def run_res (iter_index,
json_file,
exec_machine = MachineLocal) :
fp = open (json_file, 'r')
jdata = json.load (fp)
gmx_prep = jdata["gmx_prep"]
gmx_run = jdata["gmx_run"]
res_thread = jdata["res_thread"]
gmx_run = gmx_run + (" -nt %d " % res_thread)
gmx_run = gmx_run + " -plumed " + res_plm
gmx_cont_run = gmx_run + " -cpi state.cpt "
gmx_prep_log = "gmx_grompp.log"
gmx_run_log = "gmx_mdrun.log"
gmx_prep_cmd = cmd_append_log (gmx_prep, gmx_prep_log)
gmx_run_cmd = cmd_append_log (gmx_run, gmx_run_log)
gmx_cont_run_cmd = cmd_append_log (gmx_cont_run, gmx_run_log)
res_group_size = jdata['res_group_size']
batch_jobs = jdata['batch_jobs']
batch_time_limit = jdata['batch_time_limit']
batch_modules = jdata['batch_modules']
batch_sources = jdata['batch_sources']
iter_name = make_iter_name (iter_index)
res_path = iter_name + "/" + res_name + "/"
base_path = os.getcwd() + "/"
if not os.path.isdir (res_path) :
raise RuntimeError ("do not see any restrained simulation (%s)." % res_path)
all_task_propose = glob.glob(res_path + "/[0-9]*[0-9]")
if len(all_task_propose) == 0 :
return
all_task_propose.sort()
if batch_jobs :
all_task = all_task_propose
else :
all_task = []
all_cont_task = []
for ii in all_task_propose :
if not os.path.isfile(os.path.join(ii, "confout.gro")) :
if os.path.isfile(os.path.join(ii, "state.cpt")) :
all_cont_task.append(ii)
else :
all_task.append(ii)
if batch_jobs:
exec_hosts (MachineLocal, gmx_prep_cmd, 1, all_task, None)
exec_batch_group(gmx_run_cmd, res_thread, 1, all_task, task_args = None, group_size = res_group_size, time_limit = batch_time_limit, modules = batch_modules, sources = batch_sources)
else :
if len(all_task) == 1 :
exec_hosts (MachineLocal, gmx_prep_cmd, 1, all_task, None)
exec_hosts (MachineLocal, gmx_run_cmd, res_thread, all_task, None)
elif len(all_task) > 1 :
exec_hosts (MachineLocal, gmx_prep_cmd, 1, all_task, None)
exec_hosts_batch (exec_machine, gmx_run_cmd, res_thread, all_task, None)
if len(all_cont_task) == 1 :
exec_hosts (MachineLocal, gmx_cont_run_cmd, res_thread, all_cont_task, None)
elif len(all_cont_task) > 1 :
exec_hosts_batch (exec_machine, gmx_cont_run_cmd, res_thread, all_cont_task, None)
def run_res(iter_index, json_file, exec_machine=MachineLocal):
fp = open(json_file, 'r')
jdata = json.load(fp)
cmd_env = jdata.get("cmd_sources", [])
sits_param = jdata.get("sits_settings", None)
gmx_prep = jdata["gmx_prep"]
bPosre = jdata.get("gmx_posre", False)
if sits_param is not None:
if not bPosre:
gmx_prep += " -f grompp_sits.mdp"
else:
gmx_prep += " -f grompp_sits_restraint.mdp -r conf_init.gro"
if sits_param.get("sits_energrp", None) not in ["Protein", "MOL"]:
gmx_prep += " -n index.ndx"
gmx_run = jdata["gmx_run"]
res_thread = jdata["res_thread"]
gmx_run = gmx_run + (" -nt %d " % res_thread)
gmx_run = gmx_run + " -plumed " + res_plm
gmx_cont_run = gmx_run + " -cpi state.cpt "
gmx_prep_log = "gmx_grompp.log"
gmx_run_log = "gmx_mdrun.log"
gmx_prep_cmd = cmd_append_log(gmx_prep, gmx_prep_log, env=cmd_env)
gmx_run_cmd = cmd_append_log(gmx_run, gmx_run_log, env=cmd_env)
gmx_cont_run_cmd = cmd_append_log(gmx_cont_run, gmx_run_log, env=cmd_env)
res_group_size = jdata['res_group_size']
batch_jobs = jdata['batch_jobs']
batch_time_limit = jdata['batch_time_limit']
batch_modules = jdata['batch_modules']
batch_sources = jdata['batch_sources']
iter_name = make_iter_name(iter_index)
res_path = iter_name + "/" + res_name + "/"
base_path = os.getcwd() + "/"
if not os.path.isdir(res_path):
raise RuntimeError("do not see any restrained simulation (%s)." %
res_path)
# all_task_propose = glob.glob(res_path + "/[0-9]*[0-9]")
# assume that
# TODO
all_task_propose = list(
filter(lambda x: os.path.isdir(x),
glob.glob(res_path + "/[0-9]*[0-9]")))
# print('lib.modeling.run_res:all_task_propose:', all_task)
# print('lib.modeling.run_res:gmx_prep_cmd:', gmx_prep_cmd)
# print('lib.modeling.run_res:gmx_run_cmd:', gmx_run_cmd)
# print('lib.modeling.run_res:gmx_cont_run_cmd:', gmx_cont_run_cmd)
# raise RuntimeError('lib.modeling.run_res:debug')
if len(all_task_propose) == 0:
return
all_task_propose.sort()
if batch_jobs:
all_task = all_task_propose
else:
all_task = []
all_cont_task = []
for ii in all_task_propose:
if not os.path.isfile(os.path.join(ii, "confout.gro")):
if os.path.isfile(os.path.join(ii, "state.cpt")):
all_cont_task.append(ii)
else:
all_task.append(ii)
# if len(all_task) == 0:
# return None
# all_task.sort()
# all_task_basedir = [os.path.relpath(ii, res_path) for ii in all_task]
# lazy_local_context = LazyLocalContext(local_root='./', work_profile=None)
# slurm = Slurm(context=lazy_local_context)
# # pbs = PBS(context=lazy_local_context)
# gmx_prep_task = [Task(command=gmx_prep_cmd, task_work_path=ii, outlog='gmx_grompp.log', errlog='gmx_grompp.err') for
# ii in all_task_basedir]
# gmx_prep_submission = Submission(work_base=res_path, resources=res_resources, batch=slurm, task_list=gmx_prep_task)
# gmx_prep_submission.run_submission()
# gmx_run_task = [Task(command=gmx_run_cmd, task_work_path=ii, outlog='gmx_mdrun.log', errlog='gmx_mdrun.log') for ii
# in all_task_basedir]
# gmx_run_submission = Submission(work_base=res_path, resources=res_resources, batch=slurm, task_list=gmx_run_task)
# gmx_run_submission.run_submission()
if batch_jobs:
exec_hosts(MachineLocal, gmx_prep_cmd, 1, all_task, None)
exec_batch_group(gmx_run_cmd,
res_thread,
1,
all_task,
task_args=None,
group_size=res_group_size,
time_limit=batch_time_limit,
modules=batch_modules,
sources=batch_sources)
else:
if len(all_task) == 1:
exec_hosts(MachineLocal, gmx_prep_cmd, 1, all_task, None)
exec_hosts(MachineLocal, gmx_run_cmd, res_thread, all_task, None)
elif len(all_task) > 1:
exec_hosts(MachineLocal, gmx_prep_cmd, 1, all_task, None)
exec_hosts_batch(exec_machine, gmx_run_cmd, res_thread, all_task,
None)
if len(all_cont_task) == 1:
exec_hosts(MachineLocal, gmx_cont_run_cmd, res_thread,
all_cont_task, None)
elif len(all_cont_task) > 1:
exec_hosts_batch(exec_machine, gmx_cont_run_cmd, res_thread,
all_cont_task, None)