Added profiling for thermoEstimator

Author: keceli

thermoEstimator.py

@@ -9,7 +9,7 @@
 """
 
 import os.path
-from rmgpy.rmg.main import RMG
+from rmgpy.rmg.main import RMG, processProfileStats, makeProfileGraph
 from rmgpy.data.thermo import ThermoLibrary
 from rmgpy.chemkin import writeThermoEntry
 from rmgpy.rmg.model import makeThermoForSpecies
@@ -71,8 +71,31 @@ def runThermoEstimator(inputFile):
     parser = argparse.ArgumentParser()
     parser.add_argument('input', metavar='INPUT', type=str, nargs=1,
         help='Thermo input file')
+    parser.add_argument('-p', '--profile', action='store_true', help='run under cProfile to gather profiling statistics, and postprocess them if job completes')
+    parser.add_argument('-P', '--postprocess', action='store_true', help='postprocess profiling statistics from previous [failed] run; does not run the simulation')
+
     args = parser.parse_args()
 
     inputFile = os.path.abspath(args.input[0])
+   
+    if args.postprocess:
+        print "Postprocessing the profiler statistics (will be appended to thermo.log)"
+        args.profile = True
 
-    runThermoEstimator(inputFile)
+    if args.profile:
+        import cProfile, sys, pstats, os
+        global_vars = {}
+        local_vars = {'inputFile': inputFile,'runThermoEstimator':runThermoEstimator}
+        command = """runThermoEstimator(inputFile)"""
+        stats_file = 'thermo.profile'
+        print("Running under cProfile")
+        if not args.postprocess:
+        # actually run the program!
+            cProfile.runctx(command, global_vars, local_vars, stats_file)
+        # postprocess the stats
+        log_file = 'thermo.log'
+        processProfileStats(stats_file, log_file)
+        makeProfileGraph(stats_file)
+        
+    else:
+        runThermoEstimator(inputFile)