From e850999e31eaecf6f77ce040b6f3eba270935700 Mon Sep 17 00:00:00 2001
From: "Kurt A. O'Hearn" <ohearnk@msu.edu>
Date: Wed, 9 Jan 2019 23:34:20 -0500
Subject: [PATCH] sPuReMD: update tools/run_sim.py for running user-specified
(custom) MD simulations.
---
tools/run_sim.py | 82 +++++++++++++++++++++++++++++++++++++++++++++---
1 file changed, 77 insertions(+), 5 deletions(-)
diff --git a/tools/run_sim.py b/tools/run_sim.py
index 84426fda..5c7875fa 100644
--- a/tools/run_sim.py
+++ b/tools/run_sim.py
@@ -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',
--
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