#!/usr/local/bin/env python #============================================================================================= # MODULE DOCSTRING #============================================================================================= """ Test that forces and energies agree across platforms DESCRIPTION TODO COPYRIGHT AND LICENSE @author Mark Friedrichs All code in this repository is released under the GNU General Public License. This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . """ #============================================================================================= # GLOBAL IMPORTS #============================================================================================= import sys import traceback import os import os.path import math import doctest import time import simtk.unit as units import simtk.openmm as openmm from ValidationUtilities import ValidationUtilities from ParameterFileParser import ValidationParameterFileParser from OpenMMSystemParameters import OpenMMSystemParameters import ForceEnergyPlatformComparisonTests #============================================================================================= # Print usage (command-line arguments) #============================================================================================= def printUsage( ): """Print command line arguments ARGUMENTS """ firstTab = 1 secondTab = 19 thirdTab = 60 print "Command line arguments:\n" outputString = ' '.rjust(firstTab) + "-platform0".rjust(secondTab) + " Comparison platform (Reference, Cuda, OpenCL)\n".rjust(thirdTab) outputString += ' '.rjust(firstTab) + "-platform1".rjust(secondTab) + " Comparison platform (Reference, Cuda, OpenCL)\n".rjust(thirdTab) outputString += ' '.rjust(firstTab) + "-controlFile".rjust(secondTab) + " Control file name\n".rjust(thirdTab) outputString += ' '.rjust(firstTab) + "-systemsDirectory".rjust(secondTab) + " Systems file directory\n".rjust(thirdTab) outputString += ' '.rjust(firstTab) + "-serializeDirectory".rjust(secondTab) + " Serialize file directory\n".rjust(thirdTab) outputString += ' '.rjust(firstTab) + "-configDirectory".rjust(secondTab) + " Config file directory\n".rjust(thirdTab) outputString += ' '.rjust(firstTab) + "-dataDirectory".rjust(secondTab) + " Data file directory\n".rjust(thirdTab) outputString += ' '.rjust(firstTab) + "-deviceId".rjust(secondTab) + " device id for gpu\n".rjust(thirdTab) outputString += ' '.rjust(firstTab) + "-sleep ".rjust(secondTab) + " if nonzero, then sleep the specified time between tests\n".rjust(thirdTab) outputString += ' '.rjust(firstTab) + "-verbose".rjust(secondTab) + " if nonzero, then be verbose\n".rjust(thirdTab) outputString += ' '.rjust(firstTab) + "-testSummaryFileName".rjust(secondTab) + " summary file name\n".rjust(thirdTab) outputString += ' '.rjust(firstTab) + "-printParam".rjust(secondTab) + " if nonzero, then be print parameters\n".rjust(thirdTab) outputString += ' '.rjust(firstTab) + "-help".rjust(secondTab) + " current output\n".rjust(thirdTab) outputString += "\n\n" print outputString return # parse command-line arguments def parseCommandLine( argumentHash ): argLen = len( sys.argv ) argLenM1 = argLen - 1 skip = 0 verbose = argumentHash['Verbose'] for ii in range( 1,argLen ): if( skip ): skip = 0 continue if( sys.argv[ii].startswith('-platform0') and ii < argLenM1 ): skip = 1 argumentHash['Platform0'] = sys.argv[ii+1] elif( sys.argv[ii].startswith('-platform1') and ii < argLenM1 ): skip = 1 argumentHash['Platform1'] = sys.argv[ii+1] elif( sys.argv[ii].startswith('-systemsDirectory') and ii < argLenM1 ): skip = 1 systemsDirectory = sys.argv[ii+1] argumentHash['SystemsDirectory'] = sys.argv[ii+1] elif( sys.argv[ii].startswith('-serializeDirectory') and ii < argLenM1 ): skip = 1 serializeDirectory = sys.argv[ii+1] argumentHash['SerializeDirectory'] = sys.argv[ii+1] elif( sys.argv[ii].startswith('-configDirectory') and ii < argLenM1 ): skip = 1 argumentHash['ConfigDirectory'] = sys.argv[ii+1] elif( sys.argv[ii].startswith('-dataDirectory') and ii < argLenM1 ): skip = 1 argumentHash['DataDirectory'] = sys.argv[ii+1] elif( sys.argv[ii].startswith('-sleep') and ii < argLenM1 ): skip = 1 argumentHash['Sleep'] = sys.argv[ii+1] elif( sys.argv[ii].startswith('-deviceId') and ii < argLenM1 ): skip = 1 argumentHash['DeviceId'] = int( sys.argv[ii+1] ) elif( sys.argv[ii].startswith('-verbose') and ii < argLenM1 ): skip = 1 if( int( sys.argv[ii+1] ) > 0 ): argumentHash['Verbose'] = True else: argumentHash['Verbose'] = False elif( sys.argv[ii].startswith('-printParam') and ii < argLenM1 ): skip = 1 if( int( sys.argv[ii+1] ) > 0 ): argumentHash['PrintParam'] = True else: argumentHash['PrintParam'] = False elif( sys.argv[ii].startswith('-testSummaryFileName') and ii < argLenM1 ): skip = 1 argumentHash['TestSummaryFileName'] = sys.argv[ii+1] elif( sys.argv[ii].startswith('-showTests') and ii < argLenM1 ): skip = 1 if( int( sys.argv[ii+1] ) > 0 ): argumentHash['ShowTests'] = True else: argumentHash['ShowTests'] = False elif( sys.argv[ii].startswith('-controlFile') and ii < argLenM1 ): skip = 1 argumentHash['ControlFileName'] = sys.argv[ii+1] elif( sys.argv[ii].startswith('-help') ): printUsage() exit(-1) else: print "Argument %3d %s not recognized." % (ii,sys.argv[ii]) sys.stdout.flush() printUsage() exit(-1) if( verbose ): print "%3d %s" % (ii,sys.argv[ii]) return #============================================================================================= # Print a summary of the results to a file #============================================================================================= def printTestSummary( testSummaryFileName, testNameHash, testResults ): """Print summary of results ARGUMENTS testSummaryFileName (string) summary file name testResults (hash) testResults[testName] = testResult (EnergyForceComparisonResult object) """ firstTab = 30 summaryFile = open( testSummaryFileName, 'w') for testName,dummyArg in testNameHash.iteritems(): #012345678 012345678901234567890123456789 012345678 P/F 012345678901234567 012345678901234 01234567890 01234567890123 # Platform System Particles 1 ForceRelativeDelta NormMaxRelDelta AvgRelDelta EnergyRelDelta headerString = testName.rjust(firstTab) + "\n Platform System Particles 1 ForceRelativeDelta NormMaxRelDelta AvgRelDelta EnergyRelDelta" summaryFile.write( headerString + "\n\n" ) count = 0 average = 0.0 wtAverage = 0.0 wtStddev = 0.0 wtCount = 0.0 max = -1.0 for fullTestName, result in testResults.iteritems(): if( result.getTestName() == testName ): passed = result.testPassed( ) outputString = result.getPlatform( 1 ).rjust(9) + " " outputString += result.getSystemName().rjust(firstTab) + " " outputString += ("%6d" % result.getNumberOfParticles()).rjust(9) + " " outputString += repr(passed).rjust(3) + " " outputString += ("%10.3e" % result.getMaxRelativeDeltaInForce()).rjust(18) + " " sys.stdout.flush() outputString += ("%10.3e" % result.getMaxRelativeDeltaInForceNormSum()).rjust(15) + " " outputString += ("%10.3e" % result.getAvgRelativeDeltaInForce()).rjust(11) + " " sys.stdout.flush() outputString += ("%10.3e" % result.getRelativeDeltaPotentialEnergy()).rjust(14) + " " outputString += "Tol=" + ("%8.2e" % result.getTolerance()) average += result.getMaxRelativeDeltaInForce() count += 1 wtAverage += result.getAvgRelativeDeltaInForce()*result.getCntRelativeDeltaInForce() wtStddev += result.getStdRelativeDeltaInForce()*result.getCntRelativeDeltaInForce() wtCount += result.getCntRelativeDeltaInForce() if( result.getMaxRelativeDeltaInForce() > max ): max = result.getMaxRelativeDeltaInForce() summaryFile.write( outputString + "\n" ) if( count > 0 ): average = average/count if( wtCount > 0 ): wtAverage /= wtCount wtStddev /= wtCount outputString = "\n%40s Max %10.3e Average %10.3e Count %d\n" % (testName, max, average, count) outputString += "%40s Weighted Average %10.3e Stdev %10.3e Count %d\n" % (testName, wtAverage, wtStddev, wtCount) summaryFile.write( outputString + "\n\n\n" ) summaryFile.close() return #============================================================================================= # Build tests objects given name and args #============================================================================================= def forceEnergyComparisonTestFactory( testName, systemParameters, testParameterHash, verbose ): """Build test ARGUMENTS test name test name systemParameters systemParameters testParameterHash testParameterHash verbose if true, be verbose RETURN if testName is valid, return test object; else return None """ if( testName == 'HarmonicBondForceTest' ): forceTest = ForceEnergyPlatformComparisonTests.HarmonicBondForceTest( systemParameters, testParameterHash, verbose ) elif( testName == 'HarmonicAngleForceTest' ): forceTest = ForceEnergyPlatformComparisonTests.HarmonicAngleForceTest( systemParameters, testParameterHash, verbose ) elif( testName == 'PeriodicTorsionForceTest' ): forceTest = ForceEnergyPlatformComparisonTests.PeriodicTorsionForceTest( systemParameters, testParameterHash, verbose ) elif( testName == 'RBTorsionForceTest' ): forceTest = ForceEnergyPlatformComparisonTests.RBTorsionForceTest( systemParameters, testParameterHash, verbose ) elif( testName == 'NonbondedForceNoCutoffTest' ): forceTest = ForceEnergyPlatformComparisonTests.NonbondedForceNoCutoffTest( systemParameters, testParameterHash, verbose ) elif( testName == 'NonbondedForceCutoffNonPeriodicTest' ): forceTest = ForceEnergyPlatformComparisonTests.NonbondedForceCutoffNonPeriodicTest( systemParameters, testParameterHash, verbose ) elif( testName == 'NonbondedForceCutoffPeriodicTest' ): forceTest = ForceEnergyPlatformComparisonTests.NonbondedForceCutoffPeriodicTest( systemParameters, testParameterHash, verbose ) elif( testName == 'NonbondedForceEwaldTest' ): forceTest = ForceEnergyPlatformComparisonTests.NonbondedForceEwaldTest( systemParameters, testParameterHash, verbose ) elif( testName == 'NonbondedForcePMETest' ): forceTest = ForceEnergyPlatformComparisonTests.NonbondedForcePMETest( systemParameters, testParameterHash, verbose ) elif( testName == 'GbsaObcForceNoCutoffTest' ): forceTest = ForceEnergyPlatformComparisonTests.GbsaObcForceNoCutoffTest( systemParameters, testParameterHash, verbose ) elif( testName == 'GbsaObcForceCutoffNonPeriodicTest' ): forceTest = ForceEnergyPlatformComparisonTests.GbsaObcForceCutoffNonPeriodicTest( systemParameters, testParameterHash, verbose ) elif( testName == 'GbsaObcForceCutoffPeriodicTest' ): forceTest = ForceEnergyPlatformComparisonTests.GbsaObcForceCutoffPeriodicTest( systemParameters, testParameterHash, verbose ) elif( testName == 'GbviForceNoCutoffTest' ): forceTest = ForceEnergyPlatformComparisonTests.GbviForceNoCutoffTest( systemParameters, testParameterHash, verbose ) elif( testName == 'CustomBondForceTest' ): forceTest = ForceEnergyPlatformComparisonTests.CustomBondForceTest( systemParameters, testParameterHash, verbose ) elif( testName == 'CustomAngleForceTest' ): forceTest = ForceEnergyPlatformComparisonTests.CustomAngleForceTest( systemParameters, testParameterHash, verbose ) elif( testName == 'CustomTorsionForceTest' ): forceTest = ForceEnergyPlatformComparisonTests.CustomTorsionForceTest( systemParameters, testParameterHash, verbose ) elif( testName == 'CMAPTorsionForceTest' ): forceTest = ForceEnergyPlatformComparisonTests.CMAPTorsionForceTest( systemParameters, testParameterHash, verbose ) elif( testName == 'CustomExternalForceTest' ): forceTest = ForceEnergyPlatformComparisonTests.CustomExternalForceTest( systemParameters, testParameterHash, verbose ) elif( testName == 'CustomNonbondedForceNonPeriodicCutoffTest' ): forceTest = ForceEnergyPlatformComparisonTests.CustomNonbondedForceNonPeriodicCutoffTest( systemParameters, testParameterHash, verbose ) elif( testName == 'CustomNonbondedForcePeriodicCutoffTest' ): forceTest = ForceEnergyPlatformComparisonTests.CustomNonbondedForcePeriodicCutoffTest( systemParameters, testParameterHash, verbose ) elif( testName == 'CustomNonbondedForceNoCutoffTest' ): forceTest = ForceEnergyPlatformComparisonTests.CustomNonbondedForceNoCutoffTest( systemParameters, testParameterHash, verbose ) elif( testName == 'CustomGbsaForceNonPeriodicCutoffTest' ): forceTest = ForceEnergyPlatformComparisonTests.CustomGbsaForceNonPeriodicCutoffTest( systemParameters, testParameterHash, verbose ) elif( testName == 'CustomGbsaForcePeriodicCutoffTest' ): forceTest = ForceEnergyPlatformComparisonTests.CustomGbsaForcePeriodicCutoffTest( systemParameters, testParameterHash, verbose ) elif( testName == 'CustomNonbondedForceNoModificationTest' ): forceTest = ForceEnergyPlatformComparisonTests.CustomNonbondedForceNoModificationTest( systemParameters, testParameterHash, verbose ) elif( testName == 'CustomGbsaForceNoCutoffTest' ): forceTest = ForceEnergyPlatformComparisonTests.CustomGbsaForceNoCutoffTest( systemParameters, testParameterHash, verbose ) elif( testName == 'AmoebaGeneralizedKirkwoodForceTest' ): forceTest = ForceEnergyPlatformComparisonTests.AmoebaGeneralizedKirkwoodForceTest( systemParameters, testParameterHash, verbose ) elif( testName == 'AmoebaHarmonicAngleForceTest' ): forceTest = ForceEnergyPlatformComparisonTests.AmoebaHarmonicAngleForceTest( systemParameters, testParameterHash, verbose ) elif( testName == 'AmoebaHarmonicBondForceTest' ): forceTest = ForceEnergyPlatformComparisonTests.AmoebaHarmonicBondForceTest( systemParameters, testParameterHash, verbose ) elif( testName == 'AmoebaOutOfPlaneBendForceTest' ): forceTest = ForceEnergyPlatformComparisonTests.AmoebaOutOfPlaneBendForceTest( systemParameters, testParameterHash, verbose ) elif( testName == 'AmoebaHarmonicInPlaneAngleForceTest' ): forceTest = ForceEnergyPlatformComparisonTests.AmoebaHarmonicInPlaneAngleForceTest( systemParameters, testParameterHash, verbose ) elif( testName == 'AmoebaMultipoleForceTest' ): forceTest = ForceEnergyPlatformComparisonTests.AmoebaMultipoleForceTest( systemParameters, testParameterHash, verbose ) elif( testName == 'AmoebaPiTorsionForceTest' ): forceTest = ForceEnergyPlatformComparisonTests.AmoebaPiTorsionForceTest( systemParameters, testParameterHash, verbose ) elif( testName == 'AmoebaTorsionForceTest' ): forceTest = ForceEnergyPlatformComparisonTests.AmoebaTorsionForceTest( systemParameters, testParameterHash, verbose ) elif( testName == 'AmoebaTorsionTorsionForceTest' ): forceTest = ForceEnergyPlatformComparisonTests.AmoebaTorsionTorsionForceTest( systemParameters, testParameterHash, verbose ) elif( testName == 'AmoebaStretchBendForceTest' ): forceTest = ForceEnergyPlatformComparisonTests.AmoebaStretchBendForceTest( systemParameters, testParameterHash, verbose ) elif( testName == 'AmoebaUreyBradleyForceTest' ): forceTest = ForceEnergyPlatformComparisonTests.AmoebaUreyBradleyForceTest( systemParameters, testParameterHash, verbose ) elif( testName == 'AmoebaVdwForceTest' ): forceTest = ForceEnergyPlatformComparisonTests.AmoebaVdwForceTest( systemParameters, testParameterHash, verbose ) elif( testName == 'AmoebaWcaDispersionForceTest' ): forceTest = ForceEnergyPlatformComparisonTests.AmoebaWcaDispersionForceTest( systemParameters, testParameterHash, verbose ) else: forceTest = None print "%s test not recognized." % testName return forceTest #============================================================================================= # MAIN #============================================================================================= # set Validation directory argumentHash = {} validationUtilities = ValidationUtilities(False) validationDirectory = os.path.join(os.getenv('PYOPENMM_SOURCE_DIR'), 'test', 'validation') useXml = 1 if( useXml ): parameterFileSuffix = '.xml' systemsDirectory = os.path.join(validationDirectory, 'systems_xml') else: parameterFileSuffix = '.txt' systemsDirectory = os.path.join(validationDirectory, 'systems') configDirectory = os.path.join(validationDirectory, 'config') dataDirectory = os.path.join(validationDirectory, 'data') testListFileName = 'ForceEnergyComparisonTestNames.txt' systemListFileName = 'SystemNames.txt' argumentHash['ValidationDirectory'] = validationDirectory argumentHash['ConfigDirectory'] = configDirectory argumentHash['DataDirectory'] = dataDirectory argumentHash['TestListFileName'] = testListFileName argumentHash['SystemListFileName'] = systemListFileName argumentHash['SystemsDirectory'] = systemsDirectory argumentHash['Platform0'] = 'Reference' argumentHash['Platform1'] = 'Cuda' #argumentHash['Platform1'] = 'OpenCL' argumentHash['Verbose'] = False argumentHash['Verbose'] = True argumentHash['PrintParam'] = False argumentHash['ShowTests'] = False argumentHash['TestSummaryFileName'] = 'NA' argumentHash['Sleep'] = 0 # parse command line parseCommandLine( argumentHash ) systemsDirectory = argumentHash['SystemsDirectory'] if( 'SerializeDirectory' in argumentHash ): serializeDirectory = argumentHash['SerializeDirectory'] else: serializeDirectory = 0 # track number of tests that do not run numberOfTestsThatDidNotRun = 0 defaultParameterHash = { 'Active' : 1, 'Tolerance' : 1.0e-02, 'MinForceNormCutoff' : 1.0e+00, 'MinEnergyNormCutoff' : 1.0e+00, } verbose = argumentHash['Verbose'] validationUtilities.setVerbose( verbose ) printParam = argumentHash['PrintParam'] comparisonPlatformList = [ ] comparisonPlatformList.append( argumentHash['Platform0'] ) comparisonPlatformList.append( argumentHash['Platform1'] ) if( argumentHash['TestSummaryFileName'] != 'NA' ): testSummaryFileName = argumentHash['TestSummaryFileName'] else: testSummaryFileName = comparisonPlatformList[0] + comparisonPlatformList[1] + 'ForceEnergyComparisonSummary.txt' fullTestListFileName = os.path.join( argumentHash['DataDirectory'], argumentHash['TestListFileName'] ) testList = validationUtilities.getListFromFile( fullTestListFileName ) fullSystemListFileName = os.path.join( argumentHash['DataDirectory'], argumentHash['SystemListFileName'] ) systemList = validationUtilities.getListFromFile( fullSystemListFileName ) testHash = validationUtilities.buildDefaultTestHash( testList, systemList, defaultParameterHash ) if( 'ControlFileName' in argumentHash ): fullControlFileName = os.path.join( argumentHash['ConfigDirectory'], argumentHash['ControlFileName'] ) validationUtilities.editTestHashBasedOnControlFile( fullControlFileName, testHash ) if( verbose or printParam ): print "%s" % validationUtilities.printHash( argumentHash, "Arguments\n" ) print "%s" % validationUtilities.printTestHash( testHash, 1 ) if( printParam ):exit(0) testResults = {} testNameHash = {} # loop over tests for fullTestName, testParameterHash in testHash.iteritems(): if( argumentHash['ShowTests'] and testParameterHash['Active'] != 0 ): print "%s %s active=%d" % ( testParameterHash['SystemName'], testParameterHash['TestName'], testParameterHash['Active'] ) #print "%s %s active=%d" % ( testParameterHash['SystemName'], testParameterHash['TestName'], testParameterHash['Active'] ) # skip CustomGB tests on Cuda -- not implmented! if( testParameterHash['Active'] != 0 and testParameterHash['TestName'].startswith('CustomGbsaForce') and ( comparisonPlatformList[0].startswith('Cuda') or comparisonPlatformList[1].startswith('Cuda') ) ): if( verbose ): print "Skipping comparison of %s %s test=%s on %s since CustomGbsaForce is not implemented on Cuda" % (comparisonPlatformList[0], comparisonPlatformList[1], testParameterHash['TestName'], testParameterHash['SystemName']) testParameterHash['Active'] = 0 elif( testParameterHash['Active'] > 0 ): systemName = testParameterHash['SystemName'] testName = testParameterHash['TestName'] testNameHash[testName] = 1 print '*' * 80 print "%30s %30s" % (systemName, testName ) # read parameter file. parameterFileName = systemName + parameterFileSuffix fullParameterFileName = os.path.join(systemsDirectory, parameterFileName) if( useXml ): positionFileName = systemName + '.txt' fullPositionFileName = os.path.join(systemsDirectory, positionFileName) systemParameters = OpenMMSystemParameters(fullParameterFileName, fullPositionFileName, verbose) else: systemParameters = ValidationParameterFileParser(fullParameterFileName, verbose) # loop over tests try: # get test and run print "forceTest %s %s\n" % (systemName, testName ) if( 'DeviceId' in argumentHash ): testParameterHash['DeviceId'] = argumentHash['DeviceId'] forceTest = forceEnergyComparisonTestFactory( testName, systemParameters, testParameterHash, verbose ) print "forceTest %s %s %d\n" % (systemName, testName, forceTest.isActive() ) if( forceTest is not None and forceTest.isActive() ): if( serializeDirectory ): forceTest.serialize( serializeDirectory ) forceTest.runTest( comparisonPlatformList ) fullTestName = forceTest.getFullTestName() if forceTest.getResult() is not None: testResults[fullTestName] = forceTest.getResult() else: print "%s test did not run for %s" % (testName, systemName) numberOfTestsThatDidNotRun += 1 if( 'Sleep' in argumentHash and argumentHash['Sleep'] > 0 ): if( verbose ): print "Sleeping %s seconds." % (str(argumentHash['Sleep'])) sys.stdout.flush() time.sleep(float(argumentHash['Sleep'])) except: print "%s test did not run for %s" % (testName, systemName) print repr(traceback.print_exception( sys.exc_info()[0], sys.exc_info()[1], sys.exc_info()[2])) numberOfTestsThatDidNotRun += 1 if( argumentHash['ShowTests'] ): exit(0) # output results print '*' * 80 numberOfTestsThatPassed = 0 numberOfTestsThatFailed = 0 for testName,result in testResults.iteritems(): if( result.testPassed( ) ): numberOfTestsThatPassed += 1 else: numberOfTestsThatFailed += 1 print "\nSummary:\n" print " %d tests passed" % numberOfTestsThatPassed print " %d tests failed" % numberOfTestsThatFailed print " %d tests did not run" % numberOfTestsThatDidNotRun # print summary file try: printTestSummary( testSummaryFileName, testNameHash, testResults ) except: print repr(traceback.print_exception( sys.exc_info()[0], sys.exc_info()[1], sys.exc_info()[2])) # exit w/ flag signalling success if numberOfTestsThatFailed > 0 or numberOfTestsThatDidNotRun > 0: sys.exit(1) else: sys.exit(0)