Merge pull request #312 from LLNL/bugfix/fix_none_type_options

Parsing and testing improvements

RELEASE_NOTES.md

@@ -48,6 +48,8 @@ Notable changes include:
     * Clang C++ warnings have eliminated, so the Clang CI tests have been updated to treat warnings as errors.
     * Fix for installing libraries when building individual package WITH ENABLE_DEV_BUILD=On.
     * Bugfix for RZ solid CRKSPH with compatible energy.
+    * Parsing of None string now always becomes None python type. Tests have been updated accordingly.
+    * IO for checkpoints and visuzalization can now be properly turned off through SpheralController input options.
 
 Version v2024.06.1 -- Release date 2024-07-09
 ==============================================

src/PYB11/Utilities/Utilities_PYB11.py

@@ -819,7 +819,7 @@ def clippedVolume(poly = "const Dim<3>::FacetedVolume&",
                        ("long", "Long"),
                        ("double", "Scalar"),
                        ("std::string", "String")):
-    exec("""
-adiak_value%(label)s = PYB11TemplateFunction(adiak_value, "%(value)s")
-adiak_value2%(label)s = PYB11TemplateFunction(adiak_value2, "%(value)s", pyname="adiak_value%(label)s")
-""" % {"label" : label, "value" : value})
+    exec(f"""
+adiak_value{label} = PYB11TemplateFunction(adiak_value, "{value}", pyname="adiak_value")
+adiak_value2{label} = PYB11TemplateFunction(adiak_value2, "{value}", pyname="adiak_value")
+""")

src/SimulationControl/CMakeLists.txt

@@ -60,6 +60,7 @@ spheral_install_python_files(
   SpheralPolytopeSiloDump.py
   Spheral1dVizDump.py
   SpheralMatplotlib.py
+  SpheralTimingParser.py
   findLastRestart.py
   Pnorm.py
   filearraycmp.py

src/SimulationControl/SpheralController.py

@@ -5,6 +5,7 @@
 
 from SpheralCompiledPackages import *
 from SpheralTimer import SpheralTimer
+from SpheralUtilities import adiak_value
 from SpheralConservation import SpheralConservation
 from GzipFileIO import GzipFileIO
 from SpheralTestUtilities import globalFrame
@@ -52,6 +53,7 @@ def __init__(self, integrator,
                  volumeType = RKVolumeType.RKVoronoiVolume,
                  facetedBoundaries = None,
                  printAllTimers = False):
+        self.restartBaseName = restartBaseName
         self.restart = RestartableObject(self)
         self.integrator = integrator
         self.restartObjects = restartObjects
@@ -80,6 +82,7 @@ def __init__(self, integrator,
 
         # Determine the dimensionality of this run, based on the integrator.
         self.dim = "%id" % self.integrator.dataBase.nDim
+        adiak_value("dim", self.dim)
 
         # Determine the visualization method.
         if self.dim == "1d":
@@ -100,8 +103,11 @@ def __init__(self, integrator,
         self.insertDistributedBoundary(integrator.physicsPackages())
 
         # Should we look for the last restart set?
-        if restoreCycle == -1:
-            restoreCycle = findLastRestart(restartBaseName)
+        if restartBaseName:
+            if restoreCycle == -1:
+                restoreCycle = findLastRestart(restartBaseName)
+        else:
+            restoreCycle = None
 
         # Generic initialization work.
         self.reinitializeProblem(restartBaseName,
@@ -181,7 +187,8 @@ def reinitializeProblem(self, restartBaseName, vizBaseName,
         self._periodicTimeWork = []
 
         # Set the restart file base name.
-        self.setRestartBaseName(restartBaseName)
+        if restartBaseName:
+            self.setRestartBaseName(restartBaseName)
 
         # Set the simulation time.
         self.integrator.currentTime = initialTime
@@ -393,9 +400,12 @@ def advance(self, goalTime, maxSteps=None):
         numActualGhostNodes = 0
         for bc in bcs:
             numActualGhostNodes += bc.numGhostNodes
-        print("Total number of (internal, ghost, active ghost) nodes : (%i, %i, %i)" % (mpi.allreduce(db.numInternalNodes, mpi.SUM),
-                                                                                        mpi.allreduce(db.numGhostNodes, mpi.SUM),
-                                                                                        mpi.allreduce(numActualGhostNodes, mpi.SUM)))
+        numInternal = db.globalNumInternalNodes
+        numGhost = db.globalNumGhostNodes
+        numActGhost = mpi.allreduce(numActualGhostNodes, mpi.SUM)
+        print(f"Total number of (internal, ghost, active ghost) nodes : ({numInternal}, {numGhost}, {numActGhost})")
+        adiak_value("total_internal_nodes", numInternal)
+        adiak_value("total_ghost_nodes", numGhost)
 
         # Print how much time was spent per integration cycle.
         self.stepTimer.printStatus()
@@ -566,6 +576,8 @@ def findname(thing):
     #--------------------------------------------------------------------------
     def dropRestartFile(self):
 
+        if not self.restartBaseName:
+            return
         # First find out if the requested directory exists.
         import os
         dire = os.path.dirname(os.path.abspath(self.restartBaseName))
@@ -594,6 +606,8 @@ def dropRestartFile(self):
     def loadRestartFile(self, restoreCycle,
                         frameDict=None):
 
+        if not self.restartBaseName:
+            return
         # Find out if the requested file exists.
         import os
         fileName = self.restartBaseName + "_cycle%i" % restoreCycle

src/SimulationControl/SpheralOptionParser.py

@@ -7,36 +7,41 @@
 from SpheralCompiledPackages import *
 
 from SpheralTestUtilities import globalFrame
-from SpheralUtilities import TimerMgr
+import SpheralTimingParser
+
+def parse_value(value):
+    gd = globalFrame().f_globals
+    try:
+        return eval(value, gd)
+    except:
+        return value
 
 def commandLine(**options):
 
     # Build a command line parser with the keyword arguments passed to us.
     parser = argparse.ArgumentParser()
-    for key in options:
-        parser.add_argument("--" + key,
-                            dest = key,
-                            default = options[key])
+    for key, default in options.items():
+        if default == "None":
+            raise SyntaxError(f"ERROR: {key}, None as a default value cannot be a string")
+        elif type(default) is str:
+            parser.add_argument(f"--{key}", type = str, default = default)
+        else:
+            parser.add_argument(f"--{key}", type = parse_value, default = default)
 
     # Add the universal options supported by all Spheral++ scripts.
     parser.add_argument("-v", "--verbose",
                         action = "store_true",
                         dest = "verbose",
                         default = False,
                         help = "Verbose output -- print all options that were set.")
-    parser.add_argument("--caliperConfig", default="", type=str)
-    parser.add_argument("--caliperFilename", default="", type=str)
-    parser.add_argument("--caliperConfigJSON", default="", type=str)
+
+    # Parse Caliper and Adiak inputs
+    SpheralTimingParser.add_timing_args(parser)
+
     # Evaluate the command line.
     args = parser.parse_args()
     arg_dict = vars(args)
 
-    if (not TimerMgr.timers_usable()):
-        if (args.caliperConfig or args.caliperFilename or args.caliperConfigJSON):
-            print("WARNING: Caliper command line inputs provided for "+\
-                  "non-timer install. Reconfigure the install with "+\
-                  "-DENABLE_TIMER=ON to be able to use Caliper timers.")
-
     # Verbose output?
     if args.verbose:
         print("All parameters set:")
@@ -46,46 +51,12 @@ def commandLine(**options):
                     print("  *  ", key, " = ", val)
                 else:
                     print("     ", key, " = ", val)
-        if (args.caliperConfig):
-            print("  *  caliperConfig = ", args.caliperConfig)
-        if (args.caliperFilename):
-            print("  *  caliperFilename = ", args.caliperFilename)
-        if (args.caliperConfigJSON):
-            print("  *  caliperConfigJSON = ", args.caliperConfigJSON)
     # Set all the variables.
     gd = globalFrame().f_globals
     for key, val in arg_dict.items():
-        if key in options:
-            if (type(val) != type(options[key])):
-                val = eval(val, gd)
+        if val == "None":
+            val = None
         gd[key] = val
-    # Initialize timers
-    InitTimers(args.caliperConfig, args.caliperFilename, args.caliperConfigJSON)
-    return
-
-def InitTimers(caliper_config, filename, caliper_json):
-    if(caliper_json):
-        TimerMgr.load(caliper_json)
-        if(not caliper_config):
-            raise RuntimeError("SpheralOptionParser: specifying a configuration file without using one of the configurations means no timers are started")
-    off_tests = ["none", "off", "disable", "disabled", "0"]
-    if (caliper_config.lower() in off_tests):
-        return
-    elif (caliper_config):
-        TimerMgr.add(caliper_config)
-        TimerMgr.start()
-    else:
-        import os, sys
-        if (filename):
-            testname = filename
-        else:
-            from datetime import datetime
-            # Append the current day and time to the filename
-            unique_digits = datetime.now().strftime("_%Y_%m_%d_%H%M%S_%f")
-            # Name file based on name of python file being run
-            testname = os.path.splitext(os.path.basename(sys.argv[0]))[0]
-            testname += unique_digits + ".cali"
-        TimerMgr.default_start(testname)
-    adiak_valueInt("threads_per_rank", omp_get_num_threads())
-    adiak_valueInt("num_ranks", mpi.procs)
+    # Initialize timers and add inputs as Adiak metadata
+    SpheralTimingParser.init_timer(args)
     return

src/SimulationControl/SpheralTimingParser.py

@@ -0,0 +1,100 @@
+#-------------------------------------------------------------------------------
+# Functions for adding Caliper and Adiak parsing arguments and initializing
+# the timer manager
+#-------------------------------------------------------------------------------
+
+import argparse, mpi
+from SpheralUtilities import TimerMgr
+from SpheralUtilities import adiak_value
+import SpheralOpenMP
+
+cali_args = ["caliperConfig", "caliperFilename", "caliperConfigJSON"]
+
+def parse_dict(string):
+    """
+    Function to parse a dictionary provided through the command line
+    """
+    try:
+        inp_dict = dict(item.split(":") for item in string.split(","))
+    except:
+        raise SyntaxError("Input to --adiakData must be in key:value format, separated by commas")
+    new_dict = {}
+    for ikey, ival in inp_dict.items():
+        try:
+            key = eval(ikey)
+        except:
+            key = ikey.strip()
+        try:
+            val = eval(ival)
+        except:
+            val = ival.strip()
+        new_dict.update({key: val})
+    return new_dict
+
+def add_timing_args(parser):
+    """
+    Add Caliper and Adiak arguments to the parser
+    """
+    # Allow Adiak values to be set on the command line
+    # Inputs are a string that can be evaluated into a dictionary
+    # For example, --adiakData "testname: ShockTube1, testing:3"
+    parser.add_argument("--adiakData", default=None,
+                        type=parse_dict)
+    # This logic checks if the user already set a Caliper
+    # argument and default value and prevents adding the argument
+    # if it already exists
+    arg_list = [action.dest for action in parser._actions]
+    for ca in cali_args:
+        if (ca not in arg_list):
+            parser.add_argument(f"--{ca}", default="", type=str)
+
+def init_timer(args):
+    """
+    Initializes the timing manager and adds input values to Adiak from parsed arguments
+    """
+    if args.verbose:
+        if (args.caliperConfig):
+            print("  *  caliperConfig = ", args.caliperConfig)
+        if (args.caliperFilename):
+            print("  *  caliperFilename = ", ars.caliperFilename)
+        if (args.caliperConfigJSON):
+            print("  *  caliperConfigJSON = ", args.caliperConfigJSON)
+    if (not TimerMgr.timers_usable()):
+        if (args.caliperConfig or args.caliperFilename or args.caliperConfigJSON):
+            print("WARNING: Caliper command line inputs provided for "+\
+                  "non-timer install. Reconfigure the install with "+\
+                  "-DENABLE_TIMER=ON to be able to use Caliper timers.")
+    if(args.caliperConfigJSON):
+        TimerMgr.load(args.caliperConfigJSON)
+        if(not args.caliperConfig):
+            raise RuntimeError("SpheralOptionParser: specifying a configuration file without "+\
+                               "using one of the configurations means no timers are started")
+    off_tests = ["none", "off", "disable", "disabled", "0"]
+    # Check if Caliper is turned off
+    if (args.caliperConfig):
+        if (args.caliperConfig.lower() in off_tests):
+            return
+        TimerMgr.add(args.caliperConfig)
+        TimerMgr.start()
+    else:
+        import os, sys
+        # If output name for Caliper is given, use it
+        if (args.caliperFilename):
+            testname = args.caliperFilename
+        else:
+            from datetime import datetime
+            # Append the current day and time to the filename
+            unique_digits = datetime.now().strftime("_%Y_%m_%d_%H%M%S_%f")
+            # Name file based on name of python file being run
+            testname = os.path.splitext(os.path.basename(sys.argv[0]))[0]
+            testname += unique_digits + ".cali"
+        TimerMgr.default_start(testname)
+    # Add number of ranks and threads per rank
+    adiak_value("threads_per_rank", SpheralOpenMP.omp_get_num_threads())
+    adiak_value("num_ranks", mpi.procs)
+
+    # Add --adiakData inputs as Adiak metadata
+    if (args.adiakData):
+        for key, val in args.adiakData.items():
+            adiak_value(key, val)
+    return

tests/functional/Damage/TensileDisk/TensileDisk-2d.py

@@ -75,7 +75,7 @@
     plotFlaws = False,
     clearDirectories = False,
     dataDirBase = "dumps-TensileDisk-2d",
-    outputFile = "None",
+    outputFile = None,
 
     # Should we restart (-1 => find most advanced available restart)
     restoreCycle = -1,

tests/functional/Damage/TensileRod/TensileRod-1d.py

@@ -171,8 +171,8 @@ def restoreState(self, file, path):
             clearDirectories = False,
             referenceFile = "Reference/TensileRod-GradyKippOwen-1d-1proc-reproducing-20240816.gnu",
             dataDirBase = "dumps-TensileRod-1d",
-            outputFile = "None",
-            comparisonFile = "None",
+            outputFile = None,
+            comparisonFile = None,
             )
 
 # On the IBM BlueOS machines we have some tolerance issues...
@@ -744,7 +744,7 @@ def restoreState(self, file, path):
 #-------------------------------------------------------------------------------
 # If requested, write out the state in a global ordering to a file.
 #-------------------------------------------------------------------------------
-if outputFile != "None":
+if outputFile:
     from SpheralTestUtilities import multiSort
     state = State(db, integrator.physicsPackages())
     outputFile = os.path.join(dataDir, outputFile)
@@ -786,7 +786,7 @@ def restoreState(self, file, path):
         # Also we can optionally compare the current results with another file for
         # bit level consistency.
         #---------------------------------------------------------------------------
-        if comparisonFile != "None" and BuildData.cxx_compiler_id != "IntelLLVM":
+        if comparisonFile and BuildData.cxx_compiler_id != "IntelLLVM":
             comparisonFile = os.path.join(dataDir, comparisonFile)
             import filecmp
             assert filecmp.cmp(outputFile, comparisonFile)

tests/functional/Damage/TensileRod/TensileRod-2d.py

@@ -166,7 +166,7 @@ def restoreState(self, file, path):
 
             clearDirectories = False,
             dataDirBase = "dumps-TensileRod-2d",
-            outputFile = "None",
+            outputFile = None,
             )
 
 dx = xlength/nx

tests/functional/Gravity/CollisionlessSphereCollapse.py

@@ -263,7 +263,7 @@
 #-------------------------------------------------------------------------------
 # If requested, write out the profiles
 #-------------------------------------------------------------------------------
-if outputFile != "None" and mpi.rank == 0:
+if outputFile and mpi.rank == 0:
     outputFile = os.path.join(dataDir, outputFile)
     f = open(outputFile, "w")
     f.write(("# " + 14*"%15s " + "\n") % ("r", "x", "y", "z", "vx", "vy", "vz", "Hxx", "Hxy", "Hxz", "Hyy", "Hyz", "Hzz", "phi"))