diff --git a/environ/param.gpu.water b/environ/param.gpu.water
index 90288d3da7b9a108722c74a061ce47dd1d76c5e8..edd2784aa4f0a7a25df38e415d070f9cc392083c 100644
--- a/environ/param.gpu.water
+++ b/environ/param.gpu.water
@@ -35,7 +35,7 @@ compress 0.008134 ! in ps^2 * A / amu ( 4.5X10^(-5
press_mode 0 ! 0: internal + external pressure, 1: ext only, 2: int only
geo_format 1 ! 0: xyz, 1: pdb, 2: bgf
-write_freq 1000 ! write trajectory after so many steps
+write_freq 0 ! write trajectory after so many steps
traj_compress 0 ! 0: no compression 1: uses zlib to compress trajectory output
traj_format 0 ! 0: our own format (below options apply to this only), 1: xyz, 2: bgf, 3: pdb
traj_title WATER_NVT ! (no white spaces)
diff --git a/tools/run_sim.py b/tools/run_sim.py
index de1c0372609af6c4eccce3c8a2b8dd95a531a03e..39342fdb03a3f71591453199b561fbc9ca9ba7c8 100644
--- a/tools/run_sim.py
+++ b/tools/run_sim.py
@@ -1,91 +1,197 @@
#!/usr/bin/env python
from fileinput import input
+from itertools import product
from re import sub
from subprocess import Popen, PIPE
-from os import getcwd, environ, path, rename
+from os import getcwd, environ, path, remove, rename, rmdir
from sys import exit
+from tempfile import mkdtemp
from time import time
-base_dir = getcwd()
-control_dir = path.join(base_dir, 'environ')
-data_dir = path.join(base_dir, 'data/benchmarks')
-puremd_args = [ \
-# (path.join(data_dir, 'water/water_6540.pdb'), path.join(data_dir, 'water/ffield.water'), path.join(control_dir, 'param.gpu.water')), \
-# (path.join(data_dir, 'water/water_78480.pdb'), path.join(data_dir, 'water/ffield.water'), path.join(control_dir, 'param.gpu.water')), \
-# (path.join(data_dir, 'water/water_327000.geo'), path.join(data_dir, 'water/ffield.water'), path.join(control_dir, 'param.gpu.water')), \
-# (path.join(data_dir, 'bilayer/bilayer_56800.pdb'), path.join(data_dir, 'bilayer/ffield-bio'), path.join(control_dir, 'param.gpu.water')), \
- (path.join(data_dir, 'dna/dna_19733.pdb'), path.join(data_dir, 'dna/ffield-dna'), path.join(control_dir, 'param.gpu.water')), \
- (path.join(data_dir, 'silica/silica_6000.pdb'), path.join(data_dir, 'silica/ffield-bio'), path.join(control_dir, 'param.gpu.water')), \
-# (path.join(data_dir, 'silica/silica_72000.geo'), path.join(data_dir, 'silica/ffield-bio'), path.join(control_dir, 'param.gpu.water')), \
-# (path.join(data_dir, 'silica/silica_300000.geo'), path.join(data_dir, 'silica/ffield-bio'), path.join(control_dir, 'param.gpu.water')), \
-# (path.join(data_dir, 'petn/petn_48256.pdb'), path.join(data_dir, 'petn/ffield.petn'), path.join(control_dir, 'param.gpu.water')), \
-]
-
-header_fmt_str = '{:20}|{:5}|{:5}|{:5}|{:10}|{:10}|{:10}|{:10}|{:10}|{:10}'
-body_fmt_str = '{:20} {:5} {:5} {:5} {:10.6f} {:10.6f} {:10.6f} {:10.6f} {:10} {:10.6f}'
-
-steps = ['20'] #['100']
-qeq_solver_tol = ['1e-6'] #['1e-6', '1e-8', '1e-10', '1e-14']
-pre_comp_type = ['2'] #['0', '1', '2']
-threads = ['1', '2', '4', '12', '24']
-patterns = [ \
- lambda l, x: sub(r'(?P<key>simulation_name\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
- lambda l, x: sub(r'(?P<key>nsteps\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
- lambda l, x: sub(r'(?P<key>qeq_solver_q_err\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
- lambda l, x: sub(r'(?P<key>pre_comp_type\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
- lambda l, x: sub(r'(?P<key>geo_format\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
-]
-d = dict(environ)
-
-print header_fmt_str.format('Data Set', 'Steps', 'Q Tol', 'Pre T', 'Pre Comp',
- 'Pre App', 'Iters', 'SpMV', 'Threads', 'Time (s)')
-
-for i in xrange(len(puremd_args)):
- for s in xrange(len(steps)):
- for j in xrange(len(qeq_solver_tol)):
- for t in xrange(len(pre_comp_type)):
- for k in xrange(len(threads)):
- for line in input(puremd_args[i][2], inplace=1):
- line = line.rstrip()
- line = patterns[0](line, path.basename(puremd_args[i][0]).split('.')[0]
- + '_' + 'tol' + qeq_solver_tol[j] + '_precomp' + pre_comp_type[t] + '_thread' + threads[k])
- line = patterns[1](line, steps[s])
- line = patterns[2](line, qeq_solver_tol[j])
- line = patterns[3](line, pre_comp_type[t])
- print line
-
- d['OMP_NUM_THREADS'] = threads[k]
- start = time()
- p = Popen([path.join(base_dir, 'sPuReMD/bin/spuremd')] + list(puremd_args[i]),
- stdout=PIPE, stderr=PIPE, env=d)
- stdout, stderr = p.communicate()
- stop = time()
-
- iters = 0.
- pre_comp = 0.
- pre_app = 0.
- spmv = 0.
- cnt = 0
- with open(path.basename(puremd_args[i][0]).split('.')[0]
- + '_' + 'tol' + qeq_solver_tol[j] + '_precomp' + pre_comp_type[t] + '_thread'
- + threads[k] + '.log', 'r') as fp:
- for line in fp:
- line = line.split()
- try:
- iters = iters + float(line[7])
- pre_comp = pre_comp + float(line[8])
- pre_app = pre_app + float(line[9])
- spmv = spmv + float(line[10])
- cnt = cnt + 1
- except Exception:
+
+class TestCase():
+ def __init__(self, geo_file, ffield_file, control_file, params={}, result_header_fmt='',
+ result_header='', result_body_fmt='', result_file='results.txt'):
+ self.__geo_file = geo_file
+ self.__ffield_file = ffield_file
+ self.__control_file = control_file
+ self.__param_names = sorted(params.keys())
+ self.__params = params
+ self.__result_header_fmt = result_header_fmt
+ self.__result_header = result_header
+ self.__result_body_fmt = result_body_fmt
+ self.__result_file = result_file
+ self.__control_res = { \
+ '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(
+ r'(?P<key>ensemble_type\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'nsteps': lambda l, x: sub(
+ r'(?P<key>nsteps\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'qeq_solver_type': lambda l, x: sub(
+ r'(?P<key>qeq_solver_type\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'qeq_solver_q_err': lambda l, x: sub(
+ r'(?P<key>qeq_solver_q_err\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'pre_comp_type': lambda l, x: sub(
+ r'(?P<key>pre_comp_type\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'pre_comp_refactor': lambda l, x: sub(
+ r'(?P<key>pre_comp_refactor\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'pre_comp_sweeps': lambda l, x: sub(
+ r'(?P<key>pre_comp_sweeps\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'pre_app_type': lambda l, x: sub(
+ r'(?P<key>pre_app_type\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'pre_app_jacobi_iters': lambda l, x: sub(
+ r'(?P<key>pre_app_jacobi_iters\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'geo_format': lambda l, x: sub(
+ r'(?P<key>geo_format\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ }
+
+ def _setup(self, param, temp_file):
+ fp = open(self.__control_file, 'r')
+ lines = fp.read()
+ fp.close()
+ for k in self.__control_res.keys():
+ try:
+ lines = self.__control_res[k](lines, param[k])
+ except KeyError:
pass
- cnt = cnt - 1
- iters = iters / cnt
- pre_comp = pre_comp / cnt
- pre_app = pre_app / cnt
- spmv = spmv / cnt
-
- print body_fmt_str.format(path.basename(puremd_args[i][0]).split('.')[0],
- steps[s], qeq_solver_tol[j], pre_comp_type[t], pre_comp, pre_app, iters, spmv,
- threads[k], stop - start)
+ fp_temp = open(temp_file, 'w', 0)
+ fp_temp.write(lines)
+ fp_temp.close()
+
+ def run(self, bin_file='sPuReMD/bin/spuremd'):
+ base_dir = getcwd()
+ bin_path = path.join(base_dir, bin_file)
+ env = dict(environ)
+
+ write_header = True
+ if path.exists(self.__result_file):
+ write_header = False
+ fout = open(self.__result_file, 'a', 0)
+ if write_header:
+ fout.write(self.__result_header_fmt.format(*self.__result_header))
+
+ temp_dir = mkdtemp()
+ temp_file = path.join(temp_dir, path.basename(self.__control_file))
+
+ 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] \
+ + '_step' + param_dict['nsteps'] + '_tol' + param_dict['qeq_solver_q_err'] \
+ + '_precomp' + param_dict['pre_comp_type'] + '_thread' + param_dict['threads']
+
+ self._setup(param_dict, temp_file)
+
+ env['OMP_NUM_THREADS'] = param_dict['threads']
+ start = time()
+ proc_handle = Popen([bin_path, self.__geo_file, self.__ffield_file, temp_file],
+ stdout=PIPE, stderr=PIPE, env=env)
+ #TODO: handle outputs?
+ stdout, stderr = proc_handle.communicate()
+ stop = time()
+
+ self._process_result(fout, stop - start, param_dict)
+
+ fout.close()
+ remove(temp_file)
+ rmdir(temp_dir)
+
+ def _process_result(self, fout, time, param):
+ qeq = 0.
+ iters = 0.
+ pre_comp = 0.
+ pre_app = 0.
+ spmv = 0.
+ cnt = 0
+ with open(param['name'] + '.log', 'r') as fp:
+ for line in fp:
+ line = line.split()
+ try:
+ qeq = qeq + float(line[6])
+ iters = iters + float(line[7])
+ pre_comp = pre_comp + float(line[8])
+ pre_app = pre_app + float(line[9])
+ spmv = spmv + float(line[10])
+ cnt = cnt + 1
+ except Exception:
+ pass
+ cnt = cnt - 1
+ qeq = qeq / cnt
+ iters = iters / cnt
+ pre_comp = pre_comp / cnt
+ pre_app = pre_app / cnt
+ spmv = spmv / cnt
+
+ fout.write(self.__result_body_fmt.format(path.basename(self.__geo_file).split('.')[0],
+ param['nsteps'], param['qeq_solver_q_err'], param['pre_comp_type'], pre_comp, pre_app, iters, spmv,
+ qeq, param['threads'], time))
+
+
+if __name__ == '__main__':
+ base_dir = getcwd()
+ control_dir = path.join(base_dir, 'environ')
+ data_dir = path.join(base_dir, 'data/benchmarks')
+
+ header_fmt_str = '{:20}|{:5}|{:5}|{:5}|{:10}|{:10}|{:10}|{:10}|{:10}|{:10}|{:10}\n'
+ header_str = ['Data Set', 'Steps', 'Q Tol', 'Pre T', 'Pre Comp',
+ 'Pre App', 'Iters', 'SpMV', 'QEq', 'Threads', 'Time (s)']
+ body_fmt_str = '{:20} {:5} {:5} {:5} {:10.6f} {:10.6f} {:10.6f} {:10.6f} {:10.6f} {:10} {:10.6f}\n'
+
+ params = {
+ 'ensemble_type': ['0'],
+ 'nsteps': ['20', '100', '500', '1000'],
+ 'qeq_solver_type': ['0'],
+ 'qeq_solver_q_err': ['1e-6', '1e-10'],
+# 'qeq_solver_q_err': ['1e-6', '1e-8', '1e-10', '1e-14'],
+ 'pre_comp_type': ['0'],
+# 'pre_comp_type': ['0', '1', '2'],
+ 'pre_comp_refactor': ['1'],
+# 'pre_comp_sweeps': ['3'],
+# 'pre_app_type': ['0'],
+# 'pre_app_jacobi_iters': ['50'],
+ 'threads': ['12'],
+# 'threads': ['1', '2', '4', '12', '24'],
+ 'geo_format': ['1'],
+ }
+
+ test_cases = [
+ TestCase(path.join(data_dir, 'water/water_6540.pdb'),
+ path.join(data_dir, 'water/ffield.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),
+# TestCase(path.join(data_dir, 'water/water_78480.pdb'),
+# path.join(data_dir, 'water/ffield.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),
+# TestCase(path.join(data_dir, 'water/water_327000.geo'),
+# path.join(data_dir, 'water/ffield.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),
+ 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),
+ 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),
+ 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),
+# 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),
+# 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),
+ 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),
+ ]
+ for test in test_cases:
+ test.run(bin_file='sPuReMD/bin/spuremd')