Skip to content
Snippets Groups Projects
Commit e850999e authored by Kurt A. O'Hearn's avatar Kurt A. O'Hearn
Browse files

sPuReMD: update tools/run_sim.py for running user-specified (custom) MD simulations.

parent 6ea9210e
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
Showing
with 77 additions and 5 deletions
tools/run_sim.py
+ 77
− 5
View file @ e850999e
......@@ -108,6 +108,14 @@ class TestCase():
r'(?P<key>\bcompress\b\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
'press_mode': lambda l, x: sub(
r'(?P<key>\bpress_mode\b\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
'write_freq': lambda l, x: sub(
r'(?P<key>\bwrite_freq\b\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
'traj_compress': lambda l, x: sub(
r'(?P<key>\btraj_compress\b\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
'traj_format': lambda l, x: sub(
r'(?P<key>\btraj_format\b\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
'traj_title': lambda l, x: sub(
r'(?P<key>\btraj_title\b\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
}
self.__params['geo_format'] = geo_format
self.__min_step = min_step
......@@ -258,7 +266,7 @@ restart_freq 0 ! 0: do not output any restart f
def _create_output_file_base(self, run_type, param_dict):
if run_type == 'serial' or run_type == 'openmp':
param_dict['name'] = path.basename(self.__geo_file).split('.')[0] \
name = path.basename(self.__geo_file).split('.')[0] \
+ '_cm' + param_dict['charge_method'] \
+ '_s' + param_dict['nsteps'] \
+ '_q' + param_dict['cm_solver_type'] \
......@@ -273,7 +281,7 @@ restart_freq 0 ! 0: do not output any restart f
+ '_paji' + param_dict['cm_solver_pre_app_jacobi_iters'] \
+ '_t' + param_dict['threads']
elif run_type == 'mpi' or run_type == 'mpi+gpu':
param_dict['name'] = path.basename(self.__geo_file).split('.')[0] \
name = path.basename(self.__geo_file).split('.')[0] \
+ '_cm' + param_dict['charge_method'] \
+ '_s' + param_dict['nsteps'] \
+ '_proc' + param_dict['proc_by_dim'].replace(':', '_') \
......@@ -289,8 +297,10 @@ restart_freq 0 ! 0: do not output any restart f
+ '_pcsai' + param_dict['cm_solver_pre_comp_sai_thres'] \
+ '_pa' + param_dict['cm_solver_pre_app_type'] \
+ '_paji'+ str(param_dict['cm_solver_pre_app_jacobi_iters'])
else:
name = 'default_sim'
return param_dict
return name
def run_md(self, binary, run_type, mpi_cmd):
from itertools import product
......@@ -305,7 +315,9 @@ restart_freq 0 ! 0: do not output any restart f
# create Cartesian product of all supplied sets of parameter values
for p in product(*[self.__params[k] for k in self.__param_names]):
param_dict = dict((k, v) for (k, v) in zip(self.__param_names, p))
param_dict = self._create_output_file_base(run_type, param_dict)
param_dict['name'] = self._create_output_file_base(run_type, param_dict)
if not param_dict['traj_title']:
param_dict['traj_title'] = param_dict['name'] + '.trj'
temp_file = path.join(temp_dir, 'control')
self._create_control_file(param_dict, temp_file)
......@@ -407,7 +419,7 @@ restart_freq 0 ! 0: do not output any restart f
# create Cartesian product of all supplied sets of parameter values
for p in product(*[self.__params[k] for k in self.__param_names]):
param_dict = dict((k, v) for (k, v) in zip(self.__param_names, p))
param_dict = self._create_output_file_base(run_type, param_dict)
param_dict['name'] = self._create_output_file_base(run_type, param_dict)
self._process_result(fout, param_dict, self.__min_step, self.__max_step)
......@@ -521,6 +533,7 @@ if __name__ == '__main__':
parser = argparse.ArgumentParser(description='Molecular dynamics simulation tools used with specified data sets.')
subparsers = parser.add_subparsers(help="Actions.")
run_md_parser = subparsers.add_parser("run_md")
run_md_custom_parser = subparsers.add_parser("run_md_custom")
parse_results_parser = subparsers.add_parser("parse_results")
submit_jobs_parser = subparsers.add_parser("submit_jobs")
......@@ -538,6 +551,22 @@ if __name__ == '__main__':
choices=DATA_SETS, help='Data set(s) used for the MD simulation(s).')
run_md_parser.set_defaults(func=run_md)
run_md_custom_parser.add_argument('-b', '--binary', metavar='binary', default=None, nargs=1,
help='Binary file used for running the MD simulation(s).')
run_md_custom_parser.add_argument('-p', '--params', metavar='params', action='append', default=None, nargs=2,
help='Paramater name and value pairs for the simulation as defined in the control file.'
+ ' Multiple values for a parameter can be specified using commas, and each'
+ ' value will constitute a separate MD simulation.')
run_md_custom_parser.add_argument('-m', '--mpi_cmd', metavar='mpi_cmd', default=['mpirun'], nargs=1,
help='MPI command type and arguments. Examples: \'mpirun\', \'srun:1:32:1\'.')
run_md_custom_parser.add_argument('run_type', nargs=1,
choices=RUN_TYPES, help='Run type for the MD simulation(s).')
run_md_custom_parser.add_argument('geo_file', nargs=1,
help='Geometry file used for the MD simulation.')
run_md_custom_parser.add_argument('ffield_file', nargs=1,
help='Force field parameter file used for the MD simulation.')
run_md_custom_parser.set_defaults(func=run_md_custom)
parse_results_parser.add_argument('-f', '--out_file', metavar='out_file', default=None, nargs=1,
help='Output file to write results.')
parse_results_parser.add_argument('-p', '--params', metavar='params', action='append', default=None, nargs=2,
......@@ -616,6 +645,10 @@ if __name__ == '__main__':
'pt_mass': ['5000.0'],
'compress': ['0.008134'],
'press_mode': ['0'],
'write_freq': ['0'],
'traj_format': ['0'],
'traj_compress': ['0'],
'traj_title': [None],
}
return data_dir, control_params_dict
......@@ -754,6 +787,45 @@ if __name__ == '__main__':
for test in test_cases:
test.run_md(binary, args.run_type[0], args.mpi_cmd[0].split(':'))
def run_md_custom(args):
if args.binary:
binary = args.binary[0]
# remove executable and back up two directory levels
base_dir = path.dirname(path.dirname(path.dirname(path.abspath(binary))))
else:
base_dir = getcwd()
if args.run_type[0] == 'serial' or args.run_type[0] == 'openmp':
binary = path.join(base_dir, 'sPuReMD/bin/spuremd')
elif args.run_type[0] == 'mpi':
binary = path.join(base_dir, 'PuReMD/bin/puremd')
elif args.run_type[0] == 'mpi+gpu':
binary = path.join(base_dir, 'PG-PuReMD/bin/pg-puremd')
_, control_params_dict = setup_defaults(base_dir)
# overwrite default control file parameter values if supplied via command line args
if args.params:
for param in args.params:
if param[0] in control_params_dict:
control_params_dict[param[0]] = param[1].split(',')
else:
print("ERROR: Invalid parameter {0}. Terminating...".format(param[0]))
exit(-1)
geo_base, geo_ext = path.splitext(args.geo_file[0])
if geo_ext == '.pdb':
geo_format = ['1']
elif geo_ext == '.geo':
geo_format = ['0']
else:
print("ERROR: unrecognized geometry format {0}. Terminating...".format(ext))
exit(-1)
test_case = TestCase(geo_base, args.geo_file[0], args.ffield_file[0],
params=control_params_dict, geo_format=geo_format)
test_case.run_md(binary, args.run_type[0], args.mpi_cmd[0].split(':'))
def parse_results(args):
header_fmt_str = '{:15}|{:5}|{:5}|{:5}|{:5}|{:5}|{:5}|{:5}|{:5}|{:5}|{:5}|{:5}|{:10}|{:10}|{:10}|{:10}|{:10}|{:3}|{:10}\n'
header_str = ['Data Set', 'Steps', 'CM', 'Solvr', 'Q Tol', 'QDS', 'PreCT', 'PreCD', 'PreCS', 'PCSAI', 'PreAT', 'PreAJ', 'Pre Comp',
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment