void write_hdf(const std::string &filename, double* &data, int &m_rows, int &m_cols){
hid_t file_id, dataset_id, space_id, property_id;
herr_t status;
hsize_t dims[2] = {m_rows,m_cols};
//Create a new file using the default properties.
file_id = H5Fcreate (filename.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
//Create dataspace. Setting maximum size to NULL sets the maximum
//size to be the current size.
space_id = H5Screate_simple (2, dims, NULL);
//Create the dataset creation property list, set the layout to compact.
property_id = H5Pcreate (H5P_DATASET_CREATE);
status = H5Pset_layout (property_id, H5D_CONTIGUOUS);
// Create the dataset.
dataset_id = H5Dcreate (file_id, "x", H5T_NATIVE_DOUBLE, space_id, H5P_DEFAULT, property_id, H5P_DEFAULT);
//Write the data to the dataset.
status = H5Dwrite (dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
status = H5Sclose(space_id);
status = H5Dclose(dataset_id);
status = H5Fclose(file_id);
status = H5Pclose(property_id);
}
hid_t InfiniteDimensionalMCMCSampler::_create_scalar_dataset(const std::string & name)
{
// Only subprocess with rank 0 manipulates the output file
if ((this->m_env).subRank() == 0) {
// Create a 1D dataspace. Unlimited size. Initially set to 0. We will
// extend it later
const int ndims = 1;
hsize_t dims[ndims] = {0}; // dataset dimensions at creation
hsize_t maxdims[ndims] = {H5S_UNLIMITED};
hid_t file_space = H5Screate_simple(ndims, dims, maxdims);
// Create dataset creation property list. Unlimited datasets must be
// chunked. Choosing the chunk size is an issue, here we set it to 1
hsize_t chunk_dims[ndims] = {1};
hid_t plist = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_layout(plist, H5D_CHUNKED);
H5Pset_chunk(plist, ndims, chunk_dims);
// Create the dataset
hid_t dset = H5Dcreate(this->_outfile, name.c_str(), H5T_NATIVE_DOUBLE,
file_space, H5P_DEFAULT, plist, H5P_DEFAULT);
// We don't need the property list anymore. We also don't need the file
// dataspace anymore because we'll extend it later, making this one
// invalild anyway.
H5Pclose(plist);
H5Sclose(file_space);
return dset;
}
}
void write(const std::string &filename, std::vector<int> &data)
{
// HDF5 handles
hid_t file_id, dataset_id, space_id, property_id;
herr_t status;
hsize_t dims[1] = {data.size()};
//Create a new file using the default properties.
file_id = H5Fcreate (filename.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
//Create dataspace. Setting maximum size to NULL sets the maximum
//size to be the current size.
space_id = H5Screate_simple (1, dims, NULL);
//Create the dataset creation property list, set the layout to compact.
property_id = H5Pcreate (H5P_DATASET_CREATE);
status = H5Pset_layout (property_id, H5D_COMPACT);
// Create the dataset.
dataset_id = H5Dcreate (file_id, "DATASET", H5T_STD_I32LE, space_id, H5P_DEFAULT, property_id, H5P_DEFAULT);
//Write the data to the dataset.
status = H5Dwrite (dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, &data[0]);
status = H5Sclose(space_id);
status = H5Dclose(dataset_id);
status = H5Fclose(file_id);
status = H5Pclose(property_id);
}
hid_t seissol::checkpoint::h5::Fault::initFile(int odd, const char* filename)
{
hid_t h5file;
if (loaded()) {
// Open the file
h5file = open(filename, false);
checkH5Err(h5file);
// Fault writer
m_h5timestepFault[odd] = H5Aopen(h5file, "timestep_fault", H5P_DEFAULT);
checkH5Err(m_h5timestepFault[odd]);
// Data
for (unsigned int i = 0; i < NUM_VARIABLES; i++) {
m_h5data[odd][i] = H5Dopen(h5file, VAR_NAMES[i], H5P_DEFAULT);
checkH5Err(m_h5data[odd][i]);
}
} else {
// Create the file
hid_t h5plist = H5Pcreate(H5P_FILE_ACCESS);
checkH5Err(h5plist);
checkH5Err(H5Pset_libver_bounds(h5plist, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST));
#ifdef USE_MPI
checkH5Err(H5Pset_fapl_mpio(h5plist, comm(), MPI_INFO_NULL));
#endif // USE_MPI
h5file = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, h5plist);
checkH5Err(h5file);
checkH5Err(H5Pclose(h5plist));
// Create scalar dataspace for attributes
hid_t h5spaceScalar = H5Screate(H5S_SCALAR);
checkH5Err(h5spaceScalar);
// Fault writer
m_h5timestepFault[odd] = H5Acreate(h5file, "timestep_fault",
H5T_STD_I32LE, h5spaceScalar, H5P_DEFAULT, H5P_DEFAULT);
checkH5Err(m_h5timestepFault[odd]);
int t = 0;
checkH5Err(H5Awrite(m_h5timestepFault[odd], H5T_NATIVE_INT, &t));
checkH5Err(H5Sclose(h5spaceScalar));
// Variables
for (unsigned int i = 0; i < NUM_VARIABLES; i++) {
h5plist = H5Pcreate(H5P_DATASET_CREATE);
checkH5Err(h5plist);
checkH5Err(H5Pset_layout(h5plist, H5D_CONTIGUOUS));
checkH5Err(H5Pset_alloc_time(h5plist, H5D_ALLOC_TIME_EARLY));
m_h5data[odd][i] = H5Dcreate(h5file, VAR_NAMES[i], H5T_IEEE_F64LE, m_h5fSpaceData,
H5P_DEFAULT, h5plist, H5P_DEFAULT);
checkH5Err(m_h5data[odd][i]);
checkH5Err(H5Pclose(h5plist));
}
}
return h5file;
}
//--------------------------------------------------------------------------
// Function: DSetCreatPropList::setLayout
///\brief Sets the type of storage used store the raw data for a dataset.
///\param layout - IN: Type of storage layout for raw data
///\exception H5::PropListIException
///\par Description
/// For information on valid layout types, please refer to
/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-SetLayout
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
void DSetCreatPropList::setLayout(H5D_layout_t layout) const
{
herr_t ret_value = H5Pset_layout( id, layout );
if( ret_value < 0 )
{
throw PropListIException("DSetCreatPropList::setLayout",
"H5Pset_layout failed");
}
}
void HDF5Output::open(const std::string& filename) {
file = H5Fcreate(filename.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
sid = H5Tcreate(H5T_COMPOUND, sizeof(OutputRow));
H5Tinsert(sid, "D", HOFFSET(OutputRow, D), H5T_NATIVE_DOUBLE);
H5Tinsert(sid, "z", HOFFSET(OutputRow, z), H5T_NATIVE_DOUBLE);
H5Tinsert(sid, "SN", HOFFSET(OutputRow, SN), H5T_NATIVE_UINT64);
H5Tinsert(sid, "ID", HOFFSET(OutputRow, ID), H5T_NATIVE_INT32);
H5Tinsert(sid, "E", HOFFSET(OutputRow, E), H5T_NATIVE_DOUBLE);
H5Tinsert(sid, "X", HOFFSET(OutputRow, X), H5T_NATIVE_DOUBLE);
H5Tinsert(sid, "Y", HOFFSET(OutputRow, Y), H5T_NATIVE_DOUBLE);
H5Tinsert(sid, "Z", HOFFSET(OutputRow, Z), H5T_NATIVE_DOUBLE);
H5Tinsert(sid, "Px", HOFFSET(OutputRow, Px), H5T_NATIVE_DOUBLE);
H5Tinsert(sid, "Py", HOFFSET(OutputRow, Py), H5T_NATIVE_DOUBLE);
H5Tinsert(sid, "Pz", HOFFSET(OutputRow, Pz), H5T_NATIVE_DOUBLE);
H5Tinsert(sid, "SN0", HOFFSET(OutputRow, SN0), H5T_NATIVE_UINT64);
H5Tinsert(sid, "ID0", HOFFSET(OutputRow, ID0), H5T_NATIVE_INT32);
H5Tinsert(sid, "E0", HOFFSET(OutputRow, E0), H5T_NATIVE_DOUBLE);
H5Tinsert(sid, "X0", HOFFSET(OutputRow, X0), H5T_NATIVE_DOUBLE);
H5Tinsert(sid, "Y0", HOFFSET(OutputRow, Y0), H5T_NATIVE_DOUBLE);
H5Tinsert(sid, "Z0", HOFFSET(OutputRow, Z0), H5T_NATIVE_DOUBLE);
H5Tinsert(sid, "P0x", HOFFSET(OutputRow, P0x), H5T_NATIVE_DOUBLE);
H5Tinsert(sid, "P0y", HOFFSET(OutputRow, P0y), H5T_NATIVE_DOUBLE);
H5Tinsert(sid, "P0z", HOFFSET(OutputRow, P0z), H5T_NATIVE_DOUBLE);
H5Tinsert(sid, "SN1", HOFFSET(OutputRow, SN1), H5T_NATIVE_UINT64);
H5Tinsert(sid, "ID1", HOFFSET(OutputRow, ID1), H5T_NATIVE_INT32);
H5Tinsert(sid, "E1", HOFFSET(OutputRow, E1), H5T_NATIVE_DOUBLE);
H5Tinsert(sid, "X1", HOFFSET(OutputRow, X1), H5T_NATIVE_DOUBLE);
H5Tinsert(sid, "Y1", HOFFSET(OutputRow, Y1), H5T_NATIVE_DOUBLE);
H5Tinsert(sid, "Z1", HOFFSET(OutputRow, Z1), H5T_NATIVE_DOUBLE);
H5Tinsert(sid, "P1x", HOFFSET(OutputRow, P1x), H5T_NATIVE_DOUBLE);
H5Tinsert(sid, "P1y", HOFFSET(OutputRow, P1y), H5T_NATIVE_DOUBLE);
H5Tinsert(sid, "P1z", HOFFSET(OutputRow, P1z), H5T_NATIVE_DOUBLE);
// chunked prop
hid_t plist = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_layout(plist, H5D_CHUNKED);
hsize_t chunk_dims[RANK] = {BUFFER_SIZE};
H5Pset_chunk(plist, RANK, chunk_dims);
H5Pset_deflate(plist, 5);
hsize_t dims[RANK] = {0};
hsize_t max_dims[RANK] = {H5S_UNLIMITED};
dataspace = H5Screate_simple(RANK, dims, max_dims);
dset = H5Dcreate2(file, "CRPROPA3", sid, dataspace, H5P_DEFAULT, plist, H5P_DEFAULT);
H5Pclose(plist);
buffer.reserve(BUFFER_SIZE);
}
void write_file(const std::string & filename, double * image, int r, int c)
{
hid_t file_id, dataset_id, space_id, property_id;
herr_t status;
hsize_t dims[2] = {r, c};
file_id = H5Fcreate (filename.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
space_id = H5Screate_simple (2, dims, NULL);
property_id = H5Pcreate (H5P_DATASET_CREATE);
status = H5Pset_layout (property_id, H5D_CONTIGUOUS);
dataset_id = H5Dcreate (file_id, "DATASET", H5T_STD_I32LE, space_id, H5P_DEFAULT, property_id, H5P_DEFAULT);
status = H5Dwrite (dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, image);
status = H5Sclose(space_id);
status = H5Dclose(dataset_id);
status = H5Fclose(file_id);
status = H5Pclose(property_id);
}
/*-------------------------------------------------------------------------
* Function: gent_compact
*
* Purpose: Generate a compact dataset in LOC_ID
*
*-------------------------------------------------------------------------
*/
static void gent_compact(hid_t loc_id)
{
hid_t sid, did, pid;
hsize_t dims[1] = {6};
int buf[6] = {1,2,3,4,5,6};
/* create dataspace */
sid = H5Screate_simple(1, dims, NULL);
/* create property plist */
pid = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_layout (pid,H5D_COMPACT);
/* create dataset */
did = H5Dcreate2(loc_id, DATASET_COMPACT, H5T_NATIVE_INT, sid, H5P_DEFAULT, pid, H5P_DEFAULT);
/* write */
H5Dwrite(did, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
/* close */
H5Sclose(sid);
H5Dclose(did);
H5Pclose(pid);
}
hid_t seissol::checkpoint::h5::Wavefield::initFile(int odd, const char* filename)
{
hid_t h5file;
if (loaded()) {
// Open the old file
h5file = open(filename, false);
checkH5Err(h5file);
// Time
m_h5time[odd] = H5Aopen(h5file, "time", H5P_DEFAULT);
checkH5Err(m_h5time[odd]);
// Wavefield writer
m_h5timestepWavefield[odd] = H5Aopen(h5file, "timestep_wavefield", H5P_DEFAULT);
checkH5Err(m_h5timestepWavefield[odd]);
// Data
m_h5data[odd] = H5Dopen(h5file, "values", H5P_DEFAULT);
checkH5Err(m_h5data[odd]);
} else {
// Create the file
hid_t h5plist = H5Pcreate(H5P_FILE_ACCESS);
checkH5Err(h5plist);
checkH5Err(H5Pset_libver_bounds(h5plist, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST));
hsize_t align = utils::Env::get<hsize_t>("SEISSOL_CHECKPOINT_ALIGNMENT", 0);
if (align > 0)
checkH5Err(H5Pset_alignment(h5plist, 1, align));
#ifdef USE_MPI
MPIInfo info;
checkH5Err(H5Pset_fapl_mpio(h5plist, seissol::MPI::mpi.comm(), info.get()));
#endif // USE_MPI
h5file = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, h5plist);
checkH5Err(h5file);
checkH5Err(H5Pclose(h5plist));
// Create scalar dataspace for attributes
hid_t h5spaceScalar = H5Screate(H5S_SCALAR);
checkH5Err(h5spaceScalar);
// Time
m_h5time[odd] = H5Acreate(h5file, "time", H5T_IEEE_F64LE, h5spaceScalar,
H5P_DEFAULT, H5P_DEFAULT);
checkH5Err(m_h5time[odd]);
// Partitions
hid_t h5partitions = H5Acreate(h5file, "partitions", H5T_STD_I32LE, h5spaceScalar,
H5P_DEFAULT, H5P_DEFAULT);
checkH5Err(h5partitions);
int p = partitions();
checkH5Err(H5Awrite(h5partitions, H5T_NATIVE_INT, &p));
checkH5Err(H5Aclose(h5partitions));
// Wavefield writer
m_h5timestepWavefield[odd] = H5Acreate(h5file, "timestep_wavefield",
H5T_STD_I32LE, h5spaceScalar, H5P_DEFAULT, H5P_DEFAULT);
checkH5Err(m_h5timestepWavefield[odd]);
int t = 0;
checkH5Err(H5Awrite(m_h5timestepWavefield[odd], H5T_NATIVE_INT, &t));
checkH5Err(H5Sclose(h5spaceScalar));
// Variable
h5plist = H5Pcreate(H5P_DATASET_CREATE);
checkH5Err(h5plist);
checkH5Err(H5Pset_layout(h5plist, H5D_CONTIGUOUS));
checkH5Err(H5Pset_alloc_time(h5plist, H5D_ALLOC_TIME_EARLY));
m_h5data[odd] = H5Dcreate(h5file, "values", H5T_IEEE_F64LE, m_h5fSpaceData,
H5P_DEFAULT, h5plist, H5P_DEFAULT);
checkH5Err(m_h5data[odd]);
checkH5Err(H5Pclose(h5plist));
}
return h5file;
}
int apply_filters(const char* name, /* object name from traverse list */
int rank, /* rank of dataset */
hsize_t *dims, /* dimensions of dataset */
size_t msize, /* size of type */
hid_t dcpl_id, /* dataset creation property list */
pack_opt_t *options, /* repack options */
int *has_filter) /* (OUT) object NAME has a filter */
{
int nfilters; /* number of filters in DCPL */
hsize_t chsize[64]; /* chunk size in elements */
H5D_layout_t layout;
int i;
pack_info_t obj;
*has_filter = 0;
if (rank==0) /* scalar dataset, do not apply */
return 0;
/*-------------------------------------------------------------------------
* initialize the assigment object
*-------------------------------------------------------------------------
*/
init_packobject(&obj);
/*-------------------------------------------------------------------------
* find options
*-------------------------------------------------------------------------
*/
if (aux_assign_obj(name,options,&obj)==0)
return 0;
/* get information about input filters */
if ((nfilters = H5Pget_nfilters(dcpl_id))<0)
return -1;
/*-------------------------------------------------------------------------
* check if we have filters in the pipeline
* we want to replace them with the input filters
* only remove if we are inserting new ones
*-------------------------------------------------------------------------
*/
if (nfilters && obj.nfilters )
{
*has_filter = 1;
if (H5Premove_filter(dcpl_id,H5Z_FILTER_ALL)<0)
return -1;
}
/*-------------------------------------------------------------------------
* check if there is an existent chunk
* read it only if there is not a requested layout
*-------------------------------------------------------------------------
*/
if (obj.layout == -1 )
{
if ((layout = H5Pget_layout(dcpl_id))<0)
return -1;
if (layout == H5D_CHUNKED)
{
if ((rank = H5Pget_chunk(dcpl_id,NELMTS(chsize),chsize/*out*/))<0)
return -1;
obj.layout = H5D_CHUNKED;
obj.chunk.rank = rank;
for ( i = 0; i < rank; i++)
obj.chunk.chunk_lengths[i] = chsize[i];
}
}
/*-------------------------------------------------------------------------
* the type of filter and additional parameter
* type can be one of the filters
* H5Z_FILTER_NONE 0 , uncompress if compressed
* H5Z_FILTER_DEFLATE 1 , deflation like gzip
* H5Z_FILTER_SHUFFLE 2 , shuffle the data
* H5Z_FILTER_FLETCHER32 3 , fletcher32 checksum of EDC
* H5Z_FILTER_SZIP 4 , szip compression
* H5Z_FILTER_NBIT 5 , nbit compression
* H5Z_FILTER_SCALEOFFSET 6 , scaleoffset compression
*-------------------------------------------------------------------------
*/
if (obj.nfilters)
{
/*-------------------------------------------------------------------------
* filters require CHUNK layout; if we do not have one define a default
*-------------------------------------------------------------------------
*/
if (obj.layout==-1)
{
/* stripmine info */
hsize_t sm_size[H5S_MAX_RANK]; /*stripmine size */
hsize_t sm_nbytes; /*bytes per stripmine */
obj.chunk.rank = rank;
/*
* determine the strip mine size. The strip mine is
* a hyperslab whose size is manageable.
*/
sm_nbytes = msize;
for ( i = rank; i > 0; --i)
{
hsize_t size = H5TOOLS_BUFSIZE / sm_nbytes;
if ( size == 0) /* datum size > H5TOOLS_BUFSIZE */
size = 1;
sm_size[i - 1] = MIN(dims[i - 1], size);
sm_nbytes *= sm_size[i - 1];
assert(sm_nbytes > 0);
}
for ( i = 0; i < rank; i++)
{
obj.chunk.chunk_lengths[i] = sm_size[i];
}
}
for ( i=0; i<obj.nfilters; i++)
{
switch (obj.filter[i].filtn)
{
default:
break;
/*-------------------------------------------------------------------------
* H5Z_FILTER_DEFLATE 1 , deflation like gzip
*-------------------------------------------------------------------------
*/
case H5Z_FILTER_DEFLATE:
{
unsigned aggression; /* the deflate level */
aggression = obj.filter[i].cd_values[0];
/* set up for deflated data */
if(H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths)<0)
return -1;
if(H5Pset_deflate(dcpl_id,aggression)<0)
return -1;
}
break;
/*-------------------------------------------------------------------------
* H5Z_FILTER_SZIP 4 , szip compression
*-------------------------------------------------------------------------
*/
case H5Z_FILTER_SZIP:
{
unsigned options_mask;
unsigned pixels_per_block;
options_mask = obj.filter[i].cd_values[0];
pixels_per_block = obj.filter[i].cd_values[1];
/* set up for szip data */
if(H5Pset_chunk(dcpl_id,obj.chunk.rank,obj.chunk.chunk_lengths)<0)
return -1;
if (H5Pset_szip(dcpl_id,options_mask,pixels_per_block)<0)
return -1;
}
break;
/*-------------------------------------------------------------------------
* H5Z_FILTER_SHUFFLE 2 , shuffle the data
*-------------------------------------------------------------------------
*/
case H5Z_FILTER_SHUFFLE:
if(H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths)<0)
return -1;
if (H5Pset_shuffle(dcpl_id)<0)
return -1;
break;
/*-------------------------------------------------------------------------
* H5Z_FILTER_FLETCHER32 3 , fletcher32 checksum of EDC
*-------------------------------------------------------------------------
*/
case H5Z_FILTER_FLETCHER32:
if(H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths)<0)
return -1;
if (H5Pset_fletcher32(dcpl_id)<0)
return -1;
break;
/*----------- -------------------------------------------------------------
* H5Z_FILTER_NBIT , NBIT compression
*-------------------------------------------------------------------------
*/
case H5Z_FILTER_NBIT:
if(H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths)<0)
return -1;
if (H5Pset_nbit(dcpl_id)<0)
return -1;
break;
/*----------- -------------------------------------------------------------
* H5Z_FILTER_SCALEOFFSET , scale+offset compression
*-------------------------------------------------------------------------
*/
case H5Z_FILTER_SCALEOFFSET:
{
H5Z_SO_scale_type_t scale_type;
int scale_factor;
scale_type = (H5Z_SO_scale_type_t)obj.filter[i].cd_values[0];
scale_factor = obj.filter[i].cd_values[1];
if(H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths)<0)
return -1;
if (H5Pset_scaleoffset(dcpl_id,scale_type,scale_factor)<0)
return -1;
}
break;
} /* switch */
}/*i*/
}
/*obj.nfilters*/
/*-------------------------------------------------------------------------
* layout
*-------------------------------------------------------------------------
*/
if (obj.layout>=0)
{
/* a layout was defined */
if (H5Pset_layout(dcpl_id, obj.layout)<0)
return -1;
if (H5D_CHUNKED == obj.layout)
{
if(H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths)<0)
return -1;
}
else if (H5D_COMPACT == obj.layout)
{
if (H5Pset_alloc_time(dcpl_id, H5D_ALLOC_TIME_EARLY)<0)
return -1;
}
/* remove filters for the H5D_CONTIGUOUS case */
else if (H5D_CONTIGUOUS == obj.layout)
{
if (H5Premove_filter(dcpl_id,H5Z_FILTER_ALL)<0)
return -1;
}
}
return 0;
}
int
main(int argc, char **argv)
{
printf("\n*** Testing HDF5/NetCDF-4 interoperability...\n");
printf("*** testing HDF5 compatibility...");
{
#define GRPA_NAME "grpa"
#define VAR_NAME "vara"
#define NDIMS 2
int nrowCur = 7; /* current size */
int ncolCur = 3;
int nrowMax = nrowCur + 0; /* maximum size */
int ncolMax = ncolCur + 0;
hid_t xdimId;
hid_t ydimId;
hsize_t xscaleDims[1];
hsize_t yscaleDims[1];
hid_t xdimSpaceId, spaceId;
hid_t fileId;
hid_t fapl;
hsize_t curDims[2];
hsize_t maxDims[2];
hid_t dataTypeId, dsPropertyId, grpaId, grpaPropId, dsId;
hid_t ydimSpaceId;
const char * dimNameBase
= "This is a netCDF dimension but not a netCDF variable.";
char dimNameBuf[1000];
char *varaName = "/grpa/vara";
short amat[nrowCur][ncolCur];
int ii, jj;
xscaleDims[0] = nrowCur;
yscaleDims[0] = ncolCur;
if ((xdimSpaceId = H5Screate_simple(1, xscaleDims, NULL)) < 0) ERR;
/* With the SEMI close degree, the HDF5 file close will fail if
* anything is left open. */
if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR;
if (H5Pset_fclose_degree(fapl, H5F_CLOSE_SEMI)) ERR;
/* Create file */
if((fileId = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC,
H5Pcreate(H5P_FILE_CREATE), fapl)) < 0) ERR;
if (H5Pclose(fapl) < 0) ERR;
/* Create data space */
curDims[0] = nrowCur;
curDims[1] = ncolCur;
maxDims[0] = nrowMax;
maxDims[1] = ncolMax;
if ((spaceId = H5Screate_simple(2, curDims, maxDims)) < 0) ERR;
if ((dataTypeId = H5Tcopy(H5T_NATIVE_SHORT)) < 0) ERR;
if ((dsPropertyId = H5Pcreate(H5P_DATASET_CREATE)) < 0) ERR;
if ((grpaPropId = H5Pcreate(H5P_GROUP_CREATE)) < 0) ERR;
if ((grpaId = H5Gcreate2(fileId, GRPA_NAME, H5P_DEFAULT,
grpaPropId, H5P_DEFAULT)) < 0) ERR;
if (H5Pclose(grpaPropId) < 0) ERR;
/* Create vara dataset */
if ((dsId = H5Dcreate2(fileId, varaName, dataTypeId, spaceId,
H5P_DEFAULT, dsPropertyId,
H5P_DEFAULT)) < 0) ERR;
if (H5Pclose(dsPropertyId) < 0) ERR;
if (H5Tclose(dataTypeId) < 0) ERR;
if ((ydimSpaceId = H5Screate_simple(1, yscaleDims, NULL)) < 0) ERR;
/* Create xdim dimension dataset */
if ((xdimId = H5Dcreate2(fileId, "/xdim", H5T_IEEE_F32BE,
xdimSpaceId, H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT)) < 0) ERR;
if (H5Sclose(xdimSpaceId) < 0) ERR;
/* Create ydim dimension dataset */
if ((ydimId = H5Dcreate2(fileId, "/ydim", H5T_IEEE_F32BE,
ydimSpaceId, H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT)) < 0) ERR;
if (H5Sclose(ydimSpaceId) < 0) ERR;
/* Create xdim scale */
sprintf(dimNameBuf, "%s%10d", dimNameBase, nrowCur);
if (H5DSset_scale(xdimId, dimNameBuf) < 0) ERR;
/* Create ydim scale */
sprintf(dimNameBuf, "%s%10d", dimNameBase, ncolCur);
if (H5DSset_scale(ydimId, dimNameBuf) < 0) ERR;
/* Attach dimension scales to the dataset */
if (H5DSattach_scale(dsId, xdimId, 0) < 0) ERR;
if (H5DSattach_scale(dsId, ydimId, 1) < 0) ERR;
/* Close stuff. */
if (H5Dclose(xdimId) < 0) ERR;
if (H5Dclose(ydimId) < 0) ERR;
if (H5Dclose(dsId) < 0) ERR;
if (H5Gclose(grpaId) < 0) ERR;
if (H5Sclose(spaceId) < 0) ERR;
if (H5Fclose(fileId) < 0) ERR;
/* Create some data */
for (ii = 0; ii < nrowCur; ii++)
for (jj = 0; jj < ncolCur; jj++)
amat[ii][jj] = 100 * ii + jj;
/* Re-open file */
if ((fileId = H5Fopen(FILE_NAME, H5F_ACC_RDWR, H5P_DEFAULT)) < 0) ERR;
if ((grpaId = H5Gopen2(fileId, GRPA_NAME, H5P_DEFAULT)) < 0) ERR;
if ((dsId = H5Dopen2(grpaId, varaName, H5P_DEFAULT)) < 0) ERR;
/* Write dataset */
if (H5Dwrite(dsId, H5T_NATIVE_SHORT, H5S_ALL, H5S_ALL, H5P_DEFAULT,
amat) < 0) ERR;
/* Write dimension values for both xdim, ydim */
{
short xydimMat[ nrowCur >= ncolCur ? nrowCur : ncolCur];
for (ii = 0; ii < nrowCur; ii++)
xydimMat[ii] = 0; /*#### 100 * ii; */
/* Write xdim */
if ((xdimId = H5Dopen2(fileId, "/xdim", H5P_DEFAULT)) < 0) ERR;
if (H5Dwrite(xdimId, H5T_NATIVE_SHORT, H5S_ALL, H5S_ALL,
H5P_DEFAULT, xydimMat) < 0) ERR;
if (H5Dclose(xdimId) < 0) ERR;
/* Write ydim */
if ((ydimId = H5Dopen2(fileId, "/ydim", H5P_DEFAULT)) < 0) ERR;
if (H5Dwrite(ydimId, H5T_NATIVE_SHORT, H5S_ALL, H5S_ALL,
H5P_DEFAULT, xydimMat) < 0) ERR;
if (H5Dclose(ydimId) < 0) ERR;
}
if (H5Dclose(dsId) < 0) ERR;
if (H5Gclose(grpaId) < 0) ERR;
if (H5Fclose(fileId) < 0) ERR;
{
int ncid, grpid, nvars, ngatts, ndims, unlimdimid, ngrps;
char name_in[NC_MAX_NAME + 1];
nc_type xtype_in;
int ndims_in, natts_in, dimid_in[NDIMS];
/* nc_set_log_level(5);*/
if (nc_open(FILE_NAME, NC_NOWRITE, &ncid)) ERR;
if (nc_inq(ncid, &ndims, &nvars, &ngatts, &unlimdimid)) ERR;
if (ndims != 2 || nvars != 0 || ngatts != 0 || unlimdimid != -1) ERR;
if (nc_inq_grps(ncid, &ngrps, &grpid)) ERR;
if (ngrps != 1) ERR;
if (nc_inq(grpid, &ndims, &nvars, &ngatts, &unlimdimid)) ERR;
if (ndims != 0 || nvars != 1 || ngatts != 0 || unlimdimid != -1) ERR;
if (nc_inq_var(grpid, 0, name_in, &xtype_in, &ndims_in, dimid_in,
&natts_in)) ERR;
if (strcmp(name_in, VAR_NAME) || xtype_in != NC_SHORT || ndims_in != NDIMS ||
dimid_in[0] != 0 || dimid_in[1] != 1 || natts_in != 0) ERR;
if (nc_close(ncid)) ERR;
}
}
SUMMARIZE_ERR;
#ifdef USE_SZIP
printf("*** testing HDF5 compatibility with szip...");
{
#define DEFLATE_LEVEL 9
#define MAX_NAME 100
#define NUM_CD_ELEM 10
/* HDF5 defines this... */
#define DEFLATE_NAME "deflate"
#define DIM1_LEN 3000
#define GRP_NAME "George_Washington"
#define BATTLE_RECORD "Battle_Record"
hid_t fileid, grpid, spaceid, datasetid;
int data_out[DIM1_LEN], data_in[DIM1_LEN];
hsize_t dims[1] = {DIM1_LEN};
hid_t propid;
char name_in[MAX_NAME + 1];
int ncid, ndims_in, nvars_in, ngatts_in, unlimdimid_in, ngrps_in;
int nc_grpid;
int dimid_in[1], natts_in;
nc_type xtype_in;
int i;
for (i = 0; i < DIM1_LEN; i++)
data_out[i] = i;
/* Open file and create group. */
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT,
H5P_DEFAULT)) < 0) ERR;
if ((grpid = H5Gcreate(fileid, GRP_NAME, 0)) < 0) ERR;
/* Write an array of bools, with szip compression. */
if ((propid = H5Pcreate(H5P_DATASET_CREATE)) < 0) ERR;
if (H5Pset_layout(propid, H5D_CHUNKED)) ERR;
if (H5Pset_chunk(propid, 1, dims)) ERR;
if (H5Pset_szip(propid, H5_SZIP_EC_OPTION_MASK, 32)) ERR;
if ((spaceid = H5Screate_simple(1, dims, dims)) < 0) ERR;
if ((datasetid = H5Dcreate(grpid, BATTLE_RECORD, H5T_NATIVE_INT,
spaceid, propid)) < 0) ERR;
if (H5Dwrite(datasetid, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT,
data_out) < 0) ERR;
if (H5Dclose(datasetid) < 0 ||
H5Pclose(propid) < 0 ||
H5Sclose(spaceid) < 0 ||
H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0)
ERR;
/* Open the file with netCDF and check it. */
if (nc_open(FILE_NAME, NC_NOWRITE, &ncid)) ERR;
if (nc_inq(ncid, &ndims_in, &nvars_in, &ngatts_in, &unlimdimid_in)) ERR;
if (ndims_in != 0 || nvars_in != 0 || ngatts_in != 0 || unlimdimid_in != -1) ERR;
if (nc_inq_grps(ncid, &ngrps_in, &nc_grpid)) ERR;
if (ngrps_in != 1) ERR;
if (nc_inq(nc_grpid, &ndims_in, &nvars_in, &ngatts_in, &unlimdimid_in)) ERR;
if (ndims_in != 1 || nvars_in != 1 || ngatts_in != 0 || unlimdimid_in != -1) ERR;
/* Check the variable. */
if (nc_inq_var(nc_grpid, 0, name_in, &xtype_in, &ndims_in, dimid_in,
&natts_in)) ERR;
if (strcmp(name_in, BATTLE_RECORD) || xtype_in != NC_INT || ndims_in != 1 ||
dimid_in[0] != 0 || natts_in != 0) ERR;
/* Check the data. */
if (nc_get_var(nc_grpid, 0, data_in)) ERR;
for (i = 0; i < DIM1_LEN; i++)
if (data_in[i] != data_out[i]) ERR;
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
#endif /* USE_SZIP */
FINAL_RESULTS;
}
hid_t H5Dataset::create(H5Object & loc, const std::string & name, const hid_t type, const hid_t targettype, const hid_t srcspace, const hid_t targetspace, void * data, const bool chunked)
{
herr_t err;
hid_t dataset;
if (H5Lexists(loc.getH5Id(), name.c_str(), H5P_DEFAULT) > 0)
{
dataset = H5Oopen(loc.getH5Id(), name.c_str(), H5P_DEFAULT);
if (dataset < 0)
{
throw H5Exception(__LINE__, __FILE__, _("Cannot open the dataset: %s"), name.c_str());
}
if (targetspace > 0)
{
hid_t space = H5Dget_space(dataset);
if (space < 0)
{
throw H5Exception(__LINE__, __FILE__, _("Cannot get the dataspace associated with dataset named %s."), name.c_str());
}
hsize_t * dims = 0;
hsize_t * ddims = 0;
hsize_t * maxdims = 0;
hsize_t * dmaxdims = 0;
try
{
herr_t err;
int ndims = H5Sget_simple_extent_ndims(space);
if (ndims < 0)
{
throw H5Exception(__LINE__, __FILE__, _("Invalid source space"));
}
int dndims = H5Sget_simple_extent_ndims(targetspace);
if (dndims < 0)
{
throw H5Exception(__LINE__, __FILE__, _("Invalid target space"));
}
hsize_t * dims = new hsize_t[ndims];
hsize_t * ddims = new hsize_t[dndims];
hsize_t * maxdims = new hsize_t[ndims];
hsize_t * dmaxdims = new hsize_t[dndims];
H5Sget_simple_extent_dims(space, dims, maxdims);
H5Sget_simple_extent_dims(targetspace, ddims, dmaxdims);
H5Sclose(space);
if (ndims != dndims)
{
throw H5Exception(__LINE__, __FILE__, _("Wrong dimensions."));
}
else
{
for (int i = 0; i < ndims; i++)
{
if (maxdims[i] != dmaxdims[i])
{
throw H5Exception(__LINE__, __FILE__, _("Cannot modify maximum dimensions."));
}
if (ddims[i] > dims[i])
{
err = H5Dset_extent(dataset, ddims);
if (err < 0)
{
throw H5Exception(__LINE__, __FILE__, _("Cannot modify dimension %d."), i);
}
break;
}
}
}
delete[] dims;
delete[] ddims;
delete[] maxdims;
delete[] dmaxdims;
}
catch (const H5Exception & /*e*/)
{
delete[] dims;
delete[] ddims;
delete[] maxdims;
delete[] dmaxdims;
throw;
}
}
}
else
{
if (chunked)
{
herr_t err;
int ndims = H5Sget_simple_extent_ndims(targetspace);
if (ndims < 0)
{
throw H5Exception(__LINE__, __FILE__, _("Invalid target space"));
}
hsize_t * dims = new hsize_t[ndims];
H5Sget_simple_extent_dims(targetspace, dims, 0);
hid_t dcpl = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_layout(dcpl, H5D_CHUNKED);
err = H5Pset_chunk(dcpl, ndims, dims);
delete[] dims;
if (err < 0)
{
H5Pclose(dcpl);
throw H5Exception(__LINE__, __FILE__, _("Cannot set the chunk dimensions: %s"), name.c_str());
}
dataset = H5Dcreate(loc.getH5Id(), name.c_str(), targettype, targetspace == -1 ? srcspace : targetspace, H5P_DEFAULT, dcpl, H5P_DEFAULT);
H5Pclose(dcpl);
}
else
{
dataset = H5Dcreate(loc.getH5Id(), name.c_str(), targettype, targetspace == -1 ? srcspace : targetspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
}
if (dataset < 0)
{
throw H5Exception(__LINE__, __FILE__, _("Cannot create the dataset: %s"), name.c_str());
}
}
err = H5Dwrite(dataset, type, srcspace, targetspace == -1 ? H5S_ALL : targetspace, H5P_DEFAULT, data);
if (err < 0)
{
throw H5Exception(__LINE__, __FILE__, _("Cannot write data in the dataset."));
}
return dataset;
}
/*
* To exercise the coding for the re-read of the object header for SWMR access.
* When the object header is read in H5O_load() of H5Ocache.c, the library initially reads
* 512 bytes for decoding, then reads the remaining bytes later if the object header is
* greater than 512 bytes. For SWMR access, the read should be done all at one time.
*/
static herr_t
test_ohdr_swmr(void)
{
hid_t fid = -1; /* File ID */
hid_t fapl = -1; /* File access property list */
hid_t did = -1; /* Dataset ID */
hid_t sid = -1; /* Dataspace ID */
hid_t plist = -1; /* Dataset creation property list */
size_t compact_size = 1024; /* The size of compact dataset */
int wbuf[1024]; /* Buffer for writing */
hsize_t dims[1]; /* Dimension sizes */
unsigned int n = 0, u; /* Locatl index variable */
H5O_info_t obj_info; /* Information for the object */
TESTING("exercise the coding for the re-read of the object header for SWMR access");
/* File access property list */
if((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
FAIL_STACK_ERROR
/* Set to use latest library format */
if(H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0)
FAIL_STACK_ERROR
/* Initialize data */
for(u = 0; u < compact_size; u++)
wbuf[u] = n++;
/* Create the file with the latest format (ensure version 2 object header for SWMR) */
if((fid = H5Fcreate(FILE_OHDR_SWMR, H5F_ACC_TRUNC, H5P_DEFAULT, fapl)) < 0)
TEST_ERROR
/* Create a small data space for compact dataset */
dims[0] = (hsize_t)compact_size;
if((sid = H5Screate_simple(1, dims, NULL)) < 0)
FAIL_STACK_ERROR
/* Create property list for compact dataset creation */
if((plist = H5Pcreate(H5P_DATASET_CREATE)) < 0)
FAIL_STACK_ERROR
/* Set the layout for the compact dataset */
if(H5Pset_layout(plist, H5D_COMPACT) < 0)
FAIL_STACK_ERROR
/* Create a compact dataset */
if((did = H5Dcreate2(fid, DSET_NAME, H5T_NATIVE_INT, sid, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0)
FAIL_STACK_ERROR
/* Write to the compact dataset */
if(H5Dwrite(did, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, wbuf) < 0)
FAIL_STACK_ERROR
/* Close the dataset */
if(H5Dclose(did) < 0)
FAIL_STACK_ERROR
/* Close the file */
if(H5Fclose(fid) < 0)
FAIL_STACK_ERROR
/* Open the file for SWMR write and latest format */
if((fid = H5Fopen(FILE_OHDR_SWMR, H5F_ACC_RDWR|H5F_ACC_SWMR_WRITE, fapl)) < 0)
FAIL_STACK_ERROR
/* Open the compact dataset */
if((did = H5Dopen2(fid, DSET_NAME, H5P_DEFAULT)) < 0)
FAIL_STACK_ERROR
/* Get the object information */
if(H5Oget_info(did, &obj_info) < 0)
FAIL_STACK_ERROR
/* The size of object header should be greater than the speculative read size of 512 */
/* This will exercise the coding for the re-read of the object header for SWMR access */
if(obj_info.hdr.space.total < 512)
TEST_ERROR;
/* Close the dataset */
if(H5Dclose(did) < 0)
FAIL_STACK_ERROR
/* Close the file */
if(H5Fclose(fid) < 0)
FAIL_STACK_ERROR
/* Close the dataspace */
if(H5Sclose(sid) < 0)
FAIL_STACK_ERROR
/* Close the dataset creation property list */
if(H5Pclose(plist) < 0)
FAIL_STACK_ERROR
/* Close the file access property list */
if(H5Pclose(fapl) < 0)
FAIL_STACK_ERROR
/* Remove the test file */
if(HDremove(FILE_OHDR_SWMR) < 0)
FAIL_STACK_ERROR
PASSED();
return 0;
error:
H5E_BEGIN_TRY {
H5Fclose(fid);
H5Dclose(did);
H5Sclose(sid);
H5Pclose(plist);
H5Pclose(fapl);
HDremove(FILE_OHDR_SWMR);
} H5E_END_TRY;
return -1;
} /* test_ohdr_swmr() */
int main(int argc, char **argv) {
struct rlimit rlim;
getrlimit(RLIMIT_STACK, &rlim);
rlim.rlim_cur = 1024 * 1024 * 1024;
setrlimit(RLIMIT_STACK, &rlim);
hid_t file_id, dataset_id, dataspace_id, status, property_id;
hsize_t dims[2];
if(argc < 4) {
usage(stderr, argv[0]);
exit(1);
}
file_id = H5Fopen(argv[1], H5F_ACC_RDONLY, H5P_DEFAULT);
dataset_id = H5Dopen2(file_id, "x", H5P_DEFAULT);
dataspace_id = H5Dget_space(dataset_id);
status = H5Sget_simple_extent_dims(dataspace_id, dims, NULL);
hsize_t a_rows = dims[0], a_cols = dims[1];
double a[a_rows][a_cols];
status = H5Dread(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, a);
status = H5Sclose(dataspace_id);
status = H5Dclose(dataset_id);
status = H5Fclose(file_id);
file_id = H5Fopen(argv[2], H5F_ACC_RDONLY, H5P_DEFAULT);
dataset_id = H5Dopen2(file_id, "x", H5P_DEFAULT);
dataspace_id = H5Dget_space(dataset_id);
status = H5Sget_simple_extent_dims(dataspace_id, dims, NULL);
hsize_t b_rows = dims[0], b_cols = dims[1];
double b[b_rows][b_cols];
status = H5Dread(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, b);
status = H5Sclose(dataspace_id);
status = H5Dclose(dataset_id);
status = H5Fclose(file_id);
if(a_cols != b_rows) {
fprintf(stderr, "Error: matrix dimension mismatch.\n");
exit(1);
}
size_t m = a_rows;
size_t n = a_cols;
size_t p = b_cols;
double c[m][p];
matrix_multiply_block(&a[0][0], &b[0][0], &c[0][0], m, n, p, BLOCKSIZE);
// Write out the output
dims[0] = m;
dims[1] = p;
file_id = H5Fcreate(argv[3], H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
status = H5Screate_simple(2, dims, NULL);
property_id = H5Pcreate(H5P_DATASET_CREATE);
status = H5Pset_layout(property_id, H5D_CONTIGUOUS);
dataset_id = H5Dcreate(file_id, "x", H5T_NATIVE_DOUBLE, dataspace_id, H5P_DEFAULT, property_id, H5P_DEFAULT);
status = H5Dwrite(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, &c[0][0]);
status = H5Sclose(dataspace_id);
status = H5Dclose(dataset_id);
status = H5Fclose(file_id);
status = H5Pclose(property_id);
}
/****************************************************************
**
** test_compact_vlstring(): Test code for storing VL strings in
** compact datasets.
**
****************************************************************/
static void
test_compact_vlstring(void)
{
const char *wdata[SPACE1_DIM1] = {"one", "two", "three", "four"};
char *rdata[SPACE1_DIM1]; /* Information read in */
hid_t fid1; /* HDF5 File IDs */
hid_t dataset; /* Dataset ID */
hid_t sid1; /* Dataspace ID */
hid_t tid1; /* Datatype ID */
hid_t plist; /* Dataset creation property list */
hsize_t dims1[] = {SPACE1_DIM1};
unsigned i; /* counting variable */
herr_t ret; /* Generic return value */
/* Output message about test being performed */
MESSAGE(5, ("Testing VL Strings in compact dataset\n"));
/* Create file */
fid1 = H5Fcreate(DATAFILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
CHECK(fid1, FAIL, "H5Fcreate");
/* Create dataspace for datasets */
sid1 = H5Screate_simple(SPACE1_RANK, dims1, NULL);
CHECK(sid1, FAIL, "H5Screate_simple");
/* Create a datatype to refer to */
tid1 = H5Tcopy (H5T_C_S1);
CHECK(tid1, FAIL, "H5Tcopy");
ret = H5Tset_size (tid1,H5T_VARIABLE);
CHECK(ret, FAIL, "H5Tset_size");
plist = H5Pcreate(H5P_DATASET_CREATE);
CHECK(plist, FAIL, "H5Pcreate");
ret = H5Pset_layout(plist, H5D_COMPACT);
CHECK(ret, FAIL, "H5Pset_layout");
/* Create a dataset */
dataset = H5Dcreate2(fid1, "Dataset5", tid1, sid1, H5P_DEFAULT, plist, H5P_DEFAULT);
CHECK(dataset, FAIL, "H5Dcreate2");
/* Write dataset to disk */
ret = H5Dwrite(dataset, tid1, H5S_ALL, H5S_ALL, H5P_DEFAULT, wdata);
CHECK(ret, FAIL, "H5Dwrite");
/* Read dataset from disk */
ret = H5Dread(dataset, tid1, H5S_ALL, H5S_ALL, H5P_DEFAULT, rdata);
CHECK(ret, FAIL, "H5Dread");
/* Compare data read in */
for(i = 0; i < SPACE1_DIM1; i++) {
if(HDstrlen(wdata[i]) != HDstrlen(rdata[i])) {
TestErrPrintf("VL data length don't match!, strlen(wdata[%d])=%d, strlen(rdata[%d])=%d\n",(int)i,(int)strlen(wdata[i]),(int)i,(int)strlen(rdata[i]));
continue;
} /* end if */
if(HDstrcmp(wdata[i], rdata[i]) != 0) {
TestErrPrintf("VL data values don't match!, wdata[%d]=%s, rdata[%d]=%s\n",(int)i,wdata[i],(int)i,rdata[i]);
continue;
} /* end if */
} /* end for */
/* Reclaim the read VL data */
ret = H5Dvlen_reclaim(tid1, sid1, H5P_DEFAULT, rdata);
CHECK(ret, FAIL, "H5Dvlen_reclaim");
/* Close Dataset */
ret = H5Dclose(dataset);
CHECK(ret, FAIL, "H5Dclose");
/* Close datatype */
ret = H5Tclose(tid1);
CHECK(ret, FAIL, "H5Tclose");
/* Close disk dataspace */
ret = H5Sclose(sid1);
CHECK(ret, FAIL, "H5Sclose");
/* Close dataset create property list */
ret = H5Pclose(plist);
CHECK(ret, FAIL, "H5Pclose");
/* Close file */
ret = H5Fclose(fid1);
CHECK(ret, FAIL, "H5Fclose");
} /*test_compact_vlstrings*/
int
main()
{
printf("\n*** Checking HDF5 dimscales detach.\n");
printf("*** Creating a file with two vars with one dimension scale...");
{
#if 0
hid_t cparmsid;
#endif
hid_t fileid, grpid, spaceid, var1_id, var2_id, dimscaleid;
hid_t fcpl_id, fapl_id, create_propid, access_propid;
hsize_t dims[NDIMS] = {DIM_LEN};
char dimscale_wo_var[STR_LEN];
float data = 42;
/* Create file. */
if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR;
if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_STRONG)) ERR;
if (H5Pset_cache(fapl_id, 0, CHUNK_CACHE_NELEMS, CHUNK_CACHE_SIZE,
CHUNK_CACHE_PREEMPTION) < 0) ERR;
if (H5Pset_libver_bounds(fapl_id, H5F_LIBVER_18, H5F_LIBVER_18) < 0) ERR;
if ((fcpl_id = H5Pcreate(H5P_FILE_CREATE)) < 0) ERR;
if (H5Pset_link_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED |
H5P_CRT_ORDER_INDEXED)) < 0) ERR;
if (H5Pset_attr_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED |
H5P_CRT_ORDER_INDEXED)) < 0) ERR;
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, fcpl_id, fapl_id)) < 0) ERR;
if (H5Pclose(fapl_id) < 0) ERR;
if (H5Pclose(fcpl_id) < 0) ERR;
if ((grpid = H5Gopen2(fileid, "/", H5P_DEFAULT)) < 0) ERR;
/* Create dimension scale. */
if ((create_propid = H5Pcreate(H5P_DATASET_CREATE)) < 0) ERR;
if (H5Pset_attr_creation_order(create_propid, H5P_CRT_ORDER_TRACKED|
H5P_CRT_ORDER_INDEXED) < 0) ERR;
if ((spaceid = H5Screate_simple(1, dims, dims)) < 0) ERR;
if ((dimscaleid = H5Dcreate1(grpid, DIMSCALE_NAME, H5T_IEEE_F32BE,
spaceid, create_propid)) < 0) ERR;
if (H5Sclose(spaceid) < 0) ERR;
if (H5Pclose(create_propid) < 0) ERR;
sprintf(dimscale_wo_var, "%s%10d", DIM_WITHOUT_VARIABLE, DIM_LEN);
if (H5DSset_scale(dimscaleid, dimscale_wo_var) < 0) ERR;
/* Create a variable that uses this dimension scale. */
if ((access_propid = H5Pcreate(H5P_DATASET_ACCESS)) < 0) ERR;
if (H5Pset_chunk_cache(access_propid, CHUNK_CACHE_NELEMS,
CHUNK_CACHE_SIZE, CHUNK_CACHE_PREEMPTION) < 0) ERR;
if ((create_propid = H5Pcreate(H5P_DATASET_CREATE)) < 0) ERR;
if (H5Pset_fill_value(create_propid, H5T_NATIVE_FLOAT, &data) < 0) ERR;
if (H5Pset_layout(create_propid, H5D_CONTIGUOUS) < 0) ERR;
if (H5Pset_attr_creation_order(create_propid, H5P_CRT_ORDER_TRACKED|
H5P_CRT_ORDER_INDEXED) < 0) ERR;
if ((spaceid = H5Screate_simple(NDIMS, dims, dims)) < 0) ERR;
if ((var1_id = H5Dcreate2(grpid, VAR1_NAME, H5T_NATIVE_FLOAT, spaceid,
H5P_DEFAULT, create_propid, access_propid)) < 0) ERR;
if (H5Pclose(create_propid) < 0) ERR;
if (H5Pclose(access_propid) < 0) ERR;
if (H5Sclose(spaceid) < 0) ERR;
if (H5DSattach_scale(var1_id, dimscaleid, 0) < 0) ERR;
/* Create another variable that uses this dimension scale. */
if ((access_propid = H5Pcreate(H5P_DATASET_ACCESS)) < 0) ERR;
if (H5Pset_chunk_cache(access_propid, CHUNK_CACHE_NELEMS,
CHUNK_CACHE_SIZE, CHUNK_CACHE_PREEMPTION) < 0) ERR;
if ((create_propid = H5Pcreate(H5P_DATASET_CREATE)) < 0) ERR;
if (H5Pset_fill_value(create_propid, H5T_NATIVE_FLOAT, &data) < 0) ERR;
if (H5Pset_layout(create_propid, H5D_CONTIGUOUS) < 0) ERR;
if (H5Pset_attr_creation_order(create_propid, H5P_CRT_ORDER_TRACKED|
H5P_CRT_ORDER_INDEXED) < 0) ERR;
if ((spaceid = H5Screate_simple(NDIMS, dims, dims)) < 0) ERR;
if ((var2_id = H5Dcreate2(grpid, VAR2_NAME, H5T_NATIVE_FLOAT, spaceid,
H5P_DEFAULT, create_propid, access_propid)) < 0) ERR;
if (H5Pclose(create_propid) < 0) ERR;
if (H5Pclose(access_propid) < 0) ERR;
if (H5Sclose(spaceid) < 0) ERR;
if (H5DSattach_scale(var2_id, dimscaleid, 0) < 0) ERR;
/* Now detach the scales and remove the dimscale. This doesn't
* work if I reverse the order of the statements. */
if (H5DSdetach_scale(var2_id, dimscaleid, 0) < 0) ERR;
if (H5DSdetach_scale(var1_id, dimscaleid, 0) < 0) ERR;
/* Fold up our tents. */
if (H5Dclose(var1_id) < 0) ERR;
if (H5Dclose(dimscaleid) < 0) ERR;
if (H5Gclose(grpid) < 0) ERR;
if (H5Fclose(fileid) < 0) ERR;
/* /\* Now read the file and check it. *\/ */
/* { */
/* hid_t fileid, spaceid = 0, datasetid = 0; */
/* hsize_t num_obj, i; */
/* int obj_class; */
/* char obj_name[STR_LEN + 1]; */
/* char dimscale_name[STR_LEN+1]; */
/* htri_t is_scale; */
/* char label[STR_LEN+1]; */
/* int num_scales; */
/* hsize_t dims[1], maxdims[1]; */
/* H5G_stat_t statbuf; */
/* HDF5_OBJID_T dimscale_obj, vars_dimscale_obj; */
/* struct nc_hdf5_link_info link_info; */
/* hsize_t idx = 0; */
/* /\* Open the file. *\/ */
/* if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDWR, H5P_DEFAULT)) < 0) ERR; */
/* if ((grpid = H5Gopen2(fileid, "/", H5P_DEFAULT)) < 0) ERR; */
/* /\* Loop through objects in the root group. *\/ */
/* if (H5Gget_num_objs(fileid, &num_obj) < 0) ERR; */
/* for (i = 0; i < num_obj; i++) */
/* { */
/* if (H5Literate(grpid, H5_INDEX_CRT_ORDER, H5_ITER_INC, */
/* &idx, visit_link, (void *)&link_info) < 0) ERR; */
/* printf("Encountered: HDF5 object link_info.name %s\n", link_info.name); */
/* /\* Deal with object based on its obj_class. *\/ */
/* switch(link_info.obj_type) */
/* { */
/* case H5I_GROUP: */
/* break; */
/* case H5I_DATASET: */
/* /\* Open the dataset. *\/ */
/* if ((datasetid = H5Dopen1(fileid, link_info.name)) < 0) ERR; */
/* if ((spaceid = H5Dget_space(datasetid)) < 0) ERR; */
/* if (H5Sget_simple_extent_dims(spaceid, dims, maxdims) < 0) ERR; */
/* if (maxdims[0] != DIM_LEN) ERR; */
/* if (H5Sclose(spaceid) < 0) ERR; */
/* /\* Is this a dimscale? *\/ */
/* if ((is_scale = H5DSis_scale(datasetid)) < 0) ERR; */
/* if (is_scale && strcmp(link_info.name, DIMSCALE_NAME)) ERR; */
/* if (is_scale) */
/* { */
/* /\* A dimscale comes with a NAME attribute, in */
/* * addition to its real name. *\/ */
/* if (H5DSget_scale_name(datasetid, dimscale_name, STR_LEN) < 0) ERR; */
/* if (strcmp(dimscale_name, dimscale_wo_var)) ERR; */
/* /\* fileno and objno uniquely identify an object and a */
/* * HDF5 file. *\/ */
/* if (H5Gget_objinfo(datasetid, ".", 1, &statbuf) < 0) ERR; */
/* dimscale_obj.fileno[0] = statbuf.fileno[0]; */
/* dimscale_obj.objno[0] = statbuf.objno[0]; */
/* dimscale_obj.fileno[1] = statbuf.fileno[1]; */
/* dimscale_obj.objno[1] = statbuf.objno[1]; */
/* /\*printf("scale statbuf.fileno = %d statbuf.objno = %d\n", */
/* statbuf.fileno, statbuf.objno);*\/ */
/* } */
/* else */
/* { */
/* /\* Here's how to get the number of scales attached */
/* * to the dataset's dimension 0. *\/ */
/* if ((num_scales = H5DSget_num_scales(datasetid, 0)) < 0) ERR; */
/* if (num_scales != 1) ERR; */
/* /\* Go through all dimscales for this var and learn about them. *\/ */
/* if (H5DSiterate_scales(datasetid, 0, NULL, alien_visitor, */
/* &vars_dimscale_obj) < 0) ERR; */
/* /\*printf("vars_dimscale_obj.fileno = %d vars_dimscale_obj.objno = %d\n", */
/* vars_dimscale_obj.fileno, vars_dimscale_obj.objno);*\/ */
/* /\* if (vars_dimscale_obj.fileno[0] != dimscale_obj.fileno[0] || *\/ */
/* /\* vars_dimscale_obj.objno[0] != dimscale_obj.objno[0] || *\/ */
/* /\* vars_dimscale_obj.fileno[1] != dimscale_obj.fileno[1] || *\/ */
/* /\* vars_dimscale_obj.objno[1] != dimscale_obj.objno[1]) ERR; *\/ */
/* /\* There's also a label for dimension 0. *\/ */
/* if (H5DSget_label(datasetid, 0, label, STR_LEN) < 0) ERR; */
/* /\*printf("found non-scale dataset %s, label %s\n", link_info.name, label);*\/ */
/* } */
/* if (H5Dclose(datasetid) < 0) ERR; */
/* break; */
/* case H5I_DATATYPE: */
/* break; */
/* default: */
/* printf("Unknown object!"); */
/* ERR; */
/* } */
/* } */
/* /\* Close up the shop. *\/ */
/* if (H5Fclose(fileid) < 0) ERR; */
/* }*/
}
SUMMARIZE_ERR;
FINAL_RESULTS;
}
bool Hdf5Dataset::saveMap(const VecVecDouble &pose_reach, const VecVecDouble &spheres, const VecDouble &ri, const double resolution)
{
if(!checkPath(this->path_))
{
createPath(this->path_);
}
const char *filepath = this->path_.c_str();
const char *name = this->filename_.c_str();
char fullpath[100];
strcpy(fullpath, filepath);
strcat(fullpath, name);
ROS_INFO("Saving map %s", this->filename_.c_str());
this->file_ = H5Fcreate(fullpath, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
this->group_poses_ = H5Gcreate(this->file_, "/Poses", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
this->group_spheres_ = H5Gcreate(this->file_, "/Spheres", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
ROS_INFO("Saving poses in reachability map");
const hsize_t ndims = 2;
const hsize_t ncols = 10;
int posSize =pose_reach.size();
int chunk_size;
int PY = 10;
if (posSize % 2)
{
chunk_size = (posSize / 2) + 1;
}
else
{
chunk_size = (posSize / 2);
}
// Create Dataspace
hsize_t dims[ndims] = {0, ncols}; // Starting with an empty buffer
hsize_t max_dims[ndims] = {H5S_UNLIMITED, ncols}; // Creating dataspace
hid_t file_space = H5Screate_simple(ndims, dims, max_dims);
// Create Dataset Property list
hid_t plist = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_layout(plist, H5D_CHUNKED);
hsize_t chunk_dims[ndims] = {chunk_size, ncols};
H5Pset_chunk(plist, ndims, chunk_dims);
// Create the datset
this->poses_dataset_ = H5Dcreate(this->group_poses_, "poses_dataset", H5T_NATIVE_FLOAT, file_space, H5P_DEFAULT, plist, H5P_DEFAULT);
// Closing resources
H5Pclose(plist);
H5Sclose(file_space);
// Creating the first buffer
hsize_t nlines = chunk_size;
float *buffer = new float[nlines * ncols];
float **dset1_data = new float *[nlines];
for (hsize_t i = 0; i < nlines; ++i)
{
dset1_data[i] = &buffer[i * ncols];
}
// Data for the first chunk
for (int i = 0; i < chunk_size; i++)
{
for (int j = 0; j < PY; j++)
{
dset1_data[i][j] = pose_reach[i][j];
}
}
// Memory dataspace indicating size of the buffer
dims[0] = chunk_size;
dims[1] = ncols;
hid_t mem_space = H5Screate_simple(ndims, dims, NULL);
// Extending dataset
dims[0] = chunk_size;
dims[1] = ncols;
H5Dset_extent(this->poses_dataset_, dims);
// Selecting hyperslab on the dataset
file_space = H5Dget_space(this->poses_dataset_);
hsize_t start[2] = {0, 0};
hsize_t count[2] = {chunk_size, ncols};
H5Sselect_hyperslab(file_space, H5S_SELECT_SET, start, NULL, count, NULL);
// Writing buffer to the dataset
H5Dwrite(this->poses_dataset_, H5T_NATIVE_FLOAT, mem_space, file_space, H5P_DEFAULT, buffer);
// Closing file dataspace
H5Sclose(file_space);
// Data for the Second chunk
for (int i = chunk_size; i < posSize; i++)
{
for (int j = 0; j < PY; j++)
{
dset1_data[i - chunk_size][j] = pose_reach[i][j];
}
}
// Resizing new memory dataspace indicating new size of the buffer
dims[0] = posSize - chunk_size;
dims[1] = ncols;
H5Sset_extent_simple(mem_space, ndims, dims, NULL);
// Extend dataset
dims[0] = posSize;
dims[1] = ncols;
H5Dset_extent(this->poses_dataset_, dims);
// Selecting hyperslab
file_space = H5Dget_space(this->poses_dataset_);
start[0] = chunk_size;
start[1] = 0;
count[0] = posSize - chunk_size;
count[1] = ncols;
H5Sselect_hyperslab(file_space, H5S_SELECT_SET, start, NULL, count, NULL);
// Writing buffer to dataset
H5Dwrite(this->poses_dataset_, H5T_NATIVE_FLOAT, mem_space, file_space, H5P_DEFAULT, buffer);
// Closing all the resources
delete[] dset1_data;
delete[] buffer;
// Creating Sphere dataset
ROS_INFO("Saving spheres in Reachability map");
hid_t sphere_dataspace;
const int SX = spheres.size();
const int SY = 4;
hsize_t dims2[2]; // dataset dimensions
dims2[0] = SX;
dims2[1] = SY;
double dset2_data[SX][SY];
for(int i=0;i<spheres.size();++i)
{
for(int j=0;j<spheres[i].size();++j)
{
dset2_data[i][j] = spheres[i][j];
}
for (int j = 3; j < SY; j++)
{
dset2_data[i][j] = ri[i];
}
}
sphere_dataspace = H5Screate_simple(2, dims2, NULL);
this->sphere_dataset_ = H5Dcreate2(this->group_spheres_, "sphere_dataset", H5T_NATIVE_DOUBLE,
sphere_dataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Dwrite(this->sphere_dataset_, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, dset2_data);
// Creating attribute
hsize_t attr_dims;
float attr_data[1];
attr_data[0] = resolution;
attr_dims = 1;
sphere_dataspace = H5Screate_simple(1, &attr_dims, NULL);
this->attr_ = H5Acreate2(this->sphere_dataset_, "Resolution", H5T_NATIVE_FLOAT, sphere_dataspace,
H5P_DEFAULT, H5P_DEFAULT);
H5Awrite(this->attr_, H5T_NATIVE_FLOAT, attr_data);
//H5Aclose(this->attr_);
// Closing all
H5Sclose(sphere_dataspace);
H5Sclose(file_space);
H5Sclose(mem_space);
close();
}
void h5_write_unknowns_sp_(hid_t* file_identifier,
int* index, /* index of var to write */
int* nvar, /* total number of variables */
int* nxb, /* # of zones to store in x */
int* nyb, /* # of zones to store in y */
int* nzb, /* # of zones to store in z */
int* nguard, /* # of guardcells in pass */
int* maximum_blocks, /* maximum num of blocks */
float* unknowns, /* [mblk][NZB][NYB][NXB][nvar] */
char record_label[5],/* add char-null termination */
int* local_blocks,
int* total_blocks,
int* global_offset)
{
hid_t dataspace, dataset, memspace, dxfer_template, dataset_plist;
herr_t status;
int rank;
hsize_t dimens_4d[4], dimens_5d[5];
hsize_t start_4d[4];
hsize_t stride_4d[4], count_4d[4];
#ifdef CHUNK
hsize_t dimens_chunk[4];
#endif
char record_label_new[5];
int ierr;
/*
the variable names are 4 characters long -- copy this into
record_label_new, the 5th character is for the \0 termination
*/
strncpy(record_label_new, record_label,4);
*(record_label_new + 4) = '\0';
/* set the dimensions of the dataset */
rank = 4;
dimens_4d[0] = *total_blocks;
dimens_4d[1] = *nzb;
dimens_4d[2] = *nyb;
dimens_4d[3] = *nxb;
dataspace = H5Screate_simple(rank, dimens_4d, NULL);
#ifdef DEBUG_IO
printf("UNKNOWNS: dataspace = %d\n", (int) dataspace);
#endif
dataset_plist = H5Pcreate(H5P_DATASET_CREATE);
#ifdef CHUNK
/* set the layout to chunked */
ierr = H5Pset_layout(dataset_plist, H5D_CHUNKED);
/* create a chunk containing 10 blocks worth of data */
dimens_chunk[0] = 10;
dimens_chunk[1] = *nzb;
dimens_chunk[2] = *nyb;
dimens_chunk[3] = *nxb;
ierr = H5Pset_chunk(dataset_plist, 4, dimens_chunk);
#endif
dataset = H5Dcreate(*file_identifier, record_label_new,
H5T_NATIVE_FLOAT, dataspace, dataset_plist);
#ifdef DEBUG_IO
printf("UNKNOWNS: dataset = %d\n", (int) dataset);
#endif
/* create the hyperslab -- this will differ on the different processors */
start_4d[0] = (hsize_t) (*global_offset);
start_4d[1] = 0;
start_4d[2] = 0;
start_4d[3] = 0;
stride_4d[0] = 1;
stride_4d[1] = 1;
stride_4d[2] = 1;
stride_4d[3] = 1;
count_4d[0] = (hsize_t) (*local_blocks);
count_4d[1] = *nzb;
count_4d[2] = *nyb;
count_4d[3] = *nxb;
status = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, start_4d,
stride_4d, count_4d, NULL);
#ifdef DEBUG_IO
printf("UNKNOWNS: hyperslab selection = %d\n", (int) status);
#endif
/* create the memory space -- we can get away with a simple memory space
for the unknowns, since we are passing a contiguous block of memory
now, and the block count is the last index in FORTRAN */
rank = 5;
dimens_5d[0] = *local_blocks;
dimens_5d[1] = *nzb+(*nguard)*2*k3d;
dimens_5d[2] = *nyb+(*nguard)*2*k2d;
dimens_5d[3] = *nxb+(*nguard)*2;
dimens_5d[4] = *nvar;
memspace = H5Screate_simple(rank, dimens_5d, NULL);
#ifdef DEBUG_IO
printf("UNKNOWNS: memspace = %d\n", (int) memspace);
#endif
/* setting the transfer template */
flash_tune_plist(&dxfer_template);
#ifdef DEBUG_IO
printf("UNKNOWNS: dxfer_template = %d\n", (int) dxfer_template);
#endif
/* write the data */
status = H5Dwrite(dataset, H5T_NATIVE_FLOAT, memspace, dataspace,
dxfer_template, unknowns);
#ifdef DEBUG_IO
printf("UNKNOWNS: wrote unknowns, status = %d\n", (int) status);
#endif
H5Pclose(dxfer_template);
H5Sclose(memspace);
H5Sclose(dataspace);
H5Dclose(dataset);
}
int dump_hdf_file(const float *data, int docompression)
{
hid_t file_id, dataset_id, propid;
hid_t file_spaceid, mem_spaceid, access_plistid, xfer_plistid;
hsize_t dims[NDIMS] = {X_LEN, Y_LEN, Z_LEN};
hsize_t start[NDIMS] = {0, 0, 0};
hsize_t count[NDIMS] = {1, 1, Z_LEN};
/* create file */
file_id = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC,
H5P_DEFAULT, H5P_DEFAULT);
/* create property for dataset */
propid = H5Pcreate(H5P_DATASET_CREATE);
if (docompression)
{
if (H5Pset_layout(propid, H5D_CHUNKED) < 0) ERR;
if (H5Pset_chunk(propid, NDIMS, dims) < 0) ERR;
/* values[0]=9; */
/* status = H5Pset_filter(propid, H5Z_FILTER_DEFLATE,0,1,&values[0]); */
/* printf("deflat estatus is: %i\n",status); */
/* sets defalte level */
if (H5Pset_deflate(propid, 1)) ERR;
}
if ((file_spaceid = H5Screate_simple(NDIMS, dims, dims)) < 0) ERR;
/* Set up the cache. */
if ((access_plistid = H5Pcreate(H5P_DATASET_ACCESS)) < 0) ERR;
if (H5Pset_chunk_cache(access_plistid, CHUNK_CACHE_NELEMS,
CHUNK_CACHE_SIZE, CHUNK_CACHE_PREEMPTION) < 0) ERR;
/* Create the dataset. */
if ((dataset_id = H5Dcreate2(file_id, "dset", H5T_NATIVE_FLOAT, file_spaceid,
H5P_DEFAULT, propid, access_plistid)) < 0) ERR;
/* if ((file_spaceid = H5Dget_space(dataset_id)) < 0) ERR;*/
if ((mem_spaceid = H5Screate_simple(NDIMS, count, NULL)) < 0) ERR;
if ((xfer_plistid = H5Pcreate(H5P_DATASET_XFER)) < 0) ERR;
/* Write the dataset. */
for (start[0] = 0; start[0] < X_LEN; start[0]++)
for (start[1] = 0; start[1] < Y_LEN; start[1]++)
{
if (H5Sselect_hyperslab(file_spaceid, H5S_SELECT_SET, start, NULL,
count, NULL) < 0) ERR_RET;
if (H5Dwrite(dataset_id, H5T_NATIVE_FLOAT, mem_spaceid, file_spaceid,
xfer_plistid, data) < 0) ERR_RET;
}
/* Close property lists. */
if (H5Pclose(propid) < 0) ERR;
if (H5Pclose(access_plistid) < 0) ERR;
if (H5Pclose(xfer_plistid) < 0) ERR;
/* Close spaces. */
if (H5Sclose(file_spaceid) < 0) ERR;
if (H5Sclose(mem_spaceid) < 0) ERR;
/* End access to the dataset and release resources used by it. */
if (H5Dclose(dataset_id) < 0) ERR;
/* close file */
if (H5Fclose(file_id) < 0) ERR;
return 0;
}
/* Example of using PHDF5 to create, write, and read compact dataset.
*
* Changes: Updated function to use a dynamically calculated size,
* instead of the old SIZE #define. This should allow it
* to function with an arbitrary number of processors.
*
* JRM - 8/11/04
*/
void compact_dataset(void)
{
int i, j, mpi_size, mpi_rank, size, err_num=0;
hbool_t use_gpfs = FALSE;
hid_t iof, plist, dcpl, dxpl, dataset, filespace;
hsize_t file_dims [DIM];
double * outme;
double * inme;
char dname[]="dataset";
herr_t ret;
const char *filename;
size = get_size();
for ( i = 0; i < DIM; i++ )
{
file_dims[i] = size;
}
MPI_Comm_rank (MPI_COMM_WORLD, &mpi_rank);
MPI_Comm_size (MPI_COMM_WORLD, &mpi_size);
outme = HDmalloc((size_t)(size * size * sizeof(double)));
VRFY((outme != NULL), "HDmalloc succeeded for outme");
inme = HDmalloc((size_t)(size * size * sizeof(double)));
VRFY((outme != NULL), "HDmalloc succeeded for inme");
filename = GetTestParameters();
VRFY((mpi_size <= size), "mpi_size <= size");
plist = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type, use_gpfs);
iof = H5Fcreate (filename, H5F_ACC_TRUNC, H5P_DEFAULT, plist);
/* Define data space */
filespace = H5Screate_simple (DIM, file_dims, NULL);
/* Create a compact dataset */
dcpl = H5Pcreate(H5P_DATASET_CREATE);
VRFY((dcpl>=0), "dataset creation property list succeeded");
ret=H5Pset_layout(dcpl, H5D_COMPACT);
VRFY((dcpl >= 0), "set property list for compact dataset");
ret=H5Pset_alloc_time(dcpl, H5D_ALLOC_TIME_EARLY);
VRFY((ret >= 0), "set space allocation time for compact dataset");
dataset = H5Dcreate (iof, dname, H5T_NATIVE_DOUBLE, filespace, dcpl);
VRFY((dataset >= 0), "H5Dcreate succeeded");
/* set up the collective transfer properties list */
dxpl = H5Pcreate (H5P_DATASET_XFER);
VRFY((dxpl >= 0), "");
ret=H5Pset_dxpl_mpio(dxpl, H5FD_MPIO_COLLECTIVE);
VRFY((ret >= 0), "H5Pcreate xfer succeeded");
/* Recalculate data to write. Each process writes the same data. */
for (i = 0; i < size; i++)
for (j = 0; j < size; j++)
outme[(i * size) + j] = (i+j)*1000;
ret=H5Dwrite (dataset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, dxpl, outme);
VRFY((ret >= 0), "H5Dwrite succeeded");
H5Pclose (dcpl);
H5Pclose (plist);
H5Dclose (dataset);
H5Sclose (filespace);
H5Fclose (iof);
/* Open the file and dataset, read and compare the data. */
plist = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type, use_gpfs);
iof = H5Fopen(filename, H5F_ACC_RDONLY, plist);
VRFY((iof >= 0), "H5Fopen succeeded");
/* set up the collective transfer properties list */
dxpl = H5Pcreate (H5P_DATASET_XFER);
VRFY((dxpl >= 0), "");
ret=H5Pset_dxpl_mpio(dxpl, H5FD_MPIO_COLLECTIVE);
VRFY((ret >= 0), "H5Pcreate xfer succeeded");
dataset = H5Dopen(iof, dname);
VRFY((dataset >= 0), "H5Dcreate succeeded");
ret = H5Dread(dataset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, dxpl, inme);
VRFY((ret >= 0), "H5Dread succeeded");
/* Verify data value */
for (i = 0; i < size; i++)
for (j = 0; j < size; j++)
if ( inme[(i * size) + j] != outme[(i * size) + j])
if(err_num++ < MAX_ERR_REPORT || VERBOSE_MED)
printf("Dataset Verify failed at [%d][%d]: expect %f, got %f\n", i, j, outme[(i * size) + j], inme[(i * size) + j]);
H5Pclose(plist);
H5Pclose(dxpl);
H5Dclose(dataset);
H5Fclose(iof);
HDfree(inme);
HDfree(outme);
}
