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#ifdef WIN32
// Needed for unlink() on Win32 with MinGW
#include <io.h>
#endif
#include <errno.h>
#include <unistd.h>
#include <sys/stat.h>
// hdf5_simresults.h is the GMX adaptor for HDF5_SimResults
#include "hdf5_simresults.h"
#include "Nanorex/HDF5_SimResults.h"
int frameIndex = 0;
Nanorex::HDF5_SimResults* simResults = 0;
#ifdef WIN32
#include "windows.h"
/* FUNCTION: checkNamedMutexUnlocked
*
* Returns true if the mutex with the given name exists and was acquired by this
* function, false otherwise.
*/
char mutexName[32];
bool mutexNameInitialized = false;
HANDLE mutex = NULL;
bool checkNamedMutex(const char* name) {
// Add pid to mutex name so we only affect this process.
if (!mutexNameInitialized) {
sprintf(mutexName, "%s%d", name, getpid());
printf(">> mutexName=%s\n", mutexName);
mutexNameInitialized = true;
}
if (mutex == NULL)
mutex =
OpenMutex(
MUTEX_ALL_ACCESS, // request full access
FALSE, // handle not inheritable
TEXT(mutexName)); // object name
if (mutex != NULL) {
printf(">>> Mutex open\n");fflush(0);
bool gotMutexLock = false;
while (!gotMutexLock) {
DWORD result =
WaitForSingleObject(
mutex, // handle to mutex
500); // give signaller 500 ms to let us lock
if (result == WAIT_OBJECT_0) {
printf(">>> Got mutex (%s)\n", mutexName); fflush(0);
gotMutexLock = true;
} else {
printf(">>> didn't get mutex\n"), fflush(0);
}
}
return true;
} else {
printf(">>> mutex null\n");fflush(0);
}
return false;
}
#endif
/* FUNCTION: openHDF5dataStore */
void openHDF5dataStore(const char* dataStoreName) {
printf(">>> hdf5simresults.cpp: openHDF5dataStore\n");
// The dataStoreName string will be something like foo.nh5. Strip the .nh5
// off to form the directory name.
//
std::string dataStoreDirectory = dataStoreName;
dataStoreDirectory.erase(strlen(dataStoreName) - 4, 4);
// Backup old datastore file
//
char filename[128], backupFilename[128];
sprintf(backupFilename, "%s/#%s#", dataStoreDirectory.c_str(),
HDF5_SIM_RESULT_FILENAME);
unlink(backupFilename);
sprintf(filename, "%s/%s", dataStoreDirectory.c_str(),
HDF5_SIM_RESULT_FILENAME);
if (rename(filename, backupFilename) == 0)
fprintf(stderr, "\n[HDF5] Backed up %s to %s\n", filename, backupFilename);
else
if (errno != ENOENT)
fprintf(stderr, "\n[HDF5] Couldn't back up %s to %s (errno=%d)\n",
filename, backupFilename, errno);
// Create the datastore directory
//
#if defined(WIN32)
int status =
mkdir(dataStoreDirectory.c_str());
#else
int status =
mkdir(dataStoreDirectory.c_str(),
S_IRWXU | S_IRWXG | S_IROTH | S_IXOTH);
#endif
if (status == 0)
fprintf(stderr, "[HDF5] HDF5 datastore directory created: %s\n",
dataStoreDirectory.c_str());
else
if (errno != EEXIST)
fprintf(stderr, "[HDF5] Failed to create the datastore directory: %s (errno=%d)\n",
dataStoreDirectory.c_str(), errno);
else
status = 0;
// Create the HDF5 datastore
//
std::string message;
if (status == 0) {
simResults = new Nanorex::HDF5_SimResults();
status = simResults->openDataStore(dataStoreDirectory.c_str(), message);
if (status) {
fprintf(stderr, "[HDF5] Unable to open datastore %s: %d (%s)\n",
dataStoreDirectory.c_str(), status, message.c_str());
delete simResults;
simResults = 0;
}
}
// Set the run result to "still running"
status = simResults->setRunResult(1, "", message);
// Create a frame set
//
if (status == 0) {
status = simResults->addFrameSet(HDF5_FRAMESET_NAME, message);
if (status) {
fprintf(stderr, "[HDF5] Unable to create frameset %s: %d (%s)\n",
HDF5_FRAMESET_NAME, status, message.c_str());
delete simResults;
simResults = 0;
}
}
simResults->flush();
}
/* FUNCTION: addHDF5inputParameters */
void addHDF5inputParameters(const HDF5inputParameters* inputParams) {
if (simResults == 0)
return; // Short-circuit
std::string message;
simResults->setStringParameter
("GMX.pbc", inputParams->pbc, message);
simResults->setStringParameter
("GMX.integrator", inputParams->integrator, message);
simResults->setStringParameter
("GMX.ns_type", inputParams->ns_type, message);
simResults->setIntParameter
("GMX.nsteps", inputParams->nsteps, message);
simResults->setIntParameter
("GMX.nstcgsteep", inputParams->nstcgsteep, message);
simResults->setIntParameter
("GMX.nstlist", inputParams->nstlist, message);
simResults->setFloatParameter
("GMX.rlist", inputParams->rlist, message);
simResults->setFloatParameter
("GMX.rcoulomb", inputParams->rcoulomb, message);
simResults->setFloatParameter
("GMX.rvdw", inputParams->rvdw, message);
simResults->setFloatParameter
("GMX.epsilon_r", inputParams->epsilon_r, message);
simResults->setFloatParameter
("GMX.emtol", inputParams->emtol, message);
simResults->setFloatParameter
("GMX.emstep", inputParams->emstep, message);
// Hard-coded for now
simResults->setFilePath((const char*)("input.mmp"),
(const char*)("input.mmp"), message);
simResults->flush();
}
/* FUNCTION: addHDF5resultsData */
void addHDF5resultsData(const HDF5resultsData* resultsData) {
if (simResults == 0)
return; // Short-circuit
std::string message, reason;
int result = 2;
if (resultsData->converged) {
result = 0; // success
} else if (resultsData->convergedToMachinePrecision) {
result = 2; // failure
reason = "Converged to machine precision.";
} else if (resultsData->gotSIGTERM) {
result = 3; // aborted
reason = "Received SIGTERM.";
}
simResults->setRunResult(result, reason.c_str(), message);
printf(">>> addHDF5resultsData: runResult=%d\n", result);fflush(0);
simResults->setIntResult
("FinalStep", resultsData->finalStep, message);
simResults->setFloatResult
("TotalEnergy", resultsData->totalEnergy, message);
simResults->setFloatResult
("MaximumForce", resultsData->maxForce, message);
simResults->flush();
}
/* FUNCTION: addHDF5frame */
void addHDF5frame(float time) {
if (simResults == 0)
return; // Short-circuit
std::string message;
int status =
simResults->addFrame(HDF5_FRAMESET_NAME, time, frameIndex, message);
if (status) {
fprintf(stderr, "[HDF5] Unable to add frame for time=%g: %d (%s)\n",
time, status, message.c_str());
delete simResults;
simResults = 0;
}
}
/* FUNCTION: addHDF5atomIds */
void addHDF5atomIds(const unsigned int* atomIds, unsigned int atomCount) {
if (simResults == 0)
return; // Short-circuit
std::string message;
int status =
simResults->setFrameAtomIds(HDF5_FRAMESET_NAME, atomIds, atomCount,
message);
if (status) {
fprintf(stderr, "[HDF5] Unable to set atom Ids: %d (%s)\n",
status, message.c_str());
delete simResults;
simResults = 0;
}
simResults->flush();
}
/* FUNCTION: addHDF5atomicNumbers */
void addHDF5atomicNumbers(const unsigned int* atomicNumbers,
unsigned int atomCount) {
if (simResults == 0)
return; // Short-circuit
std::string message;
int status =
simResults->setFrameAtomicNumbers(HDF5_FRAMESET_NAME, atomicNumbers,
atomCount, message);
if (status) {
fprintf(stderr, "[HDF5] Unable to set atomic numbers: %d (%s)\n",
status, message.c_str());
delete simResults;
simResults = 0;
}
simResults->flush();
}
/* FUNCTION: addHDF5bonds */
void addHDF5bonds(const void* bonds, unsigned int bondCount) {
if (simResults == 0)
return; // Short-circuit
std::string message;
int status =
simResults->setFrameBonds(HDF5_FRAMESET_NAME, frameIndex, bonds,
bondCount, message);
if (status) {
fprintf(stderr, "[HDF5] Unable to add bonds to frame=%d: %d (%s)\n",
frameIndex, status, message.c_str());
delete simResults;
simResults = 0;
}
simResults->flush();
}
/* FUNCTION: addHDF5atomCoordinates */
void addHDF5atomCoordinates(const float* coordinates, unsigned int atomCount) {
if (simResults == 0)
return; // Short-circuit
std::string message;
int status =
simResults->setFrameAtomPositions(HDF5_FRAMESET_NAME, frameIndex,
coordinates, atomCount, message);
if (status) {
fprintf(stderr, "[HDF5] Unable to add atom coordinates to frame=%d: %d (%s)\n",
frameIndex, status, message.c_str());
delete simResults;
simResults = 0;
}
simResults->flush();
}
/* FUNCTION: closeHDF5dataStore */
void closeHDF5dataStore() {
delete simResults;
simResults = 0;
}
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