18c2f1a57a
Explicitly import package utilities in all packages, and corresponding fallout.
This includes:
* rename `spack.package` to `spack.package_base`
* rename `spack.pkgkit` to `spack.package`
* update all packages in builtin, builtin_mock and tutorials to include `from spack.package import *`
* update spack style
* ensure packages include the import
* automatically add the new import and remove any/all imports of `spack` and `spack.pkgkit`
from packages when using `--fix`
* add support for type-checking packages with mypy when SPACK_MYPY_CHECK_PACKAGES
is set in the environment
* fix all type checking errors in packages in spack upstream
* update spack create to include the new imports
* update spack repo to inject the new import, injection persists to allow for a deprecation period
Original message below:
As requested @adamjstewart, update all packages to use pkgkit. I ended up using isort to do this,
so repro is easy:
```console
$ isort -a 'from spack.pkgkit import *' --rm 'spack' ./var/spack/repos/builtin/packages/*/package.py
$ spack style --fix
```
There were several line spacing fixups caused either by space manipulation in isort or by packages
that haven't been touched since we added requirements, but there are no functional changes in here.
* [x] add config to isort to make sure this is maintained going forward
303 lines
11 KiB
Python
303 lines
11 KiB
Python
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack.package import *
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class Abinit(AutotoolsPackage):
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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.
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ABINIT also includes options to optimize the geometry according to the
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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 = 'https://www.abinit.org/'
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url = 'https://www.abinit.org/sites/default/files/packages/abinit-8.6.3.tar.gz'
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version('9.6.1', sha256='b6a12760fd728eb4aacca431ae12150609565bedbaa89763f219fcd869f79ac6')
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version('9.4.2', sha256='d40886f5c8b138bb4aa1ca05da23388eb70a682790cfe5020ecce4db1b1a76bc')
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version('8.10.3', sha256='ed626424b4472b93256622fbb9c7645fa3ffb693d4b444b07d488771ea7eaa75')
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version('8.10.2', sha256='4ee2e0329497bf16a9b2719fe0536cc50c5d5a07c65e18edaf15ba02251cbb73')
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version('8.8.2', sha256='15216703bd56a799a249a112b336d07d733627d3756487a4b1cb48ebb625c3e7')
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version('8.6.3', sha256='82e8d071088ab8dc1b3a24380e30b68c544685678314df1213180b449c84ca65')
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version('8.2.2', sha256='e43544a178d758b0deff3011c51ef7c957d7f2df2ce8543366d68016af9f3ea1')
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# Versions before 8.0.8b are not supported.
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version('8.0.8b', sha256='37ad5f0f215d2a36e596383cb6e54de3313842a0390ce8d6b48a423d3ee25af2')
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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('wannier90', default=False,
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description='Enables the Wannier90 library')
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variant('libxml2', default=False,
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description='Enable libxml2 support, used by multibinit')
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variant('optimization-flavor', default='standard', multi=False,
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values=('safe', 'standard', 'aggressive'),
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description='Select the optimization flavor to use.')
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variant('install-tests', default=False,
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description='Install test cases')
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# Add dependencies
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depends_on('atompaw')
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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('fftw-api')
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depends_on('netcdf-fortran')
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depends_on('netcdf-c+mpi', when='+mpi')
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depends_on('netcdf-c~mpi', when='~mpi')
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depends_on('hdf5+mpi', when='+mpi')
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depends_on('hdf5~mpi', when='~mpi')
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depends_on("wannier90+shared", when='+wannier90+mpi')
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# constrain libxc version
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depends_on('libxc')
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depends_on('libxc@:2', when='@:8')
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# libxml2
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depends_on('libxml2', when='@9:+libxml2')
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# Cannot ask for +scalapack if it does not depend on MPI
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conflicts('+scalapack', when='~mpi')
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# Cannot ask for +wannier90 if it does not depend on MPI
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conflicts('+wannier90', when='~mpi')
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# libxml2 needs version 9 and above
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conflicts('+libxml2', when='@:8')
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conflicts('%gcc@7:', when='@:8.8')
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conflicts('%gcc@9:', when='@:8.10')
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# need openmp threading for abinit+openmp
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# TODO: The logic here can be reversed with the new concretizer. Instead of
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# using `conflicts`, `depends_on` could be used instead.
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for fftw in ['amdfftw', 'cray-fftw', 'fujitsu-fftw', 'fftw']:
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conflicts('+openmp', when='^{0}~openmp'.format(fftw),
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msg='Need to request {0} +openmp'.format(fftw))
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mkl_message = 'Need to set dependent variant to threads=openmp'
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conflicts('+openmp',
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when='^intel-mkl threads=none',
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msg=mkl_message)
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conflicts('+openmp',
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when='^intel-mkl threads=tbb',
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msg=mkl_message)
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conflicts('+openmp',
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when='^intel-parallel-studio +mkl threads=none',
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msg=mkl_message)
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conflicts('+openmp',
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when='^fujitsu-ssl2 ~parallel',
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msg='Need to request fujitsu-ssl2 +parallel')
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conflicts('~openmp',
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when='^fujitsu-ssl2 +parallel',
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msg='Need to request fujitsu-ssl2 ~parallel')
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patch('rm_march_settings.patch', when='@:8')
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patch('rm_march_settings_v9.patch', when='@9:')
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# Fix detection of Fujitsu compiler
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# Fix configure not to collect the option that causes an error
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# Fix intent(out) and unnecessary rewind to avoid compile error
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patch('fix_for_fujitsu.patch', when='@:8 %fj')
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patch('fix_for_fujitsu.v9.patch', when='@9: %fj')
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def configure_args(self):
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spec = self.spec
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options = []
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options += self.with_or_without('libxml2')
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oapp = options.append
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if '@:8' in spec:
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oapp('--enable-optim={0}'
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.format(self.spec.variants['optimization-flavor'].value))
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else:
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oapp('--with-optim-flavor={0}'
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.format(self.spec.variants['optimization-flavor'].value))
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if '+wannier90' in spec:
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if '@:8' in spec:
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oapp('--with-wannier90-libs=-L{0}'
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.format(spec['wannier90'].prefix.lib + ' -lwannier -lm'))
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oapp('--with-wannier90-incs=-I{0}'
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.format(spec['wannier90'].prefix.modules))
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oapp('--with-wannier90-bins={0}'
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.format(spec['wannier90'].prefix.bin))
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oapp('--enable-connectors')
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oapp('--with-dft-flavor=atompaw+libxc+wannier90')
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else:
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options.extend([
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'WANNIER90_CPPFLAGS=-I{0}'.format(
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spec['wannier90'].prefix.modules),
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'WANNIER90_LIBS=-L{0} {1}'.format(
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spec['wannier90'].prefix.lib, '-lwannier'),
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])
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else:
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if '@:8' in spec:
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oapp('--with-dft-flavor=atompaw+libxc')
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else:
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'--without-wannier90',
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if '+mpi' in spec:
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oapp('CC={0}'.format(spec['mpi'].mpicc))
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oapp('CXX={0}'.format(spec['mpi'].mpicxx))
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oapp('FC={0}'.format(spec['mpi'].mpifc))
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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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if '@:8' in spec:
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oapp('--enable-mpi=yes')
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else:
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oapp('--with-mpi')
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else:
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if '@:8' in spec:
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oapp('--enable-mpi=no')
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else:
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oapp('--without-mpi')
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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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else:
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oapp('--enable-openmp=no')
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# BLAS/LAPACK/SCALAPACK-ELPA
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linalg = spec['lapack'].libs + spec['blas'].libs
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if '^mkl' in spec:
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linalg_flavor = 'mkl'
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elif '@9:' in spec and '^openblas' in spec:
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linalg_flavor = 'openblas'
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elif '@9:' in spec and '^fujitsu-ssl2' in spec:
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linalg_flavor = 'openblas'
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else:
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linalg_flavor = 'custom'
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if '+scalapack' in spec:
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linalg = spec['scalapack'].libs + linalg
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if '@:8' in spec:
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linalg_flavor = 'scalapack+{0}'.format(linalg_flavor)
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if '@:8' in spec:
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oapp('--with-linalg-libs={0}'.format(linalg.ld_flags))
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else:
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oapp('LINALG_LIBS={0}'.format(linalg.ld_flags))
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oapp('--with-linalg-flavor={0}'.format(linalg_flavor))
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if '^mkl' in spec:
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fftflavor = 'dfti'
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else:
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if '+openmp' in spec:
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fftflavor, fftlibs = 'fftw3-threads', '-lfftw3_omp -lfftw3 -lfftw3f'
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else:
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fftflavor, fftlibs = 'fftw3', '-lfftw3 -lfftw3f'
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oapp('--with-fft-flavor={0}'.format(fftflavor))
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if '@:8' in spec:
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if '^mkl' in spec:
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oapp('--with-fft-incs={0}'.format(spec['fftw-api'].headers.cpp_flags))
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oapp('--with-fft-libs={0}'.format(spec['fftw-api'].libs.ld_flags))
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else:
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options.extend([
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'--with-fft-incs={0}'.format(spec['fftw-api'].headers.cpp_flags),
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'--with-fft-libs=-L{0} {1}'.format(
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spec['fftw-api'].prefix.lib, fftlibs),
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])
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else:
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if '^mkl' in spec:
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options.extend([
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'FFT_CPPFLAGS={0}'.format(spec['fftw-api'].headers.cpp_flags),
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'FFT_LIBs={0}'.format(spec['fftw-api'].libs.ld_flags),
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])
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else:
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options.extend([
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'FFTW3_CPPFLAGS={0}'.format(spec['fftw-api'].headers.cpp_flags),
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'FFTW3_LIBS=-L{0} {1}'.format(
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spec['fftw-api'].prefix.lib, fftlibs),
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])
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# LibXC library
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libxc = spec['libxc:fortran']
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if '@:8' in spec:
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options.extend([
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'--with-libxc-incs={0}'.format(libxc.headers.cpp_flags),
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'--with-libxc-libs={0}'.format(libxc.libs.ld_flags + ' -lm')
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])
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else:
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oapp('--with-libxc={0}'.format(libxc.prefix))
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# Netcdf4/HDF5
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hdf5 = spec['hdf5:hl']
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netcdfc = spec['netcdf-c']
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netcdff = spec['netcdf-fortran:shared']
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if '@:8' in spec:
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oapp('--with-trio-flavor=netcdf')
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# Since version 8, Abinit started to use netcdf4 + hdf5 and we have
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# to link with the high level HDF5 library
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options.extend([
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'--with-netcdf-incs={0}'.format(
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netcdfc.headers.cpp_flags + ' ' +
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netcdff.headers.cpp_flags),
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'--with-netcdf-libs={0}'.format(
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netcdff.libs.ld_flags + ' ' + hdf5.libs.ld_flags
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),
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])
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else:
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options.extend([
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'--with-netcdf={0}'.format(netcdfc.prefix),
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'--with-netcdf-fortran={0}'.format(netcdff.prefix),
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])
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if self.spec.satisfies('%fj'):
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oapp('FCFLAGS_MODDIR=-M{0}'.format(join_path(
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self.stage.source_path, 'src/mods')))
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return options
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def check(self):
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"""This method is called after the build phase if tests have been
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explicitly activated by user.
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"""
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make('check')
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# the tests directly execute abinit. thus failing with MPI
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# TODO: run tests in tests/ via the builtin runtests.py
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# requires Python with numpy, pyyaml, pandas
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if '~mpi' in self.spec:
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make('tests_in')
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def install(self, spec, prefix):
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make('install')
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if '+install-tests' in spec:
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install_tree('tests', spec.prefix.tests)
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