diff --git a/tools/run_sim.py b/tools/run_sim.py
index 5496c1f614ae978cbb3be6457908bbcd81a2125b..9f827c3e052219c11b66d77e6c844596e9928e2f 100644
--- a/tools/run_sim.py
+++ b/tools/run_sim.py
@@ -1,20 +1,13 @@
#!/usr/bin/env python3
-import argparse
-from fileinput import input
-from itertools import product
-from re import sub
-from subprocess import Popen, PIPE
-from os import getcwd, environ, path, remove, rename, rmdir
-from sys import exit
-from tempfile import mkdtemp
-from time import time
-
class TestCase():
- def __init__(self, geo_file, ffield_file, control_file, params={}, result_header_fmt='',
+ def __init__(self, data_set, geo_file, ffield_file, control_file, params={}, result_header_fmt='',
result_header='', result_body_fmt='', result_file='results.txt', geo_format='1',
min_step=None, max_step=None):
+ from re import sub
+
+ self.__data_set = data_set
self.__geo_file = geo_file
self.__ffield_file = ffield_file
self.__control_file = control_file
@@ -24,7 +17,7 @@ class TestCase():
self.__result_header = result_header
self.__result_body_fmt = result_body_fmt
self.__result_file = result_file
- self.__control_res = { \
+ self.__control_regexes = { \
'name': lambda l, x: sub(
r'(?P<key>simulation_name\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
'ensemble_type': lambda l, x: sub(
@@ -68,42 +61,44 @@ class TestCase():
'geo_format': lambda l, x: sub(
r'(?P<key>geo_format\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
}
-
self.__params['geo_format'] = geo_format
self.__min_step = min_step
self.__max_step = max_step
- def _setup(self, param, temp_file):
- fp = open(self.__control_file, 'r')
- lines = fp.read()
- fp.close()
- for k in self.__control_res.keys():
+ def _create_control_file(self, param, new_control_file):
+ # read in template control file
+ try:
+ with open(self.__control_file, 'r') as fp:
+ lines = fp.read()
+ except Exception as e:
+ print("ERROR: Coult not read template control file!")
+ raise e
+
+ # substitute key-value pairs in the text of the control file
+ # using a dict of regexes (used to match and substitute
+ # specific key-value pairs)
+ for k in self.__control_regexes.keys():
try:
- lines = self.__control_res[k](lines, param[k])
+ lines = self.__control_regexes[k](lines, param[k])
except KeyError:
+ # if key missing from regex dict, skip for now
pass
- fp_temp = open(temp_file, 'w')
- fp_temp.write(lines)
- fp_temp.close()
- def run(self, binary, process_results=False):
- args = binary.split()
- args.append(self.__geo_file)
- args.append( self.__ffield_file)
- args.append("")
- env = dict(environ)
+ # write out new control file text using supplied file name
+ with open(new_control_file, 'w') as fp:
+ fp.write(lines)
- write_header = True
- if path.exists(self.__result_file):
- write_header = False
- fout = open(self.__result_file, 'a')
- if write_header:
- fout.write(self.__result_header_fmt.format(*self.__result_header))
- fout.flush()
+ def run(self, binary, process_results=False):
+ from itertools import product
+ from os import environ, path, remove, rmdir
+ from subprocess import Popen, PIPE
+ from tempfile import mkdtemp
+ from time import time
+ env = dict(environ)
temp_dir = mkdtemp()
- temp_file = path.join(temp_dir, path.basename(self.__control_file))
+ # 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['name'] = path.basename(self.__geo_file).split('.')[0] \
@@ -121,29 +116,33 @@ class TestCase():
+ '_paji' + param_dict['cm_solver_pre_app_jacobi_iters'] \
+ '_t' + param_dict['threads']
- if not process_results:
- self._setup(param_dict, temp_file)
-
- env['OMP_NUM_THREADS'] = param_dict['threads']
- start = time()
- args[-1] = temp_file
- proc_handle = Popen(args, stdout=PIPE, stderr=PIPE, env=env, universal_newlines=True)
- stdout, stderr = proc_handle.communicate()
- stop = time()
- if proc_handle.returncode < 0:
- print("WARNING: process terminated with code {0}".format(proc_handle.returncode))
- else:
- print('stdout:')
- print(stdout)
- print('stderr:')
- print(stderr)
+ temp_file = path.join(temp_dir, path.basename(self.__control_file))
+ self._create_control_file(param_dict, temp_file)
+ env['OMP_NUM_THREADS'] = param_dict['threads']
+
+ cmd_args = binary.split()
+ cmd_args.append(self.__geo_file)
+ cmd_args.append(self.__ffield_file)
+ cmd_args.append("")
+ cmd_args[-1] = temp_file
+
+ start = time()
+ proc_handle = Popen(cmd_args, stdout=PIPE, stderr=PIPE, env=env, universal_newlines=True)
+ stdout, stderr = proc_handle.communicate()
+ stop = time()
+
+ if proc_handle.returncode < 0:
+ print("WARNING: process terminated with code {0}".format(proc_handle.returncode))
else:
- self._process_result(fout, param_dict, self.__min_step, self.__max_step)
+ print('stdout:')
+ print(stdout)
+ print('stderr:')
+ print(stderr)
+
+ if path.exists(temp_file):
+ remove(temp_file)
- fout.close()
- if path.exists(temp_file):
- remove(temp_file)
if path.exists(temp_dir):
rmdir(temp_dir)
@@ -206,188 +205,380 @@ class TestCase():
log_file, int(param['nsteps']), max(line_cnt - 3, 0)))
fout.flush()
+ def parse_results(self):
+ from itertools import product
+ from os import path
+ write_header = True
+ if path.exists(self.__result_file):
+ write_header = False
-if __name__ == '__main__':
- DATA = [ \
- 'bilayer_56800', 'bilayer_340800', \
- 'dna_19733', \
- 'petn_48256', \
- 'silica_6000', 'silica_72000', 'silica_300000', \
- 'water_6540', 'water_78480', 'water_327000', \
- ]
-
- parser = argparse.ArgumentParser(description='Run molecular dynamics simulations on specified data sets.')
- parser.add_argument('-b', '--binary', metavar='binary', default=None, nargs=1,
- help='Binary file to run.')
- parser.add_argument('-f', '--out_file', metavar='out_file', default=None, nargs=1,
- help='Output file to write results.')
- parser.add_argument('-r', '--process_results', default=False, action='store_true',
- help='Process simulation results only (do not perform simulations).')
- parser.add_argument('-p', '--params', metavar='params', action='append', default=None, nargs=2,
- help='Paramater name and value pairs for the simulation, which multiple values comma delimited.')
- parser.add_argument('-n', '--min_step', metavar='min_step', default=None, nargs=1,
- help='Minimum simulation step to begin aggregating results.')
- parser.add_argument('-x', '--max_step', metavar='max_step', default=None, nargs=1,
- help='Maxiumum simulation step for aggregating results.')
- parser.add_argument('data', nargs='+',
- choices=DATA, help='Data sets for which to run simulations.')
-
- # parse args and take action
- args = parser.parse_args()
+ with open(self.__result_file, 'a') as fout:
+ if write_header:
+ fout.write(self.__result_header_fmt.format(*self.__result_header))
+ fout.flush()
+
+ # 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['name'] = path.basename(self.__geo_file).split('.')[0] \
+ + '_cm' + param_dict['charge_method'] \
+ + '_s' + param_dict['nsteps'] \
+ + '_q' + param_dict['cm_solver_type'] \
+ + '_qtol' + param_dict['cm_solver_q_err'] \
+ + '_qds' + param_dict['cm_domain_sparsity'] \
+ + '_pc' + param_dict['cm_solver_pre_comp_type'] \
+ + '_pcr' + param_dict['cm_solver_pre_comp_refactor'] \
+ + '_pctol' + param_dict['cm_solver_pre_comp_droptol'] \
+ + '_pcs' + param_dict['cm_solver_pre_comp_sweeps'] \
+ + '_pcsai' + param_dict['cm_solver_pre_comp_sai_thres'] \
+ + '_pa' + param_dict['cm_solver_pre_app_type'] \
+ + '_paji' + param_dict['cm_solver_pre_app_jacobi_iters'] \
+ + '_t' + param_dict['threads']
- base_dir = getcwd()
- control_dir = path.join(base_dir, 'environ')
- data_dir = path.join(base_dir, 'data/benchmarks')
-
- 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',
- 'Pre App', 'Iters', 'SpMV', 'CM', 'Thd', 'Time (s)']
- body_fmt_str = '{:15} {:5} {:5} {:5} {:5} {:5} {:5} {:5} {:5} {:5} {:5} {:5} {:10.3f} {:10.3f} {:10.3f} {:10.3f} {:10.3f} {:3} {:10.3f}\n'
-
- params = {
- 'ensemble_type': ['0'],
- 'nsteps': ['20'],
- 'tabulate_long_range': ['0'],
- 'charge_method': ['0'],
- 'cm_q_net': ['0.0'],
- 'cm_solver_type': ['0'],
- 'cm_solver_max_iters': ['20'],
- 'cm_solver_restart': ['100'],
- 'cm_solver_q_err': ['1e-6'],
- 'cm_domain_sparsity': ['1.0'],
- 'cm_init_guess_extrap1': ['3'],
- 'cm_init_guess_extrap2': ['2'],
- 'cm_solver_pre_comp_type': ['2'],
- 'cm_solver_pre_comp_refactor': ['100'],
- 'cm_solver_pre_comp_droptol': ['0.0'],
- 'cm_solver_pre_comp_sweeps': ['3'],
- 'cm_solver_pre_comp_sai_thres': ['0.1'],
- 'cm_solver_pre_app_type': ['2'],
- 'cm_solver_pre_app_jacobi_iters': ['30'],
- 'threads': ['1'],
- 'geo_format': [],
- }
-
- if args.out_file:
- result_file = args.out_file[0]
- else:
- result_file = 'result.txt'
-
- if args.binary:
- binary = args.binary[0]
- else:
- binary = path.join(base_dir, 'sPuReMD/bin/spuremd')
-
- # overwrite default params, if supplied via command line args
- if args.params:
- for param in args.params:
- if param[0] in params:
- params[param[0]] = param[1].split(',')
+ self._process_result(fout, param_dict, self.__min_step, self.__max_step)
+
+ def _build_slurm_script(self, binary, param_values):
+ job_script = """\
+#!/bin/bash -login
+
+#SBATCH --time=03:59:00
+#SBATCH --mem=120G
+#SBATCH --nodes=1
+#SBATCH --cpus-per-task=28
+#SBATCH --constraint=lac
+
+module purge
+module load GCC/7.3.0-2.30
+
+cd \${SLURM_SUBMIT_DIR}
+
+python3 tools/run_sim.py \\\
+"""
+
+ job_script += "\n -b " + binary + " \\"
+
+ for (k, v) in zip(self.__param_names, param_values):
+ job_script += "\n -p " + k + " " + v + " \\"
+
+ job_script += "\n " + self.__data_set
+
+ return job_script
+
+ def _build_pbs_script(self, binary, param_values):
+ job_script = """\
+#!/bin/bash -login
+
+#PBS -l walltime=03:59:00,nodes=1:ppn=28,mem=120gb,feature=lac
+
+module purge
+module load GCC/7.3.0-2.30
+
+cd \${PBS_O_WORKDIR}
+
+python3 tools/run_sim.py \\\
+"""
+
+ job_script += "\n -b " + binary + " \\"
+
+ for (k, v) in zip(self.__param_names, param_values):
+ job_script += "\n -p " + k + " " + v + " \\"
+
+ job_script += "\n " + self.__data_set
+
+ return job_script
+
+ def submit_jobs(self, binary, job_script_type):
+ from itertools import product
+ from subprocess import Popen, PIPE
+
+ for p in product(*[self.__params[k] for k in self.__param_names]):
+ if job_script_type == 'slurm':
+ job_script = self._build_slurm_script(binary, p)
+
+ cmd_args = ['sbatch']
+
+ if job_script_type == 'pbs':
+ job_script = self._build_pbs_script(binary, p)
+
+ cmd_args = ['qsub']
+
+ proc_handle = Popen(cmd_args, stdin=PIPE, stdout=PIPE, stderr=PIPE, universal_newlines=True)
+ stdout, stderr = proc_handle.communicate(job_script)
+
+ if proc_handle.returncode < 0:
+ print("WARNING: process terminated with code {0}".format(proc_handle.returncode))
else:
- print("[ERROR] Invalid parameter {0}. Terminating...".format(param[0]))
- exit(-1)
-
- if args.min_step:
- min_step = int(args.min_step[0])
- else:
- min_step = None
- if args.max_step:
- max_step = int(args.max_step[0])
- else:
- max_step = None
-
- test_cases = []
- if 'water_6540' in args.data:
- test_cases.append(
- TestCase(path.join(data_dir, 'water/water_6540.pdb'),
- path.join(data_dir, 'water/ffield_acks2.water'),
- path.join(control_dir, 'param.gpu.water'),
- params=params, result_header_fmt=header_fmt_str,
- result_header = header_str, result_body_fmt=body_fmt_str,
- geo_format=['1'], result_file=result_file,
- min_step=min_step, max_step=max_step))
- if 'water_78480' in args.data:
- test_cases.append(
- TestCase(path.join(data_dir, 'water/water_78480.geo'),
- path.join(data_dir, 'water/ffield_acks2.water'),
- path.join(control_dir, 'param.gpu.water'),
- params=params, result_header_fmt=header_fmt_str,
- result_header = header_str, result_body_fmt=body_fmt_str,
- geo_format=['0'], result_file=result_file,
- min_step=min_step, max_step=max_step))
- if 'water_327000' in args.data:
- test_cases.append(
- TestCase(path.join(data_dir, 'water/water_327000.geo'),
- path.join(data_dir, 'water/ffield_acks2.water'),
- path.join(control_dir, 'param.gpu.water'),
- params=params, result_header_fmt=header_fmt_str,
- result_header = header_str, result_body_fmt=body_fmt_str,
- geo_format=['0'], result_file=result_file,
- min_step=min_step, max_step=max_step))
- if 'bilayer_56800' in args.data:
- test_cases.append(
- TestCase(path.join(data_dir, 'bilayer/bilayer_56800.pdb'),
- path.join(data_dir, 'bilayer/ffield-bio'),
- path.join(control_dir, 'param.gpu.water'),
- params=params, result_header_fmt=header_fmt_str,
- result_header = header_str, result_body_fmt=body_fmt_str,
- geo_format=['1'], result_file=result_file,
- min_step=min_step, max_step=max_step))
- if 'bilayer_340800' in args.data:
- test_cases.append(
- TestCase(path.join(data_dir, 'bilayer/bilayer_340800.geo'),
- path.join(data_dir, 'bilayer/ffield-bio'),
- path.join(control_dir, 'param.gpu.water'),
- params=params, result_header_fmt=header_fmt_str,
- result_header = header_str, result_body_fmt=body_fmt_str,
- geo_format=['0'], result_file=result_file,
- min_step=min_step, max_step=max_step))
- if 'dna_19733' in args.data:
- test_cases.append(
- TestCase(path.join(data_dir, 'dna/dna_19733.pdb'),
- path.join(data_dir, 'dna/ffield-dna'),
- path.join(control_dir, 'param.gpu.water'),
- params=params, result_header_fmt=header_fmt_str,
- result_header = header_str, result_body_fmt=body_fmt_str,
- geo_format=['1'], result_file=result_file,
- min_step=min_step, max_step=max_step))
- if 'silica_6000' in args.data:
- test_cases.append(
- TestCase(path.join(data_dir, 'silica/silica_6000.pdb'),
- path.join(data_dir, 'silica/ffield-bio'),
- path.join(control_dir, 'param.gpu.water'),
- params=params, result_header_fmt=header_fmt_str,
- result_header = header_str, result_body_fmt=body_fmt_str,
- geo_format=['1'], result_file=result_file,
- min_step=min_step, max_step=max_step))
- if 'silica_72000' in args.data:
- test_cases.append(
- TestCase(path.join(data_dir, 'silica/silica_72000.geo'),
- path.join(data_dir, 'silica/ffield-bio'),
- path.join(control_dir, 'param.gpu.water'),
- params=params, result_header_fmt=header_fmt_str,
- result_header = header_str, result_body_fmt=body_fmt_str,
- geo_format=['0'], result_file=result_file,
- min_step=min_step, max_step=max_step))
- if 'silica_300000' in args.data:
- test_cases.append(
- TestCase(path.join(data_dir, 'silica/silica_300000.geo'),
- path.join(data_dir, 'silica/ffield-bio'),
- path.join(control_dir, 'param.gpu.water'),
- params=params, result_header_fmt=header_fmt_str,
- result_header = header_str, result_body_fmt=body_fmt_str,
- geo_format=['0'], result_file=result_file,
- min_step=min_step, max_step=max_step))
- if 'petn_48256' in args.data:
- test_cases.append(
- TestCase(path.join(data_dir, 'petn/petn_48256.pdb'),
- path.join(data_dir, 'petn/ffield.petn'),
- path.join(control_dir, 'param.gpu.water'),
- params=params, result_header_fmt=header_fmt_str,
- result_header = header_str, result_body_fmt=body_fmt_str,
- geo_format=['1'], result_file=result_file,
- min_step=min_step, max_step=max_step))
-
- for test in test_cases:
- test.run(binary, process_results=args.process_results)
+ print('stdout:')
+ print(stdout)
+ print('stderr:')
+ print(stderr)
+
+
+if __name__ == '__main__':
+ import argparse
+ from os import getcwd, path
+ from sys import exit
+
+ def setup_parser():
+ DATA = [ \
+ 'bilayer_56800', 'bilayer_340800', \
+ 'dna_19733', \
+ 'petn_48256', \
+ 'silica_6000', 'silica_72000', 'silica_300000', \
+ 'water_6540', 'water_78480', 'water_327000', \
+ ]
+ JOB_TYPES = ['pbs', 'slurm']
+
+ parser = argparse.ArgumentParser(description='Molecular dynamics simulation tools used with specified data sets.')
+ subparsers = parser.add_subparsers(help="Actions types.")
+ run_md_parser = subparsers.add_parser("run_md")
+ parse_results_parser = subparsers.add_parser("parse_results")
+ submit_jobs_parser = subparsers.add_parser("submit_jobs")
+
+ run_md_parser.add_argument('-b', '--binary', metavar='binary', default=None, nargs=1,
+ help='Binary file to run.')
+ run_md_parser.add_argument('-p', '--params', metavar='params', action='append', default=None, nargs=2,
+ help='Paramater name and value pairs for the simulation, with multiple values comma delimited.')
+ run_md_parser.add_argument('data_sets', nargs='+',
+ choices=DATA, help='Data sets for which to run simulations.')
+ run_md_parser.set_defaults(func=run_md)
+
+ 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,
+ help='Paramater name and value pairs for the simulation, with multiple values comma delimited.')
+ parse_results_parser.add_argument('-n', '--min_step', metavar='min_step', default=None, nargs=1,
+ help='Minimum simulation step to begin aggregating results.')
+ parse_results_parser.add_argument('-x', '--max_step', metavar='max_step', default=None, nargs=1,
+ help='Maxiumum simulation step for aggregating results.')
+ parse_results_parser.add_argument('data_sets', nargs='+',
+ choices=DATA, help='Data sets for which to parse results.')
+ parse_results_parser.set_defaults(func=parse_results)
+
+ submit_jobs_parser.add_argument('-b', '--binary', metavar='binary', default=None, nargs=1,
+ help='Binary file to run.')
+ submit_jobs_parser.add_argument('-p', '--params', metavar='params', action='append', default=None, nargs=2,
+ help='Paramater name and value pairs for the simulation, with multiple values comma delimited.')
+ submit_jobs_parser.add_argument('job_script_type', nargs=1,
+ choices=JOB_TYPES, help='Type of job script.')
+ submit_jobs_parser.add_argument('data_sets', nargs='+',
+ choices=DATA, help='Data sets for which to run simulations.')
+ submit_jobs_parser.set_defaults(func=submit_jobs)
+
+ return parser
+
+ def setup_defaults(base_dir):
+ control_dir = path.join(base_dir, 'environ')
+ data_dir = path.join(base_dir, 'data/benchmarks')
+ control_params_dict = {
+ 'ensemble_type': ['0'],
+ 'nsteps': ['20'],
+ 'tabulate_long_range': ['0'],
+ 'charge_method': ['0'],
+ 'cm_q_net': ['0.0'],
+ 'cm_solver_type': ['0'],
+ 'cm_solver_max_iters': ['20'],
+ 'cm_solver_restart': ['100'],
+ 'cm_solver_q_err': ['1e-6'],
+ 'cm_domain_sparsity': ['1.0'],
+ 'cm_init_guess_extrap1': ['3'],
+ 'cm_init_guess_extrap2': ['2'],
+ 'cm_solver_pre_comp_type': ['1'],
+ 'cm_solver_pre_comp_refactor': ['100'],
+ 'cm_solver_pre_comp_droptol': ['0.0'],
+ 'cm_solver_pre_comp_sweeps': ['3'],
+ 'cm_solver_pre_comp_sai_thres': ['0.1'],
+ 'cm_solver_pre_app_type': ['0'],
+ 'cm_solver_pre_app_jacobi_iters': ['30'],
+ 'threads': ['1'],
+ 'geo_format': [],
+ }
+ return control_dir, data_dir, control_params_dict
+
+ def setup_test_cases(data_sets, data_dir, control_dir, control_params, header_fmt_str=None,
+ header_str=None, body_fmt_str=None, result_file='result.txt', min_step=None, max_step=None):
+ test_cases = []
+
+ if 'water_6540' in data_sets:
+ test_cases.append(
+ TestCase('water_6540',
+ path.join(data_dir, 'water/water_6540.pdb'),
+ path.join(data_dir, 'water/ffield_acks2.water'),
+ path.join(control_dir, 'param.gpu.water'),
+ params=control_params, result_header_fmt=header_fmt_str,
+ result_header = header_str, result_body_fmt=body_fmt_str,
+ geo_format=['1'], result_file=result_file,
+ min_step=min_step, max_step=max_step))
+ if 'water_78480' in data_sets:
+ test_cases.append('water_78480',
+ TestCase(path.join(data_dir, 'water/water_78480.geo'),
+ path.join(data_dir, 'water/ffield_acks2.water'),
+ path.join(control_dir, 'param.gpu.water'),
+ params=control_params, result_header_fmt=header_fmt_str,
+ result_header = header_str, result_body_fmt=body_fmt_str,
+ geo_format=['0'], result_file=result_file,
+ min_step=min_step, max_step=max_step))
+ if 'water_327000' in data_sets:
+ test_cases.append(
+ TestCase('water_327000',
+ path.join(data_dir, 'water/water_327000.geo'),
+ path.join(data_dir, 'water/ffield_acks2.water'),
+ path.join(control_dir, 'param.gpu.water'),
+ params=control_params, result_header_fmt=header_fmt_str,
+ result_header = header_str, result_body_fmt=body_fmt_str,
+ geo_format=['0'], result_file=result_file,
+ min_step=min_step, max_step=max_step))
+ if 'bilayer_56800' in data_sets:
+ test_cases.append(
+ TestCase('bilayer_56800',
+ path.join(data_dir, 'bilayer/bilayer_56800.pdb'),
+ path.join(data_dir, 'bilayer/ffield-bio'),
+ path.join(control_dir, 'param.gpu.water'),
+ params=control_params, result_header_fmt=header_fmt_str,
+ result_header = header_str, result_body_fmt=body_fmt_str,
+ geo_format=['1'], result_file=result_file,
+ min_step=min_step, max_step=max_step))
+ if 'bilayer_340800' in data_sets:
+ test_cases.append(
+ TestCase('bilayer_340800',
+ path.join(data_dir, 'bilayer/bilayer_340800.geo'),
+ path.join(data_dir, 'bilayer/ffield-bio'),
+ path.join(control_dir, 'param.gpu.water'),
+ params=control_params, result_header_fmt=header_fmt_str,
+ result_header = header_str, result_body_fmt=body_fmt_str,
+ geo_format=['0'], result_file=result_file,
+ min_step=min_step, max_step=max_step))
+ if 'dna_19733' in data_sets:
+ test_cases.append(
+ TestCase('dna_19733',
+ path.join(data_dir, 'dna/dna_19733.pdb'),
+ path.join(data_dir, 'dna/ffield-dna'),
+ path.join(control_dir, 'param.gpu.water'),
+ params=control_params, result_header_fmt=header_fmt_str,
+ result_header = header_str, result_body_fmt=body_fmt_str,
+ geo_format=['1'], result_file=result_file,
+ min_step=min_step, max_step=max_step))
+ if 'silica_6000' in data_sets:
+ test_cases.append(
+ TestCase('silica_6000',
+ path.join(data_dir, 'silica/silica_6000.pdb'),
+ path.join(data_dir, 'silica/ffield-bio'),
+ path.join(control_dir, 'param.gpu.water'),
+ params=control_params, result_header_fmt=header_fmt_str,
+ result_header = header_str, result_body_fmt=body_fmt_str,
+ geo_format=['1'], result_file=result_file,
+ min_step=min_step, max_step=max_step))
+ if 'silica_72000' in data_sets:
+ test_cases.append(
+ TestCase('silica_72000',
+ path.join(data_dir, 'silica/silica_72000.geo'),
+ path.join(data_dir, 'silica/ffield-bio'),
+ path.join(control_dir, 'param.gpu.water'),
+ params=control_params, result_header_fmt=header_fmt_str,
+ result_header = header_str, result_body_fmt=body_fmt_str,
+ geo_format=['0'], result_file=result_file,
+ min_step=min_step, max_step=max_step))
+ if 'silica_300000' in data_sets:
+ test_cases.append(
+ TestCase('silica_300000',
+ path.join(data_dir, 'silica/silica_300000.geo'),
+ path.join(data_dir, 'silica/ffield-bio'),
+ path.join(control_dir, 'param.gpu.water'),
+ params=control_params, result_header_fmt=header_fmt_str,
+ result_header = header_str, result_body_fmt=body_fmt_str,
+ geo_format=['0'], result_file=result_file,
+ min_step=min_step, max_step=max_step))
+ if 'petn_48256' in data_sets:
+ test_cases.append(
+ TestCase('petn_48256',
+ path.join(data_dir, 'petn/petn_48256.pdb'),
+ path.join(data_dir, 'petn/ffield.petn'),
+ path.join(control_dir, 'param.gpu.water'),
+ params=control_params, result_header_fmt=header_fmt_str,
+ result_header = header_str, result_body_fmt=body_fmt_str,
+ geo_format=['1'], result_file=result_file,
+ min_step=min_step, max_step=max_step))
+
+ return test_cases
+
+ def run_md(args):
+ base_dir = getcwd()
+ control_dir, data_dir, control_params_dict = setup_defaults(base_dir)
+
+ if args.binary:
+ binary = args.binary[0]
+ else:
+ binary = path.join(base_dir, 'sPuReMD/bin/spuremd')
+
+ # 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)
+
+ test_cases = setup_test_cases(args.data_sets, data_dir, control_dir, control_params_dict)
+
+ for test in test_cases:
+ test.run(binary)
+
+ 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',
+ 'Pre App', 'Iters', 'SpMV', 'CM', 'Thd', 'Time (s)']
+ body_fmt_str = '{:15} {:5} {:5} {:5} {:5} {:5} {:5} {:5} {:5} {:5} {:5} {:5} {:10.3f} {:10.3f} {:10.3f} {:10.3f} {:10.3f} {:3} {:10.3f}\n'
+
+ base_dir = getcwd()
+ control_dir, data_dir, control_params_dict = setup_defaults(base_dir)
+
+ if args.out_file:
+ result_file = args.out_file[0]
+ else:
+ result_file = 'result.txt'
+
+ if args.min_step:
+ min_step = int(args.min_step[0])
+ else:
+ min_step = None
+
+ if args.max_step:
+ max_step = int(args.max_step[0])
+ else:
+ max_step = None
+
+ test_cases = setup_test_cases(args.data_sets, data_dir, control_dir, control_params_dict,
+ header_fmt_str=header_fmt_str, header_str=header_str, body_fmt_str=body_fmt_str,
+ result_file=result_file, min_step=min_step, max_step=max_step)
+
+ for test in test_cases:
+ test.parse_results()
+
+ def submit_jobs(args):
+ base_dir = getcwd()
+ control_dir, data_dir, control_params_dict = setup_defaults(base_dir)
+
+ if args.binary:
+ binary = args.binary[0]
+ else:
+ binary = path.join(base_dir, 'sPuReMD/bin/spuremd')
+
+ # 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)
+
+ test_cases = setup_test_cases(args.data_sets, data_dir, control_dir, control_params_dict)
+
+ for test in test_cases:
+ test.submit_jobs(binary, args.job_script_type[0])
+
+ parser = setup_parser()
+ args = parser.parse_args()
+ args.func(args)