# Date: October 11, 2016
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from spack import *
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class Abinit(Package):
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"""ABINIT is a package whose main program allows one to find the total
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energy, charge density and electronic structure of systems made of
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electrons and nuclei (molecules and periodic solids) within
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Density Functional Theory (DFT), using pseudopotentials and a planewave
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or wavelet basis. ABINIT also includes options to optimize the geometry
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according to the DFT forces and stresses, or to perform molecular dynamics
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simulations using these forces, or to generate dynamical matrices,
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Born effective charges, and dielectric tensors, based on Density-Functional
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Perturbation Theory, and many more properties. Excited states can be
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computed within the Many-Body Perturbation Theory (the GW approximation and
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the Bethe-Salpeter equation), and Time-Dependent Density Functional Theory
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(for molecules). In addition to the main ABINIT code, different utility
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programs are provided.
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"""
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homepage = "http://www.abinit.org"
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url = "http://ftp.abinit.org/abinit-8.0.8b.tar.gz"
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# Versions before 8.0.8b are not supported.
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version("8.0.8b", "abc9e303bfa7f9f43f95598f87d84d5d")
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variant('mpi', default=True,
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description='Builds with MPI support. Requires MPI2+')
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variant('openmp', default=False,
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description='Enables OpenMP threads. Use threaded FFTW3')
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variant('scalapack', default=False,
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description='Enables scalapack support. Requires MPI')
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# variant('elpa', default=False,
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# description='Uses elpa instead of scalapack. Requires MPI')
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# TODO: To be tested.
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# It was working before the last `git pull` but now all tests crash.
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# For the time being, the default is netcdf3 and the internal fallbacks
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variant('hdf5', default=False,
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description='Enables HDF5+Netcdf4 with MPI. WARNING: experimental')
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# Add dependencies
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# currently one cannot forward options to virtual packages, see #1712.
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# depends_on("blas", when="~openmp")
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# depends_on("blas+openmp", when="+openmp")
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depends_on('blas')
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depends_on("lapack")
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# Require MPI2+
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depends_on("mpi@2:", when="+mpi")
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depends_on("scalapack", when="+scalapack+mpi")
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# depends_on("elpa", when="+elpa+mpi~openmp")
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# depends_on("elpa+openmp", when="+elpa+mpi+openmp")
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depends_on("fftw+float", when="~openmp")
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depends_on("fftw+float+openmp", when="+openmp")
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depends_on("netcdf-fortran", when="+hdf5")
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depends_on("hdf5+mpi", when='+mpi+hdf5') # required for NetCDF-4 support
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# pin libxc version
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depends_on("libxc@2.2.1")
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def validate(self, spec):
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"""
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Checks if incompatible variants have been activated at the same time
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:param spec: spec of the package
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:raises RuntimeError: in case of inconsistencies
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"""
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error = 'you cannot ask for \'+{variant}\' when \'+mpi\' is not active'
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if '+scalapack' in spec and '~mpi' in spec:
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raise RuntimeError(error.format(variant='scalapack'))
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if '+elpa' in spec and ('~mpi' in spec or '~scalapack' in spec):
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raise RuntimeError(error.format(variant='elpa'))
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def install(self, spec, prefix):
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self.validate(spec)
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options = ['--prefix=%s' % prefix]
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oapp = options.append
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if '+mpi' in spec:
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# MPI version:
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# let the configure script auto-detect MPI support from mpi_prefix
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oapp("--with-mpi-prefix=%s" % spec["mpi"].prefix)
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oapp("--enable-mpi=yes")
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oapp("--enable-mpi-io=yes")
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# Activate OpenMP in Abinit Fortran code.
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if '+openmp' in spec:
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oapp('--enable-openmp=yes')
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# BLAS/LAPACK
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if '+scalapack' in spec:
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oapp("--with-linalg-flavor=custom+scalapack")
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linalg = (spec['scalapack'].scalapack_libs +
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spec['lapack'].lapack_libs + spec['blas'].blas_libs)
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# elif '+elpa' in spec:
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else:
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oapp("--with-linalg-flavor=custom")
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linalg = spec['lapack'].lapack_libs + spec['blas'].blas_libs
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oapp("--with-linalg-libs=%s" % linalg.ld_flags)
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# FFTW3: use sequential or threaded version if +openmp
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fftflavor, fftlibs = "fftw3", "-lfftw3 -lfftw3f"
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if '+openmp' in spec:
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fftflavor = "fftw3-threads"
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fftlibs = "-lfftw3_omp -lfftw3 -lfftw3f"
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options.extend([
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"--with-fft-flavor=%s" % fftflavor,
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"--with-fft-incs=-I%s" % spec["fftw"].prefix.include,
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"--with-fft-libs=-L%s %s" % (spec["fftw"].prefix.lib, fftlibs),
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])
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oapp("--with-dft-flavor=atompaw+libxc")
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# LibXC library
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options.extend([
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"with_libxc_incs=-I%s" % spec["libxc"].prefix.include,
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"with_libxc_libs=-L%s -lxcf90 -lxc" % spec["libxc"].prefix.lib,
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])
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# Netcdf4/HDF5
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if "+hdf5" in spec:
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oapp("--with-trio-flavor=netcdf")
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hdf_libs = "-L%s -lhdf5_hl -lhdf5" % spec["hdf5"].prefix.lib
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options.extend([
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"--with-netcdf-incs=-I%s" % (
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spec["netcdf-fortran"].prefix.include),
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"--with-netcdf-libs=-L%s -lnetcdff -lnetcdf %s" % (
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spec["netcdf-fortran"].prefix.lib, hdf_libs),
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])
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else:
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# Use internal fallbacks (netcdf3)
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oapp("--with-trio-flavor=netcdf-fallback")
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configure(*options)
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make()
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# make("check")
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# make("tests_in")
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make("install")
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63
var/spack/repos/builtin/packages/atompaw/package.py
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63
var/spack/repos/builtin/packages/atompaw/package.py
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@ -0,0 +1,63 @@
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##############################################################################
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# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/llnl/spack
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# Please also see the LICENSE file for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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class Atompaw(Package):
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"""A Projector Augmented Wave (PAW) code for generating
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atom-centered functions.
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Official website: http://pwpaw.wfu.edu
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User's guide: ~/doc/atompaw-usersguide.pdf
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"""
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homepage = "http://users.wfu.edu/natalie/papers/pwpaw/man.html"
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url = "http://users.wfu.edu/natalie/papers/pwpaw/atompaw-4.0.0.13.tar.gz"
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version('4.0.0.13', 'af4a042380356f6780183c4b325aad1d')
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version('3.1.0.3', 'c996a277e11707887177f47bbb229aa6')
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depends_on("lapack")
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depends_on("blas")
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# pin libxc version
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depends_on("libxc@2.2.1")
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def install(self, spec, prefix):
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options = ['--prefix=%s' % prefix]
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linalg = spec['lapack'].lapack_libs + spec['blas'].blas_libs
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options.extend([
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"--with-linalg-libs=%s" % linalg.ld_flags,
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"--enable-libxc",
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"--with-libxc-incs=-I%s" % spec["libxc"].prefix.include,
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"--with-libxc-libs=-L%s -lxcf90 -lxc" % spec["libxc"].prefix.lib,
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])
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configure(*options)
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make(parallel=False) # parallel build fails
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make("check")
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make("install")
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67
var/spack/repos/builtin/packages/etsf_io/package.py
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67
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##############################################################################
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# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/llnl/spack
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# Please also see the LICENSE file for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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class EtsfIo(Package):
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"""ETSF_IO is a library implementing the Nanoquanta/ETSF file
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format specifications.
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ETSF_IO enables an architecture-independent exchange of crystallographic
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data, electronic wavefunctions, densities and potentials, as well as
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spectroscopic data. It is meant to be used by quantum-physical and
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quantum-chemical applications relying upon Density Functional Theory (DFT).
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"""
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homepage = "http://www.etsf.eu/resources/software/libraries_and_tools"
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url = "https://launchpad.net/etsf-io/1.0/1.0.4/+download/etsf_io-1.0.4.tar.gz"
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version('1.0.4', '32d0f7143278bd925b334c69fa425da1')
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depends_on("netcdf-fortran")
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depends_on("hdf5+mpi~cxx", when='+mpi') # required for NetCDF-4 support
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def install(self, spec, prefix):
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options = ['--prefix=%s' % prefix]
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oapp = options.append
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# Specify installation directory for Fortran module files
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# Default is [INCLUDEDIR/FC_TYPE]
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oapp("--with-moduledir=%s" % prefix.include)
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# Netcdf4/HDF
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hdf_libs = "-L%s -lhdf5_hl -lhdf5" % spec["hdf5"].prefix.lib
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options.extend([
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"--with-netcdf-incs=-I%s" % spec["netcdf-fortran"].prefix.include,
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"--with-netcdf-libs=-L%s -lnetcdff -lnetcdf %s" % (
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spec["netcdf-fortran"].prefix.lib, hdf_libs),
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])
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configure(*options)
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make()
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make("check")
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make("install")
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@ -34,6 +34,7 @@ class Libxc(Package):
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version('3.0.0', '8227fa3053f8fc215bd9d7b0d36de03c')
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version('3.0.0', '8227fa3053f8fc215bd9d7b0d36de03c')
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version('2.2.2', 'd9f90a0d6e36df6c1312b6422280f2ec')
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version('2.2.2', 'd9f90a0d6e36df6c1312b6422280f2ec')
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version('2.2.1', '38dc3a067524baf4f8521d5bb1cd0b8f')
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def install(self, spec, prefix):
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def install(self, spec, prefix):
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# Optimizations for the Intel compiler, suggested by CP2K
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# Optimizations for the Intel compiler, suggested by CP2K
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