#!/usr/local/bin/env python #============================================================================================= # MODULE DOCSTRING #============================================================================================= """ Test that force and energy gradient agree 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 os import traceback 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 EnergyGradientTests #============================================================================================= # 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) + "-platform".rjust(secondTab) + " platform (Reference, Cuda, OpenCL) to run tests on\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) + "-configDirectory".rjust(secondTab) + " Config file directory\n".rjust(thirdTab) outputString += ' '.rjust(firstTab) + "-dataDirectory".rjust(secondTab) + " Data file directory\n".rjust(thirdTab) outputString += ' '.rjust(firstTab) + "-serializeDirectory".rjust(secondTab) + " Serialize file directory\n".rjust(thirdTab) outputString += ' '.rjust(firstTab) + "-deviceId".rjust(secondTab) + " device id for gpu\n".rjust(thirdTab) outputString += ' '.rjust(firstTab) + "-verbose".rjust(secondTab) + " if nonzero, then be verbose\n".rjust(thirdTab) outputString += ' '.rjust(firstTab) + "-printParam".rjust(secondTab) + " if nonzero, then be print parameters and exit\n".rjust(thirdTab) outputString += ' '.rjust(firstTab) + "-sleep ".rjust(secondTab) + " if nonzero, then sleep the specified time between tests\n".rjust(thirdTab) outputString += ' '.rjust(firstTab) + "-testSummaryFileName".rjust(secondTab) + " summary file name\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 print "arg %d %s" % ( ii, sys.argv[ii] ) if( sys.argv[ii].startswith('-platform') and ii < argLenM1 ): skip = 1 argumentHash['Platform'] = 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('-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('-serializeDirectory') and ii < argLenM1 ): skip = 1 serializeDirectory = sys.argv[ii+1] argumentHash['SerializeDirectory'] = 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('-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 (ForceEnergyGradientResult object) """ firstTab = 40 summaryFile = open( testSummaryFileName, 'w') for testName,dummyArg in testNameHash.iteritems(): headerString = testName.rjust(firstTab) + " Passed RelativeDelta" summaryFile.write( headerString + "\n\n" ) count = 0 average = 0.0 max = -1.0 for fullTestName, result in testResults.iteritems(): if( result.getTestName() == testName ): passed = result.testPassed( ) outputString = result.getPlatformName().rjust(8) + result.getSystemName().rjust(firstTab) + " " + repr(passed).rjust(6) + " " + ("%10.3e" % result.getRelativeDelta()).rjust(21) + " Delta " + ("%10.3e" % result.getForceStepDelta()) + " Tol " + ("%10.3e" % result.getTolerance()) average += math.log( result.getRelativeDelta() ) count += 1 if( result.getRelativeDelta() > max ): max = result.getRelativeDelta() summaryFile.write( outputString + "\n" ) if( count > 0 ): average = average/count average = math.exp( average ) outputString = "\n%40s Max %10.3e Log Average %10.3e Count %d\n" % (testName, max, average, count) summaryFile.write( outputString + "\n\n\n" ) summaryFile.close() return #============================================================================================= # Build tests objects given name and args #============================================================================================= def forceEnergyGradientTestFactory( 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 == 'HarmonicBondForceEnergyGradientTest' ): forceTest = EnergyGradientTests.HarmonicBondForceEnergyGradientTest( systemParameters, testParameterHash, verbose ) elif( testName == 'HarmonicAngleForceEnergyGradientTest' ): forceTest = EnergyGradientTests.HarmonicAngleForceEnergyGradientTest( systemParameters, testParameterHash, verbose ) elif( testName == 'PeriodicTorsionForceEnergyGradientTest' ): forceTest = EnergyGradientTests.PeriodicTorsionForceEnergyGradientTest( systemParameters, testParameterHash, verbose ) elif( testName == 'RBTorsionForceEnergyGradientTest' ): forceTest = EnergyGradientTests.RBTorsionForceEnergyGradientTest( systemParameters, testParameterHash, verbose ) elif( testName == 'NonbondedForceEnergyGradientNoCutoffTest' ): forceTest = EnergyGradientTests.NonbondedForceEnergyGradientNoCutoffTest( systemParameters, testParameterHash, verbose ) elif( testName == 'NonbondedForceEnergyGradientCutoffNonPeriodicTest' ): forceTest = EnergyGradientTests.NonbondedForceEnergyGradientCutoffNonPeriodicTest( systemParameters, testParameterHash, verbose ) elif( testName == 'NonbondedForceEnergyGradientCutoffPeriodicTest' ): forceTest = EnergyGradientTests.NonbondedForceEnergyGradientCutoffPeriodicTest( systemParameters, testParameterHash, verbose ) elif( testName == 'NonbondedForceEnergyGradientEwaldTest' ): forceTest = EnergyGradientTests.NonbondedForceEnergyGradientEwaldTest( systemParameters, testParameterHash, verbose ) elif( testName == 'NonbondedForceEnergyGradientPMETest' ): forceTest = EnergyGradientTests.NonbondedForceEnergyGradientPMETest( systemParameters, testParameterHash, verbose ) elif( testName == 'GbsaObcForceEnergyGradientNoCutoffTest' ): forceTest = EnergyGradientTests.GbsaObcForceEnergyGradientNoCutoffTest( systemParameters, testParameterHash, verbose ) elif( testName == 'GbsaObcForceEnergyGradientCutoffNonPeriodicTest' ): forceTest = EnergyGradientTests.GbsaObcForceEnergyGradientCutoffNonPeriodicTest( systemParameters, testParameterHash, verbose ) elif( testName == 'GbsaObcForceEnergyGradientCutoffPeriodicTest' ): forceTest = EnergyGradientTests.GbsaObcForceEnergyGradientCutoffPeriodicTest( systemParameters, testParameterHash, verbose ) elif( testName == 'GbviForceEnergyGradientNoCutoffTest' ): forceTest = EnergyGradientTests.GbviForceEnergyGradientNoCutoffTest( 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 = 'ForceEnergyGradientTestNames.txt' systemListFileName = 'SystemNames.txt' argumentHash['ValidationDirectory'] = validationDirectory argumentHash['ConfigDirectory'] = configDirectory argumentHash['DataDirectory'] = dataDirectory argumentHash['TestListFileName'] = testListFileName argumentHash['SystemListFileName'] = systemListFileName argumentHash['Platform'] = 'Reference' argumentHash['SystemsDirectory'] = systemsDirectory argumentHash['PrintParam'] = False argumentHash['Verbose'] = False 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' : 4.0e-02, 'ForceStepDelta' : 1.0e-03, } printParam = argumentHash['PrintParam'] verbose = argumentHash['Verbose'] validationUtilities.setVerbose( verbose ) platform = argumentHash['Platform'] 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( argumentHash['TestSummaryFileName'] != 'NA' ): testSummaryFileName = argumentHash['TestSummaryFileName'] else: testSummaryFileName = platform + 'ForceEnergyComparisonSummary.txt' 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( 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: if( 'DeviceId' in argumentHash ): testParameterHash['DeviceId'] = argumentHash['DeviceId'] # get test and run forceTest = forceEnergyGradientTestFactory( testName, systemParameters, testParameterHash, verbose ) if( forceTest is not None and forceTest.isActive() ): if( serializeDirectory ): forceTest.serialize( serializeDirectory ) forceTest.runTest( platform ) fullTestName = forceTest.getFullTestName() testResults[fullTestName] = forceTest.getResult() 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 repr(traceback.print_exception( sys.exc_info()[0], sys.exc_info()[1], sys.exc_info()[2])) print "%s test did not run for %s" % (testName, systemName) numberOfTestsThatDidNotRun += 1 # output results print '*' * 80 sys.stdout.flush() 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 printTestSummary( testSummaryFileName, testNameHash, testResults ) # exit w/ flag signalling success if numberOfTestsThatFailed > 0 or numberOfTestsThatDidNotRun > 0: sys.exit(1) else: sys.exit(0)