diff --git a/data/benchmarks/petn/petn.pdb b/data/benchmarks/petn/petn_48256.pdb
similarity index 100%
rename from data/benchmarks/petn/petn.pdb
rename to data/benchmarks/petn/petn_48256.pdb
diff --git a/sPuReMD/configure.ac b/sPuReMD/configure.ac
index 5829f0e3e1d323b8ef3d2f08f3f65551d4d53614..358dfe7eb5c0b90b1c97bd3026b5710fbe16bb9b 100644
--- a/sPuReMD/configure.ac
+++ b/sPuReMD/configure.ac
@@ -58,7 +58,7 @@ if test "x$BUILD_OPENMP" = "xyes"; then
fi
fi
-if test "x$BUILD_SUPERLU_MT" != "xno"
+if test "x$BUILD_SUPERLU_MT" != "x"
then
CPPFLAGS="${CPPFLAGS} -I${BUILD_SUPERLU_MT}/include"
LDFLAGS="${LDFLAGS} -L${BUILD_SUPERLU_MT}/lib"
diff --git a/tools/run_sim.py b/tools/run_sim.py
index a7be0e2a80ab06ff9538d933b37c29fdb4c3450d..de1c0372609af6c4eccce3c8a2b8dd95a531a03e 100644
--- a/tools/run_sim.py
+++ b/tools/run_sim.py
@@ -3,49 +3,89 @@
from fileinput import input
from re import sub
from subprocess import Popen, PIPE
-from os import environ, path, rename
+from os import getcwd, environ, path, rename
+from sys import exit
from time import time
-base_dir = os.getcwd()
+base_dir = getcwd()
control_dir = path.join(base_dir, 'environ')
-data_dir = path.join(base_dir, 'data')
+data_dir = path.join(base_dir, 'data/benchmarks')
puremd_args = [ \
- (path.join(data_dir, 'water_6540.pdb'), path.join(data_dir, 'ffield.water'), path.join(control_dir, 'param.gpu.water')), \
- (path.join(data_dir, 'water_52320.pdb'), path.join(data_dir, 'ffield.water'), path.join(control_dir, 'param.gpu.water')), \
- (path.join(data_dir, 'water_80000.geo'), path.join(data_dir, 'ffield.water'), path.join(control_dir, 'param.gpu.water')), \
- (path.join(data_dir, 'bilayer.pdb'), path.join(data_dir, 'ffield-bio'), path.join(control_dir, 'param.gpu.water')), \
- (path.join(data_dir, 'dna.pdb'), path.join(data_dir, 'ffield-dna'), path.join(control_dir, 'param.gpu.water')), \
+# (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}|{:10}|{:10}'
-body_fmt_str = '{:20} {:5} {:10} {:10d}'
+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}'
-tols = ['1e-6', '1e-8', '1e-10', '1e-14']
-threads = ['1', '2', '4', '10', '20']
+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>q_err\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l.rstrip()), \
+ 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', 'Tol', 'Threads', 'Time (ms)')
+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 j in xrange(len(tols)):
- for line in input(puremd_args[i][2], inplace=1):
- for p in patterns:
- line = p(line, tols[j])
- print line
- for k in xrange(len(threads)):
- d['OMP_NUM_THREADS'] = threads[k]
- start = time()
- p = Popen([path.join(base_dir, 'sPuReMD/spuremd')] + list(puremd_args[i]),
- stdout=PIPE, stderr=PIPE, env=d)
- stdout, stderr = p.communicate()
- stop = time()
- print body_fmt_str.format(path.basename(puremd_args[i][0]), tols[j], threads[k],
- int((stop - start) * 1000))
-
- rename('water.6.notab.log', path.basename(puremd_args[i][0]).split('.')[0]
- + '_' + tols[j] + 'tol_' + threads[k] + 'thread' + '.log')
- rename('water.6.notab.out', path.basename(puremd_args[i][0]).split('.')[0]
- + '_' + tols[j] + 'tol_' + threads[k] + 'thread' + '.out')
+ 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:
+ 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)