From 1af6b695c6e300641d81daea87b7f801d39e661e Mon Sep 17 00:00:00 2001
From: "Kurt A. O'Hearn" <ohearnk@msu.edu>
Date: Sat, 22 Sep 2018 22:35:17 -0400
Subject: [PATCH] Tools: reformat proc_by_dim and fix an issue with subprocess
command building.
---
tools/run_sim_puremd.py | 36 +++++++++++++-----------------------
1 file changed, 13 insertions(+), 23 deletions(-)
diff --git a/tools/run_sim_puremd.py b/tools/run_sim_puremd.py
index 181e06bd..b7b13774 100644
--- a/tools/run_sim_puremd.py
+++ b/tools/run_sim_puremd.py
@@ -31,15 +31,9 @@ class TestCase():
r'(?P<key>ensemble_type\s+)\S+(?P<comment>.*)', r'\g<key>{0}\g<comment>'.format(x), l), \
'nsteps': lambda l, x: sub(
r'(?P<key>nsteps\s+)\S+(?P<comment>.*)', r'\g<key>{0}\g<comment>'.format(x), l), \
- 'proc_by_dim1': lambda l, x: sub(
- r'(?P<key>proc_by_dim\s+)\S+(?P<proc_by_dim2>\s+\S+)(?P<proc_by_dim3>\s+\S+)(?P<comment>.*)',
- r'\g<key>{0}\g<proc_by_dim2>\g<proc_by_dim3>\g<comment>'.format(x), l), \
- 'proc_by_dim2': lambda l, x: sub(
- r'(?P<key>proc_by_dim\s+)(?P<proc_by_dim1>\S+\s+)\S+(?P<proc_by_dim3>\s+\S+)(?P<comment>.*)',
- r'\g<key>\g<proc_by_dim1>{0}\g<proc_by_dim3>\g<comment>'.format(x), l), \
- 'proc_by_dim3': lambda l, x: sub(
- r'(?P<key>proc_by_dim\s+)(?P<proc_by_dim1>\S+\s+)(?P<proc_by_dim2>\S+\s+)\S+(?P<comment>.*)',
- r'\g<key>\g<proc_by_dim1>\g<proc_by_dim2>{0}\g<comment>'.format(x), l), \
+ 'proc_by_dim': lambda l, x: sub(
+ r'(?P<key>proc_by_dim\s+)\S+\s+\S+\s+\S+(?P<comment>.*)',
+ r'\g<key>{0} {1} {2}\g<comment>'.format(*(x.split(':'))), l), \
'tabulate_long_range': lambda l, x: sub(
r'(?P<key>tabulate_long_range\s+)\S+(?P<comment>.*)', r'\g<key>{0}\g<comment>'.format(x), l), \
'reneighbor': lambda l, x: sub(
@@ -100,15 +94,18 @@ class TestCase():
fp_temp.close()
def run(self, binary, process_results=False):
+ from operator import mul
+ from functools import reduce
+
# command to run as subprocess
args = [
'mpirun',
'-np',
- # placeholder, substituted below
- '0',
+ '0', # placeholder, substituted below
binary,
self.__geo_file,
self.__ffield_file,
+ '', # placeholder, substituted below
]
env = dict(environ)
@@ -128,9 +125,7 @@ class TestCase():
param_dict['name'] = path.basename(self.__geo_file).split('.')[0] \
+ '_cm' + param_dict['charge_method'] \
+ '_s' + param_dict['nsteps'] \
- + '_proc' + param_dict['proc_by_dim1'] \
- + '_' + param_dict['proc_by_dim2'] \
- + '_' + param_dict['proc_by_dim3'] \
+ + '_proc' + param_dict['proc_by_dim'].replace(':', '_') \
+ '_ren' + param_dict['reneighbor'] \
+ '_skind' + param_dict['vlist_buffer'] \
+ '_q' + param_dict['cm_solver_type'] \
@@ -144,16 +139,14 @@ class TestCase():
+ '_pa' + param_dict['cm_solver_pre_app_type'] \
+ '_paji'+ str(param_dict['cm_solver_pre_app_jacobi_iters'])
- args[2] = str(int(param_dict['proc_by_dim1'])
- * int(param_dict['proc_by_dim2'])
- * int(param_dict['proc_by_dim3']));
+ args[2] = str(reduce(mul,
+ map(int, param_dict['proc_by_dim'].split(':')), 1))
if not process_results:
self._setup(param_dict, temp_file)
-
#env['OMP_NUM_THREADS'] = param_dict['threads']
start = time()
- args.append(temp_file);
+ args[6] = temp_file;
proc_handle = Popen(args, stdout=PIPE, stderr=PIPE, env=env, universal_newlines=True)
stdout, stderr = proc_handle.communicate()
stop = time()
@@ -167,7 +160,6 @@ class TestCase():
else:
self._process_result(fout, param_dict, self.__min_step, self.__max_step)
- break
fout.close()
if path.exists(temp_file):
@@ -275,9 +267,7 @@ if __name__ == '__main__':
params = {
'ensemble_type': ['0'],
'nsteps': ['100'],
- 'proc_by_dim1': ['1'],
- 'proc_by_dim2': ['1'],
- 'proc_by_dim3': ['1'],
+ 'proc_by_dim': ['1:1:1'],
'tabulate_long_range': ['0'],
'reneighbor': ['1'],
'vlist_buffer': ['0'],
--
GitLab