Option("Q", "queue", "choice", "queue for scheduling", choices=["auto",]+sorted(load_queues())),
Option("N", "nodes", "int", "number of computing cluster nodes", default=2, min_value=1),
Option("P", "ppn", "int", "number of processors per node", default=8, min_value=1),
Option("W", "walltime", "float", "job-walltime in hours", default=1.0, min_value=0.1),
Option("M", "email", "str", "email-address for notifications"),
Option("D", "dryrun", "bool", "Only generates job-file, but does not submit it", default=False),
Option("S", "subdivide", "int", "number of parallel zgf_mdrun processes started within the job", min_value=1, default=1),
])
sys.modules[__name__].__doc__ += options_desc.epytext() # for epydoc
# reuse some options from zgf_mdrun
FORWARDED_ZGF_MDRUN_OPTIONS = ("seq", "npme", "reprod", "pd", "convtest", "auto-refines")
for x in FORWARDED_ZGF_MDRUN_OPTIONS:
options_desc.append(zgf_mdrun.options_desc[x])
def is_applicable():
pool = Pool()
return(len(pool.where("state=='mdrun-able'")) > 0)
#===============================================================================
def main():
options = options_desc.parse_args(sys.argv)[0]
assert(options.nodes % options.subdivide == 0)
joblines = ["#!/bin/bash"]
joblines += ["#PBS -N zgf_job", "#PBS -j oe",]
if(options.email):
import zgf_solvate_nodes
import zgf_grompp
#===============================================================================
options_desc = OptionsList([
Option("p", "np", "int", "Number of positive ions", default=0, min_value=0),
Option("P", "pname", "str", "Name of the positive ion", default="NA"),
Option("n", "nn", "int", "Number of negative ions", default=0, min_value=0),
Option("N", "nname", "str", "Name of the negative ion", default="CL"),
Option("s", "random-seed", "str", "Seed for random number generator", default="1993"),
])
# reuse option from zgf_solvate_nodes
options_desc.append(zgf_solvate_nodes.options_desc["grompp"])
sys.modules[__name__].__doc__ += options_desc.epytext() # for epydoc
def is_applicable():
pool = Pool()
return(len(pool.where("state == 'em-mdrun-able'")) > 0)
#===============================================================================
def main():
options = options_desc.parse_args(sys.argv)[0]
pool = Pool()
needy_nodes = pool.where("state == 'em-mdrun-able'")
assert(len(needy_nodes) == len(needy_nodes.multilock())) # make sure we lock ALL nodes
"bool",
"refine all not-converged nodes",
default=False),
Option("e",
"extend-all",
"bool",
"extend all not-converged nodes",
default=False),
])
# reuse some options from zgf_create_nodes
FORWARDED_ZGF_CREATE_NODES_OPTIONS = ("numnodes", "methodnodes",
"methodalphas", "methodphifit",
"random-seed")
for x in FORWARDED_ZGF_CREATE_NODES_OPTIONS:
options_desc.append(copy(
zgf_create_nodes.options_desc[x])) # need copy to safely ...
options_desc["numnodes"].default = 2 # ... change default values
sys.modules[__name__].__doc__ += options_desc.epytext() # for epydoc
def is_applicable():
pool = Pool()
return (len(pool.where("isa_partition and is_sampled")) > 0)
#===============================================================================
# This method is also called from zgf_mdrun
def main(argv=None):
if (argv == None):
argv = sys.argv
Option("S",
"subdivide",
"int",
"number of parallel zgf_mdrun processes started within the job",
min_value=1,
default=1),
Option("A", "account", "str", "account to be debited"),
])
sys.modules[__name__].__doc__ += options_desc.epytext() # for epydoc
# reuse some options from zgf_mdrun
FORWARDED_ZGF_MDRUN_OPTIONS = ("seq", "npme", "reprod", "pd", "convtest",
"auto-refines", "multistart")
for x in FORWARDED_ZGF_MDRUN_OPTIONS:
options_desc.append(zgf_mdrun.options_desc[x])
def is_applicable():
pool = Pool()
return (len(
pool.where(
"state in ('em-mdrun-able', 'mdrun-able', 'rerun-able-converged', 'rerun-able-not-converged')"
)) > 0)
#===============================================================================
def main():
options = options_desc.parse_args(sys.argv)[0]
assert (options.nodes % options.subdivide == 0)
import zgf_setup_nodes
import zgf_grompp
import zgf_cleanup
from copy import copy
import sys
options_desc = OptionsList([
Option("r", "refine-all", "bool", "refine all not-converged nodes", default=False),
Option("e", "extend-all", "bool", "extend all not-converged nodes", default=False),
])
# reuse some options from zgf_create_nodes
FORWARDED_ZGF_CREATE_NODES_OPTIONS = ("numnodes", "methodnodes", "methodalphas", "methodphifit", "random-seed")
for x in FORWARDED_ZGF_CREATE_NODES_OPTIONS:
options_desc.append(copy(zgf_create_nodes.options_desc[x])) # need copy to safely ...
options_desc["numnodes"].default = 2 # ... change default values
sys.modules[__name__].__doc__ += options_desc.epytext() # for epydoc
def is_applicable():
pool = Pool()
return(len(pool.where("isa_partition and is_sampled")) > 0)
#===============================================================================
# This method is also called from zgf_mdrun
def main(argv=None):
if(argv==None):
argv = sys.argv
options = options_desc.parse_args(argv)[0]
options_desc = OptionsList([
Option("p", "np", "int", "Number of positive ions", default=0,
min_value=0),
Option("P", "pname", "str", "Name of the positive ion", default="NA"),
Option("n", "nn", "int", "Number of negative ions", default=0,
min_value=0),
Option("N", "nname", "str", "Name of the negative ion", default="CL"),
Option("s",
"random-seed",
"str",
"Seed for random number generator",
default="1993"),
])
# reuse option from zgf_solvate_nodes
options_desc.append(zgf_solvate_nodes.options_desc["grompp"])
sys.modules[__name__].__doc__ += options_desc.epytext() # for epydoc
def is_applicable():
pool = Pool()
return (len(pool.where("state == 'em-mdrun-able'")) > 0)
#===============================================================================
def main():
options = options_desc.parse_args(sys.argv)[0]
pool = Pool()
needy_nodes = pool.where("state == 'em-mdrun-able'")
