def run_phonon(task_type, jdata, mdata):
user = ('user_incar' in jdata.keys())
work_path = util.make_work_path(jdata, '06.phonon', False, False, user)
all_task = glob.glob(os.path.join(work_path, '.'))
#vasp
if task_type == "vasp":
mdata = decide_fp_machine(mdata)
machine, machine_type, ssh_sess, resources, command, group_size = util.get_machine_info(
mdata, task_type)
run_tasks = util.collect_task(all_task, task_type)
forward_files = ['INCAR', 'POTCAR', 'KPOINTS']
backward_files = ['OUTCAR', 'OSZICAR', 'vasprun.xml']
common_files = ['POSCAR']
_run(machine, machine_type, ssh_sess, resources, command, work_path,
run_tasks, group_size, common_files, forward_files,
backward_files)
#lammps
elif task_type in lammps_task_type:
None
else:
raise RuntimeError("unknow task %s, something wrong" % task_type)
def run_phonon(task_type,jdata,mdata):
user= ('user_incar' in jdata.keys())
work_path=util.make_work_path(jdata,'06.phonon',False,False,user)
all_task = glob.glob(os.path.join(work_path,'.'))
#vasp
if task_type == "vasp":
mdata=decide_fp_machine(mdata)
machine,resources,command,group_size=util.get_machine_info(mdata,task_type)
run_tasks = util.collect_task(all_task,task_type)
forward_files = ['INCAR', 'POTCAR','KPOINTS','KPOINTS']
backward_files = ['OUTCAR', task_type+'.out' , 'OSZICAR','vasprun.xml']
common_files=['POSCAR']
if ('cvasp' in jdata) and (jdata['cvasp'] == True):
mdata['fp_resources']['cvasp'] = True
forward_files.append('cvasp.py')
disp = make_dispatcher(machine, resources, work_path, run_tasks, group_size)
disp.run_jobs(resources,
command,
work_path,
run_tasks,
group_size,
common_files,
forward_files,
backward_files,
outlog=task_type+'.out',
errlog=task_type+'.err')
#lammps
elif task_type in lammps_task_type:
None
else:
raise RuntimeError ("unknown task %s, something wrong" % task_type)
def run_equi(task_type,jdata,mdata):
#rmprint("This module has been run !")
work_path=util.make_work_path(jdata,'00.equi',False,False,False)
all_task = glob.glob(os.path.join(work_path,'.'))
#vasp
if task_type=="vasp":
mdata=decide_fp_machine(mdata)
forward_files = ['INCAR', 'POTCAR', 'KPOINTS']
if ('cvasp' in jdata) and (jdata['cvasp'] == True):
mdata['fp_resources']['cvasp'] = True
forward_files.append('cvasp.py')
backward_files = ['OUTCAR', task_type+'.out' , 'CONTCAR','OSZICAR']
common_files=['POSCAR']
#lammps
elif task_type in lammps_task_type:
mdata = decide_model_devi_machine(mdata)
forward_files = ['conf.lmp', 'lammps.in']
backward_files = ['dump.relax','log.lammps', task_type+'.out']
fp_params = jdata['lammps_params']
model_dir = fp_params['model_dir']
model_dir = os.path.abspath(model_dir)
model_name =fp_params['model_name']
if not model_name :
models = glob.glob(os.path.join(model_dir, '*pb'))
model_name = [os.path.basename(ii) for ii in models]
else:
models = [os.path.join(model_dir,ii) for ii in model_name]
common_files = model_name
if len(model_name)>1 and task_type == 'deepmd':
backward_files = backward_files + ['model_devi.out']
else:
raise RuntimeError ("unknow task %s, something wrong" % task_type)
run_tasks = util.collect_task(all_task,task_type)
if len(run_tasks)==0: return
machine,resources,command,group_size=util.get_machine_info(mdata,task_type)
disp = make_dispatcher(machine, resources, work_path, run_tasks, group_size)
#debug#
#print(' '.join(common_files))
#print(' '.join(forward_files))
#print(' '.join(backward_files))
disp.run_jobs(resources,
command,
work_path,
run_tasks,
group_size,
common_files,
forward_files,
backward_files,
outlog=task_type+'.out',
errlog=task_type+'.err')
def run_surf(task_type,jdata,mdata):
static=jdata['static-opt']
work_path=util.make_work_path(jdata,'05.surf',False,static,False)
all_task = glob.glob(os.path.join(work_path,'struct-*'))
#vasp
if task_type == "vasp":
mdata=decide_fp_machine(mdata)
forward_files = ['INCAR', 'POSCAR','POTCAR','KPOINTS']
backward_files = ['OUTCAR', task_type+'.out' , 'OSZICAR']
common_files=['INCAR','POTCAR']
if ('cvasp' in jdata) and (jdata['cvasp'] == True):
mdata['fp_resources']['cvasp'] = True
forward_files.append('cvasp.py')
#lammps
elif task_type in lammps_task_type:
mdata = decide_model_devi_machine(mdata)
fp_params = jdata['lammps_params']
model_dir = fp_params['model_dir']
model_dir = os.path.abspath(model_dir)
model_name =fp_params['model_name']
if not model_name :
models = glob.glob(os.path.join(model_dir, '*pb'))
model_name = [os.path.basename(ii) for ii in models]
else:
models = [os.path.join(model_dir,ii) for ii in model_name]
forward_files = ['conf.lmp', 'lammps.in']+model_name
backward_files = ['log.lammps',task_type+'.out']
common_files=['lammps.in']+model_name
if len(model_name)>1 and task_type == 'deepmd':
backward_files = backward_files + ['model_devi.out']
else:
raise RuntimeError ("unknow task %s, something wrong" % task_type)
run_tasks = util.collect_task(all_task,task_type)
if len(run_tasks)==0: return
else:
run_tasks = [os.path.basename(ii) for ii in all_task]
machine,resources,command,group_size=util.get_machine_info(mdata,task_type)
disp = make_dispatcher(machine, resources, work_path, run_tasks, group_size)
disp.run_jobs(resources,
command,
work_path,
run_tasks,
group_size,
common_files,
forward_files,
backward_files,
outlog=task_type+'.out',
errlog=task_type+'.err')
def run_equi(confs,
inter_param,
mdata):
# find all POSCARs and their name like mp-xxx
# ...
conf_dirs = []
for conf in confs:
conf_dirs.extend(glob.glob(conf))
conf_dirs.sort()
# generate a list of task names like mp-xxx/relaxation/relax_task
# ...
work_path_list = []
for ii in conf_dirs:
work_path_list.append(os.path.abspath(os.path.join(ii, 'relaxation')))
all_task = []
for ii in work_path_list:
all_task.append(os.path.join(ii, 'relax_task'))
inter_type = inter_param['type']
# vasp
if inter_type == "vasp":
mdata = decide_fp_machine(mdata)
elif inter_type in lammps_task_type:
mdata = decide_model_devi_machine(mdata)
else:
raise RuntimeError("unknown task %s, something wrong" % inter_type)
# dispatch the tasks
# POSCAR here is useless
virtual_calculator = make_calculator(inter_param, "POSCAR")
forward_files = virtual_calculator.forward_files()
forward_common_files = virtual_calculator.forward_common_files()
backward_files = virtual_calculator.backward_files()
# backward_files += logs
# ...
run_tasks = util.collect_task(all_task, inter_type)
if len(run_tasks) == 0:
return
else:
run_tasks = [os.path.basename(ii) for ii in all_task]
machine, resources, command, group_size = util.get_machine_info(mdata, inter_type)
print('%d tasks will be submited '%len(run_tasks))
for ii in range(len(work_path_list)):
work_path = work_path_list[ii]
disp = make_dispatcher(machine, resources, work_path, [run_tasks[ii]], group_size)
print("%s --> Runing... "%(work_path))
disp.run_jobs(resources,
command,
work_path,
[run_tasks[ii]],
group_size,
forward_common_files,
forward_files,
backward_files,
outlog='outlog',
errlog='errlog')
def run_vacancy(task_type,jdata,mdata):
work_path=util.make_work_path(jdata,'03.vacancy',False,False,False)
all_task = glob.glob(os.path.join(work_path,'struct-*'))
#vasp
if task_type == "vasp":
mdata=decide_fp_machine(mdata)
forward_files = ['INCAR', 'POSCAR','POTCAR']
backward_files = ['OUTCAR', 'autotest.out' , 'OSZICAR']
common_files=['INCAR','POTCAR']
#lammps
elif task_type in lammps_task_type:
mdata = decide_model_devi_machine(mdata)
fp_params = jdata['lammps_params']
model_dir = fp_params['model_dir']
model_dir = os.path.abspath(model_dir)
model_name =fp_params['model_name']
if not model_name :
models = glob.glob(os.path.join(model_dir, '*pb'))
model_name = [os.path.basename(ii) for ii in models]
else:
models = [os.path.join(model_dir,ii) for ii in model_name]
common_files = model_name
forward_files = ['conf.lmp', 'lammps.in']+model_name
backward_files = ['log.lammps','autotest.out']
common_files=['lammps.in']+model_name
if len(model_name)>1 and task_type == 'deepmd':
backward_files = backward_files + ['model_devi.out']
else:
raise RuntimeError ("unknow task %s, something wrong" % task_type)
run_tasks = util.collect_task(all_task,task_type)
if len(run_tasks)==0: return
machine,machine_type,ssh_sess,resources,command,group_size=util.get_machine_info(mdata,task_type)
disp = make_dispatcher(machine)
disp.run_jobs(resources,
command,
work_path,
run_tasks,
group_size,
common_files,
forward_files,
backward_files,
outlog='autotest.out',
errlog='autotest.err')
def gen_init_surf(args):
try:
import ruamel
from monty.serialization import loadfn, dumpfn
warnings.simplefilter('ignore',
ruamel.yaml.error.MantissaNoDotYAML1_1Warning)
jdata = loadfn(args.PARAM)
if args.MACHINE is not None:
mdata = loadfn(args.MACHINE)
except:
with open(args.PARAM, 'r') as fp:
jdata = json.load(fp)
if args.MACHINE is not None:
with open(args.MACHINE, "r") as fp:
mdata = json.load(fp)
out_dir = out_dir_name(jdata)
jdata['out_dir'] = out_dir
dlog.info("# working dir %s" % out_dir)
if args.MACHINE is not None:
# Decide a proper machine
mdata = decide_fp_machine(mdata)
fp_machine = mdata['fp_machine']
fp_ssh_sess = SSHSession(fp_machine)
#stage = args.STAGE
stage_list = [int(i) for i in jdata['stages']]
for stage in stage_list:
if stage == 1:
create_path(out_dir)
make_super_cell_pymatgen(jdata)
place_element(jdata)
make_vasp_relax(jdata)
if args.MACHINE is not None:
run_vasp_relax(jdata, mdata, fp_ssh_sess)
# elif stage == 0 :
# # create_path(out_dir)
# # make_super_cell(jdata)
# # place_element(jdata)
# # make_vasp_relax(jdata)
# # make_scale(jdata)
# # pert_scaled(jdata)
# # poscar_elong('POSCAR', 'POSCAR.out', 3)
# pert_scaled(jdata)
elif stage == 2:
make_scale(jdata)
pert_scaled(jdata)
else:
raise RuntimeError("unknown stage %d" % stage)
def run_equi(confs, inter_param, mdata):
# find all POSCARs and their name like mp-xxx
# ...
conf_dirs = glob.glob(confs)
conf_dirs.sort()
# generate a list of task names like mp-xxx/relaxation
# ...
work_path_list = []
for ii in conf_dirs:
work_path_list.append(os.path.join(ii, 'relaxation'))
all_task = []
for ii in work_path_list:
all_task.append(os.path.join(ii, '.'))
inter_type = inter_param['type']
# vasp
if inter_type == "vasp":
mdata = decide_fp_machine(mdata)
elif inter_type in lammps_task_type:
mdata = decide_model_devi_machine(mdata)
else:
raise RuntimeError("unknown task %s, something wrong" % task_type)
# dispatch the tasks
forward_files, forward_common_files, backward_files = make_task_trans_files(
inter_param)
# backward_files += logs
# ...
run_tasks = util.collect_task(all_task, inter_type)
if len(run_tasks) == 0:
return
else:
run_tasks = [os.path.basename(ii) for ii in all_task]
machine, resources, command, group_size = util.get_machine_info(
mdata, inter_type)
for ii in range(len(work_path_list)):
work_path = work_path_list[ii]
disp = make_dispatcher(machine, resources, work_path,
run_tasks[ii], group_size)
disp.run_jobs(resources,
command,
work_path,
run_tasks[ii],
group_size,
forward_common_files,
forward_files,
backward_files,
outlog=inter_type + '.out',
errlog=inter_type + '.err')
def run_phonon(task_type, jdata, mdata, ssh_sess):
conf_dir = jdata['conf_dir']
fp_params = jdata['vasp_params']
kspacing = fp_params['kspacing']
conf_path = os.path.abspath(conf_dir)
task_path = re.sub('confs', '06.phonon', conf_path)
if task_type == "vasp":
work_path = os.path.join(task_path, 'vasp-k%.2f' % kspacing)
elif task_type in lammps_task_type:
work_path = os.path.join(task_path, task_type)
assert (os.path.isdir(work_path))
all_task = glob.glob(os.path.join(work_path, '.'))
#vasp
if task_type == "vasp":
mdata = decide_fp_machine(mdata)
vasp_exec = mdata['fp_command']
group_size = mdata['fp_group_size']
resources = mdata['fp_resources']
machine = mdata['fp_machine']
machine_type = mdata['fp_machine']['machine_type']
command = vasp_exec
command = cmd_append_log(command, "log")
run_tasks_ = []
for ii in all_task:
fres = os.path.join(ii, 'OUTCAR')
if os.path.isfile(fres):
if not vasp.check_finished(fres):
run_tasks_.append(ii)
else:
run_tasks_.append(ii)
run_tasks = [os.path.basename(ii) for ii in run_tasks_]
forward_files = ['INCAR', 'POTCAR', 'KPOINTS']
backward_files = ['OUTCAR', 'OSZICAR', 'vasprun.xml']
common_files = ['POSCAR']
_run(machine, machine_type, ssh_sess, resources, command, work_path,
run_tasks, group_size, common_files, forward_files,
backward_files)
#lammps
elif task_type in lammps_task_type:
None
else:
raise RuntimeError("unknow task %s, something wrong" % task_type)
def run_equi(task_type, jdata, mdata):
#rmprint("This module has been run !")
work_path = util.make_work_path(jdata, '00.equi', False, False, False)
all_task = glob.glob(os.path.join(work_path, '.'))
#vasp
if task_type == "vasp":
mdata = decide_fp_machine(mdata)
forward_files = ['INCAR', 'POTCAR']
backward_files = ['OUTCAR', 'CONTCAR', 'OSZICAR']
common_files = ['POSCAR']
#lammps
elif task_type in lammps_task_type:
mdata = decide_model_devi_machine(mdata)
forward_files = ['conf.lmp', 'lammps.in']
backward_files = ['dump.relax', 'log.lammps', 'model_devi.log']
fp_params = jdata['lammps_params']
model_dir = fp_params['model_dir']
model_dir = os.path.abspath(model_dir)
model_name = fp_params['model_name']
if not model_name:
models = glob.glob(os.path.join(model_dir, '*pb'))
model_name = [os.path.basename(ii) for ii in models]
else:
models = [os.path.join(model_dir, ii) for ii in model_name]
common_files = model_name
if len(model_name) > 1 and task_type == 'deepmd':
backward_files = backward_files + ['model_devi.out']
else:
raise RuntimeError("unknow task %s, something wrong" % task_type)
run_tasks = util.collect_task(all_task, task_type)
machine, machine_type, ssh_sess, resources, command, group_size = util.get_machine_info(
mdata, task_type)
_run(machine, machine_type, ssh_sess, resources, command, work_path,
run_tasks, group_size, common_files, forward_files, backward_files)
def run_phonon(task_type, jdata, mdata, ssh_sess):
user = ('user_incar' in jdata.keys())
work_path = make_work_path(jdata, '06.phonon', False, False, user)
all_task = glob.glob(os.path.join(work_path, '.'))
#vasp
if task_type == "vasp":
mdata = decide_fp_machine(mdata)
vasp_exec = mdata['fp_command']
group_size = mdata['fp_group_size']
resources = mdata['fp_resources']
machine = mdata['fp_machine']
machine_type = mdata['fp_machine']['machine_type']
command = vasp_exec
command = cmd_append_log(command, "log")
run_tasks_ = []
for ii in all_task:
fres = os.path.join(ii, 'OUTCAR')
if os.path.isfile(fres):
if not vasp.check_finished(fres):
run_tasks_.append(ii)
else:
run_tasks_.append(ii)
run_tasks = [os.path.basename(ii) for ii in run_tasks_]
forward_files = ['INCAR', 'POTCAR', 'KPOINTS']
backward_files = ['OUTCAR', 'OSZICAR', 'vasprun.xml']
common_files = ['POSCAR']
_run(machine, machine_type, ssh_sess, resources, command, work_path,
run_tasks, group_size, common_files, forward_files,
backward_files)
#lammps
elif task_type in lammps_task_type:
None
else:
raise RuntimeError("unknow task %s, something wrong" % task_type)
def run_property(confs, inter_param, property_list, mdata):
# find all POSCARs and their name like mp-xxx
# ...
# conf_dirs = glob.glob(confs)
# conf_dirs.sort()
processes = len(property_list)
pool = Pool(processes=processes)
print("Submit job via %d processes" % processes)
conf_dirs = []
for conf in confs:
conf_dirs.extend(glob.glob(conf))
conf_dirs.sort()
task_list = []
work_path_list = []
for ii in conf_dirs:
sepline(ch=ii, screen=True)
for jj in property_list:
# determine the suffix: from scratch or refine
# ...
if jj.get("skip", False):
continue
if 'init_from_suffix' and 'output_suffix' in jj:
suffix = jj['output_suffix']
elif 'reproduce' in jj and jj['reproduce']:
suffix = 'reprod'
else:
suffix = '00'
property_type = jj['type']
path_to_work = os.path.abspath(
os.path.join(ii, property_type + '_' + suffix))
work_path_list.append(path_to_work)
tmp_task_list = glob.glob(
os.path.join(path_to_work, 'task.[0-9]*[0-9]'))
tmp_task_list.sort()
task_list.append(tmp_task_list)
inter_param_prop = inter_param
if 'cal_setting' in jj and 'overwrite_interaction' in jj[
'cal_setting']:
inter_param_prop = jj['cal_setting']['overwrite_interaction']
# dispatch the tasks
# POSCAR here is useless
virtual_calculator = make_calculator(inter_param_prop, "POSCAR")
forward_files = virtual_calculator.forward_files(property_type)
forward_common_files = virtual_calculator.forward_common_files(
property_type)
backward_files = virtual_calculator.backward_files(property_type)
# backward_files += logs
# ...
inter_type = inter_param_prop['type']
# vasp
if inter_type == "vasp":
mdata = decide_fp_machine(mdata)
elif inter_type in lammps_task_type:
mdata = decide_model_devi_machine(mdata)
else:
raise RuntimeError("unknown task %s, something wrong" %
inter_type)
work_path = path_to_work
all_task = tmp_task_list
run_tasks = util.collect_task(all_task, inter_type)
if len(run_tasks) == 0:
return
else:
ret = pool.apply_async(worker, (
work_path,
all_task,
forward_common_files,
forward_files,
backward_files,
mdata,
inter_type,
))
# run_tasks = [os.path.basename(ii) for ii in all_task]
# machine, resources, command, group_size = util.get_machine_info(mdata, inter_type)
# disp = make_dispatcher(machine, resources, work_path, run_tasks, group_size)
# disp.run_jobs(resources,
# command,
# work_path,
# run_tasks,
# group_size,
# forward_common_files,
# forward_files,
# backward_files,
# outlog='outlog',
# errlog='errlog')
pool.close()
pool.join()
if ret.successful():
print('finished')
def _main():
parser = argparse.ArgumentParser(description="gen init confs")
parser.add_argument('PARAM',
type=str,
help="parameter file, json/yaml format")
parser.add_argument(
"MACHINE",
type=str,
help="The settings of the machine running the generator")
args = parser.parse_args()
try:
import ruamel
from monty.serialization import loadfn, dumpfn
warnings.simplefilter('ignore',
ruamel.yaml.error.MantissaNoDotYAML1_1Warning)
jdata = loadfn(args.PARAM)
mdata = loadfn(args.MACHINE)
except:
with open(args.PARAM, 'r') as fp:
jdata = json.load(fp)
with open(args.MACHINE, "r") as fp:
mdata = json.load(fp)
# Selecting a proper machine
mdata = decide_fp_machine(mdata)
fp_machine = mdata['fp_machine']
fp_ssh_sess = SSHSession(fp_machine)
# Decide work path
out_dir = out_dir_name(jdata)
jdata['out_dir'] = out_dir
print("# working dir %s" % out_dir)
# Decide whether to use a given poscar
from_poscar = False
if 'from_poscar' in jdata:
from_poscar = jdata['from_poscar']
# Verify md_nstep
md_nstep_jdata = jdata["md_nstep"]
try:
md_incar = jdata['md_incar']
if os.path.isfile(md_incar):
with open(md_incar, "r") as fr:
md_incar_lines = fr.readlines()
nsw_flag = False
for incar_line in md_incar_lines:
line = incar_line.split()
if "NSW" in line:
nsw_flag = True
nsw_steps = int(incar_line.split()[-1])
break
#print("nsw_steps is", nsw_steps)
#print("md_nstep_jdata is", md_nstep_jdata)
if nsw_flag:
if (nsw_steps != md_nstep_jdata):
print(
"WARNING: your set-up for MD steps in PARAM and md_incar are not consistent!"
)
print("MD steps in PARAM is %d" % (md_nstep_jdata))
print("MD steps in md_incar is %d" (nsw_steps))
print("DP-GEN will use settings in md_incar!")
jdata['md_nstep'] = nsw_steps
except:
pass
## correct element name
temp_elements = []
for ele in jdata['elements']:
temp_elements.append(ele[0].upper() + ele[1:])
jdata['elements'] = temp_elements
print("Elements are", jdata['elements'])
## Iteration
stage_list = [int(i) for i in jdata['stages']]
for stage in stage_list:
if stage == 1:
print("Current stage is 1, relax")
create_path(out_dir)
shutil.copy2(args.PARAM, os.path.join(out_dir, 'param.json'))
if from_poscar:
make_super_cell_poscar(jdata)
else:
make_unit_cell(jdata)
make_super_cell(jdata)
place_element(jdata)
make_vasp_relax(jdata, mdata)
run_vasp_relax(jdata, mdata, fp_ssh_sess)
elif stage == 2:
print("Current stage is 2, perturb and scale")
make_scale(jdata)
pert_scaled(jdata)
elif stage == 3:
print("Current stage is 3, run a short md")
make_vasp_md(jdata)
run_vasp_md(jdata, mdata, fp_ssh_sess)
elif stage == 4:
print("Current stage is 4, collect data")
coll_vasp_md(jdata)
else:
raise RuntimeError("unknown stage %d" % stage)
def run_task(json_file, machine_file):
with open(json_file, 'r') as fp:
jdata = json.load(fp)
with open(machine_file, 'r') as fp:
mdata = json.load(fp)
record = "record.auto_test"
model_devi_mdata = decide_model_devi_machine(mdata)
model_devi_machine = model_devi_mdata['model_devi_machine']
if ('machine_type' in model_devi_machine) and \
(model_devi_machine['machine_type'] == 'ucloud'):
model_devi_ssh_sess = None
else:
model_devi_ssh_sess = SSHSession(model_devi_machine)
fp_mdata = decide_fp_machine(mdata)
fp_machine = fp_mdata['fp_machine']
if ('machine_type' in fp_machine) and \
(fp_machine['machine_type'] == 'ucloud'):
fp_ssh_sess = None
else:
fp_ssh_sess = SSHSession(fp_machine)
confs = jdata['conf_dir']
ele_list = [key for key in jdata['potcar_map'].keys()]
key_id = jdata['key_id']
ii = jdata['task_type']
jj = jdata['task']
task_list = [
'equi', 'eos', 'elastic', 'vacancy', 'interstitial', 'surf', 'phonon',
'all'
]
task_type_list = ['vasp'] + lammps_task_type
if jj not in task_list:
raise RuntimeError("unknow task %s, something wrong" % jj)
if ii not in task_type_list:
raise RuntimeError("unknow task type %s, something wrong" % ii)
#gen_configuration
if 'confs' in confs and (not os.path.exists(confs + '/POSCAR')):
print('generate %s' % (ele_list))
if len(ele_list) == 1:
gen_confs.gen_element(ele_list[0], key_id)
else:
gen_confs.gen_alloy(ele_list, key_id)
#default task
log_iter("gen_equi", ii, "equi")
gen_equi(ii, jdata, mdata)
log_iter("run_equi", ii, "equi")
run_equi(ii, jdata, mdata, model_devi_ssh_sess)
log_iter("cmpt_equi", ii, "equi")
cmpt_equi(ii, jdata, mdata)
if jj == "eos" or jj == "all":
log_iter("gen_eos", ii, "eos")
gen_eos(ii, jdata, mdata)
log_iter("run_eos", ii, "eos")
run_eos(ii, jdata, mdata, model_devi_ssh_sess)
log_iter("cmpt_eos", ii, "eos")
cmpt_eos(ii, jdata, mdata)
if jj == "elastic" or jj == "all":
log_iter("gen_elastic", ii, "elastic")
gen_elastic(ii, jdata, mdata)
log_iter("run_elastic", ii, "elastic")
run_elastic(ii, jdata, mdata, model_devi_ssh_sess)
log_iter("cmpt_elastic", ii, "elastic")
cmpt_elastic(ii, jdata, mdata)
if jj == "vacancy" or jj == "all":
log_iter("gen_vacancy", ii, "vacancy")
gen_vacancy(ii, jdata, mdata)
log_iter("run_vacancy", ii, "vacancy")
run_vacancy(ii, jdata, mdata, model_devi_ssh_sess)
log_iter("cmpt_vacancy", ii, "vacancy")
cmpt_vacancy(ii, jdata, mdata)
if jj == "interstitial" or jj == "all":
log_iter("gen_interstitial", ii, "interstitial")
gen_interstitial(ii, jdata, mdata)
log_iter("run_interstitial", ii, "interstitial")
run_interstitial(ii, jdata, mdata, model_devi_ssh_sess)
log_iter("cmpt_interstitial", ii, "interstitial")
cmpt_interstitial(ii, jdata, mdata)
if jj == "surf" or jj == "all":
log_iter("gen_surf", ii, "surf")
gen_surf(ii, jdata, mdata)
log_iter("run_surf", ii, "surf")
run_surf(ii, jdata, mdata, model_devi_ssh_sess)
log_iter("cmpt_surf", ii, "surf")
cmpt_surf(ii, jdata, mdata)
'''
if jj=="phonon":
log_iter ("gen_phonon", ii, "phonon")
gen_phonon (ii, jdata, mdata)
log_iter ("run_phonon", ii, "phonon")
run_phonon (ii, jdata, mdata,model_devi_ssh_sess)
log_iter ("cmpt_phonon", ii, "phonon")
cmpt_phonon (ii, jdata, mdata)
'''
record_iter(record, confs, ii, jj)
def run_surf(task_type, jdata, mdata, ssh_sess):
static = jdata['static-opt']
work_path = make_work_path(jdata, '05.surf', False, static, False)
all_task = glob.glob(os.path.join(work_path, 'struct-*'))
#vasp
if task_type == "vasp":
mdata = decide_fp_machine(mdata)
vasp_exec = mdata['fp_command']
group_size = mdata['fp_group_size']
resources = mdata['fp_resources']
machine = mdata['fp_machine']
machine_type = mdata['fp_machine']['machine_type']
command = vasp_exec
command = cmd_append_log(command, "log")
run_tasks_ = []
for ii in all_task:
fres = os.path.join(ii, 'OUTCAR')
if os.path.isfile(fres):
if not vasp.check_finished(fres):
run_tasks_.append(ii)
else:
run_tasks_.append(ii)
forward_files = ['INCAR', 'POSCAR', 'POTCAR']
backward_files = ['OUTCAR', 'OSZICAR']
common_files = ['INCAR', 'POTCAR']
#lammps
elif task_type in lammps_task_type:
mdata = decide_model_devi_machine(mdata)
lmp_exec = mdata['lmp_command']
group_size = mdata['model_devi_group_size']
resources = mdata['model_devi_resources']
machine = mdata['model_devi_machine']
machine_type = mdata['model_devi_machine']['machine_type']
command = lmp_exec + " -i lammps.in"
command = cmd_append_log(command, "model_devi.log")
run_tasks_ = []
for ii in all_task:
fres = os.path.join(ii, 'log.lammps')
if os.path.isfile(fres):
with open(fres, 'r') as fp:
lines = fp.read().split('\n')
flag = False
for jj in lines:
if ("Final energy per atoms"
in jj) and (not 'print' in jj):
flag = True
if not flag:
run_tasks_.append(ii)
else:
run_tasks_.append(ii)
fp_params = jdata['lammps_params']
model_dir = fp_params['model_dir']
model_dir = os.path.abspath(model_dir)
model_name = fp_params['model_name']
if not model_name:
models = glob.glob(os.path.join(model_dir, '*pb'))
model_name = [os.path.basename(ii) for ii in models]
else:
models = [os.path.join(model_dir, ii) for ii in model_name]
forward_files = ['conf.lmp', 'lammps.in'] + model_name
backward_files = ['log.lammps', 'model_devi.log']
common_files = ['lammps.in'] + model_name
if len(model_name) > 1 and task_type == 'deepmd':
backward_files = backward_files + ['model_devi.out']
else:
raise RuntimeError("unknow task %s, something wrong" % task_type)
run_tasks = [os.path.basename(ii) for ii in run_tasks_]
_run(machine, machine_type, ssh_sess, resources, command, work_path,
run_tasks, group_size, common_files, forward_files, backward_files)
def run_iter(param_file, machine_file):
""" init (iter 0): init_pick
tasks (iter > 0):
00 make_train (same as generator)
01 run_train (same as generator)
02 post_train (same as generator)
03 make_model_devi
04 run_model_devi
05 post_model_devi
06 make_fp
07 run_fp (same as generator)
08 post_fp (same as generator)
"""
# TODO: function of handling input json should be combined as one function
try:
import ruamel
from monty.serialization import loadfn, dumpfn
warnings.simplefilter('ignore',
ruamel.yaml.error.MantissaNoDotYAML1_1Warning)
jdata = loadfn(param_file)
mdata = loadfn(machine_file)
except:
with open(param_file, 'r') as fp:
jdata = json.load(fp)
with open(machine_file, 'r') as fp:
mdata = json.load(fp)
if jdata.get('pretty_print', False):
fparam = SHORT_CMD+'_' + \
param_file.split('.')[0]+'.'+jdata.get('pretty_format', 'json')
dumpfn(jdata, fparam, indent=4)
fmachine = SHORT_CMD+'_' + \
machine_file.split('.')[0]+'.'+jdata.get('pretty_format', 'json')
dumpfn(mdata, fmachine, indent=4)
if mdata.get('handlers', None):
if mdata['handlers'].get('smtp', None):
que = queue.Queue(-1)
queue_handler = logging.handlers.QueueHandler(que)
smtp_handler = logging.handlers.SMTPHandler(
**mdata['handlers']['smtp'])
listener = logging.handlers.QueueListener(que, smtp_handler)
dlog.addHandler(queue_handler)
listener.start()
max_tasks = 10000
numb_task = 9
record = "record.dpgen"
iter_rec = [0, -1]
if os.path.isfile(record):
with open(record) as frec:
for line in frec:
iter_rec = [int(x) for x in line.split()]
dlog.info("continue from iter %03d task %02d" %
(iter_rec[0], iter_rec[1]))
cont = True
ii = -1
while cont:
ii += 1
iter_name = make_iter_name(ii)
sepline(iter_name, '=')
for jj in range(numb_task):
if ii * max_tasks + jj <= iter_rec[0] * max_tasks + iter_rec[1]:
continue
task_name = "task %02d" % jj
sepline("{} {}".format(iter_name, task_name), '-')
jdata['model_devi_jobs'] = [{} for _ in range(ii + 1)]
if ii == 0 and jj < 6:
if jj == 0:
log_iter("init_pick", ii, jj)
init_pick(ii, jdata, mdata)
dlog.info("first iter, skip step 1-5")
elif jj == 0:
log_iter("make_train", ii, jj)
make_train(ii, jdata, mdata)
elif jj == 1:
log_iter("run_train", ii, jj)
mdata = decide_train_machine(mdata)
disp = make_dispatcher(mdata['train_machine'])
run_train(ii, jdata, mdata)
elif jj == 2:
log_iter("post_train", ii, jj)
post_train(ii, jdata, mdata)
elif jj == 3:
log_iter("make_model_devi", ii, jj)
cont = make_model_devi(ii, jdata, mdata)
if not cont or ii >= jdata.get("stop_iter", ii + 1):
break
elif jj == 4:
log_iter("run_model_devi", ii, jj)
mdata = decide_model_devi_machine(mdata)
disp = make_dispatcher(mdata['model_devi_machine'])
run_model_devi(ii, jdata, mdata, disp)
elif jj == 5:
log_iter("post_model_devi", ii, jj)
post_model_devi(ii, jdata, mdata)
elif jj == 6:
log_iter("make_fp", ii, jj)
make_fp(ii, jdata, mdata)
elif jj == 7:
log_iter("run_fp", ii, jj)
if jdata.get("labeled", False):
dlog.info("already have labeled data, skip run_fp")
else:
mdata = decide_fp_machine(mdata)
disp = make_dispatcher(mdata['fp_machine'])
run_fp(ii, jdata, mdata)
elif jj == 8:
log_iter("post_fp", ii, jj)
if jdata.get("labeled", False):
dlog.info("already have labeled data, skip post_fp")
else:
post_fp(ii, jdata)
else:
raise RuntimeError("unknown task %d, something wrong" % jj)
record_iter(record, ii, jj)
def gen_init_bulk(args) :
try:
import ruamel
from monty.serialization import loadfn,dumpfn
warnings.simplefilter('ignore', ruamel.yaml.error.MantissaNoDotYAML1_1Warning)
jdata=loadfn(args.PARAM)
if args.MACHINE is not None:
mdata=loadfn(args.MACHINE)
except:
with open (args.PARAM, 'r') as fp :
jdata = json.load (fp)
if args.MACHINE is not None:
with open (args.MACHINE, "r") as fp:
mdata = json.load(fp)
if args.MACHINE is not None:
# Selecting a proper machine
mdata = decide_fp_machine(mdata)
#disp = make_dispatcher(mdata["fp_machine"])
# Decide work path
out_dir = out_dir_name(jdata)
jdata['out_dir'] = out_dir
dlog.info ("# working dir %s" % out_dir)
# Decide whether to use a given poscar
from_poscar = False
if 'from_poscar' in jdata :
from_poscar = jdata['from_poscar']
# Verify md_nstep
md_nstep_jdata = jdata["md_nstep"]
try:
md_incar = jdata['md_incar']
if os.path.isfile(md_incar):
standard_incar = incar_upper(Incar.from_file(md_incar))
nsw_flag = False
if "NSW" in standard_incar:
nsw_flag = True
nsw_steps = standard_incar['NSW']
#dlog.info("nsw_steps is", nsw_steps)
#dlog.info("md_nstep_jdata is", md_nstep_jdata)
if nsw_flag:
if (nsw_steps != md_nstep_jdata):
dlog.info("WARNING: your set-up for MD steps in PARAM and md_incar are not consistent!")
dlog.info("MD steps in PARAM is %d"%(md_nstep_jdata))
dlog.info("MD steps in md_incar is %d"%(nsw_steps))
dlog.info("DP-GEN will use settings in md_incar!")
jdata['md_nstep'] = nsw_steps
except KeyError:
pass
## correct element name
temp_elements = []
for ele in jdata['elements']:
temp_elements.append(ele[0].upper() + ele[1:])
jdata['elements'] = temp_elements
dlog.info("Elements are %s"% ' '.join(jdata['elements']))
## Iteration
stage_list = [int(i) for i in jdata['stages']]
for stage in stage_list:
if stage == 1 :
dlog.info("Current stage is 1, relax")
create_path(out_dir)
shutil.copy2(args.PARAM, os.path.join(out_dir, 'param.json'))
if from_poscar :
make_super_cell_poscar(jdata)
else :
make_unit_cell(jdata)
make_super_cell(jdata)
place_element(jdata)
if args.MACHINE is not None:
make_vasp_relax(jdata, mdata)
run_vasp_relax(jdata, mdata)
else:
make_vasp_relax(jdata, {"fp_resources":{}})
elif stage == 2 :
dlog.info("Current stage is 2, perturb and scale")
make_scale(jdata)
pert_scaled(jdata)
elif stage == 3 :
dlog.info("Current stage is 3, run a short md")
make_vasp_md(jdata)
if args.MACHINE is not None:
run_vasp_md(jdata, mdata)
elif stage == 4 :
dlog.info("Current stage is 4, collect data")
coll_vasp_md(jdata)
else :
raise RuntimeError("unknown stage %d" % stage)
def run_interstitial(task_type,jdata,mdata):
reprod_opt=jdata['reprod-opt']
work_path=util.make_work_path(jdata,'04.interstitial',reprod_opt,False,False)
all_task = glob.glob(os.path.join(work_path,'struct-*'))
#vasp
if task_type == "vasp":
mdata=decide_fp_machine(mdata)
forward_files = ['INCAR', 'POSCAR','POTCAR',"KPOINTS"]
backward_files = ['OUTCAR', task_type+'.out' , 'XDATCAR','OSZICAR']
common_files=['INCAR']
if ('cvasp' in jdata) and (jdata['cvasp'] == True):
mdata['fp_resources']['cvasp'] = True
forward_files.append('cvasp.py')
#lammps
elif task_type in lammps_task_type:
mdata = decide_model_devi_machine(mdata)
if reprod_opt:
all_frame=[]
for ii in all_task:
all_frame+=(glob.glob(os.path.join(ii,'frame.*')))
work_path = all_task
all_task = all_frame
run_tasks_ = []
for ii in all_task:
# fres = os.path.join(ii, 'log.lammps')
# if os.path.isfile(fres) :
# if not lammps.check_finished(fres):
# run_tasks_.append(ii)
# else :
# run_tasks_.append(ii)
run_tasks_.append(ii)
fp_params = jdata['lammps_params']
model_dir = fp_params['model_dir']
model_dir = os.path.abspath(model_dir)
model_name =fp_params['model_name']
if not model_name :
models = glob.glob(os.path.join(model_dir, '*pb'))
model_name = [os.path.basename(ii) for ii in models]
else:
models = [os.path.join(model_dir,ii) for ii in model_name]
forward_files = ['conf.lmp', 'lammps.in']+model_name
backward_files = ['log.lammps', task_type+'.out']
common_files=['lammps.in']+model_name
if len(model_name)>1 and task_type == 'deepmd':
backward_files = backward_files + ['model_devi.out']
else:
raise RuntimeError ("unknow task %s, something wrong" % task_type)
machine,resources,command,group_size=util.get_machine_info(mdata,task_type)
if reprod_opt:
for ii in work_path:
run_tasks=[]
for jj in run_tasks_:
if ii in jj:
run_tasks.append(os.path.basename(jj))
disp = make_dispatcher(machine, resources, work_path, run_tasks, group_size)
disp.run_jobs(resources,
command,
ii,
run_tasks,
group_size,
common_files,
forward_files,
backward_files,
outlog=task_type+'.out',
errlog=task_type+'.err')
else:
run_tasks = util.collect_task(all_task,task_type)
if len(run_tasks)==0: return
else:
run_tasks = [os.path.basename(ii) for ii in all_task]
disp = make_dispatcher(machine, resources, work_path, run_tasks, group_size)
disp.run_jobs(resources,
command,
work_path,
run_tasks,
group_size,
common_files,
forward_files,
backward_files,
outlog=task_type+'.out',
errlog=task_type+'.err')
shutil.copyfile(os.path.join(pwd,'POTCAR'),'POTCAR')
shutil.copyfile(os.path.join(pwd,'KPOINTS'),'KPOINTS')
os.chdir(pwd)
#os._exit(0)
fp_tasks = glob(os.path.join(work_path, 'task.*'))
fp_tasks.sort()
run_tasks = [os.path.basename(ii) for ii in fp_tasks]
#----------------------------------------------------
forward_files = ['POSCAR', 'INCAR', 'POTCAR','KPOINTS']
backward_files = ['OUTCAR','vasprun.xml','CONTCAR']
forward_common_files=[]
mark_failure =False
log_file='runlog'
err_file='errlog'
mdata=loadfn('machine.json')
mdata = decide_fp_machine(mdata)
#dumpfn(mdata,'new.json',indent=4)
fp_command = mdata['fp_command']
fp_group_size = mdata['fp_group_size']
#---------------------------------------------------
dispatcher = make_dispatcher(mdata['fp_machine'],
mdata_resource=mdata['fp_resources'],
work_path=work_path,
run_tasks=run_tasks,
group_size=fp_group_size)
dispatcher.run_jobs(mdata['fp_resources'],
[fp_command],
work_path,
run_tasks,
def run_property(confs, inter_param, property_list, mdata):
# find all POSCARs and their name like mp-xxx
# ...
conf_dirs = glob.glob(confs)
conf_dirs.sort()
task_list = []
work_path_list = []
for ii in conf_dirs:
for jj in property_list:
# determine the suffix: from scratch or refine
# ...
if 'init_from_suffix' and 'output_suffix' in jj:
suffix = jj['output_suffix']
else:
suffix = 0
property_type = jj['type']
path_to_work = os.path.join(ii, property_type + '_' + suffix)
work_path_list.append(path_to_work)
tmp_task_list = glob.glob(
os.path.join(path_to_work, 'task.[0-9]*[0-9]'))
tmp_task_list.sort()
task_list.append(tmp_task_list)
# dispatch the tasks
forward_files, forward_common_files, backward_files = make_task_trans_files(
inter_param)
# backward_files += logs
# ...
task_type = inter_param['type']
# vasp
if task_type == "vasp":
mdata = decide_fp_machine(mdata)
elif task_type in lammps_task_type:
mdata = decide_model_devi_machine(mdata)
else:
raise RuntimeError("unknown task %s, something wrong" % task_type)
for ii in range(len(work_path_list)):
work_path = work_path_list[ii]
all_task = task_list[ii]
run_tasks = util.collect_task(all_task, task_type)
if len(run_tasks) == 0:
return
else:
run_tasks = [os.path.basename(ii) for ii in all_task]
machine, resources, command, group_size = util.get_machine_info(
mdata, task_type)
disp = make_dispatcher(machine, resources, work_path, run_tasks,
group_size)
disp.run_jobs(resources,
command,
work_path,
run_tasks,
group_size,
forward_common_files,
forward_files,
backward_files,
outlog=task_type + '.out',
errlog=task_type + '.err')
def run_elastic(task_type, jdata, mdata, ssh_sess):
conf_dir = jdata['conf_dir']
fp_params = jdata['vasp_params']
kspacing = fp_params['kspacing']
conf_path = os.path.abspath(conf_dir)
task_path = re.sub('confs', '02.elastic', conf_path)
if task_type == "vasp":
work_path = os.path.join(task_path, 'vasp-k%.2f' % kspacing)
elif task_type in lammps_task_type:
work_path = os.path.join(task_path, task_type)
assert (os.path.isdir(work_path))
print(work_path)
all_task = glob.glob(os.path.join(work_path, "dfm-*"))
all_task.sort()
#vasp
if task_type == "vasp":
mdata = decide_fp_machine(mdata)
vasp_exec = mdata['fp_command']
group_size = mdata['fp_group_size']
resources = mdata['fp_resources']
machine = mdata['fp_machine']
machine_type = mdata['fp_machine']['machine_type']
command = vasp_exec
command = cmd_append_log(command, "log")
run_tasks_ = []
for ii in all_task:
fres = os.path.join(ii, 'OUTCAR')
if os.path.isfile(fres):
if not vasp.check_finished(fres):
run_tasks_.append(ii)
else:
run_tasks_.append(ii)
forward_files = ['INCAR', 'POSCAR', 'POTCAR', 'KPOINTS']
backward_files = ['OUTCAR', 'CONTCAR', 'OSZICAR']
common_files = ['INCAR', 'POTCAR', 'KPOINTS']
#lammps
elif task_type in lammps_task_type:
mdata = decide_model_devi_machine(mdata)
lmp_exec = mdata['lmp_command']
group_size = mdata['model_devi_group_size']
resources = mdata['model_devi_resources']
machine = mdata['model_devi_machine']
machine_type = mdata['model_devi_machine']['machine_type']
command = lmp_exec + " -i lammps.in"
command = cmd_append_log(command, "model_devi.log")
run_tasks_ = []
for ii in all_task:
fres = os.path.join(ii, 'log.lammps')
if os.path.isfile(fres):
with open(fres, 'r') as fp:
lines = fp.read().split('\n')
flag = False
for jj in lines:
if ('Final Stress' in jj) and (not 'print' in jj):
flag = True
if not flag:
run_tasks_.append(ii)
else:
run_tasks_.append(ii)
fp_params = jdata['lammps_params']
model_dir = fp_params['model_dir']
model_dir = os.path.abspath(model_dir)
model_name = fp_params['model_name']
if not model_name:
models = glob.glob(os.path.join(model_dir, '*pb'))
model_name = [os.path.basename(ii) for ii in models]
else:
models = [os.path.join(model_dir, ii) for ii in model_name]
forward_files = ['conf.lmp', 'lammps.in', 'strain.out'] + model_name
backward_files = ['log.lammps', 'model_devi.log']
common_files = ['lammps.in'] + model_name
if len(model_name) > 1:
backward_files = backward_files + ['model_devi.out']
else:
raise RuntimeError("unknow task %s, something wrong" % task_type)
run_tasks = [os.path.basename(ii) for ii in run_tasks_]
_run(machine, machine_type, ssh_sess, resources, command, work_path,
run_tasks, group_size, common_files, forward_files, backward_files)
def run_interstitial(task_type, jdata, mdata, ssh_sess):
conf_dir = jdata['conf_dir']
fp_params = jdata['vasp_params']
kspacing = fp_params['kspacing']
reprod_opt = jdata['reprod-opt']
conf_path = os.path.abspath(conf_dir)
task_path = re.sub('confs', '04.interstitial', conf_path)
if task_type == "vasp":
work_path = os.path.join(task_path, 'vasp-k%.2f' % kspacing)
elif task_type in lammps_task_type:
work_path = os.path.join(task_path, task_type)
if reprod_opt:
work_path = os.path.join(task_path,
'%s-reprod-k%.2f' % (task_type, kspacing))
assert (os.path.isdir(work_path))
all_task = glob.glob(os.path.join(work_path, 'struct-*'))
#vasp
if task_type == "vasp":
mdata = decide_fp_machine(mdata)
vasp_exec = mdata['fp_command']
group_size = mdata['fp_group_size']
resources = mdata['fp_resources']
machine = mdata['fp_machine']
machine_type = mdata['fp_machine']['machine_type']
command = vasp_exec
command = cmd_append_log(command, "log")
run_tasks_ = []
for ii in all_task:
fres = os.path.join(ii, 'OUTCAR')
if os.path.isfile(fres):
if not vasp.check_finished(fres):
run_tasks_.append(ii)
else:
run_tasks_.append(ii)
forward_files = ['INCAR', 'POSCAR', 'POTCAR']
backward_files = ['OUTCAR', 'XDATCAR', 'OSZICAR']
common_files = ['INCAR']
#lammps
elif task_type in lammps_task_type:
mdata = decide_model_devi_machine(mdata)
lmp_exec = mdata['lmp_command']
group_size = mdata['model_devi_group_size']
resources = mdata['model_devi_resources']
machine = mdata['model_devi_machine']
machine_type = mdata['model_devi_machine']['machine_type']
command = lmp_exec + " -i lammps.in"
command = cmd_append_log(command, "model_devi.log")
if reprod_opt:
all_frame = []
for ii in all_task:
all_frame += (glob.glob(os.path.join(ii, 'frame.*')))
work_path = all_task
all_task = all_frame
run_tasks_ = []
for ii in all_task:
fres = os.path.join(ii, 'log.lammps')
if os.path.isfile(fres):
with open(fres, 'r') as fp:
lines = fp.read().split('\n')
flag = False
for jj in lines:
if ("Final energy per atoms"
in jj) and (not 'print' in jj):
flag = True
if not flag:
run_tasks_.append(ii)
else:
run_tasks_.append(ii)
fp_params = jdata['lammps_params']
model_dir = fp_params['model_dir']
model_dir = os.path.abspath(model_dir)
model_name = fp_params['model_name']
if not model_name:
models = glob.glob(os.path.join(model_dir, '*pb'))
model_name = [os.path.basename(ii) for ii in models]
else:
models = [os.path.join(model_dir, ii) for ii in model_name]
forward_files = ['conf.lmp', 'lammps.in'] + model_name
backward_files = ['log.lammps', 'model_devi.log']
common_files = ['lammps.in'] + model_name
if len(model_name) > 1:
backward_files = backward_files + ['model_devi.out']
else:
raise RuntimeError("unknow task %s, something wrong" % task_type)
if reprod_opt:
for ii in work_path:
run_tasks = []
for jj in run_tasks_:
if ii in jj:
run_tasks.append(os.path.basename(jj))
_run(machine, machine_type, ssh_sess, resources, command, ii,
run_tasks, group_size, common_files, forward_files,
backward_files)
else:
run_tasks = [os.path.basename(ii) for ii in run_tasks_]
_run(machine, machine_type, ssh_sess, resources, command, work_path,
run_tasks, group_size, common_files, forward_files,
backward_files)
