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Commit 38c2015e authored by Mark Friedrichs's avatar Mark Friedrichs
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Update to nonbonded and implicit solvent tests

parent 7b5344db
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Showing with 143 additions and 240 deletions
platforms/cuda/src/kernels/kCalculateGBVIBornSum.cu
View file @ 38c2015e
......@@ -242,6 +242,10 @@ void kReduceGBVIBornSum(gpuContext gpu)
LAUNCHERROR("kReduceGBVIBornSum");
}
static int isNanOrInfinity( float number ){
return (number != number || number == std::numeric_limits<float>::infinity() || number == -std::numeric_limits<float>::infinity()) ? 1 : 0;
}
void kPrintGBVI( gpuContext gpu, std::string callId, int call, FILE* log)
{
......@@ -252,6 +256,26 @@ void kPrintGBVI( gpuContext gpu, std::string callId, int call, FILE* log)
gpu->psPosq4->Download();
gpu->psSigEps2->Download();
int printOnlyOnNan = 1;
int foundNan = 0;
if( printOnlyOnNan ){
for( int ii = 0; ii < gpu->sim.paddedNumberOfAtoms && foundNan == 0; ii++ ){
foundNan += isNanOrInfinity( gpu->psBornRadii->_pSysData[ii] );
foundNan += isNanOrInfinity( gpu->psBornForce->_pSysData[ii] );
foundNan += isNanOrInfinity( gpu->psGBVISwitchDerivative->_pSysData[ii] );
}
if( foundNan ){
log = stderr;
(void) fprintf( log, "kPrintGBVI found nan \n", gpu->sim.paddedNumberOfAtoms );
for( int ii = 0; ii < gpu->sim.paddedNumberOfAtoms; ii++ ){
(void) fprintf( log, "%6d %15.7e %15.7e %15.7e\n", ii,
gpu->psPosq4->_pSysData[ii].x,
gpu->psPosq4->_pSysData[ii].y,
gpu->psPosq4->_pSysData[ii].z );
}
}
}
if( !printOnlyOnNan || foundNan ){
(void) fprintf( log, "kPrintGBVI Cuda comp bR bF prm sigeps2\n" );
(void) fprintf( stderr, "kCalculateGBVIBornSum: bOutputBufferPerWarp=%u blks=%u th/blk=%u wu=%u %u shrd=%u\n", gpu->bOutputBufferPerWarp,
gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block, gpu->sim.workUnits, gpu->psWorkUnit->_pSysStream[0][0],
......@@ -271,6 +295,10 @@ void kPrintGBVI( gpuContext gpu, std::string callId, int call, FILE* log)
gpu->psSigEps2->_pSysData[ii].y );
}
if( foundNan ){
exit(0);
}
}
}
......
platforms/cuda/tests/CMakeLists.txt
View file @ 38c2015e
......@@ -15,7 +15,6 @@ IF( INCLUDE_SERIALIZATION )
SET( SHARED_OPENMM_SERIALIZATION OpenMMSerialization )
ENDIF( INCLUDE_SERIALIZATION )
# Automatically create tests using files named "Test*.cpp"
FILE(GLOB TEST_PROGS "*Test*.cpp")
# TestCudaRandom has never worked on windows, so let's stop polluting the dashboard with it.
......@@ -28,9 +27,17 @@ FOREACH(TEST_PROG ${TEST_PROGS})
GET_FILENAME_COMPONENT(TEST_ROOT ${TEST_PROG} NAME_WE)
# Link with shared library
CUDA_ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_TARGET})
# Three tests are created from the file TestCudaGBVIForce2.cpp by
# setting preprocessor definitions
# TestCudaNonbondForce2
# TestCudaGBSAOBCForce2
# TestCudaGBVIForce2
IF( ${TEST_ROOT} STREQUAL "TestCudaGBVIForce2" )
# serialize
......@@ -38,9 +45,6 @@ FOREACH(TEST_PROG ${TEST_PROGS})
SET(DEFINE_STRING "-DTEST_PLATFORM=0 ")
IF( INCLUDE_SERIALIZATION )
SET(DEFINE_STRING "${DEFINE_STRING} -DOPENMM_SERIALIZE ")
SET(TARGET_LINK_LIBRARIES_STRING "${SHARED_TARGET} ${SHARED_OPENMM_SERIALIZATION}")
ELSE( INCLUDE_SERIALIZATION )
SET(TARGET_LINK_LIBRARIES_STRING "${SHARED_TARGET}")
ENDIF( INCLUDE_SERIALIZATION )
# obc
......@@ -48,12 +52,6 @@ FOREACH(TEST_PROG ${TEST_PROGS})
SET(OBC_DEFINE_STRING "${DEFINE_STRING} -DIMPLICIT_SOLVENT=1")
SET(OBC_TEST "TestCudaGBSAOBCForce2")
CUDA_ADD_EXECUTABLE(${OBC_TEST} ${TEST_PROG})
IF( INCLUDE_SERIALIZATION )
TARGET_LINK_LIBRARIES(${OBC_TEST} ${SHARED_TARGET} ${SHARED_OPENMM_SERIALIZATION} )
ELSE( INCLUDE_SERIALIZATION )
TARGET_LINK_LIBRARIES(${OBC_TEST} ${SHARED_TARGET})
ENDIF( INCLUDE_SERIALIZATION )
SET_TARGET_PROPERTIES(${OBC_TEST} PROPERTIES COMPILE_FLAGS ${OBC_DEFINE_STRING} )
ADD_TEST(${OBC_TEST} ${EXECUTABLE_OUTPUT_PATH}/${OBC_TEST})
......@@ -62,12 +60,6 @@ FOREACH(TEST_PROG ${TEST_PROGS})
SET(NONBOND_DEFINE_STRING "${DEFINE_STRING} -DIMPLICIT_SOLVENT=0")
SET(NONBOND_TEST "TestCudaNonbondForce2")
CUDA_ADD_EXECUTABLE(${NONBOND_TEST} ${TEST_PROG})
IF( INCLUDE_SERIALIZATION )
TARGET_LINK_LIBRARIES(${NONBOND_TEST} ${SHARED_TARGET} ${SHARED_OPENMM_SERIALIZATION} )
ELSE( INCLUDE_SERIALIZATION )
TARGET_LINK_LIBRARIES(${NONBOND_TEST} ${SHARED_TARGET})
ENDIF( INCLUDE_SERIALIZATION )
SET_TARGET_PROPERTIES(${NONBOND_TEST} PROPERTIES COMPILE_FLAGS ${NONBOND_DEFINE_STRING} )
ADD_TEST(${NONBOND_TEST} ${EXECUTABLE_OUTPUT_PATH}/${NONBOND_TEST})
......@@ -76,6 +68,18 @@ FOREACH(TEST_PROG ${TEST_PROGS})
SET(DEFINE_STRING "${DEFINE_STRING} -DIMPLICIT_SOLVENT=2")
SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES COMPILE_FLAGS ${DEFINE_STRING} )
# libs
IF( INCLUDE_SERIALIZATION )
TARGET_LINK_LIBRARIES(${OBC_TEST} ${SHARED_TARGET} ${SHARED_OPENMM_SERIALIZATION} )
TARGET_LINK_LIBRARIES(${NONBOND_TEST} ${SHARED_TARGET} ${SHARED_OPENMM_SERIALIZATION} )
TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_TARGET} ${SHARED_OPENMM_SERIALIZATION} )
ELSE( INCLUDE_SERIALIZATION )
TARGET_LINK_LIBRARIES(${OBC_TEST} ${SHARED_TARGET})
TARGET_LINK_LIBRARIES(${NONBOND_TEST} ${SHARED_TARGET})
TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_TARGET})
ENDIF( INCLUDE_SERIALIZATION )
ENDIF( ${TEST_ROOT} STREQUAL "TestCudaGBVIForce2" )
#MESSAGE( "vcm ${TEST_ROOT} ${DEFINE_STRING}" )
......@@ -94,11 +98,6 @@ FOREACH(TEST_PROG ${TEST_PROGS})
ENDFOREACH(TEST_PROG ${TEST_PROGS})
SET(TEST_PROG TstCudaUsingParameterFile.cpp)
SET(TEST_STATIC ${TEST_ROOT}Static)
SET(INCLUDE_CUDA_STATIC 1)
#ENDIF(INCLUDE_CUDA_STATIC)
install(TARGETS TestCudaHarmonicBondForce
RUNTIME DESTINATION bin)
platforms/cuda/tests/TestCudaGBVIForce2.cpp
View file @ 38c2015e
......@@ -824,7 +824,7 @@ void PositionGenerator::getSortedDistances( int periodicBoundaryConditions, int
for( unsigned int ii = 0; ii < positions.size(); ii++ ){
if( ii == positionIndex )continue;
double distance = periodicBoundaryConditions ? getPeriodicDistance( positionIndex, ii, positions) : getDistance( positionIndex, ii, positions);
sortVector.push_back( IntDoublePair(ii,sqrt(distance) ) );
sortVector.push_back( IntDoublePair( ii, distance ) );
}
std::sort( sortVector.begin(), sortVector.end(), TestIntDoublePair );
......@@ -2115,158 +2115,6 @@ static Force* copyForce( const Force& force, FILE* log ){
return forceCopy;
}
/**---------------------------------------------------------------------------------------
*
* Copy NonbondedSoftcoreForce
*
* @param nonbondedSoftcoreForce NonbondedSoftcoreForce to copy
*
* @return copy of nonbondedSoftcoreForce
*
--------------------------------------------------------------------------------------- */
#ifdef USE_SOFTCORE
static NonbondedSoftcoreForce* copyNonbondedSoftcoreForce( const NonbondedSoftcoreForce& nonbondedSoftcoreForce ){
NonbondedSoftcoreForce* copyNonbondedSoftcoreForce = new NonbondedSoftcoreForce( nonbondedSoftcoreForce );
/*
copyNonbondedSoftcoreForce->setNonbondedMethod( nonbondedSoftcoreForce.getNonbondedMethod() );
copyNonbondedSoftcoreForce->setCutoffDistance( nonbondedSoftcoreForce.getCutoffDistance() );
copyNonbondedSoftcoreForce->setReactionFieldDielectric( nonbondedSoftcoreForce.getReactionFieldDielectric() );
// particle parameters
for( unsigned int ii = 0; ii < nonbondedSoftcoreForce.getNumParticles(); ii++ ){
double charge;
double sigma;
double epsilon;
double softcoreLJLambda;
nonbondedSoftcoreForce.getParticleParameters(ii, charge, sigma, epsilon, softcoreLJLambda);
copyNonbondedSoftcoreForce->addParticle( charge, sigma, epsilon, softcoreLJLambda);
}
// exceptions
for( unsigned int ii = 0; ii < nonbondedSoftcoreForce.getNumExceptions(); ii++ ){
int particle1, particle2;
double chargeProd;
double sigma;
double epsilon;
double softcoreLJLambda;
nonbondedSoftcoreForce.getExceptionParameters( ii, particle1, particle2, chargeProd, sigma, epsilon, softcoreLJLambda );
copyNonbondedSoftcoreForce->addException( particle1, particle2, chargeProd, sigma, epsilon, softcoreLJLambda );
}
*/
return copyNonbondedSoftcoreForce;
}
static GBVISoftcoreForce* copyGbviSoftcoreForce( const GBVISoftcoreForce& gbviSoftcoreForce ){
GBVISoftcoreForce* copyGbviSoftcoreForce = new GBVISoftcoreForce(gbviSoftcoreForce);
/*
GBVISoftcoreForce* copyGbviSoftcoreForce = new GBVISoftcoreForce();
copyGbviSoftcoreForce->setNonbondedMethod( gbviSoftcoreForce.getNonbondedMethod() );
copyGbviSoftcoreForce->setCutoffDistance( gbviSoftcoreForce.getCutoffDistance() );
copyGbviSoftcoreForce->setSolventDielectric( gbviSoftcoreForce.getSolventDielectric() );
copyGbviSoftcoreForce->setSoluteDielectric( gbviSoftcoreForce.getSoluteDielectric() );
copyGbviSoftcoreForce->setBornRadiusScalingMethod( gbviSoftcoreForce.getBornRadiusScalingMethod() );
copyGbviSoftcoreForce->setQuinticLowerLimitFactor( gbviSoftcoreForce.getQuinticLowerLimitFactor() );
copyGbviSoftcoreForce->setQuinticUpperBornRadiusLimit( gbviSoftcoreForce.getQuinticUpperBornRadiusLimit() );
// particle parameters
for( unsigned int ii = 0; ii < gbviSoftcoreForce.getNumParticles(); ii++ ){
double charge;
double sigma;
double gamma;
double softcoreLJLambda;
gbviSoftcoreForce.getParticleParameters(ii, charge, sigma, gamma, softcoreLJLambda);
copyGbviSoftcoreForce->addParticle( charge, sigma, gamma, softcoreLJLambda);
}
// bonds
for( unsigned int ii = 0; ii < gbviSoftcoreForce.getNumBonds(); ii++ ){
int particle1, particle2;
double distance;
gbviSoftcoreForce.getBondParameters( ii, particle1, particle2, distance);
copyGbviSoftcoreForce->addBond( particle1, particle2, distance );
}
*/
return copyGbviSoftcoreForce;
}
static GBSAOBCSoftcoreForce* copyGBSAOBCSoftcoreForce( const GBSAOBCSoftcoreForce& gbviSoftcoreForce ){
return new GBSAOBCSoftcoreForce(gbviSoftcoreForce);
}
#endif
/**---------------------------------------------------------------------------------------
*
* Copy NonbondedForce
*
* @param nonbondedForce NonbondedForce to copy
*
* @return copy of nonbondedForce
*
--------------------------------------------------------------------------------------- */
static NonbondedForce* copyNonbondedForce( const NonbondedForce& nonbondedForce ){
NonbondedForce* copyNonbondedForce = new NonbondedForce( nonbondedForce );
/*
copyNonbondedForce->setNonbondedMethod( nonbondedForce.getNonbondedMethod() );
copyNonbondedForce->setCutoffDistance( nonbondedForce.getCutoffDistance() );
copyNonbondedForce->setReactionFieldDielectric( nonbondedForce.getReactionFieldDielectric() );
// particle parameters
for( unsigned int ii = 0; ii < nonbondedForce.getNumParticles(); ii++ ){
double charge;
double sigma;
double epsilon;
double softcoreLJLambda;
nonbondedForce.getParticleParameters(ii, charge, sigma, epsilon, softcoreLJLambda);
copyNonbondedForce->addParticle( charge, sigma, epsilon, softcoreLJLambda);
}
// exceptions
for( unsigned int ii = 0; ii < nonbondedForce.getNumExceptions(); ii++ ){
int particle1, particle2;
double chargeProd;
double sigma;
double epsilon;
double softcoreLJLambda;
nonbondedForce.getExceptionParameters( ii, particle1, particle2, chargeProd, sigma, epsilon, softcoreLJLambda );
copyNonbondedForce->addException( particle1, particle2, chargeProd, sigma, epsilon, softcoreLJLambda );
}
*/
return copyNonbondedForce;
}
static GBVIForce* copyGbviForce( const GBVIForce& gbviForce ){
return new GBVIForce(gbviForce);
}
static GBSAOBCForce* copyGbsaObcForce( const GBSAOBCForce& gbviForce ){
return new GBSAOBCForce(gbviForce);
}
/**
* Return copy of system (but not forces)
*
......@@ -2891,6 +2739,25 @@ static void getPlatformName( int platformId, std::string& platformName ){
return;
}
/**
* Get lib name
*
* @param libPrefix lib prefix (lib or "")
* @param libSuffix lib suffix (.so, .dylib, .dll)
* @param baseName base name
*
* @return libname
*
*/
static std::string getLibName( const std::string& libPrefix, const std::string& libSuffix, const std::string& baseName ){
std::string fullName = libPrefix;
fullName.append( baseName );
fullName.append( libSuffix );
return fullName;
}
/**
* Get nonbonded method name
*
......@@ -3044,9 +2911,9 @@ void runSystemComparisonTest( System& system1, System& system2,
Platform& platform2 = Platform::getPlatformByName( platformName2 );
if( deviceId2 ){
setDeviceIdUsingEnvVariable( platform2, log );
setDeviceId( platform2, deviceId2, log );
}
setDeviceIdUsingEnvVariable( platform2, log );
Context context2( system2, integrator2, platform2 );
context2.setPositions(positions);
......@@ -3298,22 +3165,21 @@ void runTests( MapStringToDouble& inputArgumentMap, FILE* log ){
double distanceTolerance = 1.0e-04;
IntVector positionIndexVector;
positionIndexVector.push_back( 0 );
positionIndexVector.push_back( 2266 );
positionIndexVector.push_back( 2656 );
positionIndexVector.push_back( 5713 );
positionIndexVector.push_back( 6291 );
positionIndexVector.push_back( 3191 );
positionIndexVector.push_back( 3769 );
positionIndexVector.push_back( static_cast<int>(positions.size())-1 );
//positionGenerator.showMinMaxDistances( positions, periodicBoundaryConditions, showIndex, positionIndexVector);
positionGenerator.showMinMaxDistances( positions, periodicBoundaryConditions, showIndex, positionIndexVector);
positionGenerator.showMinMaxDistances( positions, periodicBoundaryConditions, showIndex );
positionGenerator.showParticlesWithinDistance( positions, periodicBoundaryConditions, 2266, cutoffDistance, distanceTolerance );
positionGenerator.showParticlesWithinDistance( positions, periodicBoundaryConditions, 5713, cutoffDistance, distanceTolerance );
positionGenerator.showParticlesWithinDistance( positions, periodicBoundaryConditions, 6291, cutoffDistance, distanceTolerance );
IntIntPairVector pairs;
pairs.push_back( IntIntPair( 2266, 2656 ) );
pairs.push_back( IntIntPair( 2266, 2264 ) );
pairs.push_back( IntIntPair( 2266, 2292 ) );
pairs.push_back( IntIntPair( 2266, 1872 ) );
pairs.push_back( IntIntPair( 2266, 1847 ) );
pairs.push_back( IntIntPair( 2266, 2658 ) );
pairs.push_back( IntIntPair( 2266, 2294 ) );
pairs.push_back( IntIntPair( 2266, 2236 ) );
pairs.push_back( IntIntPair( 5713, 6291 ) );
pairs.push_back( IntIntPair( 5713, 3191 ) );
pairs.push_back( IntIntPair( 5713, 3769 ) );
pairs.push_back( IntIntPair( 6291, 3191 ) );
positionGenerator.showDistances( pairs, positions );
}
......@@ -3431,18 +3297,18 @@ void runTests( MapStringToDouble& inputArgumentMap, FILE* log ){
System systemCopy;
copySystem( standardSystem, systemCopy, log );
// perform comparison
std::stringstream idString;
idString << "Nb " << nonbondedMethod << " l2 " << std::fixed << setprecision(2) << lambda2;
runSystemComparisonTest( standardSystem, systemCopy, positions, inputArgumentMap, idString.str(), log );
// serialize
baseFileName << "_N" << positions.size();
baseFileName << "_Nb" << nonbondedMethod;
serializeSystemAndPositions( standardSystem, positions, baseFileName.str(), log);
// perform comparison
std::stringstream idString;
idString << "Nb " << nonbondedMethod << " l2 " << std::fixed << setprecision(2) << lambda2;
runSystemComparisonTest( standardSystem, systemCopy, positions, inputArgumentMap, idString.str(), log );
}
int main() {
......@@ -3505,9 +3371,9 @@ int main() {
}
DoubleVector nonbondedMethod;
//nonbondedMethod.push_back( NoCutoff_OpenMMTest );
nonbondedMethod.push_back( NoCutoff_OpenMMTest );
nonbondedMethod.push_back( CutoffNonPeriodic_OpenMMTest );
//nonbondedMethod.push_back( CutoffPeriodic_OpenMMTest );
nonbondedMethod.push_back( CutoffPeriodic_OpenMMTest );
#if IMPLICIT_SOLVENT == TEST_NONBONDED
nonbondedMethod.push_back( Ewald_OpenMMTest );
nonbondedMethod.push_back( PME_OpenMMTest );
......@@ -3529,16 +3395,26 @@ int main() {
// check that required libs are available for platform to be tested
// if unavailable, skip tests
std::string libPrefix = "lib";
std::string libSuffix = ".so";
#ifdef _MSC_VER
libPrefix = "";
libSuffix = ".dll";
#endif
#ifdef __APPLE__
libSuffix = ".dylib";
#endif
StringVector requiredLibs;
for( unsigned int kk = 0; kk < platformId2s.size(); kk++ ){
if( platformId2s[kk] == OpenCL_OpenMMTest ){
requiredLibs.push_back( "libOpenMMOpenCL.so" );
requiredLibs.push_back( getLibName( libPrefix, libSuffix, "OpenMMOpenCL" ) );
}
if( platformId2s[kk] == Cuda_OpenMMTest ){
requiredLibs.push_back( "libOpenMMCuda.so" );
requiredLibs.push_back( getLibName( libPrefix, libSuffix, "OpenMMCuda") );
#ifdef USE_SOFTCORE
requiredLibs.push_back( "libOpenMMFreeEnergy.so" );
requiredLibs.push_back( "libOpenMMFreeEnergyCuda.so" );
requiredLibs.push_back( getLibName( libPrefix, libSuffix, "OpenMMFreeEnergy" ) );
requiredLibs.push_back( getLibName( libPrefix, libSuffix, "OpenMMFreeEnergyCuda" ) );
#endif
}
}
......
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