void openH5File()
{
if (dataCollector == NULL)
{
DataSpace<simDim> mpi_pos;
DataSpace<simDim> mpi_size;
Dimensions splashMpiPos;
Dimensions splashMpiSize;
GridController<simDim> &gc = Environment<simDim>::get().GridController();
mpi_pos = gc.getPosition();
mpi_size = gc.getGpuNodes();
splashMpiPos.set(0, 0, 0);
splashMpiSize.set(1, 1, 1);
for (uint32_t i = 0; i < simDim; ++i)
{
splashMpiPos[i] = mpi_pos[i];
splashMpiSize[i] = mpi_size[i];
}
const uint32_t maxOpenFilesPerNode = 1;
dataCollector = new ParallelDomainCollector(
gc.getCommunicator().getMPIComm(),
gc.getCommunicator().getMPIInfo(),
splashMpiSize,
maxOpenFilesPerNode);
// set attributes for datacollector files
DataCollector::FileCreationAttr h5_attr;
h5_attr.enableCompression = false;
h5_attr.fileAccType = DataCollector::FAT_CREATE;
h5_attr.mpiPosition.set(splashMpiPos);
h5_attr.mpiSize.set(splashMpiSize);
}
// open datacollector
try
{
std::string filename = (foldername + std::string("/makroParticlePerSupercell"));
log<picLog::INPUT_OUTPUT > ("HDF5 open DataCollector with file: %1%") %
filename;
dataCollector->open(filename.c_str(), h5_attr);
}
catch (DCException e)
{
std::cerr << e.what() << std::endl;
throw std::runtime_error("Failed to open datacollector");
}
}
int detectFileMPISize(Options& options, Dimensions &fileMPISizeDim)
{
int result = RESULT_OK;
DataCollector *dc = NULL;
#if (SPLASH_SUPPORTED_PARALLEL==1)
if (options.parallelFile)
dc = new ParallelDataCollector(MPI_COMM_WORLD, MPI_INFO_NULL,
Dimensions(options.mpiSize, 1, 1), 1);
else
#endif
dc = new SerialDataCollector(1);
DataCollector::FileCreationAttr fileCAttr;
DataCollector::initFileCreationAttr(fileCAttr);
fileCAttr.fileAccType = DataCollector::FAT_READ;
try
{
dc->open(options.filename.c_str(), fileCAttr);
dc->getMPISize(fileMPISizeDim);
dc->close();
} catch (DCException e)
{
std::cerr << "[0] Detecting file MPI size failed!" << std::endl <<
e.what() << std::endl;
fileMPISizeDim.set(0, 0, 0);
result = RESULT_ERROR;
}
delete dc;
dc = NULL;
return result;
}
void DCDataSet::read(Dimensions dstBuffer,
Dimensions dstOffset,
Dimensions srcSize,
Dimensions srcOffset,
Dimensions& sizeRead,
uint32_t& srcNDims,
void* dst)
throw (DCException)
{
log_msg(2, "DCDataSet::read (%s)", name.c_str());
if (!opened)
throw DCException(getExceptionString("read: Dataset has not been opened/created"));
if (dstBuffer.getScalarSize() == 0)
dstBuffer.set(srcSize);
// dst buffer is allowed to be NULL
// in this case, only the size of the dataset is returned
// if the dataset is empty, return just its size as there is nothing to read
if ((dst != NULL) && (getNDims() > 0))
{
log_msg(3,
" ndims = %llu\n"
" logical_size = %s\n"
" physical_size = %s\n"
" dstBuffer = %s\n"
" dstOffset = %s\n"
" srcSize = %s\n"
" srcOffset = %s\n",
(long long unsigned) ndims,
getLogicalSize().toString().c_str(),
getPhysicalSize().toString().c_str(),
dstBuffer.toString().c_str(),
dstOffset.toString().c_str(),
srcSize.toString().c_str(),
srcOffset.toString().c_str());
dstBuffer.swapDims(ndims);
dstOffset.swapDims(ndims);
srcSize.swapDims(ndims);
srcOffset.swapDims(ndims);
hid_t dst_dataspace = H5Screate_simple(ndims, dstBuffer.getPointer(), NULL);
if (dst_dataspace < 0)
throw DCException(getExceptionString("read: Failed to create target dataspace"));
if (H5Sselect_hyperslab(dst_dataspace, H5S_SELECT_SET, dstOffset.getPointer(), NULL,
srcSize.getPointer(), NULL) < 0 ||
H5Sselect_valid(dst_dataspace) <= 0)
throw DCException(getExceptionString("read: Target dataspace hyperslab selection is not valid!"));
if (H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, srcOffset.getPointer(), NULL,
srcSize.getPointer(), NULL) < 0 ||
H5Sselect_valid(dataspace) <= 0)
throw DCException(getExceptionString("read: Source dataspace hyperslab selection is not valid!"));
if (srcSize.getScalarSize() == 0)
H5Sselect_none(dataspace);
if (H5Dread(dataset, this->datatype, dst_dataspace, dataspace, dsetReadProperties, dst) < 0)
throw DCException(getExceptionString("read: Failed to read dataset"));
H5Sclose(dst_dataspace);
srcSize.swapDims(ndims);
}
// swap dimensions if necessary
sizeRead.set(srcSize);
srcNDims = this->ndims;
log_msg(3, " returns ndims = %llu", (long long unsigned) ndims);
log_msg(3, " returns sizeRead = %s", sizeRead.toString().c_str());
}