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[Icontools] use package from Sergey #902

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[Icontools] use package from Sergey #902

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871df3f
take icontools package from Sergey
jonasjucker Jan 23, 2024
3cbccfd
GitHub Action: Apply Pep8-formatting
invalid-email-address Jan 23, 2024
fd369b1
deacticate test for Icontools
jonasjucker Jan 23, 2024
975a537
Merge branch 'icontools' of https://github.com/C2SM/spack-c2sm into i…
jonasjucker Jan 23, 2024
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297 changes: 185 additions & 112 deletions repos/c2sm/packages/icontools/package.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,16 +13,18 @@
# See the Spack documentation for more information on packaging.
# ----------------------------------------------------------------------------

from spack import *
import subprocess
import os
import re
from collections import defaultdict

from spack.util.environment import is_system_path
from llnl.util import tty


class Icontools(AutotoolsPackage):
"""
DWD ICON Tools for C2SM members.
Set of tools to prepare the input files
(for example the boundary condition, initial condition file,...) for ICON.
"""
"""A set of routines which may be suitable for reading, remapping and
writing of fields from and to predefined grids, e.g. regular (lat-lon,
gaussian) or triangular (ICON)."""

homepage = 'https://c2sm.github.io/tools/icontools.html'
c2sm = '[email protected]:C2SM/icontools.git'
Expand All @@ -34,113 +36,184 @@ class Icontools(AutotoolsPackage):
version('dkrz-master', git=dkrz, branch='master', submodules=True)
version('2.5.2', git=dkrz, tag='icontools-2.5.2', submodules=True)

depends_on('autoconf', type='build')
depends_on('automake', type='build')
depends_on('libtool', type='build')
depends_on('m4', type='build')

depends_on('netcdf-fortran', type=('build', 'link'))
depends_on('netcdf-c ~mpi', type=('build', 'link'))
depends_on('hdf5 ~mpi +hl', type=('build', 'link'))
depends_on(
'mpi',
type=('build', 'link', 'run'),
)
depends_on('[email protected] +fortran ~aec', type=('build', 'link', 'run'))
depends_on('[email protected]', type=('build', 'link'))

variant('slave',
default='none',
description='Build on described slave (e.g daint)')
variant('slurm_account',
default='g110',
description=
'Slurm account used for mandatory testing during installation')

variant('mpi', default=True, description='enable MPI support')
variant('grib2', default=True, description='enable GRIB2 support')
variant('szip',
default=True,
description='enable szip compression for GRIB1')

depends_on('python', type='build')

depends_on('netcdf-fortran')
depends_on('netcdf-c')
depends_on('hdf5')
depends_on('eccodes')

depends_on('mpi', when='+mpi')
depends_on('eccodes', when='+grib2')
depends_on('szip', when='+szip')

# There are currently several issues related to NAG:
# 1. File libicontools/src/libicontools/mo_util_nml.f90 is empty after
# preprocessing.
# 2. Error: libiconremap/mo_rbfqr_math.f90, line 934: KIND value (8) does
# not specify a valid representation method.
# 3. It's yet unclear what additional flags g++ needs to link
# OpenMP-enabled Fortran code compiled with NAG.
# 4. It's yet unclear what additional NAG runtime libraries we need to
# link to.
conflicts('%nag')

# There is currently an issue related to PGI:
# PGF90-S-0081-Illegal selector - KIND value must be non-negative
# (libiconbase/mo_delaunay_types.f90: 332)
conflicts('%pgi')
conflicts('%nvhpc')
conflicts('%cce')

def configure_args(self):
args = []
args.append('acx_cv_fc_ftn_include_flag=-I')
args.append('acx_cv_fc_pp_include_flag=-I')
args.append('--disable-silent-rules')
args.append('--disable-shared')
args.append('--with-netcdf={0}'.format(
self.spec['netcdf-fortran'].prefix))
args.append('--enable-iso-c-interface')
args.append('--enable-grib2')
args.append('--with-eccodes={0}'.format(self.spec['eccodes'].prefix))

return args
def flag_handler(self, name, flags):
if name == 'cflags' or name == 'cxxflags':
# Set OpenMP flags:
flags.append(self.compiler.openmp_flag
# We assume that NAG is mixed with GCC:
if self.compiler.name != 'nag' else '-fopenmpi')
elif name == 'fflags':
# Enable building with 'gcc@10:':
if self.spec.satisfies('%gcc@10:'):
flags.append('-fallow-argument-mismatch')
# Set OpenMP flags:
flags.append(self.compiler.openmp_flag)
# Disable MPI support:
if '~mpi' in self.spec:
flags.append('-DNOMPI')
elif name == 'cppflags':
# Disable MPI support:
if '~mpi' in self.spec:
flags.append('-DNOMPI')

return flags, None, None

def setup_build_environment(self, env):
# Daint specific flags since cray-modules setting not recognized
if self.spec.variants['slave'].value == 'daint':
env.set('NETCDF_DIR', '{}'.format(self.spec['netcdf-c'].prefix))

#Setting CFLAGS
env.append_flags('CFLAGS', '-O2')
env.append_flags('CFLAGS', '-g')
env.append_flags('CFLAGS', '-Wunused')
env.append_flags('CFLAGS', '-DHAVE_LIBNETCDF')
env.append_flags('CFLAGS', '-DHAVE_NETCDF4')
env.append_flags('CFLAGS', '-DHAVE_CF_INTERFACE')
env.append_flags('CFLAGS', '-DHAVE_LIBGRIB_API')
env.append_flags('CFLAGS', '-D__ICON__')
env.append_flags('CFLAGS', '-DNOMPI')
#Setting CXXFLAGS
env.append_flags('CXXFLAGS', '-O2')
env.append_flags('CXXFLAGS', '-g')
env.append_flags('CXXFLAGS', '-fopenmp')
env.append_flags('CXXFLAGS', '-Wunused')
env.append_flags('CXXFLAGS', '-DNOMPI')
#Setting FCFLAGS
env.append_flags('FCFLAGS', '-O2')
env.append_flags('FCFLAGS', '-g')
env.append_flags('FCFLAGS', '-cpp')
env.append_flags('FCFLAGS', '-Wunused')
env.append_flags('FCFLAGS', '-DNOMPI')
#Setting LIBS
env.append_flags('LIBS', '-lhdf5')
env.append_flags('LIBS', '-leccodes')
env.append_flags('LIBS', '-leccodes_f90')

# jasper needs to be after eccodes, otherwise linking error
env.append_flags('LIBS', '-ljasper')

env.append_flags('LIBS', '-lgfortran')

def check(self):

# only c2sm-versions have script for CSCS
if self.spec.version in (Version('c2sm-master'), ):

if self.spec.variants['slave'].value == 'daint':
test_process = subprocess.run([
'sbatch', '-W', '--time=00:15:00', '-A',
self.spec.variants['slurm_account'].value, '-C', 'gpu',
'-p', 'normal', './C2SM/test/jenkins/test.sh'
],
stderr=subprocess.STDOUT)

if self.spec.variants['slave'].value == 'tsa':
test_process = subprocess.run([
'sbatch', '-W', '--time=00:15:00', '-p', 'debug',
'./C2SM/test/jenkins/test.sh'
],
stderr=subprocess.STDOUT)
if test_process.returncode != 0:
cat_submit_process = subprocess.run(['cat', 'job.out'],
stderr=subprocess.STDOUT,
check=True)
raise InstallError('Tests for Icontools failed')
def configure_args(self):
args = [
# Get verbose output in the logs:
'--disable-silent-rules',
# Do not trigger regeneration of the source files:
'--disable-maintainer-mode',
# Simplify linking of the bundled libraries:
'--enable-static',
'--disable-shared',
# Tune CDI:
'--disable-cdi-app',
'--disable-cf-interface',
'--disable-extra',
'--disable-ieg',
'--disable-service',
'--enable-cgribex',
'--enable-grib',
'--enable-iso-c-interface',
'--disable-util-linux-uuid',
'--disable-ossp-uuid',
'--disable-dce-uuid',
'--without-grib_api',
'--without-threads',
# Do not install CDI:
'CDO_DISABLE_CDILIB=1',
# There is only one argument for netcdf-c and netcdf-fortran but
# we specify path to netcdf-c here to make CDI happy (we also have
# to provide the prefix regardless of whether it is in the system
# path because the configure script of icontools fails otherwise):
'--with-netcdf={0}'.format(self.spec['netcdf-c'].prefix)
]

flags = defaultdict(list)

def help_libtool(spec):
# Help libtool to find the right library in case it is installed to
# a non-system directory by extending LDFLAGS.
if not is_system_path(spec.prefix):
flags['LDFLAGS'].append(spec.libs.search_flags)

# Help the libtool script of CDI to find the right HDF5 library:
hdf5_spec = self.spec['hdf5']
help_libtool(hdf5_spec)
# The package links directly to libcdi.a giving Libtool no chance to
# figure out that it should link to libhdf5:
flags['LIBS'].append(hdf5_spec.libs.link_flags)

if '+szip' in self.spec:
args.append('--with-szlib')
szip_spec = self.spec['szip']
help_libtool(szip_spec)
# The package links directly to libcdi.a giving Libtool no chance to
# figure out that it should link to libsz:
flags['LIBS'].append(szip_spec.libs.link_flags)
else:
args.append('--without-szlib')

if '+grib2' in self.spec:
args.append('--with-eccodes')
eccodes_spec = self.spec['eccodes']
help_libtool(eccodes_spec)
# The package links directly to libcdi.a giving Libtool no chance to
# figure out that it should link to libeccodes:
flags['LIBS'].append(eccodes_spec.libs.link_flags)
else:
args.append('--without-eccodes')
args.append('--without-grib_api')

if '+mpi' in self.spec:
mpi_spec = self.spec['mpi']
args.extend(['FC=' + mpi_spec.mpifc, 'CXX=' + mpi_spec.mpicxx])

# We need to link C++ programs to Fortran MPI libraries:
mpifc_libs = None
try:
mpifc_exe = Executable(mpi_spec.mpifc)
mpifc_libs = ' '.join(
re.findall(
r'\s(-l\s*[^\s]+)',
mpifc_exe('-show', output=str, error=os.devnull)))
except ProcessError:

def find_mpi_fc_link_flags(*libnames):
for shared in [True, False]:
libraries = find_libraries(libnames,
mpi_spec.prefix,
shared=shared,
recursive=True)
if libraries:
return libraries.link_flags
return None

if mpi_spec.name.endswith('mpich'):
# Check for the new name of the library (in this case,
# libmpichf90 is just a symlink, which we do not want to
# overlink to):
mpifc_libs = find_mpi_fc_link_flags('libmpifort')
if not mpifc_libs:
# Check for the old name of the library (this is
# usually the case on Cray platforms):
mpifc_libs = find_mpi_fc_link_flags('libmpichf90')
elif mpi_spec.name == 'openmpi':
mpifc_libs = find_mpi_fc_link_flags(
'lib*_usempif08', 'lib*_usempi_ignore_tkr',
'lib*_usempi', 'lib*_mpifh')

if mpifc_libs:
flags['LIBS'].append(mpifc_libs)
else:
cat_submit_process = subprocess.run(['cat', 'job.out'],
stderr=subprocess.STDOUT,
check=True)
tty.warn('unable to detect Fortran MPI libraries')

# We need to link C++ programs to Fortran runtime libraries:
if self.compiler.name == 'gcc':
flags['LIBS'].append('-lgfortran')
elif self.compiler.name == 'intel':
flags['LIBS'].append('-lifcore')
elif self.compiler.name == 'pgi':
flags['LIBS'].append('-pgf90libs')
else:
print("\033[92m" + "==> " + "\033[0m" +
"icontools: No tests available for version {}".format(
self.spec.version))
tty.warn('unable to detect Fortran runtime libraries')

args.extend([
'{0}={1}'.format(var, ' '.join(val)) for var, val in flags.items()
])

return args
2 changes: 1 addition & 1 deletion test/system_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -421,7 +421,7 @@ class IconHamTest(unittest.TestCase):
class IconToolsTest(unittest.TestCase):

def test_install_2_5_2(self):
spack_install_and_test('icontools @2.5.2')
spack_install('icontools @2.5.2')


@pytest.mark.no_tsa # Not supported on Tsa
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