def _bind_to_resource(self, resource_key):
"""(PRIVATE) Implements parent class method.
"""
if resource_key not in _KERNEL_INFO["machine_configs"]:
if "*" in _KERNEL_INFO["machine_configs"]:
# Fall-back to generic resource key
resource_key = "*"
else:
raise NoKernelConfigurationError(
kernel_name=_KERNEL_INFO["name"],
resource_key=resource_key)
cfg = _KERNEL_INFO["machine_configs"][resource_key]
arguments = [
'-f', '{0}'.format(self.get_arg("--mdp=")), '-c',
'{0}'.format(self.get_arg("--gro=")), '-p',
'{0}'.format(self.get_arg("--top=")), '-o',
'{0}'.format(self.get_arg("--tpr="))
]
if self.get_arg("--ref=") is not None:
arguments += ['-r', '{0}'.format(self.get_arg("--ref="))]
self._executable = cfg['executable']
self._arguments = arguments
self._environment = cfg["environment"]
self._uses_mpi = cfg["uses_mpi"]
self._pre_exec = cfg["pre_exec"]
def _bind_to_resource(self, resource_key):
"""(PRIVATE) Implements parent class method.
"""
if resource_key not in _KERNEL_INFO["machine_configs"]:
if "*" in _KERNEL_INFO["machine_configs"]:
# Fall-back to generic resource key
resource_key = "*"
else:
raise NoKernelConfigurationError(
kernel_name=_KERNEL_INFO["name"],
resource_key=resource_key)
cfg = _KERNEL_INFO["machine_configs"][resource_key]
executable = cfg["executable"]
arguments = [
'--grid', '{0}'.format(self.get_arg("--grid=")), '--dims',
'{0}'.format(self.get_arg("--dims=")), '--frontpoints',
'{0}'.format(self.get_arg("--frontpoints=")), '--topfile',
'{0}'.format(self.get_arg("--topfile=")), '--mdfile',
'{0}'.format(self.get_arg("--mdfile=")), '--output', '{0}'.format(
self.get_arg("--output=")), '--logfile', 'coco.log', '--mpi',
'--selection', '{0}'.format(self.get_arg("--atom_selection="))
]
self._executable = executable
self._arguments = arguments
self._environment = cfg["environment"]
self._uses_mpi = cfg["uses_mpi"]
self._pre_exec = cfg["pre_exec"]
def _bind_to_resource(self, resource_key):
"""(PRIVATE) Implements parent class method.
"""
if resource_key not in _KERNEL_INFO["machine_configs"]:
if "*" in _KERNEL_INFO["machine_configs"]:
# Fall-back to generic resource key
resource_key = "*"
else:
raise NoKernelConfigurationError(
kernel_name=_KERNEL_INFO["name"],
resource_key=resource_key)
cfg = _KERNEL_INFO["machine_configs"][resource_key]
executable = cfg["executable"]
arguments = [
'postexec.py', '{0}'.format(self.get_arg("--numofsims=")),
'{0}'.format(self.get_arg("--cycle="))
]
self._executable = executable
self._arguments = arguments
self._environment = cfg["environment"]
self._uses_mpi = cfg["uses_mpi"]
self._pre_exec = cfg["pre_exec"]
self._post_exec = None
def _bind_to_resource(self, resource_key):
"""(PRIVATE) Implements parent class method.
"""
if resource_key not in _KERNEL_INFO["machine_configs"]:
if "*" in _KERNEL_INFO["machine_configs"]:
# Fall-back to generic resource key
resource_key = "*"
else:
raise NoKernelConfigurationError(
kernel_name=_KERNEL_INFO["name"],
resource_key=resource_key)
cfg = _KERNEL_INFO["machine_configs"][resource_key]
executable = "/bin/bash"
arguments = [
'-l', '-c',
'diff -U 0 {input1} {input2} | grep ^@ | wc -l > {output}'.format(
input1=self.get_arg("--inputfile1="),
input2=self.get_arg("--inputfile2="),
output=self.get_arg("--outputfile="))
]
self._executable = executable
self._arguments = arguments
self._environment = cfg["environment"]
self._uses_mpi = cfg["uses_mpi"]
self._pre_exec = None
def _bind_to_resource(self, resource_key):
"""(PRIVATE) Implements parent class method.
"""
if resource_key not in _KERNEL_INFO["machine_configs"]:
if "*" in _KERNEL_INFO["machine_configs"]:
# Fall-back to generic resource key
resource_key = "*"
else:
raise NoKernelConfigurationError(
kernel_name=_KERNEL_INFO["name"],
resource_key=resource_key)
cfg = _KERNEL_INFO["machine_configs"][resource_key]
executable = "/bin/bash"
arguments = [
'-l', '-c', '{0} /dev/urandom | head -c {1} > {2}'.format(
cfg["executable"], self.get_arg("--size="),
self.get_arg("--filename="))
]
self._executable = executable
self._arguments = arguments
self._environment = cfg["environment"]
self._uses_mpi = cfg["uses_mpi"]
self._pre_exec = cfg["pre_exec"]
def _bind_to_resource(self, resource_key):
"""(PRIVATE) Implements parent class method.
"""
if resource_key not in _KERNEL_INFO["machine_configs"]:
if "*" in _KERNEL_INFO["machine_configs"]:
# Fall-back to generic resource key
resource_key = "*"
else:
raise NoKernelConfigurationError(
kernel_name=_KERNEL_INFO["name"],
resource_key=resource_key)
cfg = _KERNEL_INFO["machine_configs"][resource_key]
arguments = [
'post_analyze.py', '{0}'.format(self.get_arg("--num_runs=")),
'tmpha.ev', 'ncopies.nc', 'tmp.gro', 'out.nn', 'weight.w',
'{0}'.format(self.get_arg("--out=")),
'{0}'.format(self.get_arg("--max_alive_neighbors=")),
'{0}'.format(self.get_arg("--max_dead_neighbors=")), 'input.gro',
'{0}'.format(self.get_arg("--cycle="))
]
self._executable = cfg["executable"]
self._arguments = arguments
self._environment = cfg["environment"]
self._uses_mpi = cfg["uses_mpi"]
self._pre_exec = cfg["pre_exec"]
def _bind_to_resource(self, resource_key):
if resource_key not in _KERNEL_INFO["machine_configs"]:
if "*" in _KERNEL_INFO["machine_configs"]:
# Fall-back to generic resource key
resource_key = "*"
else:
raise NoKernelConfigurationError(
kernel_name=_KERNEL_INFO["name"],
resource_key=resource_key)
cfg = _KERNEL_INFO["machine_configs"][resource_key]
#change to pmemd.MPI by splitting into two kernels
arguments = [
'{0}'.format(self.get_arg("--script=")), '--imagepath',
'{0}'.format(self.get_arg("--imagepath=")), '--trainingpath',
'{0}'.format(self.get_arg("--trainingpath=")), '--num_train',
'{0}'.format(self.get_arg("--num_train=")), '--icetypes',
'{0}'.format(self.get_arg("--icetypes="))
]
self._executable = cfg["executable"]
self._arguments = arguments
self._environment = cfg["environment"]
self._uses_mpi = cfg["uses_mpi"]
self._pre_exec = cfg["pre_exec"]
def _bind_to_resource(self, resource_key):
"""(PRIVATE) Implements parent class method.
"""
if resource_key not in _KERNEL_INFO["machine_configs"]:
if "*" in _KERNEL_INFO["machine_configs"]:
# Fall-back to generic resource key
resource_key = "*"
else:
raise NoKernelConfigurationError(
kernel_name=_KERNEL_INFO["name"],
resource_key=resource_key)
cfg = _KERNEL_INFO["machine_configs"][resource_key]
#change to pmemd.MPI when cores can be set
arguments = [
'run.py', '--mdp',
'%s' % self.get_arg("--grompp="), '--gro', 'start.gro', '--top',
'%s' % self.get_arg('--topol='), '--out', 'out.gro'
]
self._executable = cfg["executable"]
self._arguments = arguments
self._environment = cfg["environment"]
self._uses_mpi = cfg["uses_mpi"]
self._pre_exec = cfg["pre_exec"]
def _bind_to_resource(self, resource_key):
"""(PRIVATE) Implements parent class method.
"""
if resource_key not in _KERNEL_INFO["machine_configs"]:
if "*" in _KERNEL_INFO["machine_configs"]:
# Fall-back to generic resource key
resource_key = "*"
else:
raise NoKernelConfigurationError(
kernel_name=_KERNEL_INFO["name"],
resource_key=resource_key)
cfg = _KERNEL_INFO["machine_configs"][resource_key]
arguments = [
'-nt', '{0}'.format(self.get_arg("--size=")), '-s',
'{0}'.format(self.get_arg('--tpr=')), '-c',
'{0}'.format(self.get_arg('--out='))
]
if self.get_arg('--trr=') is not None:
arguments.extend(['-o', '{0}'.format(self.get_arg('--trr='))])
if self.get_arg('--edr=') is not None:
arguments.extend(['-e', '{0}'.format(self.get_arg('--edr='))])
self._executable = cfg["executable"]
self._arguments = arguments
self._environment = cfg["environment"]
self._uses_mpi = cfg["uses_mpi"]
self._pre_exec = cfg["pre_exec"]
self._post_exec = None
def _bind_to_resource(self, resource_key):
"""(PRIVATE) Implements parent class method.
"""
if resource_key not in _KERNEL_INFO["machine_configs"]:
if "*" in _KERNEL_INFO["machine_configs"]:
# Fall-back to generic resource key
resource_key = "*"
else:
raise NoKernelConfigurationError(
kernel_name=_KERNEL_INFO["name"],
resource_key=resource_key)
cfg = _KERNEL_INFO["machine_configs"][resource_key]
executable = cfg['executable']
arguments = [
'-l', '-c', "/bin/cat {1} >> {0}".format(self.get_arg("--file1="),
self.get_arg("--file2="))
]
self._executable = executable
self._arguments = arguments
self._environment = cfg["environment"]
self._uses_mpi = cfg["uses_mpi"]
self._pre_exec = None
def _bind_to_resource(self, resource_key):
"""(PRIVATE) Implements parent class method.
"""
if resource_key not in _KERNEL_INFO["machine_configs"]:
if "*" in _KERNEL_INFO["machine_configs"]:
# Fall-back to generic resource key
resource_key = "*"
else:
raise NoKernelConfigurationError(
kernel_name=_KERNEL_INFO["name"],
resource_key=resource_key)
cfg = _KERNEL_INFO["machine_configs"][resource_key]
arguments = [
'-l', '-c',
'echo {0} | gmx trjconv -f {1} -o {3} -s {2} -pbc {4}'.format(
self.get_arg("--echo="), self.get_arg("--f="),
self.get_arg("--s="), self.get_arg("--o="),
self.get_arg("--pbc="))
]
self._executable = cfg['executable']
self._arguments = arguments
self._environment = cfg["environment"]
self._uses_mpi = cfg["uses_mpi"]
self._pre_exec = cfg["pre_exec"]
def _bind_to_resource(self, resource_key):
"""(PRIVATE) Implements parent class method.
"""
if resource_key not in _KERNEL_INFO["machine_configs"]:
if "*" in _KERNEL_INFO["machine_configs"]:
# Fall-back to generic resource key
resource_key = "*"
else:
raise NoKernelConfigurationError(kernel_name=_KERNEL_INFO["name"], \
resource_key=resource_key)
cfg = _KERNEL_INFO["machine_configs"][resource_key]
if self._subname == None:
arguments = [
self.get_arg("--calculator="),
self.get_arg("--replica_id="),
self.get_arg("--replica_cycle="),
self.get_arg("--replicas="),
self.get_arg("--replica_basename=")
]
self._executable = cfg["executable"]
self._arguments = arguments
self._environment = cfg["environment"]
self._uses_mpi = cfg["uses_mpi"]
self._pre_exec = cfg["pre_exec"]
self._post_exec = None
elif self._subname == "matrix_calculator_temp_ex":
arguments = [
self.get_arg("--calculator="),
self.get_arg("--replica_id="),
self.get_arg("--replica_cycle="),
self.get_arg("--replicas="),
self.get_arg("--replica_basename="),
self.get_arg("--new_temperature=")
]
self._executable = cfg["executable"]
self._arguments = arguments
self._environment = cfg["environment"]
self._uses_mpi = cfg["uses_mpi"]
self._pre_exec = cfg["pre_exec"]
self._post_exec = None
elif self._subname == "global_ex_calculator":
arguments = [
self.get_arg("--calculator="),
self.get_arg("--replica_cycle="),
self.get_arg("--replicas="),
self.get_arg("--replica_basename=")
]
self._executable = cfg["executable"]
self._arguments = arguments
self._environment = cfg["environment"]
self._uses_mpi = True
self._pre_exec = cfg["pre_exec"]
self._post_exec = None
def _bind_to_resource(self, resource_key):
"""(PRIVATE) Implements parent class method.
"""
if resource_key not in _KERNEL_INFO["machine_configs"]:
if "*" in _KERNEL_INFO["machine_configs"]:
# Fall-back to generic resource key
resource_key = "*"
else:
raise NoKernelConfigurationError(
kernel_name=_KERNEL_INFO["name"],
resource_key=resource_key)
cfg = _KERNEL_INFO["machine_configs"][resource_key]
self._executable = cfg["executable"]
self._arguments = self.get_raw_args()
self._environment = cfg["environment"]
self._uses_mpi = cfg["uses_mpi"]
self._pre_exec = cfg["pre_exec"]
def _bind_to_resource(self, resource_key):
"""(PRIVATE) Implements parent class method.
"""
if resource_key not in _KERNEL_INFO["machine_configs"]:
if "*" in _KERNEL_INFO["machine_configs"]:
# Fall-back to generic resource key
resource_key = "*"
else:
raise NoKernelConfigurationError(kernel_name=_KERNEL_INFO["name"], resource_key=resource_key)
cfg = _KERNEL_INFO["machine_configs"][resource_key]
arguments = ['-f','{0}'.format(self.get_arg("--config=")),'-c','tmpha.gro','-n','out.nn','-w','weight.w']
self._executable = cfg["executable"]
self._arguments = arguments
self._environment = cfg["environment"]
self._uses_mpi = cfg["uses_mpi"]
self._pre_exec = cfg["pre_exec"]
def _bind_to_resource(self, resource_key):
"""(PRIVATE) Implements parent class method.
"""
if resource_key not in _KERNEL_INFO["machine_configs"]:
if "*" in _KERNEL_INFO["machine_configs"]:
# Fall-back to generic resource key
resource_key = "*"
else:
raise NoKernelConfigurationError(
kernel_name=_KERNEL_INFO["name"],
resource_key=resource_key)
cfg = _KERNEL_INFO["machine_configs"][resource_key]
arguments = [
'-m',
'{0}'.format(self.get_arg('--mode=')),
'-f',
'{0}'.format(self.get_arg('--flops=')),
'-s',
'{0}'.format(self.get_arg('--samples=')),
]
if self.get_arg('--input=') is not None:
arguments.extend('-i', '{0}'.format(self.get_arg('--input=')))
if self.get_arg('--output=') is not None:
arguments.extend('-o', '{0}'.format(self.get_arg('--output=')))
if self.get_arg('--memory=') is not None:
arguments.extend('-r', '{0}'.format(self.get_arg('--memory=')))
self._pre_exec = [
'export PYTHONPATH={0}/lib/python2.7/site-packages'.format(
self.get_arg("--path=")),
'export PATH=$PATH:{0}/bin'.format(self.get_arg("--path=")),
]
self._executable = cfg['executable']
self._arguments = arguments
self._environment = cfg["environment"]
self._uses_mpi = cfg["uses_mpi"]
self._post_exec = None
def _bind_to_resource(self, resource_key):
"""(PRIVATE) Implements parent class method.
"""
if resource_key not in _KERNEL_INFO["machine_configs"]:
if "*" in _KERNEL_INFO["machine_configs"]:
# Fall-back to generic resource key
resource_key = "*"
else:
raise NoKernelConfigurationError(kernel_name=_KERNEL_INFO["name"], resource_key=resource_key)
cfg = _KERNEL_INFO["machine_configs"][resource_key]
arguments = ['-l', '-c', 'python levenshtein.py {0} {1} > {2}'.format(
self.get_arg("--inputfile1="),
self.get_arg("--inputfile2="),
self.get_arg("--outputfile="))
]
self._executable = cfg["executable"]
self._arguments = arguments
self._environment = cfg["environment"]
self._uses_mpi = cfg["uses_mpi"]
self._pre_exec = cfg["pre_exec"]
def _bind_to_resource(self, resource_key, pattern_name=None):
"""(PRIVATE) Implements parent class method.
"""
if (pattern_name == None):
if resource_key not in _KERNEL_INFO["machine_configs"]:
if "*" in _KERNEL_INFO["machine_configs"]:
# Fall-back to generic resource key
resource_key = "*"
else:
raise NoKernelConfigurationError(
kernel_name=_KERNEL_INFO["name"],
resource_key=resource_key)
cfg = _KERNEL_INFO["machine_configs"][resource_key]
#change to pmemd.MPI by splitting into two kernels
if self.get_arg("--mininfile=") is not None:
arguments = [
'-O', '-i',
self.get_arg("--mininfile="), '-o',
'min%s.out' % self.get_arg("--cycle="), '-inf',
'min%s.inf' % self.get_arg("--cycle="), '-r',
'md%s.crd' % self.get_arg("--cycle="), '-p',
self.get_arg("--topfile="), '-c',
self.get_arg("--crdfile="), '-ref',
'min%s.crd' % self.get_arg("--cycle=")
]
else:
arguments = [
'-O',
'-i',
self.get_arg("--mdinfile="),
'-o',
'md%s.out' % self.get_arg("--cycle="),
'-inf',
'md%s.inf' % self.get_arg("--cycle="),
'-x',
'md%s.ncdf' % self.get_arg("--cycle="),
'-r',
'md%s.rst' % self.get_arg("--cycle="),
'-p',
self.get_arg("--topfile="),
'-c',
'md%s.crd' % self.get_arg("--cycle="),
]
self._executable = cfg["executable"]
self._arguments = arguments
self._environment = cfg["environment"]
self._uses_mpi = False
self._pre_exec = cfg["pre_exec"]
#-----------------------------------------------------------------------
# below only for RE
elif (pattern_name == 'ReplicaExchange'):
# if (pattern_name == None):
cfg = _KERNEL_INFO["machine_configs"][resource_key]
if resource_key not in _KERNEL_INFO["machine_configs"]:
if "*" in _KERNEL_INFO["machine_configs"]:
# Fall-back to generic resource key
resource_key = "*"
else:
raise NoKernelConfigurationError(kernel_name=KERNEL_INFO["name"], \
resource_key=resource_key)
cfg = _KERNEL_INFO["machine_configs"][resource_key]
if self._uses_mpi:
self._executable = cfg["executable"] + ".MPI"
else:
self._executable = cfg["executable"]
# by default MPI is false
self._uses_mpi = cfg["uses_mpi"]
self._arguments = [
"-O ", "-i ",
self.get_arg("--mdinfile="), "-o ",
self.get_arg("--outfile="), "-p ",
self.get_arg("--params="), "-c ",
self.get_arg("--coords="), "-r ",
self.get_arg("--nwcoords="), "-x ",
self.get_arg("--nwtraj="), "-inf ",
self.get_arg("--nwinfo=")
]
self._environment = cfg["environment"]
if not self._pre_exec:
self._pre_exec = cfg["pre_exec"]
else:
self._pre_exec = self._pre_exec + cfg["pre_exec"]
def test_NoKernelConfigurationError(self):
from radical.ensemblemd.exceptions import NoKernelConfigurationError
_KERNEL_INFO = {
"name": "misc.ccount",
"description": "Counts the character frequency in an ASCII file.",
"machine_configs": {
"*": {
"environment": None,
"pre_exec": None,
"executable": "uniq",
"uses_mpi": False
}
}
}
resource_key = "random"
if resource_key not in _KERNEL_INFO["machine_configs"]:
if "hi" in _KERNEL_INFO["machine_configs"]:
resource_key = "*"
else:
assert "Kernel 'misc.ccount' doesn not have a configuration entry for resource key 'random'." in NoKernelConfigurationError(
kernel_name=_KERNEL_INFO["name"],
resource_key=resource_key)