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Update abinit package (#23670)

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This PR updates the abinit package. The underlying build system has
several changes from previous versions, which are reflected in the
package recipe.

- added version 9.4.2
- removed commented out code
- add new libxml2 variant, with dependency and conflicts
- add dependency on atompaw
- depend on fftw-api when ~openmp
  This allows other fftw implementations to be used. This PR adds MKL.
- depend on netcdf explicitly
- remove hdf5 variant as hdf5 is required
- only use wannier90 if +mpi as the wannier90 spack package is MPI only
- allow newer versions of libxc for abinit 9
- split configure options for versions before and after abinit 9
- always use MPI compiler wrappers
- add patch to remove march settings for version 9
- Set conflict for fftw~openmp if abinit+openmp
  This allows the virtual fftw-api to be used for the dependency. If fftw
  is the fftw-api provider then bail if fftw~openmp is set when
  abinit+openmp is used.
- Set conflicts for +openmp and mkl
- Be explicit about +mkl for intel-parallel-studio
- Add TODO entry for switching conflicts/depends_on logic
This commit is contained in:
Glenn Johnson 2021-05-22 08:35:58 -05:00 committed by GitHub
parent cd61b2352d
commit 1000deb5f9
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GPG Key ID: 4AEE18F83AFDEB23
2 changed files with 195 additions and 74 deletions
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199
var/spack/repos/builtin/packages/abinit/package.py
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@ -30,6 +30,7 @@ class Abinit(AutotoolsPackage):
homepage = 'http://www.abinit.org'
url = 'https://www.abinit.org/sites/default/files/packages/abinit-8.6.3.tar.gz'
version('9.4.2', sha256='d40886f5c8b138bb4aa1ca05da23388eb70a682790cfe5020ecce4db1b1a76bc')
version('8.10.3', sha256='ed626424b4472b93256622fbb9c7645fa3ffb693d4b444b07d488771ea7eaa75')
version('8.10.2', sha256='4ee2e0329497bf16a9b2719fe0536cc50c5d5a07c65e18edaf15ba02251cbb73')
version('8.8.2', sha256='15216703bd56a799a249a112b336d07d733627d3756487a4b1cb48ebb625c3e7')
@ -44,26 +45,14 @@ class Abinit(AutotoolsPackage):
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
# FIXME: rename (trio?) and use multivalued variants to cover
# --with-trio-flavor={netcdf, none}
# Note that Abinit@8: does not support etsf_io anymore because it is not
# compatible with HDF5 and MPI-IO
variant('hdf5', default=False,
description='Enables HDF5+Netcdf4 with MPI. WARNING: experimental')
variant('wannier90', default=False,
description='Enables the Wannier90 library')
variant('libxml2', default=False,
description='Enable libxml2 support, used by multibinit')
# 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('atompaw')
depends_on('blas')
depends_on('lapack')
@ -72,29 +61,53 @@ class Abinit(AutotoolsPackage):
depends_on('scalapack', when='+scalapack+mpi')
# depends_on('elpa~openmp', when='+elpa+mpi~openmp')
# depends_on('elpa+openmp', when='+elpa+mpi+openmp')
depends_on('fftw-api')
depends_on('fftw precision=float,double')
depends_on('fftw~openmp', when='~openmp')
depends_on('fftw+openmp', when='+openmp')
depends_on('netcdf-fortran')
depends_on('netcdf-c+mpi', when='+mpi')
depends_on('netcdf-c~mpi', when='~mpi')
depends_on('hdf5+mpi', when='+mpi')
depends_on('hdf5~mpi', when='~mpi')
depends_on("wannier90+shared", when='+wannier90+mpi')
depends_on('netcdf-fortran', when='+hdf5')
depends_on('hdf5+mpi', when='+mpi+hdf5') # required for NetCDF-4 support
# constrain libxc version
depends_on('libxc')
depends_on('libxc@:2', when='@:8')
# pin libxc version
depends_on("libxc@2.2.2")
# libxml2
depends_on('libxml2', when='@9:')
# Cannot ask for +scalapack if it does not depend on MPI
conflicts('+scalapack', when='~mpi')
depends_on("wannier90+shared", when='+wannier90')
# Cannot ask for +wannier90 if it does not depend on MPI
conflicts('+wannier90', when='~mpi')
# Elpa is a substitute for scalapack and needs mpi
# conflicts('+elpa', when='~mpi')
# conflicts('+elpa', when='+scalapack')
# libxml2 needs version 9 and above
conflicts('+libxml2', when='@:8')
patch('rm_march_settings.patch')
conflicts('%gcc@7:', when='@:8.8')
conflicts('%gcc@9:', when='@:8.10')
# need openmp threading for abinit+openmp
# TODO: The logic here can be reversed with the new concretizer. Instead of
# using `conflicts`, `depends_on` could be used instead.
mkl_message = 'Need to set dependent variant to threads=openmp'
conflicts('+openmp',
when='^fftw~openmp',
msg='Need to request fftw +openmp')
conflicts('+openmp',
when='^intel-mkl threads=none',
msg=mkl_message)
conflicts('+openmp',
when='^intel-mkl threads=tbb',
msg=mkl_message)
conflicts('+openmp',
when='^intel-parallel-studio +mkl threads=none',
msg=mkl_message)
patch('rm_march_settings.patch', when='@:8')
patch('rm_march_settings_v9.patch', when='@9:')
# Fix detection of Fujitsu compiler
# Fix configure not to collect the option that causes an error
@ -106,9 +119,12 @@ def configure_args(self):
spec = self.spec
options = []
options += self.with_or_without('libxml2')
oapp = options.append
if '+wannier90' in spec:
if '@:8' in spec:
oapp('--with-wannier90-libs=-L{0}'
.format(spec['wannier90'].prefix.lib + ' -lwannier -lm'))
oapp('--with-wannier90-incs=-I{0}'
@ -116,65 +132,125 @@ def configure_args(self):
oapp('--with-wannier90-bins={0}'
.format(spec['wannier90'].prefix.bin))
oapp('--enable-connectors')
oapp('--with-dft-flavor=wannier90')
oapp('--with-dft-flavor=atompaw+libxc+wannier90')
else:
options.extend([
'WANNIER90_CPPFLAGS=-I{0}'.format(
spec['wannier90'].prefix.modules),
'WANNIER90_LIBS=-L{0} {1}'.format(
spec['wannier90'].prefix.lib, '-lwannier'),
])
else:
if '@:8' in spec:
oapp('--with-dft-flavor=atompaw+libxc')
else:
'--without-wannier90',
if '+mpi' in spec:
# MPI version:
# let the configure script auto-detect MPI support from mpi_prefix
oapp('--enable-mpi=yes')
if self.spec.satisfies('%fj'):
oapp('CC={0}'.format(spec['mpi'].mpicc))
oapp('CXX={0}'.format(spec['mpi'].mpicxx))
oapp('FC={0}'.format(spec['mpi'].mpifc))
# MPI version:
# let the configure script auto-detect MPI support from mpi_prefix
if '@:8' in spec:
oapp('--enable-mpi=yes')
else:
oapp('--with-mpi-prefix={0}'.format(spec['mpi'].prefix))
oapp('--enable-mpi-io=yes')
oapp('MPIFC={0}'.format(spec['mpi'].mpifc))
if '~wannier90' in spec:
oapp('--with-dft-flavor=atompaw+libxc')
oapp('--with-mpi')
else:
if '@:8' in spec:
oapp('--enable-mpi=no')
else:
oapp('--without-mpi')
# Activate OpenMP in Abinit Fortran code.
if '+openmp' in spec:
oapp('--enable-openmp=yes')
else:
oapp('--enable-openmp=no')
# BLAS/LAPACK/SCALAPACK-ELPA
linalg = spec['lapack'].libs + spec['blas'].libs
if '+scalapack' in spec:
oapp('--with-linalg-flavor=custom+scalapack')
linalg = spec['scalapack'].libs + linalg
# elif '+elpa' in spec:
if '^mkl' in spec:
linalg_flavor = 'mkl'
elif '@9:' in spec and '^openblas' in spec:
linalg_flavor = 'openblas'
else:
oapp('--with-linalg-flavor=custom')
linalg_flavor = 'custom'
if '+scalapack' in spec:
linalg = spec['scalapack'].libs + linalg
if '@:8' in spec:
linalg_flavor = 'scalapack+{0}'.format(linalg_flavor)
if '@:8' in spec:
oapp('--with-linalg-libs={0}'.format(linalg.ld_flags))
else:
oapp('LINALG_LIBS={0}'.format(linalg.ld_flags))
# FFTW3: use sequential or threaded version if +openmp
fftflavor, fftlibs = 'fftw3', '-lfftw3 -lfftw3f'
oapp('--with-linalg-flavor={0}'.format(linalg_flavor))
# FFTW3: use sequential from fftw3 or MKL
if '@:8' in spec:
if '+openmp' in spec:
fftflavor = 'fftw3-threads'
fftlibs = '-lfftw3_omp -lfftw3 -lfftw3f'
fftflavor, fftlibs = 'fftw3-threads', '-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),
'--with-fft-incs={0}'.format(spec['fftw'].headers.cpp_flags),
'--with-fft-libs=-L{0} {1}'.format(
spec['fftw'].prefix.lib, fftlibs),
])
else:
oapp('--with-fft-incs={0}'.format(spec['fftw-api'].headers.cpp_flags))
if '^mkl' in spec:
fftflavor = 'dfti'
oapp('--with-fft-libs={0}'.format(spec['fftw-api'].libs.ld_flags))
elif '^fftw' in spec:
fftflavor, fftlibs = 'fftw3', '-lfftw3 -lfftw3f'
oapp('--with-fft-libs=-L{0} {1}'.format(
spec['fftw-api'].prefix.lib, fftlibs))
else:
if '+openmp' in spec:
fftflavor, fftlibs = 'fftw3-threads', '-lfftw3_omp -lfftw3 -lfftw3f'
options.extend([
'FFTW3_CPPFLAGS={0}'.format(spec['fftw'].headers.cpp_flags),
'FFTW3_LIBS=-L{0} {1}'.format(
spec['fftw'].prefix.lib, fftlibs),
])
else:
if '^mkl' in spec:
fftflavor = 'dfti'
options.extend([
'FFT_CPPFLAGS={0}'.format(spec['fftw-api'].headers.cpp_flags),
'FFT_LIBs={0}'.format(spec['fftw-api'].libs.ld_flags),
])
elif '^fftw' in spec:
fftflavor, fftlibs = 'fftw3', '-lfftw3 -lfftw3f'
options.extend([
'FFTW3_CPPFLAGS={0}'.format(spec['fftw-api'].headers.cpp_flags),
'FFTW3_LIBS=-L{0} {1}'.format(
spec['fftw-api'].prefix.lib, fftlibs),
])
oapp('--with-fft-flavor={0}'.format(fftflavor))
# LibXC library
libxc = spec['libxc:fortran']
if '@:8' in spec:
options.extend([
'with_libxc_incs={0}'.format(libxc.headers.cpp_flags),
'with_libxc_libs={0}'.format(libxc.libs.ld_flags + ' -lm')
'--with-libxc-incs={0}'.format(libxc.headers.cpp_flags),
'--with-libxc-libs={0}'.format(libxc.libs.ld_flags + ' -lm')
])
else:
oapp('--with-libxc={0}'.format(libxc.prefix))
# Netcdf4/HDF5
if '+hdf5' in spec:
hdf5 = spec['hdf5:hl']
netcdfc = spec['netcdf-c']
netcdff = spec['netcdf-fortran:shared']
if '@:8' in spec:
oapp('--with-trio-flavor=netcdf')
# Since version 8, Abinit started to use netcdf4 + hdf5 and we have
# to link with the high level HDF5 library
hdf5 = spec['hdf5:hl']
netcdff = spec['netcdf-fortran:shared']
options.extend([
'--with-netcdf-incs={0}'.format(netcdff.headers.cpp_flags),
'--with-netcdf-libs={0}'.format(
@ -182,9 +258,10 @@ def configure_args(self):
),
])
else:
# In Spack we do our best to avoid building any internally provided
# dependencies, such as netcdf3 in this case.
oapp('--with-trio-flavor=none')
options.extend([
'--with-netcdf={0}'.format(netcdfc.prefix),
'--with-netcdf-fortran={0}'.format(netcdff.prefix),
])
if self.spec.satisfies('%fj'):
oapp('FCFLAGS_MODDIR=-M{0}'.format(join_path(

44
var/spack/repos/builtin/packages/abinit/rm_march_settings_v9.patch Normal file
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@ -0,0 +1,44 @@
--- a/configure 2021-04-30 04:25:20.000000000 -0500
+++ b/configure 2021-05-14 17:34:11.666320745 -0500
@@ -16794,11 +16794,11 @@
;;
standard)
abi_optim_flavor_opt="standard"
- CFLAGS_OPTIM="-O2 -mtune=native -march=native"
+ CFLAGS_OPTIM="-O2"
;;
aggressive)
abi_optim_flavor_opt="aggressive"
- CFLAGS_OPTIM="-O3 -mtune=native -march=native"
+ CFLAGS_OPTIM="-O3"
;;
esac # [case: abi_optim_flavor, indent: 2, item: True]
;;
@@ -16947,11 +16947,11 @@
;;
standard)
abi_optim_flavor_opt="standard"
- CXXFLAGS_OPTIM="-O2 -mtune=native -march=native"
+ CXXFLAGS_OPTIM="-O2"
;;
aggressive)
abi_optim_flavor_opt="aggressive"
- CXXFLAGS_OPTIM="-O3 -mtune=native -march=native"
+ CXXFLAGS_OPTIM="-O3"
;;
esac # [case: abi_optim_flavor, indent: 2, item: True]
;;
@@ -17100,11 +17100,11 @@
;;
standard)
abi_optim_flavor_opt="standard"
- FCFLAGS_OPTIM="-O2 -mtune=native -march=native"
+ FCFLAGS_OPTIM="-O2"
;;
aggressive)
abi_optim_flavor_opt="aggressive"
- FCFLAGS_OPTIM="-O3 -mtune=native -march=native -funroll-loops -faggressive-function-elimination"
+ FCFLAGS_OPTIM="-O3 -funroll-loops -faggressive-function-elimination"
;;
esac # [case: abi_optim_flavor, indent: 2, item: True]
;;