octopus: update to 11.4 and add tests (#30321)
* octopus: adding versions up to 11.4
* octopus: add smoke tests
* octopus: add necessary flags for gcc@10
* octopus: update to compilation and dependencies
* octopus: adding new variants
* octopus: remove 'poke' (as this poke is not in spack [yet])
* octopus: allow compilation from git repo develop branch
* octopus: adapt to spack style requirements
* octopus: add maintainer
* octopus: make tests after install optional
Thank you @tldahlgren
* octopus: follow recommended practice for test input data
Move the two configuration files we use for smoke tests into `test`
subdirectory. Thanks @tldahlgren.
* Adding maintainer
with their agreement by email
* octopus: reduce duplication of flags
- part of code review
* octopus: https is preferred over http
* octopus: remove .99 from versioning information
Thanks to https://github.com/spack/spack/pull/26402, we can drop the
"2:3.99" notation when we mean all versions 2.x and 3.x
Examples: b9e72557e8 (diff-b8373d30b3a141c495c2281273ee6184fc513413142afaf2adac1f406cd6b0d7)
(from review)
* octopus: args.extend([x]) -> args.append(x)
(hint from review)
This commit is contained in:
Hans Fangohr
GitHub
parent
e88396e5ed
commit
9a33121859
@ -3,6 +3,8 @@
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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import os
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import llnl.util.tty as tty
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from spack import *
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@ -13,14 +15,26 @@ class Octopus(Package, CudaPackage):
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theory code."""
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homepage = "https://octopus-code.org/"
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url = "http://octopus-code.org/down.php?file=6.0/octopus-6.0.tar.gz"
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url = "https://octopus-code.org/down.php?file=6.0/octopus-6.0.tar.gz"
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git = "https://gitlab.com/octopus-code/octopus"
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maintainers = ['fangohr', 'RemiLacroix-IDRIS']
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version('11.4', sha256='73bb872bff8165ddd8efc5b891f767cb3fe575b5a4b518416c834450a4492da7')
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version('11.3', sha256='0c98417071b5e38ba6cbdd409adf917837c387a010e321c0a7f94d9bd9478930')
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version('11.1', sha256='d943cc2419ca409dda7459b7622987029f2af89984d0d5f39a6b464c3fc266da')
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version('10.5', sha256='deb92e3491b0c6ac5736960d075b44cab466f528b69715ed44968ecfe2953ec4')
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version('10.4', sha256='4de9dc6f5815a45e43320e4abc7ef3e501e34bc327441376ea20ca1a992bdb72')
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version('10.3', sha256='4633490e21593b51b60a8391b8aa0ed17fa52a3a0030630de123b67a41f88b33')
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version('10.2', sha256='393e2ba7b18af1b736ad6deb339ba0cef18c6417671da7a6f1fcc3a5d8f7586b')
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version('10.1', sha256='b6a660a99ed593c1d491e2d11cfff9ce87f0d80d527d9ff47fd983533d45adc6')
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version('10.0', sha256='ccf62200e3f37911bfff6d127ebe74220996e9c09383a10b1420c81d931dcf23')
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version('7.3', sha256='ad843d49d4beeed63e8b9a2ca6bfb2f4c5a421f13a4f66dc7b02f6d6a5c4d742')
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version('6.0', sha256='4a802ee86c1e06846aa7fa317bd2216c6170871632c9e03d020d7970a08a8198')
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version('5.0.1', sha256='3423049729e03f25512b1b315d9d62691cd0a6bd2722c7373a61d51bfbee14e0')
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version('develop', branch='develop')
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variant('scalapack', default=False,
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description='Compile with Scalapack')
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variant('metis', default=False,
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@ -31,26 +45,62 @@ class Octopus(Package, CudaPackage):
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description='Compile with Netcdf')
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variant('arpack', default=False,
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description='Compile with ARPACK')
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variant('cgal', default=False,
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description='Compile with CGAL library support')
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variant('pfft', default=False,
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description='Compile with PFFT')
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# poke here refers to https://gitlab.e-cam2020.eu/esl/poke
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# variant('poke', default=False,
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# description='Compile with poke (not available in spack yet)')
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variant('python', default=False,
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description='Activates Python support')
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variant('likwid', default=False,
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description='Compile with likwid')
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variant('libvdwxc', default=False,
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description='Compile with libvdwxc')
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variant('libyaml', default=False,
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description='Compile with libyaml')
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variant('elpa', default=False,
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description='Compile with ELPA')
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variant('nlopt', default=False,
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description='Compile with nlopt')
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variant('debug', default=False,
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description='Compile with debug flags')
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depends_on('autoconf', type='build')
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depends_on('automake', type='build')
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depends_on('libtool', type='build')
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depends_on('m4', type='build')
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depends_on('blas')
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depends_on('gsl@1.9:')
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depends_on('lapack')
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depends_on('libxc@2.0:2', when='@:5')
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depends_on('libxc@2.0:3', when='@6:7')
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depends_on('libxc@2.0:4', when='@8:9')
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depends_on('libxc@3:5.0.0', when='@10:')
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depends_on('libxc@2:2', when='@:5')
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depends_on('libxc@2:3', when='@6:7')
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depends_on('libxc@2:4', when='@8:9')
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depends_on('libxc@5.1.0:', when='@10:')
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depends_on('libxc@5.1.0:', when='@develop')
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depends_on('mpi')
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depends_on('fftw@3:+mpi+openmp', when='@8:9')
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depends_on('fftw-api@3:', when='@10:')
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depends_on('metis@5:', when='+metis')
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depends_on('parmetis', when='+parmetis')
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depends_on('fftw-api@3:+mpi+openmp', when='@10:')
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depends_on('py-numpy', when='+python')
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depends_on('py-mpi4py', when='+python')
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depends_on('metis@5:+int64', when='+metis')
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depends_on('parmetis+int64', when='+parmetis')
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depends_on('scalapack', when='+scalapack')
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depends_on('netcdf-fortran', when='+netcdf')
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depends_on('arpack-ng', when='+arpack')
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depends_on('cgal', when='+cgal')
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depends_on('pfft', when='+pfft')
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depends_on('likwid', when='+likwid')
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depends_on('libvdwxc', when='+libvdwxc')
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depends_on('libyaml', when='+libyaml')
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depends_on('elpa', when='+elpa')
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depends_on('nlopt', when='+nlopt')
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# optional dependencies:
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# TODO: etsf-io, sparskit,
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# feast, libfm, pfft, isf, pnfft
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# feast, libfm, pfft, isf, pnfft, poke
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def install(self, spec, prefix):
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lapack = spec['lapack'].libs
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@ -65,19 +115,20 @@ def install(self, spec, prefix):
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'CC=%s' % spec['mpi'].mpicc,
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'FC=%s' % spec['mpi'].mpifc,
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'--enable-mpi',
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'--enable-openmp',
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])
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if '^fftw' in spec:
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args.extend([
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'--with-fftw-prefix=%s' % spec['fftw'].prefix,
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])
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args.append(
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'--with-fftw-prefix=%s' % spec['fftw'].prefix
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)
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elif '^mkl' in spec:
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# As of version 10.0, Octopus depends on fftw-api instead
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# of FFTW. If FFTW is not in the dependency tree, then
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# it ought to be MKL as it is currently the only providers
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# available for fftw-api.
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args.extend([
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args.append(
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'FCFLAGS_FFTW=-I%s' % spec['mkl'].prefix.include.fftw
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])
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)
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else:
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# To be foolproof, fail with a proper error message
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# if neither FFTW nor MKL are in the dependency tree.
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@ -85,13 +136,13 @@ def install(self, spec, prefix):
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'currently only FFTW and MKL are supported.\n'
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"Please report this issue on Spack's repository.")
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if '+metis' in spec:
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args.extend([
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'--with-metis-prefix=%s' % spec['metis'].prefix,
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])
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args.append(
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'--with-metis-prefix=%s' % spec['metis'].prefix
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)
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if '+parmetis' in spec:
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args.extend([
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'--with-parmetis-prefix=%s' % spec['parmetis'].prefix,
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])
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args.append(
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'--with-parmetis-prefix=%s' % spec['parmetis'].prefix
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)
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if '+netcdf' in spec:
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args.extend([
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'--with-netcdf-prefix=%s' % spec['netcdf-fortran'].prefix,
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@ -100,13 +151,13 @@ def install(self, spec, prefix):
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])
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if '+arpack' in spec:
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arpack_libs = spec['arpack-ng'].libs.joined()
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args.extend([
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args.append(
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'--with-arpack={0}'.format(arpack_libs),
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])
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)
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if '+mpi' in spec['arpack-ng']:
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args.extend([
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'--with-parpack={0}'.format(arpack_libs),
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])
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args.append(
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'--with-parpack={0}'.format(arpack_libs)
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)
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if '+scalapack' in spec:
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args.extend([
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@ -114,10 +165,53 @@ def install(self, spec, prefix):
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'--with-scalapack=%s' % spec['scalapack'].libs
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])
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if '+cgal' in spec:
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args.append(
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'--with-cgal-prefix=%s' % spec['cgal'].prefix
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)
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if '+likwid' in spec:
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args.append(
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'--with-likwid-prefix=%s' % spec['likwid'].prefix
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)
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if '+pfft' in spec:
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args.append(
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'--with-pfft-prefix=%s' % spec['pfft'].prefix,
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)
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# if '+poke' in spec:
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# args.extend([
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# '--with-poke-prefix=%s' % spec['poke'].prefix,
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# ])
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if '+libvdwxc' in spec:
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args.append(
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'--with-libvdwxc-prefix=%s' % spec['libvdwxc'].prefix
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)
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if '+libyaml' in spec:
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args.append(
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'--with-libyaml-prefix=%s' % spec['libyaml'].prefix
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)
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if '+elpa' in spec:
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args.append(
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'--with-elpa-prefix=%s' % spec['elpa'].prefix
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)
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if '+nlopt' in spec:
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args.append(
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'--with-nlopt-prefix=%s' % spec['nlopt'].prefix
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)
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if '+cuda' in spec:
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args.extend([
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args.append(
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'--enable-cuda'
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])
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)
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if '+python' in spec:
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args.append('--enable-python')
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# --with-etsf-io-prefix=
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# --with-sparskit=${prefix}/lib/libskit.a
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@ -134,12 +228,112 @@ def install(self, spec, prefix):
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if (spec.satisfies('%apple-clang') or
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spec.satisfies('%clang') or
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spec.satisfies('%gcc')):
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args.extend([
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'FCFLAGS=-O2 -ffree-line-length-none'
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])
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# In case of GCC version 10, we will have errors because of
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# argument mismatching. Need to provide a flag to turn this into a
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# warning and build sucessfully
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fcflags = 'FCFLAGS=-O2 -ffree-line-length-none'
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fflags = 'FFLAGS=O2 -ffree-line-length-none'
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if (spec.satisfies('%gcc@10:')):
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gcc10_extra = '-fallow-argument-mismatch -fallow-invalid-boz'
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args.append(fcflags + ' ' + gcc10_extra)
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args.append(fflags + ' ' + gcc10_extra)
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else:
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args.append(fcflags)
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args.append(fflags)
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autoreconf('-i')
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configure(*args)
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make()
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# short tests take forever...
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# make('check-short')
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make('install')
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@run_after('install')
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@on_package_attributes(run_tests=True)
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def smoke_tests_after_install(self):
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"""Function stub to run tests after install if desired
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(for example through `spack install --test=root octopus`)
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"""
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self.smoke_tests()
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def test(self):
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"""Entry point for smoke tests run through `spack test run octopus`.
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"""
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self.smoke_tests()
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def smoke_tests(self):
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"""Actual smoke tests for Octopus."""
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#
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# run "octopus --version"
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#
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exe = join_path(self.spec.prefix.bin, "octopus")
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options = ["--version"]
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purpose = "Check octopus can execute (--version)"
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# Example output:
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#
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# spack-v0.17.2$ octopus --version
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# octopus 11.3 (git commit )
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expected = ["octopus "]
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self.run_test(
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exe,
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options=options,
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expected=expected,
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status=[0],
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installed=False,
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purpose=purpose,
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skip_missing=False)
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# Octopus expects a file with name `inp` in the current working
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# directory to read configuration information for a simulation run from
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# that file. We copy the relevant configuration file in a dedicated
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# subfolder for each test.
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#
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# As we like to be able to run these tests also with the
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# `spack install --test=root` command, we cannot rely on
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# self.test_suite.current_test_data_dir, and need to copy the test
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# input files manually (see below).
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#
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# run recipe example
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#
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expected = ["Running octopus", "CalculationMode = recipe",
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"DISCLAIMER: The authors do not "
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"guarantee that the implementation",
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'recipe leads to an edible dish, '
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'for it is clearly "system-dependent".',
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"Calculation ended on"]
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options = []
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purpose = "Run Octopus recipe example"
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with working_dir("example-recipe", create=True):
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print("Current working directory (in example-recipe)")
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copy(join_path(os.path.dirname(__file__), "test", "recipe.inp"), "inp")
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self.run_test(exe,
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options=options,
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expected=expected,
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status=[0],
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installed=False,
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purpose=purpose,
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skip_missing=False)
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#
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# run He example
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#
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expected = ["Running octopus", "Info: Starting calculation mode.",
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"CalculationMode = gs",
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'''Species "helium" is a user-defined potential.''',
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"Info: Writing states.", "Calculation ended on"]
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options = []
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purpose = "Run tiny calculation for He"
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with working_dir("example-he", create=True):
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print("Current working directory (in example-he)")
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copy(join_path(os.path.dirname(__file__), "test", "he.inp"), "inp")
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self.run_test(exe,
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options=options,
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expected=expected,
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status=[0],
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installed=False,
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purpose=purpose,
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skip_missing=False)
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20
var/spack/repos/builtin/packages/octopus/test/he.inp
Normal file
20
var/spack/repos/builtin/packages/octopus/test/he.inp
Normal file
@ -0,0 +1,20 @@
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CalculationMode = gs
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Dimensions = 2
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TheoryLevel = independent_particles
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BoxShape = parallelepiped
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Lsize = 8
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Spacing = 0.1
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%Output
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wfs | plane_z
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%
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%Species
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"helium" | species_user_defined | potential_formula | "-2/(1+x^2)^(1/2)-2/(1+y^2)^(1/2)+1/(1+(x-y)^2)^(1/2)" | valence | 1
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%
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%Coordinates
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"helium"| 0 | 0
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%
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1
var/spack/repos/builtin/packages/octopus/test/recipe.inp
Normal file
1
var/spack/repos/builtin/packages/octopus/test/recipe.inp
Normal file
@ -0,0 +1 @@
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CalculationMode = recipe
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