def __init__(self):
SimQueue.__init__(self)
ProtocolInterface.__init__(self)
self._arg('ngpu',
'int',
'Number of GPUs',
default=0,
validator=Number(int, '0POS'))
self._arg('ncpu',
'int',
'Number of CPUs',
default=1,
validator=Number(int, '0POS'))
self._arg('memory',
'int',
'Amount of memory (MB)',
default=1000,
validator=Number(int, 'POS'))
self._arg('max_jobs',
'int',
'Maximum number of concurent jobs',
default=sys.maxsize,
validator=Number(int, 'POS'))
self._arg('token',
'str',
'PM token',
required=True,
validator=String())
self._arg('app', 'str', 'App name', required=True, validator=String())
self._dirs = {}
def __init__(self):
SimQueue.__init__(self)
ProtocolInterface.__init__(self)
self._arg(
"datadir",
"str",
"The path in which to store completed trajectories.",
None,
val.String(),
)
self._arg(
"trajext",
"str",
"Extension of trajectory files. This is needed to copy them to datadir.",
"xtc",
val.String(),
)
self._arg(
"copy",
"list",
"A list of file names or globs for the files to copy to datadir",
("*.xtc", ),
val.String(),
nargs="*",
)
self._cmdDeprecated("trajext", "copy")
self._states = dict()
self._queue = None
self._shutdown = False
def __init__(self,
_configapp=None,
_configfile=None,
_findExecutables=True,
_logger=True):
from playmolecule import Session, Job
SimQueue.__init__(self)
ProtocolInterface.__init__(self)
self._arg(
"parentjob",
"playmolecule.job.Job",
"Spawn all jobs as children of this job",
default=None,
required=False,
validator=val.Object(Job),
)
self._arg(
"session",
"playmolecule.session.Session",
"The current PMWS Session object",
required=True,
validator=val.Object(Session),
)
self._arg("jobname", "str", "Job name (identifier)", None,
val.String())
self._arg("group", "str", "Group name (identifier)", None,
val.String())
self._arg(
"ngpu",
"int",
"Number of GPUs",
default=0,
validator=val.Number(int, "0POS"),
)
self._arg(
"ncpu",
"int",
"Number of CPUs",
default=1,
validator=val.Number(int, "0POS"),
)
self._arg(
"memory",
"int",
"Amount of memory (MB)",
default=1000,
validator=val.Number(int, "POS"),
)
self._arg("app",
"str",
"App name",
required=True,
validator=val.String())
self._arg(
"configname",
"str",
"Name of the file containing the individual job configurations yaml or json. Not a filepath, just the name. All submitted folders must contain this file.",
None,
val.String(),
)
self._arg(
"retrievedir",
"str",
"Directory in which to retrieve the results of jobs",
None,
val.String(),
)
self._arg(
"datadir",
"str",
"Directory in which to copy or symlink the output directory.",
None,
val.String(),
)
self._arg(
"symlink",
"bool",
"Set to False to copy instead of symlink the directories from the retrievedir to datadir",
True,
val.Boolean(),
)
self._arg(
"copy",
"list",
"A list of file names or globs for the files to copy or symlink from retrievedir to datadir.",
("/", ),
val.String(),
nargs="*",
)
loadConfig(self, "playmolecule", _configfile, _configapp, _logger)
def __init__(self,
_configapp=None,
_configfile=None,
_findExecutables=True,
_logger=True):
SimQueue.__init__(self)
ProtocolInterface.__init__(self)
self._arg("jobname", "str", "Job name (identifier)", None,
val.String())
self._arg(
"queue",
"list",
"The queue or list of queues to run on. If list, it attempts to submit the job to "
"the first queue listed",
self._defaults["queue"],
val.String(),
nargs="*",
)
self._arg(
"ngpu",
"int",
"Number of GPUs to use for a single job",
self._defaults["ngpu"],
val.Number(int, "0POS"),
)
self._arg(
"ncpu",
"int",
"Number of CPUs to use for a single job",
self._defaults["ncpu"],
val.Number(int, "0POS"),
)
self._arg(
"memory",
"int",
"Amount of memory per job (MiB)",
self._defaults["memory"],
val.Number(int, "0POS"),
)
self._arg(
"walltime",
"int",
"Job timeout (hour:min or min)",
self._defaults["walltime"],
val.Number(int, "0POS"),
)
self._arg(
"pe",
"str",
"SGE Parallel Environment",
self._defaults["pe"],
val.String(),
)
self._arg(
"resources",
"list",
"Resources of the queue",
self._defaults["resources"],
val.String(),
nargs="*",
)
self._cmdDeprecated("environment", "prerun")
self._arg(
"outputstream",
"str",
"Output stream.",
"$REQUEST.oJID[.TASKID]",
val.String(),
)
self._arg(
"errorstream",
"str",
"Error stream.",
"$REQUEST.eJID[.TASKID]",
val.String(),
)
self._arg(
"datadir",
"str",
"The path in which to store completed trajectories.",
None,
val.String(),
)
self._arg(
"trajext",
"str",
"Extension of trajectory files. This is needed to copy them to datadir.",
"xtc",
val.String(),
)
self._arg(
"envvars",
"str",
"Envvars to propagate from submission node to the running node (comma-separated)",
self._defaults["envvars"],
val.String(),
)
self._arg(
"prerun",
"list",
"Shell commands to execute on the running node before the job (e.g. "
"loading modules)",
self._defaults["prerun"],
val.String(),
nargs="*",
)
# Load SGE configuration profile
loadConfig(self, "sge", _configfile, _configapp, _logger)
# Find executables
if _findExecutables:
self._qsubmit = SgeQueue._find_binary("qsub")
self._qinfo = SgeQueue._find_binary("qhost")
self._qcancel = SgeQueue._find_binary("qdel")
self._qstatus = SgeQueue._find_binary("qstat")
self._checkQueue()
def __init__(self,
_configapp=None,
_configfile=None,
_findExecutables=True,
_logger=True):
SimQueue.__init__(self)
ProtocolInterface.__init__(self)
self._arg(
"version",
"int",
"LSF major version",
self._defaults["version"],
valid_values=[9, 10],
)
self._arg("jobname", "str", "Job name (identifier)", None,
val.String())
self._arg(
"queue",
"list",
"The queue or list of queues to run on. If list, it attempts to submit the job to "
"the first queue listed",
self._defaults["queue"],
val.String(),
nargs="*",
)
self._arg("app", "str", "The application profile",
self._defaults["app"], val.String())
self._arg(
"ngpu",
"int",
"Number of GPUs to use for a single job",
self._defaults["ngpu"],
val.Number(int, "0POS"),
)
self._arg(
"gpu_options",
"dict",
"Number of GPUs to use for a single job",
self._defaults["gpu_options"],
val.Dictionary(
key_type=str,
valid_keys=["mode", "mps", "j_exclusive"],
value_type={
"mode": str,
"mps": str,
"j_exclusive": str
},
valid_values={
"mode": ["shared", "exclusive_process"],
"mps": ["yes", "no"],
"j_exclusive": ["yes", "no"],
},
),
)
self._arg(
"ncpu",
"int",
"Number of CPUs to use for a single job",
self._defaults["ncpu"],
val.Number(int, "0POS"),
)
self._arg(
"memory",
"int",
"Amount of memory per job (KB)",
self._defaults["memory"],
val.Number(int, "0POS"),
)
self._arg(
"walltime",
"int",
"Job timeout (hour:min or min)",
self._defaults["walltime"],
val.Number(int, "0POS"),
)
self._arg(
"resources",
"list",
"Resources of the queue",
self._defaults["resources"],
val.String(),
nargs="*",
)
self._cmdDeprecated("environment", "prerun")
self._arg("outputstream", "str", "Output stream.", "lsf.%J.out",
val.String())
self._arg("errorstream", "str", "Error stream.", "lsf.%J.err",
val.String())
self._arg(
"datadir",
"str",
"The path in which to store completed trajectories.",
None,
val.String(),
)
self._arg(
"trajext",
"str",
"Extension of trajectory files. This is needed to copy them to datadir.",
"xtc",
val.String(),
)
self._arg(
"envvars",
"str",
"Envvars to propagate from submission node to the running node (comma-separated)",
self._defaults["envvars"],
val.String(),
)
self._arg(
"prerun",
"list",
"Shell commands to execute on the running node before the job (e.g. "
"loading modules)",
self._defaults["prerun"],
val.String(),
nargs="*",
)
# Load LSF configuration profile
loadConfig(self, "lsf", _configfile, _configapp, _logger)
# Find executables
if _findExecutables:
self._qsubmit = LsfQueue._find_binary("bsub")
self._qinfo = LsfQueue._find_binary("bqueues")
self._qcancel = LsfQueue._find_binary("bkill")
self._qstatus = LsfQueue._find_binary("bjobs")
def __init__(
self, _configapp=None, _configfile=None, _findExecutables=True, _logger=True
):
SimQueue.__init__(self)
ProtocolInterface.__init__(self)
self._arg("jobname", "str", "Job name (identifier)", None, val.String())
self._arg(
"partition",
"str",
"The queue (partition) or list of queues to run on. If list, the one offering "
"earliest initiation will be used.",
self._defaults["partition"],
val.String(),
nargs="*",
)
self._arg(
"priority", "str", "Job priority", self._defaults["priority"], val.String()
)
self._arg(
"ngpu",
"int",
"Number of GPUs to use for a single job",
self._defaults["ngpu"],
val.Number(int, "0POS"),
)
self._arg(
"ncpu",
"int",
"Number of CPUs to use for a single job",
self._defaults["ncpu"],
val.Number(int, "POS"),
)
self._arg(
"memory",
"int",
"Amount of memory per job (MiB)",
self._defaults["memory"],
val.Number(int, "POS"),
)
self._arg(
"gpumemory",
"int",
"Only run on GPUs with at least this much memory. Needs special setup of SLURM. "
"Check how to define gpu_mem on SLURM.",
None,
val.Number(int, "0POS"),
)
self._arg(
"walltime",
"int",
"Job timeout (minutes)",
self._defaults["walltime"],
val.Number(int, "POS"),
)
self._cmdDeprecated("environment", "envvars")
self._arg(
"mailtype",
"str",
"When to send emails. Separate options with commas like 'END,FAIL'.",
None,
val.String(),
)
self._arg("mailuser", "str", "User email address.", None, val.String())
self._arg(
"outputstream", "str", "Output stream.", "slurm.%N.%j.out", val.String()
)
self._arg(
"errorstream", "str", "Error stream.", "slurm.%N.%j.err"
), val.String()
self._arg(
"datadir",
"str",
"The path in which to store completed trajectories.",
None,
val.String(),
)
self._arg(
"trajext",
"str",
"Extension of trajectory files. This is needed to copy them to datadir.",
"xtc",
val.String(),
)
self._arg(
"nodelist",
"list",
"A list of nodes on which to run every job at the *same time*! Careful! The jobs"
" will be duplicated!",
None,
val.String(),
nargs="*",
)
self._arg(
"exclude",
"list",
"A list of nodes on which *not* to run the jobs. Use this to select nodes on "
"which to allow the jobs to run on.",
None,
val.String(),
nargs="*",
)
self._arg(
"envvars",
"str",
"Envvars to propagate from submission node to the running node (comma-separated)",
self._defaults["envvars"],
val.String(),
)
self._arg(
"prerun",
"list",
"Shell commands to execute on the running node before the job (e.g. "
"loading modules)",
self._defaults["prerun"],
val.String(),
nargs="*",
)
self._arg(
"account",
"str",
"Charge resources used by the jobs to specified account.",
None,
val.String(),
)
self._arg(
"user",
"str",
"The SLURM user submitting and managing jobs",
getpass.getuser(),
val.String(),
)
# Load Slurm configuration profile
loadConfig(self, "slurm", _configfile, _configapp, _logger)
# Find executables
if _findExecutables:
self._qsubmit = SlurmQueue._find_binary("sbatch")
self._qinfo = SlurmQueue._find_binary("sinfo")
self._qcancel = SlurmQueue._find_binary("scancel")
self._qstatus = SlurmQueue._find_binary("squeue")
self._qjobinfo = SlurmQueue._find_binary("sacct")
self._checkQueue()