def module(command, *arguments):
"""
`module` wrapper for the LMOD based modules function.
Args:
command (str): The `module` command that we're executing. i.e., `load`, `unload`, `swap`, etc.
*arguments : Variable length argument list.
Returns:
int: status indicating success or failure. 0 = success, nonzero for failure
For now, because the LMOD `module()` command returns nothing (`NoneType`)
and provides no way to determine success or failure, we will only return 0.
Raises:
Any exception thrown by env_modules_python.module() will get caught and passed along.
"""
output = 0
try:
status = env_modules_python.module(command, *arguments)
except BaseException as error:
print("")
print("An ERROR occurred during execution of module command")
print("")
raise error
return output
def loadModules(self, modules, testDef):
# Logging of results from the environment modules usage is the responsibility of the plugin that is making use of this utility.
if self.env_module_wrapper is None:
# cannot perform this operation
return (1, None, "Module capability was not found")
# Load the lmod python module() definition
sys.path.insert(0, os.path.dirname(self.env_module_link))
try:
from env_modules_python import module
except:
return (1, None, "No module named env_modules_python found")
# We have to run this in the same python context for it to take effect and be propagated to future children
# Redirect the sys.stdout and sys.stderr for the module loads and unloads.
saved_stdout = sys.stdout
saved_stderr = sys.stderr
load_stdout = sys.stdout = StringIO()
load_stderr = sys.stderr = StringIO()
modules = modules.split()
for mod in modules:
mod = mod.strip()
try:
module("load", mod)
except:
# If a module name is not found the module python flow will trigger this exception.
return (1, None, "Attempt to load environment module " + mod +
" failed")
# Restore sys.stdout and sys.stderr
sys.stdout = saved_stdout
sys.stderr = saved_stderr
status = load_stderr.seek(0, os.SEEK_END)
stdout = load_stdout.getvalue()
stderr = load_stderr.getvalue()
load_stdout.close()
load_stderr.close()
return (status, stdout, stderr)
def unloadModules(self, modules, testDef):
if self.env_module_wrapper is None:
# cannot perform this operation
return (1, None, "Module capability was not found")
# Load the lmod python module() definition
sys.path.insert(0, os.path.dirname(self.env_module_link))
try:
from env_modules_python import module
except:
return (1, None, "No module named env_modules_python found")
# We have to run this in the same python context for it to take effect and be propagated to future children
# Redirect the sys.stdout and sys.stderr for the module loads and unloads.
saved_stdout = sys.stdout
saved_stderr = sys.stderr
unload_stdout = sys.stdout = StringIO()
unload_stderr = sys.stderr = StringIO()
modules = modules.split()
for mod in modules:
mod = mod.strip()
try:
module("unload", mod)
except:
# Unlike the load, the module python flow will not cause an exception if the module can not be found.
# Add this to catch any other unexpected exceptions.
return (1, None, "Attempt to unload environment module " +
mod + " failed")
# Restore sys.stdout and sys.stderr
sys.stdout = saved_stdout
sys.stderr = saved_stderr
status = unload_stderr.seek(0, os.SEEK_END)
stdout = unload_stdout.getvalue()
stderr = unload_stderr.getvalue()
unload_stdout.close()
unload_stderr.close()
return (status, stdout, stderr)
def loadModules(self, modules, testDef):
# Logging of results from the environment modules usage is the responsibility
# of the plugin that is making use of this utility.
if self.env_module_wrapper is None:
# cannot perform this operation
return (1, None, "Module capability was not found")
# Load the lmod python module() definition
sys.path.insert(0, os.path.dirname(self.env_module_link))
try:
from env_modules_python import module
except:
return (1, None, "No module named env_modules_python found")
# We have to run this in the same python context for it to take effect and be propagated to future children
# Redirect the sys.stdout and sys.stderr for the module loads and unloads.
saved_stdout = sys.stdout
saved_stderr = sys.stderr
load_stdout = sys.stdout = StringIO()
load_stderr = sys.stderr = StringIO()
modules = modules.split()
for mod in modules:
mod = mod.strip()
try:
module("load", mod)
except:
# If a module name is not found the module python flow will trigger this exception.
return (1, None, "Attempt to load environment module " + mod + " failed")
# Restore sys.stdout and sys.stderr
sys.stdout = saved_stdout
sys.stderr = saved_stderr
status = load_stderr.seek(0, os.SEEK_END)
stdout = load_stdout.getvalue()
stderr = load_stderr.getvalue()
load_stdout.close()
load_stderr.close()
return (status, stdout, stderr)
def unloadModules(self, modules, testDef):
if self.env_module_wrapper is None:
# cannot perform this operation
return (1, None, "Module capability was not found")
# Load the lmod python module() definition
sys.path.insert(0, os.path.dirname(self.env_module_link))
try:
from env_modules_python import module
except:
return (1, None, "No module named env_modules_python found")
# We have to run this in the same python context for it to take effect and be propagated to future children
# Redirect the sys.stdout and sys.stderr for the module loads and unloads.
saved_stdout = sys.stdout
saved_stderr = sys.stderr
unload_stdout = sys.stdout = StringIO()
unload_stderr = sys.stderr = StringIO()
modules = modules.split()
for mod in modules:
mod = mod.strip()
try:
module("unload", mod)
except:
# Unlike the load, the module python flow will not cause an exception if the module can not be found.
# Add this to catch any other unexpected exceptions.
return (1, None, "Attempt to unload environment module " + mod + " failed")
# Restore sys.stdout and sys.stderr
sys.stdout = saved_stdout
sys.stderr = saved_stderr
status = unload_stderr.seek(0, os.SEEK_END)
stdout = unload_stdout.getvalue()
stderr = unload_stderr.getvalue()
unload_stdout.close()
unload_stderr.close()
return (status, stdout, stderr)
def setBuildEnviron(arguments):
moduleMap = {
'Trilinos_pullrequest_gcc_4.8.4': [
'sems-env', 'sems-git/2.10.1', 'sems-gcc/4.8.4',
'sems-openmpi/1.10.1', 'sems-python/2.7.9',
'sems-boost/1.63.0/base', 'sems-zlib/1.2.8/base',
'sems-hdf5/1.8.12/parallel', 'sems-netcdf/4.4.1/exo_parallel',
'sems-parmetis/4.0.3/parallel',
'sems-scotch/6.0.3/nopthread_64bit_parallel',
'sems-superlu/4.3/base', 'sems-cmake/3.10.3', 'atdm-env',
'atdm-ninja_fortran/1.7.2'
],
'Trilinos_pullrequest_gcc_4.9.3_SERIAL': [
'sems-env', 'sems-git/2.10.1', 'sems-gcc/4.9.3',
'sems-python/2.7.9', 'sems-boost/1.63.0/base',
'sems-zlib/1.2.8/base', 'sems-hdf5/1.8.12/base',
'sems-netcdf/4.4.1/exo', 'sems-metis/5.1.0/base',
'sems-superlu/4.3/base', 'sems-cmake/3.10.3', 'atdm-env',
'atdm-ninja_fortran/1.7.2'
],
'Trilinos_pullrequest_python_2': [
'sems-git/2.10.1', 'sems-gcc/7.2.0', ('', 'sems-python/2.7.9'),
'sems-cmake/3.10.3', 'atdm-env', 'atdm-ninja_fortran/1.7.2'
],
'Trilinos_pullrequest_python_3': [
'sems-git/2.10.1', 'sems-gcc/7.2.0', ('', 'sems-python/2.7.9'),
'sems-cmake/3.10.3', 'atdm-env', 'atdm-ninja_fortran/1.7.2'
],
'Trilinos_pullrequest_gcc_7.2.0': [
'sems-env', 'sems-git/2.10.1', 'sems-gcc/7.2.0',
'sems-openmpi/1.10.1', 'sems-python/2.7.9',
'sems-boost/1.63.0/base', 'sems-zlib/1.2.8/base',
'sems-hdf5/1.8.12/parallel', 'sems-netcdf/4.4.1/exo_parallel',
'sems-parmetis/4.0.3/parallel',
'sems-scotch/6.0.3/nopthread_64bit_parallel',
'sems-superlu/4.3/base', 'sems-cmake/3.10.3', 'atdm-env',
'atdm-ninja_fortran/1.7.2'
],
'Trilinos_pullrequest_gcc_8.3.0': [
'sems-env', 'sems-git/2.10.1', 'sems-gcc/8.3.0',
'sems-openmpi/1.10.1', 'sems-python/2.7.9',
'sems-boost/1.66.0/base', 'sems-zlib/1.2.8/base',
'sems-hdf5/1.8.12/parallel', 'sems-netcdf/4.4.1/exo_parallel',
'sems-parmetis/4.0.3/parallel',
'sems-scotch/6.0.3/nopthread_64bit_parallel',
'sems-superlu/4.3/base', 'sems-cmake/3.10.3', 'atdm-env',
'atdm-ninja_fortran/1.7.2'
],
'Trilinos_pullrequest_intel_17.0.1': [
'sems-env', 'sems-git/2.10.1', 'sems-gcc/4.9.3',
'sems-intel/17.0.1', 'sems-mpich/3.2', 'sems-python/2.7.9',
'sems-boost/1.63.0/base', 'sems-zlib/1.2.8/base',
'sems-hdf5/1.8.12/parallel', 'sems-netcdf/4.4.1/exo_parallel',
'sems-parmetis/4.0.3/parallel',
'sems-scotch/6.0.3/nopthread_64bit_parallel',
'sems-superlu/4.3/base', 'sems-cmake/3.10.3', 'atdm-env',
'atdm-ninja_fortran/1.7.2'
],
'Trilinos_pullrequest_cuda_9.2': [
'git/2.10.1',
'devpack/20180521/openmpi/2.1.2/gcc/7.2.0/cuda/9.2.88',
('openblas/0.2.20/gcc/7.2.0', 'netlib/3.8.0/gcc/7.2.0')
]
}
environMap = {
'Trilinos_pullrequest_gcc_4.8.4': {
'OMP_NUM_THREADS': '2'
},
'Trilinos_pullrequest_gcc_4.9.3_SERIAL': {
'OMP_NUM_THREADS': '2'
},
'Trilinos_pullrequest_python_2': {
'PYTHONPATH':
os.path.join(os.path.sep, 'projects', 'sierra', 'linux_rh7',
'install', 'Python', 'extras', 'lib', 'python2.7',
'site-packages'),
'MANPATH':
os.path.join(os.path.sep, 'projects', 'sierra', 'linux_rh7',
'install', 'Python', '2.7.15', 'share', 'man'),
'PATH':
os.path.join(os.path.sep, 'projects', 'sierra', 'linux_rh7',
'install', 'Python', '2.7.15', 'bin') + os.pathsep +
os.path.join(os.path.sep, 'projects', 'sierra', 'linux_rh7',
'install', 'Python', 'extras'
'bin')
},
'Trilinos_pullrequest_python_3': {
'PYTHONPATH':
os.path.join(os.path.sep, 'projects', 'sierra', 'linux_rh7',
'install', 'Python', 'extras', 'lib', 'python3.6',
'site-packages'),
'MANPATH':
os.path.join(os.path.sep, 'projects', 'sierra', 'linux_rh7',
'install', 'Python', '3.6.3', 'share', 'man'),
'PATH':
os.path.join(os.path.sep, 'projects', 'sierra', 'linux_rh7',
'install', 'Python', '3.6.3', 'bin') + os.pathsep +
os.path.join(os.path.sep, 'projects', 'sierra', 'linux_rh7',
'install', 'Python', 'extras'
'bin')
},
'Trilinos_pullrequest_gcc_7.2.0': {
'SEMS_FORCE_LOCAL_COMPILER_VERSION': '4.9.3',
'OMP_NUM_THREADS': '2'
},
'Trilinos_pullrequest_gcc_8.3.0': {
'SEMS_FORCE_LOCAL_COMPILER_VERSION': '4.9.3',
'OMP_NUM_THREADS': '2'
},
'Trilinos_pullrequest_intel_17.0.1': {
'SEMS_FORCE_LOCAL_COMPILER_VERSION': '4.9.3',
'OMP_NUM_THREADS': '2'
},
'Trilinos_pullrequest_cuda_9.2': {
'OMPI_CXX':
os.path.join(os.environ['WORKSPACE'], 'Trilinos', 'packages',
'kokkos', 'bin', 'nvcc_wrapper'),
'OMPI_CC':
os.environ.get('CC', ''),
'OMPI_FC':
os.environ.get('FC', ''),
'CUDA_LAUNCH_BLOCKING':
'1',
'CUDA_MANAGED_FORCE_DEVICE_ALLOC':
'1',
'PATH':
os.path.join(os.path.sep, 'ascldap', 'users', 'rabartl', 'install',
'white-ride', 'cmake-3.11.2', 'bin') + os.pathsep +
os.path.join(os.path.sep, 'ascldap', 'users', 'rabartl', 'install',
'white-ride', 'ninja-1.8.2', 'bin')
}
}
try:
moduleList = moduleMap[arguments.job_base_name]
l_environMap = environMap[arguments.job_base_name]
except KeyError:
sys.exit(
"""ERROR: Unable to find matching environment for job: Trilinos_pullrequest_UNKOWN
Error code was: 42""")
if 'sems-env' == moduleList[0]:
module('use', '/projects/sems/modulefiles/projects')
for mod in moduleList:
if isinstance(mod, str):
module('load', mod)
else:
unl_mod, load_mod = mod
if '' == unl_mod:
module('unload', load_mod)
else:
module('swap', unl_mod, load_mod)
if 'OMPI_CC' in l_environMap:
l_environMap['OMPI_CC'] = os.environ.get('CC', '')
if 'OMPI_FC' in l_environMap:
l_environMap['OMPI_FC'] = os.environ.get('FC', '')
for key, value in l_environMap.items():
if key in os.environ:
# we are assuming these are paths to be prepended
os.environ[key] = value + os.pathsep + os.environ[key]
else:
os.environ[key] = value
confirmGitVersion()
print("Environment:\n", file=sys.stdout)
print(" pwd = {cwd}".format(cwd=os.getcwd()), file=sys.stdout)
print("", file=sys.stdout)
for key in os.environ:
print(key + ' = ' + os.environ[key], file=sys.stdout)
print(
"\n==========================================================================================",
file=sys.stdout)
print(module('list'))
def load_module(mach, compiler, module_name):
logger = logging.getLogger(__name__)
logger.info("Building with %s on %s" % (compiler, mach))
logger.info("Loading module %s..." % module_name)
if mach == 'yellowstone':
sys.path.insert(
0,
os.path.join(os.sep, 'glade', 'apps', 'opt', 'lmod', 'lmod',
'init'))
from env_modules_python import module
module('purge')
module('load', module_name)
module('load', 'ncarcompilers')
module('load', 'ncarbinlibs')
if mach == 'cheyenne':
sys.path.insert(
0,
os.path.join(os.sep, 'glade', 'u', 'apps', 'ch', 'opt', 'lmod',
'7.2.1', 'lmod', 'lmod', 'init'))
from env_modules_python import module
module('purge')
module('load', module_name)
module('load', 'ncarcompilers')
module('load', 'mpt/2.15')
if mach == 'hobart':
sys.path.insert(
0, os.path.join(os.sep, 'usr', 'share', 'Modules', 'init'))
from python import module
module('purge')
module(['load', module_name])
if mach == 'edison':
sys.path.insert(
0, os.path.join(os.sep, 'opt', 'modules', 'default', 'init'))
from python import module
module('purge')
module(['load', 'craype/2.5.12'])
module(['load', module_name])
def setBuildEnviron(arguments):
"""
TODO: Needs explanation.
- How is environMap structured?
- How is moduleMap structured?
TODO: wcm: Could it be possible to offload environMap and moduleMap into a
JSON or Yaml file? (Yaml allows comments which is more helpful
than JSON IMO.)
"""
moduleMap = {"Trilinos_pullrequest_gcc_4.8.4":
["sems-env",
"sems-git/2.10.1",
"sems-gcc/4.8.4",
"sems-openmpi/1.10.1",
"sems-python/2.7.9",
"sems-boost/1.63.0/base",
"sems-zlib/1.2.8/base",
"sems-hdf5/1.10.6/parallel",
"sems-netcdf/4.7.3/parallel",
"sems-parmetis/4.0.3/parallel",
"sems-scotch/6.0.3/nopthread_64bit_parallel",
"sems-superlu/4.3/base",
"sems-cmake/3.10.3",
"atdm-env",
"atdm-ninja_fortran/1.7.2"],
"Trilinos_pullrequest_gcc_4.9.3_SERIAL":
["sems-env",
"sems-git/2.10.1",
"sems-gcc/4.9.3",
"sems-python/2.7.9",
"sems-boost/1.63.0/base",
"sems-zlib/1.2.8/base",
"sems-hdf5/1.10.6/base",
"sems-netcdf/4.7.3/base",
"sems-metis/5.1.0/base",
"sems-superlu/4.3/base",
"sems-cmake/3.10.3",
"atdm-env",
"atdm-ninja_fortran/1.7.2"],
"Trilinos_pullrequest_python_2":
["sems-git/2.10.1",
"sems-gcc/7.2.0",
("", "sems-python/2.7.9"),
"sems-cmake/3.10.3",
"atdm-env",
"atdm-ninja_fortran/1.7.2"],
"Trilinos_pullrequest_python_3":
["sems-git/2.10.1",
"sems-gcc/7.2.0",
("", "sems-python/2.7.9"),
"sems-cmake/3.10.3",
"atdm-env",
"atdm-ninja_fortran/1.7.2"],
"Trilinos_pullrequest_gcc_7.2.0":
["sems-env",
"sems-git/2.10.1",
"sems-gcc/7.2.0",
"sems-openmpi/1.10.1",
"sems-python/2.7.9",
"sems-boost/1.63.0/base",
"sems-zlib/1.2.8/base",
"sems-hdf5/1.10.6/parallel",
"sems-netcdf/4.7.3/parallel",
"sems-parmetis/4.0.3/parallel",
"sems-scotch/6.0.3/nopthread_64bit_parallel",
"sems-superlu/4.3/base",
"sems-cmake/3.10.3",
"atdm-env",
"atdm-ninja_fortran/1.7.2"],
"Trilinos_pullrequest_gcc_7.2.0_debug":
["sems-env",
"sems-git/2.10.1",
"sems-gcc/7.2.0",
"sems-openmpi/1.10.1",
"sems-python/2.7.9",
"sems-boost/1.63.0/base",
"sems-zlib/1.2.8/base",
"sems-hdf5/1.10.6/parallel",
"sems-netcdf/4.7.3/parallel",
"sems-parmetis/4.0.3/parallel",
"sems-scotch/6.0.3/nopthread_64bit_parallel",
"sems-superlu/4.3/base",
"sems-cmake/3.10.3",
"atdm-env",
"atdm-ninja_fortran/1.7.2"],
"Trilinos_pullrequest_gcc_8.3.0":
["sems-env",
"sems-git/2.10.1",
"sems-gcc/8.3.0",
"sems-openmpi/1.10.1",
"sems-python/2.7.9",
"sems-boost/1.66.0/base",
"sems-zlib/1.2.8/base",
"sems-hdf5/1.10.6/parallel",
"sems-netcdf/4.7.3/parallel",
"sems-parmetis/4.0.3/parallel",
"sems-scotch/6.0.3/nopthread_64bit_parallel",
"sems-superlu/4.3/base",
"sems-cmake/3.17.1",
"sems-ninja_fortran/1.10.0",
"atdm-env"
],
"Trilinos_pullrequest_intel_17.0.1":
["sems-env",
"sems-git/2.10.1",
"sems-gcc/4.9.3",
"sems-intel/17.0.1",
"sems-mpich/3.2",
"sems-python/2.7.9",
"sems-boost/1.63.0/base",
"sems-zlib/1.2.8/base",
"sems-hdf5/1.10.6/parallel",
"sems-netcdf/4.7.3/parallel",
"sems-parmetis/4.0.3/parallel",
"sems-scotch/6.0.3/nopthread_64bit_parallel",
"sems-superlu/4.3/base",
"sems-cmake/3.10.3",
"atdm-env",
"atdm-ninja_fortran/1.7.2"],
"Trilinos_pullrequest_clang_7.0.1":
["sems-env",
"sems-git/2.10.1",
"sems-gcc/5.3.0",
"sems-clang/7.0.1",
"sems-openmpi/1.10.1",
"sems-python/2.7.9",
"sems-boost/1.63.0/base",
"sems-zlib/1.2.8/base",
"sems-hdf5/1.10.6/parallel",
"sems-netcdf/4.7.3/parallel",
"sems-parmetis/4.0.3/parallel",
"sems-scotch/6.0.3/nopthread_64bit_parallel",
"sems-superlu/4.3/base",
"sems-cmake/3.12.2",
"atdm-env",
"atdm-ninja_fortran/1.7.2"],
"Trilinos_pullrequest_clang_9.0.0":
["sems-env",
"sems-git/2.10.1",
"sems-gcc/5.3.0",
"sems-clang/9.0.0",
"sems-openmpi/1.10.1",
"sems-python/2.7.9",
"sems-boost/1.63.0/base",
"sems-zlib/1.2.8/base",
"sems-hdf5/1.10.6/parallel",
"sems-netcdf/4.7.3/parallel",
"sems-parmetis/4.0.3/parallel",
"sems-scotch/6.0.3/nopthread_64bit_parallel",
"sems-superlu/4.3/base",
"sems-cmake/3.12.2",
"atdm-env",
"atdm-ninja_fortran/1.7.2"],
"Trilinos_pullrequest_clang_10.0.0":
["sems-env",
"sems-git/2.10.1",
"sems-gcc/5.3.0",
"sems-clang/10.0.0",
"sems-openmpi/1.10.1",
"sems-python/2.7.9",
"sems-boost/1.69.0/base",
"sems-zlib/1.2.8/base",
"sems-hdf5/1.10.6/parallel",
"sems-netcdf/4.7.3/parallel",
"sems-parmetis/4.0.3/parallel",
"sems-scotch/6.0.3/nopthread_64bit_parallel",
"sems-superlu/4.3/base",
"sems-cmake/3.17.1",
"sems-ninja_fortran/1.10.0"],
"Trilinos_pullrequest_cuda_9.2":
["git/2.10.1",
"devpack/20180521/openmpi/2.1.2/gcc/7.2.0/cuda/9.2.88",
("openblas/0.2.20/gcc/7.2.0", "netlib/3.8.0/gcc/7.2.0")]}
environMap = {
"Trilinos_pullrequest_gcc_4.8.4":
{"OMP_NUM_THREADS": "2"},
"Trilinos_pullrequest_gcc_4.9.3_SERIAL":
{"OMP_NUM_THREADS": "2"},
"Trilinos_pullrequest_python_2":
{"PYTHONPATH":
os.path.join(os.path.sep,
"projects",
"sierra",
"linux_rh7",
"install",
"Python",
"extras",
"lib",
"python2.7",
"site-packages"),
"MANPATH":
os.path.join(os.path.sep,
"projects",
"sierra",
"linux_rh7",
"install",
"Python",
"2.7.15",
"share",
"man"),
"PATH": os.path.join(os.path.sep,
"projects",
"sierra",
"linux_rh7",
"install",
"Python",
"2.7.15",
"bin") + os.pathsep +
os.path.join(os.path.sep,
"projects",
"sierra",
"linux_rh7",
"install",
"Python",
"extras"
"bin")},
"Trilinos_pullrequest_python_3":
{"PYTHONPATH":
os.path.join(os.path.sep,
"projects",
"sierra",
"linux_rh7",
"install",
"Python",
"extras",
"lib",
"python3.6",
"site-packages"),
"MANPATH":
os.path.join(os.path.sep,
"projects",
"sierra",
"linux_rh7",
"install",
"Python",
"3.6.3",
"share",
"man"),
"PATH": os.path.join(os.path.sep,
"projects",
"sierra",
"linux_rh7",
"install",
"Python",
"3.6.3",
"bin") + os.pathsep +
os.path.join(os.path.sep,
"projects",
"sierra",
"linux_rh7",
"install",
"Python",
"extras"
"bin")},
"Trilinos_pullrequest_gcc_7.2.0":
{"SEMS_FORCE_LOCAL_COMPILER_VERSION": "4.9.3",
"OMP_NUM_THREADS": "2"},
"Trilinos_pullrequest_gcc_7.2.0_debug":
{"SEMS_FORCE_LOCAL_COMPILER_VERSION": "4.9.3",
"OMP_NUM_THREADS": "2"},
"Trilinos_pullrequest_gcc_8.3.0":
{"SEMS_FORCE_LOCAL_COMPILER_VERSION": "4.9.3",
"OMP_NUM_THREADS": "2"},
"Trilinos_pullrequest_intel_17.0.1":
{"SEMS_FORCE_LOCAL_COMPILER_VERSION": "4.9.3",
"OMP_NUM_THREADS": "2"},
"Trilinos_pullrequest_clang_7.0.1":
{"SEMS_FORCE_LOCAL_COMPILER_VERSION": "5.3.0",
"OMP_NUM_THREADS": "2"},
"Trilinos_pullrequest_clang_9.0.0":
{"SEMS_FORCE_LOCAL_COMPILER_VERSION": "5.3.0",
"OMP_NUM_THREADS": "2"},
"Trilinos_pullrequest_clang_10.0.0":
{"SEMS_FORCE_LOCAL_COMPILER_VERSION": "5.3.0",
"OMP_NUM_THREADS": "2"},
"Trilinos_pullrequest_cuda_9.2":
{"OMPI_CXX":
os.path.join(os.environ["WORKSPACE"],
"Trilinos",
"packages",
"kokkos",
"bin",
"nvcc_wrapper"),
"OMPI_CC": os.environ.get("CC", ""),
"OMPI_FC": os.environ.get("FC", ""),
"CUDA_LAUNCH_BLOCKING": "1",
"CUDA_MANAGED_FORCE_DEVICE_ALLOC": "1",
"PATH": os.path.join(os.path.sep,
"ascldap",
"users",
"rabartl",
"install",
"white-ride",
"cmake-3.11.2",
"bin") + os.pathsep +
os.path.join(os.path.sep,
"ascldap",
"users",
"rabartl",
"install",
"white-ride",
"ninja-1.8.2",
"bin")}
}
try:
moduleList = moduleMap[arguments.job_base_name]
l_environMap = environMap[arguments.job_base_name]
except KeyError:
sys.exit(dedent("""\
ERROR: Unable to find matching environment for job: Trilinos_pullrequest_UNKOWN
Error code was: 42"""))
if 'sems-env' == moduleList[0]:
module('use', '/projects/sems/modulefiles/projects')
for mod in moduleList:
if isinstance(mod, str):
module('load', mod)
else:
unl_mod, load_mod = mod
if '' == unl_mod:
module('unload', load_mod)
else:
module('swap', unl_mod, load_mod)
if 'OMPI_CC' in l_environMap:
l_environMap['OMPI_CC'] = os.environ.get('CC', '')
if 'OMPI_FC' in l_environMap:
l_environMap['OMPI_FC'] = os.environ.get('FC', '')
for key, value in l_environMap.items():
if key in os.environ:
# we are assuming these are paths to be prepended
os.environ[key] = str(value) + os.pathsep + os.environ[key]
else:
os.environ[key] = str(value)
confirmGitVersion()
print ("Environment:\n")
print(" pwd = {cwd}".format(cwd=os.getcwd()))
print("")
for key in os.environ:
print(key + ' = ' + os.environ[key],
file=sys.stdout)
print("\n"+"="*90)
print(module('list'))
return None
################################################################################
### Helper functions to generate LD info using PLINK and the 1000G
### data provided with LocusZoom 1.4
import os
import sys
################################################################################
### MAGIC ENVIRONMENT MODULE STUFF
### Automatically load plink environment module when this module is loaded
if "LMOD_PACKAGE_PATH" in os.environ:
sys.path.insert(0,
os.path.join(os.environ["LMOD_PACKAGE_PATH"], "lmod/init"))
from env_modules_python import module
module('load', 'plink')
################################################################################
# LOCUSZOOM_1000G_DIR = "locuszoom-1.4/locuszoom/data/1000G/genotypes/2014-10-14" # EUR
################################################################################
def invoke_system(command_parameters):
cmd = ' '.join(command_parameters)
errcode = os.system(cmd)
if 0 != errcode:
raise Exception("ERROR: failed (returns {errcode}):".format(
errcode=errcode) + cmd + '\n')
def source_g5_modules(g5_modules, fout=None):
"""
#---------------------------------------------------------------------------
# def source_g5_modules(g5_modules, fout):
#
# source_g5_modules is a wrapper for the csh script g5_modules. It
# queries the csh script for basedir, modules and modinit, adds basedir
# to os.environ and loads library modules
#
# Input:
# g5_modules: full path of g5_modules
# fout: handle of (open) log file, if None - set to sys.stdout
#---------------------------------------------------------------------------
"""
if not fout: fout = sys.stdout
# check if g5_modules exists
# --------------------------
if not os.path.isfile(g5_modules):
raise Exception('g5_modules does not exist')
# part of the command to run
# --------------------------
cmd = ['/bin/csh', g5_modules]
# query for basedir
# -----------------
run = sp.Popen(cmd + ['basedir'], stdout=sp.PIPE, stderr=sp.PIPE)
output = run.communicate()
rtrnCode = run.wait()
if rtrnCode != 0:
print('0:')
print(output[0])
print('1:')
print(output[1])
raise Exception('cant query g5_modules for basedir')
#BASEDIR = output[0].strip()
BASEDIR = output[0].split('\n')[0].strip()
# query for modules to load
# -------------------------
run = sp.Popen(cmd + ['modules'], stdout=sp.PIPE, stderr=sp.PIPE)
output = run.communicate()
rtrnCode = run.wait()
if rtrnCode != 0:
print('0:')
print(output[0])
print('1:')
print(output[1])
raise Exception('cant query g5_modules for modules')
#MODULES = output[0].strip().split()
MODULES = output[0].split('\n')[0].strip().split()
#print("MATMAT MODULES: ", MODULES)
# query for modinit
# -----------------
run = sp.Popen(cmd + ['modinit'], stdout=sp.PIPE, stderr=sp.PIPE)
output = run.communicate()
rtrnCode = run.wait()
if rtrnCode != 0:
print('0:')
print(output[0])
print('1:')
print(output[1])
raise Exception('cant query g5_modules for modinit')
# MODINIT = output[0].strip().replace('csh', 'python')
# For Matt, modinit query results in '/usr/share/modules/init/csh\n/usr/..'
tmpdir = output[0].split('\n')[0].strip()
newdir = tmpdir.split('/')
HOST = get_hostname()
# MAT On anvil, at least, the modules has python.py
if HOST == 'PLEIADES' or HOST == 'DESKTOP':
newdir[-1] = 'python.py'
else:
newdir[-1] = 'python'
MODINIT = '/'.join(newdir)
# set BASEDIR
# -----------
ARCH = os.uname()[0]
writemsg(' %s: Setting BASEDIR' % os.path.basename(g5_modules), fout)
os.environ['BASEDIR'] = BASEDIR # this only modifies the local environment
BASELIB = '%s/%s/lib' % (BASEDIR, ARCH)
if 'LD_LIBRARY_PATH' in os.environ:
os.environ['LD_LIBRARY_PATH'] += os.pathsep + BASELIB
else:
os.environ['LD_LIBRARY_PATH'] = BASELIB
# load library modules
# --------------------
if (os.path.isfile(MODINIT)):
writemsg(' and modules.\n', fout)
exec(open(MODINIT).read())
module('purge')
for mod in MODULES:
module('load', mod)
# At NAS something weird is happening with python
# if you force it to load this at the end, things work
#if HOST=='PLEIADES':
#module('load','python/2.7.15')
#module('list')
elif os.environ.get('LMOD_PKG') is not None:
writemsg(' and modules.\n', fout)
sys.path.insert(0, os.path.join(os.environ['LMOD_PKG'], "init"))
from env_modules_python import module
module('purge')
for mod in MODULES:
module('load', mod)
else:
raise Exception('could not load required modules')
# set ESMA_FC to gfortran, if needed
# ----------------------------------
if BASEDIR.split(os.sep)[-1].split('_')[0] == 'gfortran':
writemsg(' Setting ESMA_FC to gfortran\n', fout)
os.environ['ESMA_FC'] = 'gfortran'
# set ESMA_FC to pgfortran, if needed
# -----------------------------------
if BASEDIR.split(os.sep)[-1].split('_')[0] == 'pgfortran':
writemsg(' Setting ESMA_FC to pgfortran\n', fout)
os.environ['ESMA_FC'] = 'pgfortran'
os.environ[
'PGI_LOCALRC'] = '/discover/swdev/mathomp4/PGILocalRC/linux86-64/17.10/bin/localrc.60300'
writemsg(' Setting PGI_LOCALRC to %s\n' % os.environ['PGI_LOCALRC'],
fout)
