Rename benchmark. Fix SuperLU-MT build. Update benchmark script.

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"

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)