def run_temp(iter_index, json_file):
iter_name = make_iter_name(iter_index)
work_path = iter_name + "/" + temp_name + "/"
fp = open(json_file, 'r')
jdata = json.load(fp)
gmx_prep = jdata["gmx_prep"]
gmx_run = jdata["gmx_run"]
temp_thread = jdata["temp_thread"]
gmx_run = gmx_run + (" -nt %d " % temp_thread)
gmx_prep_log = "gmx_grompp.log"
gmx_run_log = "gmx_mdrun.log"
gmx_run = gmx_run + " -plumed " + temp_plm
gmx_prep_cmd = cmd_append_log(gmx_prep, gmx_prep_log)
gmx_run_cmd = cmd_append_log(gmx_run, gmx_run_log)
numb_walkers = jdata["numb_walkers"]
all_task = glob.glob(work_path + "/[0-9]*[0-9]")
all_task.sort()
global exec_machine
exec_hosts(MachineLocal, gmx_prep_cmd, 1, all_task, None)
if len(all_task) == 1:
exec_hosts(MachineLocal, gmx_run_cmd, temp_thread, all_task, None)
else:
exec_hosts_batch(exec_machine, gmx_run_cmd, temp_thread, all_task,
None)
def post_enhc(iter_index, json_file):
iter_name = make_iter_name(iter_index)
work_path = iter_name + "/" + enhc_name + "/"
fp = open(json_file, 'r')
jdata = json.load(fp)
gmx_split = jdata["gmx_split_traj"]
gmx_split_log = "gmx_split.log"
gmx_split_cmd = cmd_append_log(gmx_split, gmx_split_log)
all_task = glob.glob(work_path + "/[0-9]*[0-9]")
all_task.sort()
cwd = os.getcwd()
numb_walkers = jdata["numb_walkers"]
for ii in range(numb_walkers):
walker_path = work_path + make_walker_name(ii) + "/"
os.chdir(walker_path)
if os.path.isdir("confs"):
shutil.rmtree("confs")
os.makedirs("confs")
os.chdir(cwd)
global exec_machine
exec_hosts(MachineLocal, gmx_split_cmd, 1, all_task, None)
for ii in range(numb_walkers):
walker_path = work_path + make_walker_name(ii) + "/"
angles = np.loadtxt(walker_path + enhc_out_plm)
np.savetxt(walker_path + enhc_out_angle, angles[:, 1:], fmt="%.6f")
def run_enhc(iter_index, json_file):
iter_name = make_iter_name(iter_index)
work_path = iter_name + "/" + enhc_name + "/"
fp = open(json_file, 'r')
jdata = json.load(fp)
gmx_prep = jdata["gmx_prep"]
gmx_run = jdata["gmx_run"]
enhc_thread = jdata["bias_thread"]
gmx_run = gmx_run + (" -nt %d " % enhc_thread)
gmx_prep_log = "gmx_grompp.log"
gmx_run_log = "gmx_mdrun.log"
# assuming at least one walker
graph_files = glob.glob(work_path + (make_walker_name(0)) + "/*.pb")
if len(graph_files) != 0:
gmx_run = gmx_run + " -plumed " + enhc_plm
else:
gmx_run = gmx_run + " -plumed " + enhc_bf_plm
gmx_prep_cmd = cmd_append_log(gmx_prep, gmx_prep_log)
gmx_run_cmd = cmd_append_log(gmx_run, gmx_run_log)
numb_walkers = jdata["numb_walkers"]
batch_jobs = jdata['batch_jobs']
batch_time_limit = jdata['batch_time_limit']
batch_modules = jdata['batch_modules']
batch_sources = jdata['batch_sources']
all_task = glob.glob(work_path + "/[0-9]*[0-9]")
all_task.sort()
global exec_machine
exec_hosts(MachineLocal, gmx_prep_cmd, 1, all_task, None)
if batch_jobs:
exec_batch(gmx_run_cmd,
enhc_thread,
1,
all_task,
task_args=None,
time_limit=batch_time_limit,
modules=batch_modules,
sources=batch_sources)
else:
if len(all_task) == 1:
exec_hosts(MachineLocal, gmx_run_cmd, enhc_thread, all_task, None)
else:
exec_hosts_batch(exec_machine, gmx_run_cmd, enhc_thread, all_task,
None)
def post_temp(iter_index, json_file):
iter_name = make_iter_name(iter_index)
work_path = iter_name + "/" + temp_name + "/"
fp = open(json_file, 'r')
jdata = json.load(fp)
gmx_split = jdata["gmx_split_traj"]
gmx_split_log = "gmx_split.log"
gmx_split_cmd = cmd_append_log(gmx_split, gmx_split_log)
temp_test_intvl = jdata['temp_test_intvl']
dev_trust_lvl = jdata['dev_trust_lvl']
temp_incr_ratio = jdata['temp_incr_ratio']
temp_decr_ratio = jdata['temp_decr_ratio']
temp_incr_lvl = jdata['temp_incr_lvl']
temp_decr_lvl = jdata['temp_decr_lvl']
phys_temp = jdata['phys_temp']
max_temp = jdata['max_temp']
all_task = glob.glob(work_path + "/[0-9]*[0-9]")
all_task.sort()
cwd = os.getcwd()
numb_walkers = jdata["numb_walkers"]
for ii in range(numb_walkers):
walker_path = work_path + make_walker_name(ii) + "/"
os.chdir(walker_path)
if os.path.isdir("confs"):
shutil.rmtree("confs")
os.makedirs("confs")
os.chdir(cwd)
global exec_machine
exec_hosts(MachineLocal, gmx_split_cmd, 1, all_task, None)
walker_stop_flags = []
for ii in range(numb_walkers):
walker_path = work_path + make_walker_name(ii) + "/"
angles = np.loadtxt(walker_path + temp_out_plm)
angles = angles[:, 1:]
np.savetxt(walker_path + temp_out_angle, angles, fmt="%.6f")
graph_files = glob.glob(walker_path + "/*.pb")
cur_temp = np.loadtxt(os.path.join(walker_path, 'cur.temp'))
if len(graph_files) != 0:
next_temp, dec_list, model_dev\
= make_next_temp(graph_files,
cur_temp,
angles,
temp_test_intvl,
dev_trust_lvl,
temp_incr_ratio,
temp_decr_ratio,
temp_incr_lvl,
temp_decr_lvl,
phys_temp,
max_temp)
model_dev = np.concatenate(
(angles, np.reshape(model_dev, [-1, 1])), axis=1)
np.savetxt(os.path.join(walker_path, 'model.devi'), model_dev)
np.savetxt(os.path.join(walker_path, 'dec_list'), dec_list)
else:
next_temp = cur_temp
np.savetxt(os.path.join(walker_path, 'next.temp'), [next_temp])
if cur_temp == max_temp and next_temp == max_temp:
walker_stop_flags.append(True)
else:
walker_stop_flags.append(False)
# return if the iteration continues
if all(walker_stop_flags):
return False
else:
return True
def run_enhc(iter_index, json_file):
iter_name = make_iter_name(iter_index)
work_path = iter_name + "/" + enhc_name + "/"
fp = open(json_file, 'r')
jdata = json.load(fp)
bPosre = jdata.get("gmx_posre", False)
gmx_prep = jdata["gmx_prep"]
if bPosre:
gmx_prep += " -f grompp_restraint.mdp -r conf_init.gro"
gmx_run = jdata["gmx_run"]
enhc_thread = jdata["bias_thread"]
gmx_run = gmx_run + (" -nt %d " % enhc_thread)
gmx_prep_log = "gmx_grompp.log"
gmx_run_log = "gmx_mdrun.log"
# assuming at least one walker
graph_files = glob.glob(work_path + (make_walker_name(0)) + "/*.pb")
if len(graph_files) != 0:
gmx_run = gmx_run + " -plumed " + enhc_plm
else:
gmx_run = gmx_run + " -plumed " + enhc_bf_plm
gmx_prep_cmd = cmd_append_log(gmx_prep, gmx_prep_log)
gmx_run_cmd = cmd_append_log(gmx_run, gmx_run_log)
numb_walkers = jdata["numb_walkers"]
batch_jobs = jdata['batch_jobs']
batch_time_limit = jdata['batch_time_limit']
batch_modules = jdata['batch_modules']
batch_sources = jdata['batch_sources']
# print('debug', glob.glob(work_path + "/[0-9]*[0-9]"))
# all_task = glob.glob(work_path + "/[0-9]*[0-9]")
all_task = list(
filter(lambda x: os.path.isdir(x),
glob.glob(work_path + "/[0-9]*[0-9]")))
all_task.sort()
# all_task_basedir = [os.path.relpath(ii, work_path) for ii in all_task]
# print('run_enhc:work_path', work_path)
# print('run_enhc:gmx_prep_cmd:', gmx_prep_cmd)
# print('run_enhc:gmx_run_cmd:', gmx_run_cmd)
# print('run_enhc:all_task:', all_task)
# print('run_enhc:all_task_basedir:', all_task_basedir)
# print('run_enhc:batch_jobs:', batch_jobs)
#
# lazy_local_context = LazyLocalContext(local_root='./', work_profile=None)
# # pbs = PBS(context=lazy_local_context)
# slurm = Slurm(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=work_path, resources=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=work_path, resources=resources, batch=slurm, task_list=gmx_run_task)
# gmx_run_submission.run_submission()
global exec_machine
exec_hosts(MachineLocal, gmx_prep_cmd, 1, all_task, None)
if batch_jobs:
exec_batch(gmx_run_cmd,
enhc_thread,
1,
all_task,
task_args=None,
time_limit=batch_time_limit,
modules=batch_modules,
sources=batch_sources)
else:
if len(all_task) == 1:
exec_hosts(MachineLocal, gmx_run_cmd, enhc_thread, all_task, None)
else:
exec_hosts_batch(exec_machine, gmx_run_cmd, enhc_thread, all_task,
None)
