def prepare_step(self, *args, **kwargs):
"""Custom prepare step for LAMMPS."""
super(EB_LAMMPS, self).prepare_step(*args, **kwargs)
# Unset LIBS when using both KOKKOS and CUDA - it will mix lib paths otherwise
if self.cfg['kokkos'] and get_software_root('CUDA'):
env.unset_env_vars(['LIBS'])
def correct_mpich_build_env(self):
"""
Method to correctly set the environment for MPICH and derivatives
"""
env_vars = [
'CFLAGS', 'CPPFLAGS', 'CXXFLAGS', 'FCFLAGS', 'FFLAGS', 'LDFLAGS',
'LIBS'
]
vars_to_unset = ['F90', 'F90FLAGS']
for envvar in env_vars:
envvar_val = os.getenv(envvar)
if envvar_val:
new_envvar = 'MPICHLIB_%s' % envvar
new_envvar_val = os.getenv(new_envvar)
vars_to_unset.append(envvar)
if envvar_val == new_envvar_val:
self.log.debug("$%s == $%s, just defined $%s as empty",
envvar, new_envvar, envvar)
elif new_envvar_val is None:
env.setvar(new_envvar, envvar_val)
else:
raise EasyBuildError(
"Both $%s and $%s set, can I overwrite $%s with $%s (%s) ?",
envvar, new_envvar, new_envvar, envvar, envvar_val)
env.unset_env_vars(vars_to_unset)
def correct_mpich_build_env(self):
"""
Method to correctly set the environment for MPICH and derivatives
"""
env_vars = ["CFLAGS", "CPPFLAGS", "CXXFLAGS", "FCFLAGS", "FFLAGS", "LDFLAGS", "LIBS"]
vars_to_unset = ["F90", "F90FLAGS"]
for envvar in env_vars:
envvar_val = os.getenv(envvar)
if envvar_val:
new_envvar = "MPICHLIB_%s" % envvar
new_envvar_val = os.getenv(new_envvar)
vars_to_unset.append(envvar)
if envvar_val == new_envvar_val:
self.log.debug("$%s == $%s, just defined $%s as empty", envvar, new_envvar, envvar)
elif new_envvar_val is None:
env.setvar(new_envvar, envvar_val)
else:
raise EasyBuildError(
"Both $%s and $%s set, can I overwrite $%s with $%s (%s) ?",
envvar,
new_envvar,
new_envvar,
envvar,
envvar_val,
)
env.unset_env_vars(vars_to_unset)
def __init__(self, *args, **kwargs):
"""Initialize custom class variables."""
super(PerlModule, self).__init__(*args, **kwargs)
self.testcmd = None
# Environment variables PERL_MM_OPT and PERL_MB_OPT cause installations to fail.
# Therefore it is better to unset these variables.
unset_env_vars(['PERL_MM_OPT', 'PERL_MB_OPT'])
def configure_step(self):
"""
Custom configuration procedure for ParaStationMPI.
* Sets the correct options
* Calls the MPICH configure_step, disabling the default MPICH options
"""
comp_opts = {
toolchain.GCC: 'gcc',
toolchain.INTELCOMP: 'intel',
toolchain.PGI: 'pgi',
}
# ParaStationMPI defines its environment through confsets. So these should be unset
env_vars = ['CFLAGS', 'CPPFLAGS', 'CXXFLAGS', 'FCFLAGS', 'FFLAGS', 'LDFLAGS', 'LIBS']
env.unset_env_vars(env_vars)
self.log.info("Unsetting the following variables: " + ' '.join(env_vars))
# Enable CUDA
if self.cfg['cuda']:
self.log.info("Enabling CUDA-Awareness...")
self.cfg.update('configopts', ' --with-cuda')
# Set confset
comp_fam = self.toolchain.comp_family()
if comp_fam in comp_opts:
self.cfg.update('configopts', ' --with-confset=%s' % comp_opts[comp_fam])
else:
raise EasyBuildError("Compiler %s not supported. Valid options are: %s",
comp_fam, ', '.join(comp_opts.keys()))
# Enable threading, if necessary
if self.cfg['threaded']:
self.cfg.update('configopts', ' --with-threading')
# Add extra mpich options, if any
if self.cfg['mpich_opts'] is not None:
self.cfg.update('configopts', ' --with-mpichconf="%s"' % self.cfg['mpich_opts'])
# Add PGO related options, if enabled
if self.cfg['pgo']:
self.cfg.update('configopts', ' --with-profile=gen --with-profdir=%s' % self.profdir)
# Lastly, set pscom related variables
if self.cfg['pscom_allin_path'] is None:
pscom_path = get_software_root('pscom')
else:
pscom_path = self.cfg['pscom_allin_path'].strip()
self.cfg.update('configopts', ' --with-pscom-allin="%s"' % pscom_path)
pscom_flags = 'PSCOM_LDFLAGS=-L{0}/lib PSCOM_CPPFLAGS=-I{0}/include'.format(pscom_path)
self.cfg.update('preconfigopts', pscom_flags)
super(EB_psmpi, self).configure_step(add_mpich_configopts=False)
def install_step(self):
"""COMSOL install procedure using 'install' command."""
setup_script = os.path.join(self.start_dir, 'setup')
# make sure setup script is executable
adjust_permissions(setup_script, stat.S_IXUSR)
# make sure $DISPLAY is not defined, which may lead to (hard to trace) problems
# this is a workaround for not being able to specify --nodisplay to the install scripts
env.unset_env_vars(['DISPLAY'])
cmd = ' '.join([self.cfg['preinstallopts'], setup_script, '-s', self.configfile, self.cfg['installopts']])
run_cmd(cmd, log_all=True, simple=True)
def install_step(self):
"""COMSOL install procedure using 'install' command."""
setup_script = os.path.join(self.start_dir, 'setup')
# make sure setup script is executable
adjust_permissions(setup_script, stat.S_IXUSR)
# make sure $DISPLAY is not defined, which may lead to (hard to trace) problems
# this is a workaround for not being able to specify --nodisplay to the install scripts
env.unset_env_vars(['DISPLAY'])
cmd = ' '.join([self.cfg['preinstallopts'], setup_script, '-s', self.configfile, self.cfg['installopts']])
run_cmd(cmd, log_all=True, simple=True)
def configure_step(self):
"""
Configure Perl build: run ./Configure instead of ./configure with some different options
"""
# avoid that $CPATH or $C_INCLUDE_PATH include an empty entry, since that makes Perl build fail miserably
# see https://github.com/easybuilders/easybuild-easyconfigs/issues/8859
for key in ['CPATH', 'C_INCLUDE_PATH']:
value = os.getenv(key, None)
if value is not None:
paths = value.split(os.pathsep)
if '' in paths:
self.log.info(
"Found empty entry in $%s, filtering it out...", key)
os.environ[key] = os.pathsep.join(p for p in paths if p)
majver = self.version.split('.')[0]
configopts = [
self.cfg['configopts'],
'-Dcc="{0}"'.format(os.getenv('CC')),
'-Dccflags="{0}"'.format(os.getenv('CFLAGS')),
'-Dinc_version_list=none',
'-Dprefix=%(installdir)s',
# guarantee that scripts are installed in /bin in the installation directory (and not in a guessed path)
# see https://github.com/easybuilders/easybuild-easyblocks/issues/1659
'-Dinstallscript=%(installdir)s/bin',
'-Dscriptdir=%(installdir)s/bin',
'-Dscriptdirexp=%(installdir)s/bin',
# guarantee that the install directory has the form lib/perlX/
# see https://github.com/easybuilders/easybuild-easyblocks/issues/1700
"-Dinstallstyle='lib/perl%s'" % majver,
]
if self.cfg['use_perl_threads']:
configopts.append('-Dusethreads')
# see https://metacpan.org/pod/distribution/perl/INSTALL#Specifying-a-logical-root-directory
sysroot = build_option('sysroot')
if sysroot:
configopts.append('-Dsysroot=%s' % sysroot)
configopts = (' '.join(configopts)) % {'installdir': self.installdir}
# if $COLUMNS is set to 0, 'ls' produces a warning like:
# ls: ignoring invalid width in environment variable COLUMNS: 0
# this confuses Perl's Configure script and makes it fail,
# so just unset $COLUMNS if it set to 0...
if os.getenv('COLUMNS', None) == '0':
unset_env_vars(['COLUMNS'])
cmd = './Configure -de %s' % configopts
run_cmd(cmd, log_all=True, simple=True)
def test_unset_env_vars(self):
"""Test unset_env_vars function."""
os.environ['TEST_ENV_VAR'] = 'test123'
# it's fair to assume $HOME will always be set
home = os.getenv('HOME')
self.assertTrue(home)
key_not_set = 'NO_SUCH_ENV_VAR'
if key_not_set in os.environ:
del os.environ[key_not_set]
res = env.unset_env_vars(['HOME', 'NO_SUCH_ENV_VAR', 'TEST_ENV_VAR'])
self.assertFalse('HOME' in os.environ)
self.assertFalse('NO_SUCH_ENV_VAR' in os.environ)
self.assertFalse('TEST_ENV_VAR' in os.environ)
expected = {
'HOME': home,
'TEST_ENV_VAR': 'test123',
}
self.assertEqual(res, expected)
def install_step(self):
"""Custom build, test & install procedure for Amber."""
# unset $LIBS since it breaks the build
env.unset_env_vars(['LIBS'])
# define environment variables for MPI, BLAS/LAPACK & dependencies
mklroot = get_software_root('imkl')
openblasroot = get_software_root('OpenBLAS')
if mklroot:
env.setvar('MKL_HOME', mklroot)
elif openblasroot:
lapack = os.getenv('LIBLAPACK')
if lapack is None:
raise EasyBuildError(
"LIBLAPACK (from OpenBLAS) not found in environment.")
else:
env.setvar('GOTO', lapack)
mpiroot = get_software_root(self.toolchain.MPI_MODULE_NAME[0])
if mpiroot and self.toolchain.options.get('usempi', None):
env.setvar('MPI_HOME', mpiroot)
self.with_mpi = True
if self.toolchain.mpi_family() == toolchain.INTELMPI:
self.mpi_option = '-intelmpi'
else:
self.mpi_option = '-mpi'
common_configopts = [self.cfg['configopts'], '--no-updates']
if get_software_root('X11') is None:
common_configopts.append('-noX11')
if self.name == 'Amber' and self.cfg['static']:
common_configopts.append('-static')
netcdfroot = get_software_root('netCDF')
if netcdfroot:
common_configopts.extend(["--with-netcdf", netcdfroot])
netcdf_fort_root = get_software_root('netCDF-Fortran')
if netcdf_fort_root:
common_configopts.extend(["--with-netcdf-fort", netcdf_fort_root])
pythonroot = get_software_root('Python')
if pythonroot:
common_configopts.extend(
["--with-python",
os.path.join(pythonroot, 'bin', 'python')])
self.pylibdir = det_pylibdir()
pythonpath = os.environ.get('PYTHONPATH', '')
env.setvar(
'PYTHONPATH',
os.pathsep.join(
[os.path.join(self.installdir, self.pylibdir),
pythonpath]))
comp_fam = self.toolchain.comp_family()
if comp_fam == toolchain.INTELCOMP:
comp_str = 'intel'
elif comp_fam == toolchain.GCC:
comp_str = 'gnu'
else:
raise EasyBuildError(
"Don't know how to compile with compiler family '%s' -- check EasyBlock?",
comp_fam)
# The NAB compiles need openmp flag
if self.toolchain.options.get('openmp', None):
env.setvar('CUSTOMBUILDFLAGS', self.toolchain.get_flag('openmp'))
# compose list of build targets
build_targets = [('', 'test')]
if self.with_mpi:
build_targets.append((self.mpi_option, 'test.parallel'))
# hardcode to 4 MPI processes, minimal required to run all tests
env.setvar('DO_PARALLEL', 'mpirun -np 4')
cudaroot = get_software_root('CUDA')
if cudaroot:
env.setvar('CUDA_HOME', cudaroot)
self.with_cuda = True
build_targets.append(('-cuda', 'test.cuda'))
if self.with_mpi:
build_targets.append(
("-cuda %s" % self.mpi_option, 'test.cuda_parallel'))
ld_lib_path = os.environ.get('LD_LIBRARY_PATH', '')
env.setvar(
'LD_LIBRARY_PATH',
os.pathsep.join(
[os.path.join(self.installdir, 'lib'), ld_lib_path]))
for flag, testrule in build_targets:
# configure
cmd = "%s ./configure %s" % (self.cfg['preconfigopts'],
' '.join(common_configopts +
[flag, comp_str]))
(out, _) = run_cmd(cmd, log_all=True, simple=False)
# build in situ using 'make install'
# note: not 'build'
super(EB_Amber, self).install_step()
# test
if self.cfg['runtest']:
run_cmd("make %s" % testrule, log_all=True, simple=False)
# clean, overruling the normal 'build'
run_cmd("make clean")
def install_step(self):
"""Custom build, test & install procedure for Amber."""
# unset $LIBS since it breaks the build
env.unset_env_vars(['LIBS'])
# define environment variables for MPI, BLAS/LAPACK & dependencies
mklroot = get_software_root('imkl')
openblasroot = get_software_root('OpenBLAS')
if mklroot:
env.setvar('MKL_HOME', mklroot)
elif openblasroot:
lapack = os.getenv('LIBLAPACK')
if lapack is None:
raise EasyBuildError("LIBLAPACK (from OpenBLAS) not found in environment.")
else:
env.setvar('GOTO', lapack)
mpiroot = get_software_root(self.toolchain.MPI_MODULE_NAME[0])
if mpiroot and self.toolchain.options.get('usempi', None):
env.setvar('MPI_HOME', mpiroot)
self.with_mpi = True
if self.toolchain.mpi_family() == toolchain.INTELMPI:
self.mpi_option = '-intelmpi'
else:
self.mpi_option = '-mpi'
common_configopts = [self.cfg['configopts'], '--no-updates']
if get_software_root('X11') is None:
common_configopts.append('-noX11')
if self.name == 'Amber' and self.cfg['static']:
common_configopts.append('-static')
netcdfroot = get_software_root('netCDF')
if netcdfroot:
common_configopts.extend(["--with-netcdf", netcdfroot])
netcdf_fort_root = get_software_root('netCDF-Fortran')
if netcdf_fort_root:
common_configopts.extend(["--with-netcdf-fort", netcdf_fort_root])
pythonroot = get_software_root('Python')
if pythonroot:
common_configopts.extend(["--with-python", os.path.join(pythonroot, 'bin', 'python')])
self.pylibdir = det_pylibdir()
pythonpath = os.environ.get('PYTHONPATH', '')
env.setvar('PYTHONPATH', os.pathsep.join([os.path.join(self.installdir, self.pylibdir), pythonpath]))
comp_fam = self.toolchain.comp_family()
if comp_fam == toolchain.INTELCOMP:
comp_str = 'intel'
elif comp_fam == toolchain.GCC:
comp_str = 'gnu'
else:
raise EasyBuildError("Don't know how to compile with compiler family '%s' -- check EasyBlock?", comp_fam)
# The NAB compiles need openmp flag
if self.toolchain.options.get('openmp', None):
env.setvar('CUSTOMBUILDFLAGS', self.toolchain.get_flag('openmp'))
# compose list of build targets
build_targets = [('', 'test')]
if self.with_mpi:
build_targets.append((self.mpi_option, 'test.parallel'))
# hardcode to 4 MPI processes, minimal required to run all tests
env.setvar('DO_PARALLEL', 'mpirun -np 4')
cudaroot = get_software_root('CUDA')
if cudaroot:
env.setvar('CUDA_HOME', cudaroot)
self.with_cuda = True
build_targets.append(('-cuda', 'test.cuda'))
if self.with_mpi:
build_targets.append(("-cuda %s" % self.mpi_option, 'test.cuda_parallel'))
ld_lib_path = os.environ.get('LD_LIBRARY_PATH', '')
env.setvar('LD_LIBRARY_PATH', os.pathsep.join([os.path.join(self.installdir, 'lib'), ld_lib_path]))
for flag, testrule in build_targets:
# configure
cmd = "%s ./configure %s" % (self.cfg['preconfigopts'], ' '.join(common_configopts + [flag, comp_str]))
(out, _) = run_cmd(cmd, log_all=True, simple=False)
# build in situ using 'make install'
# note: not 'build'
super(EB_Amber, self).install_step()
# test
if self.cfg['runtest']:
run_cmd("make %s" % testrule, log_all=True, simple=False)
# clean, overruling the normal 'build'
run_cmd("make clean")
