int
main(void)
{
hid_t file=-1, dcpl=-1, space=-1, dset1=-1, dset2=-1;
hsize_t cur_size[2]= {8, 8};
H5D_space_status_t allocation;
int fill_val1 = 4444, fill_val2=5555;
if((file=H5Fcreate(FILENAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) <0) goto error;
if((space=H5Screate_simple(2, cur_size, cur_size)) < 0) goto error;
if((dcpl=H5Pcreate(H5P_DATASET_CREATE)) < 0) goto error;
/* Create a dataset with space being allocated and fill value written */
if(H5Pset_alloc_time(dcpl, H5D_ALLOC_TIME_EARLY) < 0) goto error;
if(H5Pset_fill_time(dcpl, H5D_FILL_TIME_ALLOC) < 0) goto error;
if(H5Pset_fill_value(dcpl, H5T_NATIVE_INT, &fill_val1) < 0) goto error;
if((dset1 = H5Dcreate2(file, "dset1", H5T_NATIVE_INT, space, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
goto error;
if(H5Dget_space_status(dset1, &allocation) < 0) goto error;
if(allocation == H5D_SPACE_STATUS_NOT_ALLOCATED) {
puts(" Got unallocated space instead of allocated.");
printf(" Got %d\n", allocation);
goto error;
}
if(H5Dclose(dset1) < 0) goto error;
/* Create a dataset with space allocation being delayed */
if(H5Pset_alloc_time(dcpl, H5D_ALLOC_TIME_LATE) < 0) goto error;
if(H5Pset_fill_time(dcpl, H5D_FILL_TIME_ALLOC) < 0) goto error;
if(H5Pset_fill_value(dcpl, H5T_NATIVE_INT, &fill_val2) < 0) goto error;
if((dset2 = H5Dcreate2(file, "dset2", H5T_NATIVE_INT, space, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
goto error;
if(H5Dget_space_status(dset2, &allocation) < 0) goto error;
if(allocation != H5D_SPACE_STATUS_NOT_ALLOCATED) {
puts(" Got allocated space instead of unallocated.");
printf(" Got %d\n", allocation);
goto error;
}
if(H5Dclose(dset2) < 0) goto error;
if(H5Sclose(space) < 0) goto error;
if(H5Pclose(dcpl) < 0) goto error;
if(H5Fclose(file) < 0) goto error;
return 0;
error:
H5E_BEGIN_TRY {
H5Pclose(dcpl);
H5Sclose(space);
H5Dclose(dset1);
H5Dclose(dset2);
H5Fclose(file);
} H5E_END_TRY;
return 1;
}
asynStatus NDFileHDF5AttributeDataset::createHDF5Dataset()
{
asynStatus status = asynSuccess;
cparm_ = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_fill_value(cparm_, datatype_, ptrFillValue_);
H5Pset_chunk(cparm_, rank_, chunk_);
dataspace_ = H5Screate_simple(rank_, dims_, maxdims_);
// Open the group by its name
hid_t dsetgroup;
if (groupName_ != ""){
dsetgroup = H5Gopen(file_, groupName_.c_str(), H5P_DEFAULT);
} else {
dsetgroup = file_;
}
// Now create the dataset
dataset_ = H5Dcreate2(dsetgroup, dsetName_.c_str(),
datatype_, dataspace_,
H5P_DEFAULT, cparm_, H5P_DEFAULT);
if (groupName_ != ""){
H5Gclose(dsetgroup);
}
memspace_ = H5Screate_simple(rank_, elementSize_, NULL);
return status;
}
//--------------------------------------------------------------------------
// Function: DSetCreatPropList::setFillValue
///\brief Sets a dataset fill value
///\param fvalue_type - IN: Data type for the value passed via \a value
///\param value - IN: Pointer to buffer containing the fill value
///\exception H5::PropListIException
///\par Description
/// The datatype may differ from that of the dataset, but it must
/// be one that the HDF5 library is able to convert \a value to
/// the dataset datatype when the dataset is created.
/// The default fill value is 0 (zero,) which is interpreted
/// according to the actual dataset datatype.
///\par
/// For information on setting fill value, please refer to the
/// C layer Reference Manual at:
/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-SetFillValue
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
void DSetCreatPropList::setFillValue( const DataType& fvalue_type, const void* value ) const
{
herr_t ret_value = H5Pset_fill_value( id, fvalue_type.getId(), value );
if( ret_value < 0 )
{
throw PropListIException("DSetCreatPropList::setFillValue",
"H5Pset_fill_value failed");
}
}
NDFileHDF5Dataset *createTestDataset(int rank, int *max_dim_size, asynUser *pasynUser, hid_t groupID, const std::string& dsetname)
{
// Add the test dataset.
hid_t datasetID = -1;
hid_t dset_access_plist = H5Pcreate(H5P_DATASET_ACCESS);
hsize_t nbytes = 1024;
hsize_t nslots = 50001;
hid_t datatype = H5T_NATIVE_INT8;
hsize_t dims[rank];
for (int i=0; i < rank-2; i++) dims[i] = 1;
for (int i=rank-2; i < rank; i++) dims[i] = max_dim_size[i];
hsize_t maxdims[rank];
for (int i=0; i < rank; i++) maxdims[i] = max_dim_size[i];
hsize_t chunkdims[rank];
for (int i=0; i < rank-2; i++) chunkdims[i] = 1;
for (int i=rank-2; i < rank; i++) chunkdims[i] = max_dim_size[i];
//hid_t dataspace = H5Screate_simple(rank, dims, maxdims);
dataspace = H5Screate_simple(rank, dims, maxdims);
hid_t cparms = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_chunk(cparms, rank, chunkdims);
void *ptrFillValue = (void*)calloc(8, sizeof(char));
*(char *)ptrFillValue = (char)0;
H5Pset_fill_value(cparms, datatype, ptrFillValue);
H5Pset_chunk_cache(dset_access_plist, (size_t)nslots, (size_t)nbytes, 1.0);
datasetID = H5Dcreate2(groupID, dsetname.c_str(), datatype, dataspace, H5P_DEFAULT, cparms, dset_access_plist);
// Now create a dataset
NDFileHDF5Dataset *dataset = new NDFileHDF5Dataset(pasynUser, dsetname, datasetID);
int extraDims = rank-2;
int extra_dims[extraDims];
for (int i=0; i < extraDims; i++) extra_dims[i] = max_dim_size[i];
int user_chunking[extraDims];
for (int i=0; i < extraDims; i++) user_chunking[i] = 1;
// Create a test array
NDArrayInfo_t arrinfo;
parr = new NDArray();
parr->dataType = NDInt8;
parr->ndims = 2;
parr->pNDArrayPool = NULL;
parr->getInfo(&arrinfo);
parr->dataSize = arrinfo.bytesPerElement;
for (unsigned int i = 0; i < 2; i++){
unsigned int dim_index = rank-(i+1);
parr->dataSize *= max_dim_size[dim_index];
parr->dims[i].size = max_dim_size[dim_index];
}
parr->pData = calloc(parr->dataSize, sizeof(char));
memset(parr->pData, 0, parr->dataSize);
parr->uniqueId = 0;
dataset->configureDims(parr, true, extraDims, extra_dims, user_chunking);
return dataset;
}
int
main()
{
printf("\n*** Checking HDF5 integer dataset with extension.\n");
printf("*** checking 1D int dataset with extend...");
{
/* Misspelling is deliberite. Please dont correct. */
#define INTERGERS "Intergers"
#define NUM_STR 1
#define NDIMS 1
hid_t fileid, grpid, spaceid;
hid_t datasetid, plistid;
hsize_t dims[NDIMS] = {NUM_STR}, max_dims[NDIMS] = {H5S_UNLIMITED};
hsize_t chunk_dims[NDIMS] = {1};
hsize_t xtend_size[NDIMS] = {2};
int data[NUM_STR] = {42};
int empty = -42;
/* Create the file, open root group. */
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT,
H5P_DEFAULT)) < 0) ERR;
if ((grpid = H5Gopen2(fileid, "/", H5P_DEFAULT)) < 0) ERR;
/* Create a space for the dataset. */
if ((spaceid = H5Screate_simple(1, dims, max_dims)) < 0) ERR;
/* Create the dataset. */
if ((plistid = H5Pcreate(H5P_DATASET_CREATE)) < 0) ERR;
if (H5Pset_chunk(plistid, 1, chunk_dims) < 0) ERR;
if (H5Pset_fill_value(plistid, H5T_NATIVE_INT32, &empty) < 0) ERR;
if ((datasetid = H5Dcreate1(grpid, INTERGERS, H5T_NATIVE_INT32,
spaceid, plistid)) < 0) ERR;
/* Now extend the dataset. */
if (H5Dextend(datasetid, xtend_size) < 0) ERR;
if (H5Dwrite(datasetid, H5T_NATIVE_INT, spaceid, spaceid,
H5P_DEFAULT, &data) < 0) ERR;
/* Close up. */
if (H5Dclose(datasetid) < 0) ERR;
if (H5Pclose(plistid) < 0) ERR;
if (H5Sclose(spaceid) < 0) ERR;
if (H5Gclose(grpid) < 0) ERR;
if (H5Fclose(fileid) < 0) ERR;
}
SUMMARIZE_ERR;
FINAL_RESULTS;
}
int main(int argc, char* argv[]) {
HDF5_CALL(H5open());
HDF5_HANDLE(plist, get_parameters(), H5Pclose);
HDF5_HANDLE(file, H5Fcreate("test.hdf5", H5F_ACC_TRUNC, H5P_DEFAULT, plist),
&H5Fclose);
hsize_t dims[D] = {0};
hsize_t cdims[D] = {64};
cdims[D - 1] = 1;
hsize_t maxs[D];
maxs[0] = H5S_UNLIMITED;
maxs[1] = H5S_UNLIMITED;
double fill = -1;
HDF5_HANDLE(space, H5Screate_simple(D, dims, maxs), &H5Sclose);
HDF5_HANDLE(dplist, H5Pcreate(H5P_DATASET_CREATE), &H5Pclose);
HDF5_CALL(H5Pset_chunk(dplist, D, cdims));
HDF5_CALL(H5Pset_fill_value(dplist, H5T_NATIVE_DOUBLE, &fill));
if (argc > 1 && argv[1][0] == '+') {
std::cout << "old" << std::endl;
HDF5_CALL(H5Pset_fill_time(dplist, H5D_FILL_TIME_IFSET));
HDF5_CALL(H5Pset_alloc_time(dplist, H5D_ALLOC_TIME_LATE));
} else if (argc > 1 && argv[1][0] == '-') {
std::cout << "new" << std::endl;
HDF5_CALL(H5Pset_fill_time(dplist, H5D_FILL_TIME_ALLOC));
HDF5_CALL(H5Pset_alloc_time(dplist, H5D_ALLOC_TIME_INCR));
} else {
std::cout << "default" << std::endl;
HDF5_CALL(H5Pset_fill_time(dplist, H5D_FILL_TIME_IFSET));
HDF5_CALL(H5Pset_alloc_time(dplist, H5D_ALLOC_TIME_EARLY));
}
HDF5_HANDLE(ds, H5Dcreate2(file, "dataset", H5T_IEEE_F64LE, space,
H5P_DEFAULT, dplist, H5P_DEFAULT),
&H5Dclose);
set_size(ds, 1, 1);
set_value(ds, 0, 0, .5);
set_size(ds, 1, 2);
set_value(ds, 0, 1, 1);
set_size(ds, 1, 3);
set_value(ds, 0, 2, 0);
set_size(ds, 3, 4);
return 0;
}
/*-------------------------------------------------------------------------
* Function: create_nbit_dsets_float
*
* Purpose: Create a dataset of FLOAT datatype with nbit filter
*
* Return: Success: 0
* Failure: -1
*
* Programmer: Raymond Lu
* 29 March 2011
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
int
create_nbit_dsets_float(hid_t fid, hid_t fsid, hid_t msid)
{
hid_t dataset = -1; /* dataset handles */
hid_t datatype = -1;
hid_t dcpl = -1;
size_t precision, offset;
float data[NX][NY]; /* data to write */
float fillvalue = -2.2f;
hsize_t chunk[RANK] = {CHUNK0, CHUNK1};
int i, j;
/*
* Data and output buffer initialization.
*/
for (j = 0; j < NX; j++) {
for (i = 0; i < NY; i++)
data[j][i] = ((float)(i + j + 1))/3;
}
/*
* Create the dataset creation property list, add the Scale-Offset
* filter, set the chunk size, and set the fill value.
*/
if((dcpl = H5Pcreate(H5P_DATASET_CREATE)) < 0)
TEST_ERROR
if(H5Pset_nbit(dcpl) < 0)
TEST_ERROR
if(H5Pset_chunk(dcpl, RANK, chunk) < 0)
TEST_ERROR
if(H5Pset_fill_value(dcpl, H5T_NATIVE_FLOAT, &fillvalue) < 0)
TEST_ERROR
/* Define user-defined single-precision floating-point type for dataset.
* A 20-bit little-endian data type. */
if((datatype = H5Tcopy(H5T_IEEE_F32LE)) < 0)
TEST_ERROR
if(H5Tset_fields(datatype, (size_t)26, (size_t)20, (size_t)6, (size_t)7, (size_t)13) < 0)
TEST_ERROR
offset = 7;
if(H5Tset_offset(datatype,offset) < 0)
TEST_ERROR
precision = 20;
if(H5Tset_precision(datatype,precision) < 0)
TEST_ERROR
if(H5Tset_size(datatype, (size_t)4) < 0)
TEST_ERROR
if(H5Tset_ebias(datatype, (size_t)31) < 0)
TEST_ERROR
/*
* Create a new dataset within the file using defined dataspace,
* user-defined datatype, and default dataset creation properties.
*/
if((dataset = H5Dcreate2(fid, DATASETNAME22, datatype, fsid,
H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
TEST_ERROR
/*
* Write the data to the dataset using default transfer properties.
*/
if(H5Dwrite(dataset, H5T_NATIVE_FLOAT, msid, fsid, H5P_DEFAULT, data) < 0)
TEST_ERROR
/* Close dataset */
if(H5Dclose(dataset) < 0)
TEST_ERROR
/* Now create a dataset with a big-endian type */
if(H5Tset_order(datatype, H5T_ORDER_BE) < 0)
TEST_ERROR
if((dataset = H5Dcreate2(fid, DATASETNAME23, datatype, fsid,
H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
TEST_ERROR
if(H5Dwrite(dataset, H5T_NATIVE_FLOAT, msid, fsid, H5P_DEFAULT, data) < 0)
TEST_ERROR
if(H5Dclose(dataset) < 0)
TEST_ERROR
/*
* Close/release resources.
*/
if(H5Pclose(dcpl) < 0)
TEST_ERROR
return 0;
error:
H5E_BEGIN_TRY {
H5Pclose(dcpl);
H5Dclose(dataset);
} H5E_END_TRY;
return -1;
}
/*-------------------------------------------------------------------------
* Function: test_refresh
*
* Purpose: This function tests refresh (evict/reload) of individual
* objects' metadata from the metadata cache.
*
* Return: 0 on Success, 1 on Failure
*
* Programmer: Mike McGreevy
* August 17, 2010
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t test_refresh(void)
{
/**************************************************************************
*
* Test Description:
*
* This test will build an HDF5 file with several objects in a varying
* hierarchical layout. It will then flush the entire file to disk. Then,
* an attribute will be added to each object in the file.
*
* One by one, this process will flush each object to disk, individually.
* It will also be coordinating with another process, which will open
* the object before it is flushed by this process, and then refresh the
* object after it's been flushed, comparing the before and after object
* information to ensure that they are as expected. (i.e., most notably,
* that an attribute has been added, and is only visible after a
* successful call to a H5*refresh function).
*
* As with the flush case, the implemention is a bit tricky as it's
* dealing with signals going back and forth between the two processes
* to ensure the timing is correct, but basically, an example:
*
* Step 1. Dataset is created.
* Step 2. Dataset is flushed.
* Step 3. Attribute on Dataset is created.
* Step 4. Another process opens the dataset and verifies that it does
* not see an attribute (as the attribute hasn't been flushed yet).
* Step 5. This process flushes the dataset again (with Attribute attached).
* Step 6. The other process calls H5Drefresh, which should evict/reload
* the object's metadata, and thus pick up the attribute that's
* attached to it. Most other before/after object information is
* compared for sanity as well.
* Step 7. Rinse and Repeat for each object in the file.
*
**************************************************************************/
/**************************************************************************
* Generated Test File will look like this:
*
* GROUP "/"
* DATASET "Dataset1"
* GROUP "Group1" {
* DATASET "Dataset2"
* GROUP "Group2" {
* DATATYPE "CommittedDatatype3"
* }
* }
* GROUP "Group3" {
* DATASET "Dataset3"
* DATATYPE "CommittedDatatype2"
* }
* DATATYPE "CommittedDatatype1"
**************************************************************************/
/* Variables */
hid_t aid,fid,sid,tid1,did,dcpl,fapl = 0;
hid_t gid,gid2,gid3,tid2,tid3,did2,did3,status = 0;
hsize_t dims[2] = {50,50};
hsize_t cdims[2] = {1,1};
int fillval = 2;
/* Testing Message */
HDfprintf(stdout, "Testing individual object refresh behavior:\n");
/* Cleanup any old error or signal files */
CLEANUP_FILES;
/* ================ */
/* CREATE TEST FILE */
/* ================ */
/* Create File */
if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) TEST_ERROR;
if (H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) TEST_ERROR;
if ((fid = H5Fcreate(FILENAME, H5F_ACC_TRUNC|H5F_ACC_SWMR_WRITE, H5P_DEFAULT, fapl)) < 0) TEST_ERROR;
/* Create data space and types */
if ((dcpl = H5Pcreate(H5P_DATASET_CREATE)) < 0) TEST_ERROR;
if ( H5Pset_chunk(dcpl, 2, cdims) < 0 ) TEST_ERROR;
if ( H5Pset_fill_value(dcpl, H5T_NATIVE_INT, &fillval) < 0 ) TEST_ERROR;
if ((sid = H5Screate_simple(2, dims, dims)) < 0) TEST_ERROR;
if ((tid1 = H5Tcopy(H5T_NATIVE_INT)) < 0) TEST_ERROR;
if ((tid2 = H5Tcopy(H5T_NATIVE_CHAR)) < 0) TEST_ERROR;
if ((tid3 = H5Tcopy(H5T_NATIVE_LONG)) < 0) TEST_ERROR;
/* Create Group1 */
if ((gid = H5Gcreate2(fid, "Group1", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0) TEST_ERROR;
/* Create Group2 */
if ((gid2 = H5Gcreate2(gid, "Group2", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0) TEST_ERROR;
/* Create Group3 */
if ((gid3 = H5Gcreate2(fid, "Group3", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0) TEST_ERROR;
/* Create Dataset1 */
if ((did = H5Dcreate2(fid, "Dataset1", tid1, sid, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0) TEST_ERROR;
/* Create Dataset2 */
if ((did2 = H5Dcreate2(gid, "Dataset2", tid3, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0) TEST_ERROR;
/* Create Dataset3 */
if ((did3 = H5Dcreate2(gid3, "Dataset3", tid2, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0) TEST_ERROR;
/* Create CommittedDatatype1 */
if ((status = H5Tcommit2(fid, "CommittedDatatype1", tid1, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0) TEST_ERROR;
/* Create CommittedDatatype2 */
if ((status = H5Tcommit2(gid2, "CommittedDatatype2", tid2, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0) TEST_ERROR;
/* Create CommittedDatatype3 */
if ((status = H5Tcommit2(gid3, "CommittedDatatype3", tid3, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0) TEST_ERROR;
/* Flush File to Disk */
if (H5Fflush(fid, H5F_SCOPE_GLOBAL) < 0) TEST_ERROR;
/* Create an attribute on each object. These will not immediately hit disk,
and thus be unavailable to another process until this process flushes
the object and the other process refreshes from disk. */
if ((aid = H5Acreate2(did, "Attribute", tid1, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0) TEST_ERROR;
if (H5Aclose(aid) < 0) TEST_ERROR;
if ((aid = H5Acreate2(did2, "Attribute", tid1, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0) TEST_ERROR;
if (H5Aclose(aid) < 0) TEST_ERROR;
if ((aid = H5Acreate2(did3, "Attribute", tid1, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0) TEST_ERROR;
if (H5Aclose(aid) < 0) TEST_ERROR;
if ((aid = H5Acreate2(gid, "Attribute", tid1, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0) TEST_ERROR;
if (H5Aclose(aid) < 0) TEST_ERROR;
if ((aid = H5Acreate2(gid2, "Attribute", tid1, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0) TEST_ERROR;
if (H5Aclose(aid) < 0) TEST_ERROR;
if ((aid = H5Acreate2(gid3, "Attribute", tid1, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0) TEST_ERROR;
if (H5Aclose(aid) < 0) TEST_ERROR;
if ((aid = H5Acreate2(tid1, "Attribute", tid1, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0) TEST_ERROR;
if (H5Aclose(aid) < 0) TEST_ERROR;
if ((aid = H5Acreate2(tid2, "Attribute", tid1, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0) TEST_ERROR;
if (H5Aclose(aid) < 0) TEST_ERROR;
if ((aid = H5Acreate2(tid3, "Attribute", tid1, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0) TEST_ERROR;
if (H5Aclose(aid) < 0) TEST_ERROR;
/* ================ */
/* Refresh Datasets */
/* ================ */
TESTING("to ensure that H5Drefresh correctly refreshes single datasets");
/* Verify First Dataset can be refreshed with H5Drefresh */
if (start_refresh_verification_process(D1) != 0) TEST_ERROR;
if (H5Oflush(did) < 0) TEST_ERROR;
if (end_refresh_verification_process() != 0) TEST_ERROR;
/* Verify Second Dataset can be refreshed with H5Drefresh */
if (start_refresh_verification_process(D2) != 0) TEST_ERROR;
if (H5Oflush(did2) < 0) TEST_ERROR;
if (end_refresh_verification_process() != 0) TEST_ERROR;
PASSED();
/* ============== */
/* Refresh Groups */
/* ============== */
TESTING("to ensure that H5Grefresh correctly refreshes single groups");
/* Verify First Group can be refreshed with H5Grefresh */
if (start_refresh_verification_process(G1) != 0) TEST_ERROR;
if (H5Oflush(gid) < 0) TEST_ERROR;
if (end_refresh_verification_process() != 0) TEST_ERROR;
/* Verify Second Group can be refreshed with H5Grefresh */
if (start_refresh_verification_process(G2) != 0) TEST_ERROR;
if (H5Oflush(gid2) < 0) TEST_ERROR;
if (end_refresh_verification_process() != 0) TEST_ERROR;
PASSED();
/* ================= */
/* Refresh Datatypes */
/* ================= */
TESTING("to ensure that H5Trefresh correctly refreshes single datatypes");
/* Verify First Committed Datatype can be refreshed with H5Trefresh */
if (start_refresh_verification_process(T1) != 0) TEST_ERROR;
if (H5Oflush(tid1) < 0) TEST_ERROR;
if (end_refresh_verification_process() != 0) TEST_ERROR;
/* Verify Second Committed Datatype can be refreshed with H5Trefresh */
if (start_refresh_verification_process(T2) != 0) TEST_ERROR;
if (H5Oflush(tid2) < 0) TEST_ERROR;
if (end_refresh_verification_process() != 0) TEST_ERROR;
PASSED();
/* =============== */
/* Refresh Objects */
/* =============== */
TESTING("to ensure that H5Orefresh correctly refreshes single objects");
/* Verify Third Dataset can be refreshed with H5Orefresh */
if (start_refresh_verification_process(D3) != 0) TEST_ERROR;
if (H5Oflush(did3) < 0) TEST_ERROR;
if (end_refresh_verification_process() != 0) TEST_ERROR;
/* Verify Third Group can be refreshed with H5Orefresh */
if (start_refresh_verification_process(G3) != 0) TEST_ERROR;
if (H5Oflush(gid3) < 0) TEST_ERROR;
if (end_refresh_verification_process() != 0) TEST_ERROR;
/* Verify Third Committed Datatype can be refreshed with H5Orefresh */
if (start_refresh_verification_process(T3) != 0) TEST_ERROR;
if (H5Oflush(tid3) < 0) TEST_ERROR;
if (end_refresh_verification_process() != 0) TEST_ERROR;
PASSED();
/* ================== */
/* Cleanup and Return */
/* ================== */
/* Close Stuff */
if (H5Pclose(fapl) < 0) TEST_ERROR;
if (H5Tclose(tid1) < 0) TEST_ERROR;
if (H5Tclose(tid2) < 0) TEST_ERROR;
if (H5Tclose(tid3) < 0) TEST_ERROR;
if (H5Dclose(did) < 0) TEST_ERROR;
if (H5Dclose(did2) < 0) TEST_ERROR;
if (H5Dclose(did3) < 0) TEST_ERROR;
if (H5Gclose(gid) < 0) TEST_ERROR;
if (H5Gclose(gid2) < 0) TEST_ERROR;
if (H5Gclose(gid3) < 0) TEST_ERROR;
if (H5Sclose(sid) < 0) TEST_ERROR;
if (H5Fclose(fid) < 0) TEST_ERROR;
/* Delete Test File */
HDremove(FILENAME);
if (end_verification() < 0) TEST_ERROR;
return SUCCEED;
error:
/* Return */
return FAIL;
} /* test_refresh() */
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;
}
int
main(void)
{
hid_t dcpl1; /* dataset create prop. list */
hid_t dapl1; /* dataset access prop. list */
hid_t dxpl1; /* dataset xfer prop. list */
hid_t gcpl1; /* group create prop. list */
hid_t ocpypl1; /* object copy prop. list */
hid_t ocpl1; /* object create prop. list */
hid_t lcpl1; /* link create prop. list */
hid_t lapl1; /* link access prop. list */
hid_t fapl1; /* file access prop. list */
hid_t fcpl1; /* file create prop. list */
hid_t strcpl1; /* string create prop. list */
hid_t acpl1; /* attribute create prop. list */
herr_t ret = 0;
hsize_t chunk_size = 16384; /* chunk size */
int fill = 2; /* Fill value */
hsize_t max_size[1]; /* data space maximum size */
size_t nslots = 521 * 2;
size_t nbytes = 1048576 * 10;
double w0 = 0.5f;
unsigned max_compact;
unsigned min_dense;
const char* c_to_f = "x+32";
int little_endian;
int word_length;
H5AC_cache_config_t my_cache_config = {
H5AC__CURR_CACHE_CONFIG_VERSION,
1 /*TRUE*/,
0 /*FALSE*/,
0 /*FALSE*/,
"temp",
1 /*TRUE*/,
0 /*FALSE*/,
( 2 * 2048 * 1024),
0.3f,
(64 * 1024 * 1024),
(4 * 1024 * 1024),
60000,
H5C_incr__threshold,
0.8f,
3.0f,
1 /*TRUE*/,
(8 * 1024 * 1024),
H5C_flash_incr__add_space,
2.0f,
0.25f,
H5C_decr__age_out_with_threshold,
0.997f,
0.8f,
1 /*TRUE*/,
(3 * 1024 * 1024),
3,
0 /*FALSE*/,
0.2f,
(256 * 2048),
H5AC_METADATA_WRITE_STRATEGY__PROCESS_0_ONLY};
H5AC_cache_image_config_t my_cache_image_config = {
H5AC__CURR_CACHE_IMAGE_CONFIG_VERSION,
TRUE,
FALSE,
-1};
/* check endianess */
{
short int word = 0x0001;
char *byte = (char *) &word;
if(byte[0] == 1)
/* little endian */
little_endian = 1;
else
/* big endian */
little_endian = 0;
}
/* check word length */
{
word_length = 8 * sizeof(void *);
}
/* Explicitly initialize the library, since we are including the private header file */
H5open();
/******* ENCODE/DECODE DCPLS *****/
if((dcpl1 = H5Pcreate(H5P_DATASET_CREATE)) < 0)
assert(dcpl1 > 0);
if((ret = encode_plist(dcpl1, little_endian, word_length, "testfiles/plist_files/def_dcpl_")) < 0)
assert(ret > 0);
if((ret = H5Pset_chunk(dcpl1, 1, &chunk_size)) < 0)
assert(ret > 0);
if((ret = H5Pset_alloc_time(dcpl1, H5D_ALLOC_TIME_LATE)) < 0)
assert(ret > 0);
ret = H5Tconvert(H5T_NATIVE_INT, H5T_STD_I32BE, (size_t)1, &fill, NULL, H5P_DEFAULT);
assert(ret >= 0);
if((ret = H5Pset_fill_value(dcpl1, H5T_STD_I32BE, &fill)) < 0)
assert(ret > 0);
max_size[0] = 100;
if((ret = H5Pset_external(dcpl1, "ext1.data", (off_t)0,
(hsize_t)(max_size[0] * sizeof(int)/4))) < 0)
assert(ret > 0);
if((ret = H5Pset_external(dcpl1, "ext2.data", (off_t)0,
(hsize_t)(max_size[0] * sizeof(int)/4))) < 0)
assert(ret > 0);
if((ret = H5Pset_external(dcpl1, "ext3.data", (off_t)0,
(hsize_t)(max_size[0] * sizeof(int)/4))) < 0)
assert(ret > 0);
if((ret = H5Pset_external(dcpl1, "ext4.data", (off_t)0,
(hsize_t)(max_size[0] * sizeof(int)/4))) < 0)
assert(ret > 0);
if((ret = encode_plist(dcpl1, little_endian, word_length, "testfiles/plist_files/dcpl_")) < 0)
assert(ret > 0);
/* release resource */
if((ret = H5Pclose(dcpl1)) < 0)
assert(ret > 0);
/******* ENCODE/DECODE DAPLS *****/
if((dapl1 = H5Pcreate(H5P_DATASET_ACCESS)) < 0)
assert(dapl1 > 0);
if((ret = encode_plist(dapl1, little_endian, word_length, "testfiles/plist_files/def_dapl_")) < 0)
assert(ret > 0);
if((ret = H5Pset_chunk_cache(dapl1, nslots, nbytes, w0)) < 0)
assert(ret > 0);
if((ret = encode_plist(dapl1, little_endian, word_length, "testfiles/plist_files/dapl_")) < 0)
assert(ret > 0);
/* release resource */
if((ret = H5Pclose(dapl1)) < 0)
assert(ret > 0);
/******* ENCODE/DECODE DXPLS *****/
if((dxpl1 = H5Pcreate(H5P_DATASET_XFER)) < 0)
assert(dxpl1 > 0);
if((ret = encode_plist(dxpl1, little_endian, word_length, "testfiles/plist_files/def_dxpl_")) < 0)
assert(ret > 0);
if((ret = H5Pset_btree_ratios(dxpl1, 0.2f, 0.6f, 0.2f)) < 0)
assert(ret > 0);
if((ret = H5Pset_hyper_vector_size(dxpl1, 5)) < 0)
assert(ret > 0);
#ifdef H5_HAVE_PARALLEL
if((ret = H5Pset_dxpl_mpio(dxpl1, H5FD_MPIO_COLLECTIVE)) < 0)
assert(ret > 0);
if((ret = H5Pset_dxpl_mpio_collective_opt(dxpl1, H5FD_MPIO_INDIVIDUAL_IO)) < 0)
assert(ret > 0);
if((ret = H5Pset_dxpl_mpio_chunk_opt(dxpl1, H5FD_MPIO_CHUNK_MULTI_IO)) < 0)
assert(ret > 0);
if((ret = H5Pset_dxpl_mpio_chunk_opt_ratio(dxpl1, 30)) < 0)
assert(ret > 0);
if((ret = H5Pset_dxpl_mpio_chunk_opt_num(dxpl1, 40)) < 0)
assert(ret > 0);
#endif/* H5_HAVE_PARALLEL */
if((ret = H5Pset_edc_check(dxpl1, H5Z_DISABLE_EDC)) < 0)
assert(ret > 0);
if((ret = H5Pset_data_transform(dxpl1, c_to_f)) < 0)
assert(ret > 0);
if((ret = encode_plist(dxpl1, little_endian, word_length, "testfiles/plist_files/dxpl_")) < 0)
assert(ret > 0);
/* release resource */
if((ret = H5Pclose(dxpl1)) < 0)
assert(ret > 0);
/******* ENCODE/DECODE GCPLS *****/
if((gcpl1 = H5Pcreate(H5P_GROUP_CREATE)) < 0)
assert(gcpl1 > 0);
if((ret = encode_plist(gcpl1, little_endian, word_length, "testfiles/plist_files/def_gcpl_")) < 0)
assert(ret > 0);
if((ret = H5Pset_local_heap_size_hint(gcpl1, 256)) < 0)
assert(ret > 0);
if((ret = H5Pset_link_phase_change(gcpl1, 2, 2)) < 0)
assert(ret > 0);
/* Query the group creation properties */
if((ret = H5Pget_link_phase_change(gcpl1, &max_compact, &min_dense)) < 0)
assert(ret > 0);
if((ret = H5Pset_est_link_info(gcpl1, 3, 9)) < 0)
assert(ret > 0);
if((ret = H5Pset_link_creation_order(gcpl1, (H5P_CRT_ORDER_TRACKED | H5P_CRT_ORDER_INDEXED))) < 0)
assert(ret > 0);
if((ret = encode_plist(gcpl1, little_endian, word_length, "testfiles/plist_files/gcpl_")) < 0)
assert(ret > 0);
/* release resource */
if((ret = H5Pclose(gcpl1)) < 0)
assert(ret > 0);
/******* ENCODE/DECODE LCPLS *****/
if((lcpl1 = H5Pcreate(H5P_LINK_CREATE)) < 0)
assert(lcpl1 > 0);
if((ret = encode_plist(lcpl1, little_endian, word_length, "testfiles/plist_files/def_lcpl_")) < 0)
assert(ret > 0);
if((ret = H5Pset_create_intermediate_group(lcpl1, 1 /*TRUE*/)) < 0)
assert(ret > 0);
if((ret = encode_plist(lcpl1, little_endian, word_length, "testfiles/plist_files/lcpl_")) < 0)
assert(ret > 0);
/* release resource */
if((ret = H5Pclose(lcpl1)) < 0)
assert(ret > 0);
/******* ENCODE/DECODE OCPYLS *****/
if((ocpypl1 = H5Pcreate(H5P_OBJECT_COPY)) < 0)
assert(ocpypl1 > 0);
if((ret = encode_plist(ocpypl1, little_endian, word_length, "testfiles/plist_files/def_ocpypl_")) < 0)
assert(ret > 0);
ret = H5Pset_copy_object(ocpypl1, H5O_COPY_EXPAND_EXT_LINK_FLAG);
assert(ret >= 0);
ret = H5Padd_merge_committed_dtype_path(ocpypl1, "foo");
assert(ret >= 0);
ret = H5Padd_merge_committed_dtype_path(ocpypl1, "bar");
assert(ret >= 0);
if((ret = encode_plist(ocpypl1, little_endian, word_length, "testfiles/plist_files/ocpypl_")) < 0)
assert(ret > 0);
/* release resource */
if((ret = H5Pclose(ocpypl1)) < 0)
assert(ret > 0);
/******* ENCODE/DECODE OCPLS *****/
if((ocpl1 = H5Pcreate(H5P_OBJECT_CREATE)) < 0)
assert(ocpl1 > 0);
if((ret = encode_plist(ocpl1, little_endian, word_length, "testfiles/plist_files/def_ocpl_")) < 0)
assert(ret > 0);
if((ret = H5Pset_attr_creation_order(ocpl1, (H5P_CRT_ORDER_TRACKED | H5P_CRT_ORDER_INDEXED))) < 0)
assert(ret > 0);
if((ret = H5Pset_attr_phase_change (ocpl1, 110, 105)) < 0)
assert(ret > 0);
if((ret = H5Pset_filter (ocpl1, H5Z_FILTER_FLETCHER32, 0, (size_t)0, NULL)) < 0)
assert(ret > 0);
if((ret = encode_plist(ocpl1, little_endian, word_length, "testfiles/plist_files/ocpl_")) < 0)
assert(ret > 0);
/* release resource */
if((ret = H5Pclose(ocpl1)) < 0)
assert(ret > 0);
/******* ENCODE/DECODE LAPLS *****/
if((lapl1 = H5Pcreate(H5P_LINK_ACCESS)) < 0)
assert(lapl1 > 0);
if((ret = encode_plist(lapl1, little_endian, word_length, "testfiles/plist_files/def_lapl_")) < 0)
assert(ret > 0);
if((ret = H5Pset_nlinks(lapl1, (size_t)134)) < 0)
assert(ret > 0);
if((ret = H5Pset_elink_acc_flags(lapl1, H5F_ACC_RDONLY)) < 0)
assert(ret > 0);
if((ret = H5Pset_elink_prefix(lapl1, "/tmpasodiasod")) < 0)
assert(ret > 0);
/* Create FAPL for the elink FAPL */
if((fapl1 = H5Pcreate(H5P_FILE_ACCESS)) < 0)
assert(fapl1 > 0);
if((ret = H5Pset_alignment(fapl1, 2, 1024)) < 0)
assert(ret > 0);
if((ret = H5Pset_elink_fapl(lapl1, fapl1)) < 0)
assert(ret > 0);
/* Close the elink's FAPL */
if((ret = H5Pclose(fapl1)) < 0)
assert(ret > 0);
if((ret = encode_plist(lapl1, little_endian, word_length, "testfiles/plist_files/lapl_")) < 0)
assert(ret > 0);
/* release resource */
if((ret = H5Pclose(lapl1)) < 0)
assert(ret > 0);
/******* ENCODE/DECODE FAPLS *****/
if((fapl1 = H5Pcreate(H5P_FILE_ACCESS)) < 0)
assert(fapl1 > 0);
if((ret = encode_plist(fapl1, little_endian, word_length, "testfiles/plist_files/def_fapl_")) < 0)
assert(ret > 0);
if((ret = H5Pset_family_offset(fapl1, 1024)) < 0)
assert(ret > 0);
if((ret = H5Pset_meta_block_size(fapl1, 2098452)) < 0)
assert(ret > 0);
if((ret = H5Pset_sieve_buf_size(fapl1, 1048576)) < 0)
assert(ret > 0);
if((ret = H5Pset_alignment(fapl1, 2, 1024)) < 0)
assert(ret > 0);
if((ret = H5Pset_cache(fapl1, 1024, 128, 10485760, 0.3f)) < 0)
assert(ret > 0);
if((ret = H5Pset_elink_file_cache_size(fapl1, 10485760)) < 0)
assert(ret > 0);
if((ret = H5Pset_gc_references(fapl1, 1)) < 0)
assert(ret > 0);
if((ret = H5Pset_small_data_block_size(fapl1, 2048)) < 0)
assert(ret > 0);
if((ret = H5Pset_libver_bounds(fapl1, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST)) < 0)
assert(ret > 0);
if((ret = H5Pset_fclose_degree(fapl1, H5F_CLOSE_WEAK)) < 0)
assert(ret > 0);
if((ret = H5Pset_multi_type(fapl1, H5FD_MEM_GHEAP)) < 0)
assert(ret > 0);
if((ret = H5Pset_mdc_config(fapl1, &my_cache_config)) < 0)
assert(ret > 0);
if((ret = H5Pset_mdc_image_config(fapl1, &my_cache_image_config)) < 0)
assert(ret > 0);
if((ret = H5Pset_core_write_tracking(fapl1, TRUE, (size_t)(1024 * 1024))) < 0)
assert(ret > 0);
if((ret = encode_plist(fapl1, little_endian, word_length, "testfiles/plist_files/fapl_")) < 0)
assert(ret > 0);
/* release resource */
if((ret = H5Pclose(fapl1)) < 0)
assert(ret > 0);
/******* ENCODE/DECODE FCPLS *****/
if((fcpl1 = H5Pcreate(H5P_FILE_CREATE)) < 0)
assert(fcpl1 > 0);
if((ret = encode_plist(fcpl1, little_endian, word_length, "testfiles/plist_files/def_fcpl_")) < 0)
assert(ret > 0);
if((ret = H5Pset_userblock(fcpl1, 1024) < 0))
assert(ret > 0);
if((ret = H5Pset_istore_k(fcpl1, 3) < 0))
assert(ret > 0);
if((ret = H5Pset_sym_k(fcpl1, 4, 5) < 0))
assert(ret > 0);
if((ret = H5Pset_shared_mesg_nindexes(fcpl1, 8) < 0))
assert(ret > 0);
if((ret = H5Pset_shared_mesg_index(fcpl1, 1, H5O_SHMESG_SDSPACE_FLAG, 32) < 0))
assert(ret > 0);
if((ret = H5Pset_shared_mesg_phase_change(fcpl1, 60, 20) < 0))
assert(ret > 0);
if((ret = H5Pset_sizes(fcpl1, 8, 4) < 0))
assert(ret > 0);
if((ret = H5Pset_file_space_strategy(fcpl1, H5F_FSPACE_STRATEGY_PAGE, TRUE, (hsize_t)1)) < 0)
assert(ret > 0);
if((ret = H5Pset_file_space_page_size(fcpl1, (hsize_t)4096)) < 0)
assert(ret > 0);
if((ret = encode_plist(fcpl1, little_endian, word_length, "testfiles/plist_files/fcpl_")) < 0)
assert(ret > 0);
/* release resource */
if((ret = H5Pclose(fcpl1)) < 0)
assert(ret > 0);
/******* ENCODE/DECODE STRCPLS *****/
strcpl1 = H5Pcreate(H5P_STRING_CREATE);
assert(strcpl1 > 0);
ret = encode_plist(strcpl1, little_endian, word_length, "testfiles/plist_files/def_strcpl_");
assert(ret > 0);
ret = H5Pset_char_encoding(strcpl1, H5T_CSET_UTF8);
assert(ret >= 0);
ret = encode_plist(strcpl1, little_endian, word_length, "testfiles/plist_files/strcpl_");
assert(ret > 0);
/* release resource */
ret = H5Pclose(strcpl1);
assert(ret >= 0);
/******* ENCODE/DECODE ACPLS *****/
acpl1 = H5Pcreate(H5P_ATTRIBUTE_CREATE);
assert(acpl1 > 0);
ret = encode_plist(acpl1, little_endian, word_length, "testfiles/plist_files/def_acpl_");
assert(ret > 0);
ret = H5Pset_char_encoding(acpl1, H5T_CSET_UTF8);
assert(ret >= 0);
ret = encode_plist(acpl1, little_endian, word_length, "testfiles/plist_files/acpl_");
assert(ret > 0);
/* release resource */
ret = H5Pclose(acpl1);
assert(ret >= 0);
return 0;
}
int main(int argc, char *argv[])
{
hid_t fid = -1;
hid_t access_plist = -1;
hid_t create_plist = -1;
hid_t cparm = -1;
hid_t datatype = -1;
hid_t dataspace = -1;
hid_t dataset = -1;
hid_t memspace = -1;
hid_t groupDetector = -1;
int rank = 1;
hsize_t chunk[2] = {10,10};
hsize_t dims[2] = {1,1};
hsize_t elementSize[2] = {1,1};
hsize_t maxdims[2] = {H5S_UNLIMITED,H5S_UNLIMITED};
int ivalue[2];
int fillValue = 0;
/* Open the source file and dataset */
/* All SWMR files need to use the latest file format */
access_plist = H5Pcreate(H5P_FILE_ACCESS);
H5Pset_fclose_degree(access_plist, H5F_CLOSE_STRONG);
#if H5_VERSION_GE(1,9,178)
H5Pset_object_flush_cb(access_plist, cFlushCallback, NULL);
#endif
H5Pset_libver_bounds(access_plist, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST);
create_plist = H5Pcreate(H5P_FILE_CREATE);
fid = H5Fcreate("test_string_swmr.h5", H5F_ACC_TRUNC, create_plist, access_plist);
/* Data */
rank = 2;
dims[0] = 10;
dims[1] = 10;
dataspace = H5Screate_simple(rank, dims, dims);
cparm = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_chunk(cparm, rank, chunk);
datatype = H5Tcopy(H5T_NATIVE_INT8);
H5Pset_fill_value(cparm, datatype, &fillValue);
groupDetector = H5Gcreate(fid, "detector", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
access_plist = H5Pcreate(H5P_DATASET_ACCESS);
H5Pset_chunk_cache(access_plist, 503, 100, 1.0);
dataset = H5Dcreate2(groupDetector, "data1",
datatype, dataspace,
H5P_DEFAULT, cparm, access_plist);
ivalue[0] = 1;
ivalue[1] = 1;
writeInt32Attribute(dataset, "NDArrayDimBinning", 2, ivalue);
ivalue[0] = 0;
ivalue[1] = 0;
writeInt32Attribute(dataset, "NDArrayDimOffset", 2, ivalue);
writeInt32Attribute(dataset, "NDArrayDimReverse", 2, ivalue);
ivalue[0] = 2;
writeInt32Attribute(dataset, "NDArrayNumDims", 1, ivalue);
H5Gclose(groupDetector);
dims[0] = 1;
dims[1] = 1;
chunk[0] = 1;
rank = 1;
/* Unique ID */
datatype = H5T_NATIVE_INT32;
cparm = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_fill_value(cparm, datatype, &fillValue);
H5Pset_chunk(cparm, rank, chunk);
dataspace = H5Screate_simple(rank, dims, maxdims);
dataset = H5Dcreate2(fid, "NDArrayUniqueId",
datatype, dataspace,
H5P_DEFAULT, cparm, H5P_DEFAULT);
memspace = H5Screate_simple(rank, elementSize, NULL);
writeStringAttribute(dataset, "NDAttrName", "NDArrayUniqueId");
writeStringAttribute(dataset, "NDAttrDescription", "The unique ID of the NDArray");
writeStringAttribute(dataset, "NDAttrSourceType", "NDAttrSourceDriver");
writeStringAttribute(dataset, "NDAttrSource", "Driver");
/* EPICS Timestemp */
datatype = H5T_NATIVE_DOUBLE;
cparm = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_fill_value(cparm, datatype, &fillValue);
H5Pset_chunk(cparm, rank, chunk);
dataspace = H5Screate_simple(rank, dims, maxdims);
dataset = H5Dcreate2(fid, "NDArrayTimeStamp",
datatype, dataspace,
H5P_DEFAULT, cparm, H5P_DEFAULT);
memspace = H5Screate_simple(rank, elementSize, NULL);
writeStringAttribute(dataset, "NDAttrName", "NDArrayTimeStamp");
writeStringAttribute(dataset, "NDAttrDescription", "The timestamp of the NDArray as float64");
writeStringAttribute(dataset, "NDAttrSourceType", "NDAttrSourceDriver");
writeStringAttribute(dataset, "NDAttrSource", "Driver");
/* EPICS TS sec */
datatype = H5T_NATIVE_UINT32;
cparm = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_fill_value(cparm, datatype, &fillValue);
H5Pset_chunk(cparm, rank, chunk);
dataspace = H5Screate_simple(rank, dims, maxdims);
dataset = H5Dcreate2(fid, "NDArrayEpicsTSSec",
datatype, dataspace,
H5P_DEFAULT, cparm, H5P_DEFAULT);
memspace = H5Screate_simple(rank, elementSize, NULL);
writeStringAttribute(dataset, "NDAttrName", "NDArrayEpicsTSSec");
writeStringAttribute(dataset, "NDAttrDescription", "The NDArray EPICS timestamp seconds past epoch");
writeStringAttribute(dataset, "NDAttrSourceType", "NDAttrSourceDriver");
writeStringAttribute(dataset, "NDAttrSource", "Driver");
/* EPICS TS nsec */
datatype = H5T_NATIVE_UINT32;
cparm = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_fill_value(cparm, datatype, &fillValue);
H5Pset_chunk(cparm, rank, chunk);
dataspace = H5Screate_simple(rank, dims, maxdims);
dataset = H5Dcreate2(fid, "NDArrayEpicsTSnSec",
datatype, dataspace,
H5P_DEFAULT, cparm, H5P_DEFAULT);
memspace = H5Screate_simple(rank, elementSize, NULL);
writeStringAttribute(dataset, "NDAttrName", "NDArrayEpicsTSnSec");
writeStringAttribute(dataset, "NDAttrDescription", "The NDArray EPICS timestamp nanoseconds");
writeStringAttribute(dataset, "NDAttrSourceType", "NDAttrSourceDriver");
writeStringAttribute(dataset, "NDAttrSource", "Driver");
/* Color mode */
datatype = H5T_NATIVE_INT32;
cparm = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_fill_value(cparm, datatype, &fillValue);
H5Pset_chunk(cparm, rank, chunk);
dataspace = H5Screate_simple(rank, dims, maxdims);
dataset = H5Dcreate2(fid, "ColorMode",
datatype, dataspace,
H5P_DEFAULT, cparm, H5P_DEFAULT);
memspace = H5Screate_simple(rank, elementSize, NULL);
writeStringAttribute(dataset, "NDAttrName", "ColorMode");
writeStringAttribute(dataset, "NDAttrDescription", "Color mode");
writeStringAttribute(dataset, "NDAttrSourceType", "NDAttrSourceDriver");
writeStringAttribute(dataset, "NDAttrSource", "Driver");
/* Camera manufacturer */
datatype = H5Tcopy(H5T_C_S1);
H5Tset_size(datatype, 256);
cparm = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_fill_value(cparm, datatype, &fillValue);
H5Pset_chunk(cparm, rank, chunk);
dataspace = H5Screate_simple(rank, dims, maxdims);
dataset = H5Dcreate2(fid, "CameraManufacturer",
datatype, dataspace,
H5P_DEFAULT, cparm, H5P_DEFAULT);
memspace = H5Screate_simple(rank, elementSize, NULL);
writeStringAttribute(dataset, "NDAttrName", "CameraManufacturer");
writeStringAttribute(dataset, "NDAttrDescription", "Camera manufacturer");
writeStringAttribute(dataset, "NDAttrSourceType", "NDAttrSourceParam");
writeStringAttribute(dataset, "NDAttrSource", "MANUFACTURER");
/* Performance data */
rank = 2;
dims[0] = 1;
dims[1] = 5;
chunk[1] = 5;
cparm = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_chunk(cparm, rank, chunk);
dataspace = H5Screate_simple(rank, dims, maxdims);
dataset = H5Dcreate2(fid, "timestamp",
H5T_NATIVE_DOUBLE, dataspace,
H5P_DEFAULT, cparm, H5P_DEFAULT);
if (!H5Iis_valid(dataset)) {
printf("Error writing performance dataset");
}
H5Sclose(dataspace);
#if H5_VERSION_GE(1,9,178)
H5Fstart_swmr_write(fid);
#endif
H5Fclose(fid);
return 0;
} /* end main */
/* Create the VDS that uses use case 1 files */
herr_t
create_3_1_vds(void)
{
hid_t src_sid = -1; /* source dataset's dataspace ID */
hid_t vds_sid = -1; /* VDS dataspace ID */
hid_t vds_dcplid = -1; /* VDS dataset property list ID */
hid_t fid = -1; /* HDF5 file ID */
hid_t did = -1; /* dataset ID */
hsize_t start[RANK]; /* source starting point for hyperslab */
hsize_t position[RANK]; /* vds mapping positions */
int i; /* iterator */
/* Create VDS dcpl */
if((vds_dcplid = H5Pcreate(H5P_DATASET_CREATE)) < 0)
UC_ERROR
if(H5Pset_fill_value(vds_dcplid, UC_31_VDS_DATATYPE,
&UC_3_VDS_FILL_VALUE) < 0)
UC_ERROR
/* Create VDS dataspace */
if((vds_sid = H5Screate_simple(RANK, UC_31_VDS_DIMS,
UC_31_VDS_MAX_DIMS)) < 0)
UC_ERROR
/* Set starting positions */
start[0] = 0;
start[1] = 0;
start[2] = 0;
position[0] = 0;
position[1] = UC_31_GAP;
position[2] = 0;
/******************************
* Create source-VDS mappings *
******************************/
for(i = 0; i < UC_1_N_SOURCES; i++) {
if((src_sid = H5Screate_simple(RANK, UC_1_DIMS[i],
UC_1_MAX_DIMS[i])) < 0)
UC_ERROR
/* set up hyperslabs for source and destination datasets */
if(H5Sselect_hyperslab(src_sid, H5S_SELECT_SET, start, NULL,
UC_1_MAX_DIMS[i], NULL) < 0)
UC_ERROR
if(H5Sselect_hyperslab(vds_sid, H5S_SELECT_SET, position,
NULL, UC_1_MAX_DIMS[i], NULL) < 0)
UC_ERROR
position[1] += UC_1_DIMS[i][1] + UC_31_GAP;
/* Add VDS mapping */
if(H5Pset_virtual(vds_dcplid, vds_sid, UC_1_FILE_NAMES[i],
UC_1_SOURCE_DSET_PATH, src_sid) < 0)
UC_ERROR
if(H5Sclose(src_sid) < 0)
UC_ERROR
} /* end for */
/*******************************
* Create VDS file and dataset *
*******************************/
/* file */
if((fid = H5Fcreate(UC_31_VDS_FILE_NAME, H5F_ACC_TRUNC,
H5P_DEFAULT, H5P_DEFAULT)) < 0)
UC_ERROR
/* dataset */
if((did = H5Dcreate2(fid, UC_3_VDS_DSET_NAME, UC_31_VDS_DATATYPE, vds_sid,
H5P_DEFAULT, vds_dcplid, H5P_DEFAULT)) < 0)
UC_ERROR
/* close */
if(H5Pclose(vds_dcplid) < 0)
UC_ERROR
if(H5Sclose(vds_sid) < 0)
UC_ERROR
if(H5Dclose(did) < 0)
UC_ERROR
if(H5Fclose(fid) < 0)
UC_ERROR
return 0;
error:
H5E_BEGIN_TRY {
if(vds_sid >= 0)
(void)H5Sclose(vds_sid);
if(vds_dcplid >= 0)
(void)H5Pclose(vds_dcplid);
if(fid >= 0)
(void)H5Fclose(fid);
if(did >= 0)
(void)H5Dclose(did);
} H5E_END_TRY
return -1;
} /* end create_3_1_vds() */
/*-------------------------------------------------------------------------
* Function: create_normal_dset
*
* Purpose: Create a regular dataset of DOUBLE datatype.
*
* Return: Success: 0
* Failure: -1
*
* Programmer: Raymond Lu
* Some time ago
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
int
create_normal_dset(hid_t fid, hid_t fsid, hid_t msid)
{
hid_t dataset = -1; /* file and dataset handles */
hid_t dcpl = -1;
float data[NX][NY]; /* data to write */
float fillvalue = -2.2f;
int i, j;
/*
* Data and output buffer initialization.
*/
for (j = 0; j < NX; j++) {
for (i = 0; i < NY; i++)
data[j][i] = ((float)(i + j + 1)) / 3;
}
/*
* 1/3 2/3 3/3 4/3 5/3 6/3
* 2/3 3/3 4/3 5/3 6/3 7/3
* 3/3 4/3 5/3 6/3 7/3 8/3
* 4/3 5/3 6/3 7/3 8/3 9/3
* 5/3 6/3 7/3 8/3 9/3 10/3
* 6/3 7/3 8/3 9/3 10/3 11/3
* -2.2 -2.2 -2.2 -2.2 -2.2 -2.2
*/
/*
* Create the dataset creation property list, set the fill value.
*/
if((dcpl = H5Pcreate(H5P_DATASET_CREATE)) < 0)
TEST_ERROR
if(H5Pset_fill_value(dcpl, H5T_NATIVE_FLOAT, &fillvalue) < 0)
TEST_ERROR
/*
* Create a new dataset within the file using defined dataspace and
* little-endian datatype and default dataset creation properties.
*/
if((dataset = H5Dcreate2(fid, DATASETNAME, H5T_IEEE_F64LE, fsid,
H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
TEST_ERROR
/*
* Write the data to the dataset using default transfer properties.
*/
if(H5Dwrite(dataset, H5T_NATIVE_FLOAT, msid, fsid, H5P_DEFAULT, data) < 0)
TEST_ERROR
/*
* Close dataset
*/
if(H5Dclose(dataset) < 0)
TEST_ERROR
/*
* Create a new dataset within the file using defined dataspace and
* big-endian datatype and default dataset creation properties.
*/
if((dataset = H5Dcreate2(fid, DATASETNAME1, H5T_IEEE_F64BE, fsid,
H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
TEST_ERROR
/*
* Write the data to the dataset using default transfer properties.
*/
if(H5Dwrite(dataset, H5T_NATIVE_FLOAT, msid, fsid, H5P_DEFAULT, data) < 0)
TEST_ERROR
/*
* Close dataset
*/
if(H5Dclose(dataset) < 0)
TEST_ERROR
/*
* Close/release resources.
*/
if(H5Pclose(dcpl) < 0)
TEST_ERROR
return 0;
error:
H5E_BEGIN_TRY {
H5Pclose(dcpl);
H5Dclose(dataset);
} H5E_END_TRY;
return -1;
}
/* ------- begin -------------------------- init_hdf5_indata.c --- */
void init_hdf5_indata_new(void)
/* Creates the netCDF file for the input data */
{
const char routineName[] = "init_hdf5_indata_new";
int i, PRD_angle_dep;
double *eweight, *eabund, *x, *y;
/* This value is harcoded for efficiency.
Maximum number of iterations ever needed */
int NMaxIter = 1500;
hid_t plist, ncid, file_dspace, ncid_input, ncid_atmos, ncid_mpi;
hsize_t dims[4];
bool_t XRD;
char startJ[MAX_LINE_SIZE], StokesMode[MAX_LINE_SIZE], angleSet[MAX_LINE_SIZE];
/* Create the file */
if (( plist = H5Pcreate(H5P_FILE_ACCESS )) < 0) HERR(routineName);
if (( H5Pset_fapl_mpio(plist, mpi.comm, mpi.info) ) < 0) HERR(routineName);
if (( ncid = H5Fcreate(INPUTDATA_FILE, H5F_ACC_TRUNC, H5P_DEFAULT,
plist) ) < 0) HERR(routineName);
if (( H5Pclose(plist) ) < 0) HERR(routineName);
/* Create groups */
if (( ncid_input = H5Gcreate(ncid, "/input", H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( ncid_atmos = H5Gcreate(ncid, "/atmos", H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( ncid_mpi = H5Gcreate(ncid, "/mpi", H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT) ) < 0) HERR(routineName);
/* --- Definitions for the root group --- */
/* dimensions as attributes */
if (( H5LTset_attribute_int(ncid, "/", "nx", &mpi.nx, 1) ) < 0)
HERR(routineName);
if (( H5LTset_attribute_int(ncid, "/", "ny", &mpi.ny, 1) ) < 0)
HERR(routineName);
if (( H5LTset_attribute_int(ncid, "/", "nz", (int *) &infile.nz, 1 )) < 0)
HERR(routineName);
/* attributes */
if (( H5LTset_attribute_string(ncid, "/", "atmosID", atmos.ID)) < 0)
HERR(routineName);
if (( H5LTset_attribute_string(ncid, "/", "rev_id", mpi.rev_id) ) < 0)
HERR(routineName);
/* --- Definitions for the INPUT group --- */
/* attributes */
if ( atmos.NPRDactive > 0)
PRD_angle_dep = input.PRD_angle_dep;
else
PRD_angle_dep=0;
XRD = (input.XRD && atmos.NPRDactive > 0);
if (( H5LTset_attribute_uchar(ncid_input, ".", "Magneto_optical",
(unsigned char *) &input.magneto_optical, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_uchar(ncid_input, ".", "PRD_angle_dep",
(unsigned char *) &PRD_angle_dep, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_uchar(ncid_input, ".", "XRD",
(unsigned char *) &XRD, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_uchar(ncid_input, ".", "Background_polarization",
(unsigned char *) &input.backgr_pol, 1)) < 0) HERR(routineName);
switch (input.startJ) {
case UNKNOWN:
strcpy(startJ, "Unknown");
break;
case LTE_POPULATIONS:
strcpy(startJ, "LTE_POPULATIONS");
break;
case ZERO_RADIATION:
strcpy(startJ, "ZERO_RADIATION");
break;
case OLD_POPULATIONS:
strcpy(startJ, "OLD_POPULATIONS");
break;
case ESCAPE_PROBABILITY:
strcpy(startJ, "ESCAPE_PROBABILITY");
break;
case NEW_J:
strcpy(startJ, "NEW_J");
break;
case OLD_J:
strcpy(startJ, "OLD_J");
break;
}
if (( H5LTset_attribute_string(ncid_input, ".", "Start_J", startJ)) < 0)
HERR(routineName);
switch (input.StokesMode) {
case NO_STOKES:
strcpy(StokesMode, "NO_STOKES");
break;
case FIELD_FREE:
strcpy(StokesMode, "FIELD_FREE");
break;
case POLARIZATION_FREE:
strcpy(StokesMode, "POLARIZATION_FREE");
break;
case FULL_STOKES:
strcpy(StokesMode, "FULL_STOKES");
break;
}
if (( H5LTset_attribute_string(ncid_input, ".", "Stokes_mode",
StokesMode) ) < 0) HERR(routineName);
switch (atmos.angleSet.set) {
case SET_VERTICAL:
strcpy(angleSet, "SET_VERTICAL");
break;
case SET_GL:
strcpy(angleSet, "SET_GL");
break;
case SET_A2:
strcpy(angleSet, "SET_A2");
break;
case SET_A4:
strcpy(angleSet, "SET_A4");
break;
case SET_A6:
strcpy(angleSet, "SET_A6");
break;
case SET_A8:
strcpy(angleSet, "SET_A8");
break;
case SET_B4:
strcpy(angleSet, "SET_B4");
break;
case SET_B6:
strcpy(angleSet, "SET_B6");
break;
case SET_B8:
strcpy(angleSet, "SET_B8");
break;
case NO_SET:
strcpy(angleSet, "NO_SET");
break;
}
if (( H5LTset_attribute_string(ncid_input, ".", "Angle_set",
angleSet) ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_input, ".", "Atmos_file",
input.atmos_input) ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_input, ".", "Abundances_file",
input.abund_input) ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_input, ".", "Kurucz_PF_data",
input.pfData) ) < 0) HERR(routineName);
if (( H5LTset_attribute_double(ncid_input, ".", "Iteration_limit",
&input.iterLimit, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_double(ncid_input, ".", "PRD_Iteration_limit",
&input.PRDiterLimit, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "N_max_iter",
&input.NmaxIter, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "Ng_delay",
&input.Ngdelay, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "Ng_order",
&input.Ngorder, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "Ng_period",
&input.Ngperiod, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "PRD_N_max_iter",
&input.PRD_NmaxIter, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "PRD_Ng_delay",
&input.PRD_Ngdelay, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "PRD_Ng_order",
&input.PRD_Ngorder, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "PRD_Ng_period",
&input.PRD_Ngperiod, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_double(ncid_input, ".", "Metallicity",
&input.metallicity, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_double(ncid_input, ".", "Lambda_reference",
&atmos.lambda_ref, 1) ) < 0) HERR(routineName);
/* --- Definitions for the ATMOS group --- */
/* dimensions */
if (( H5LTset_attribute_int(ncid_atmos, ".", "nhydr",
&atmos.H->Nlevel, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_atmos, ".", "nelements",
&atmos.Nelem, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_atmos, ".", "nrays",
&geometry.Nrays, 1) ) < 0) HERR(routineName);
/* variables*/
dims[0] = mpi.nx;
dims[1] = mpi.ny;
dims[2] = infile.nz;
if (( file_dspace = H5Screate_simple(3, dims, NULL) ) < 0) HERR(routineName);
if (( plist = H5Pcreate(H5P_DATASET_CREATE) ) < 0) HERR(routineName);
if (( H5Pset_fill_value(plist, H5T_NATIVE_FLOAT, &FILLVALUE) ) < 0)
HERR(routineName);
if (( H5Pset_alloc_time(plist, H5D_ALLOC_TIME_EARLY) ) < 0) HERR(routineName);
if (( H5Pset_fill_time(plist, H5D_FILL_TIME_ALLOC) ) < 0) HERR(routineName);
if (( io.in_atmos_T = H5Dcreate(ncid_atmos, "temperature", H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( io.in_atmos_vz = H5Dcreate(ncid_atmos, "velocity_z", H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( io.in_atmos_z = H5Dcreate(ncid_atmos, "height", H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5Pclose(plist) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
/* --- Write some data that does not depend on xi, yi, ATMOS group --- */
/* arrays of number of elements */
eweight = (double *) malloc(atmos.Nelem * sizeof(double));
eabund = (double *) malloc(atmos.Nelem * sizeof(double));
for (i=0; i < atmos.Nelem; i++) {
eweight[i] = atmos.elements[i].weight;
eabund[i] = atmos.elements[i].abund;
}
dims[0] = atmos.Nelem;
if (( H5LTmake_dataset(ncid_atmos, "element_weight", 1, dims,
H5T_NATIVE_DOUBLE, eweight) ) < 0) HERR(routineName);
if (( H5LTmake_dataset(ncid_atmos, "element_abundance", 1, dims,
H5T_NATIVE_DOUBLE, eabund) ) < 0) HERR(routineName);
/* Not writing element_id for now
dims[1] = strlen;
if (( H5LTmake_dataset(ncid_atmos, "element_id", 2, dims,
H5T_C_S1, eID) ) < 0) HERR(routineName);
*/
free(eweight);
free(eabund);
dims[0] = geometry.Nrays;
if (( H5LTmake_dataset(ncid_atmos, "muz", 1, dims,
H5T_NATIVE_DOUBLE, geometry.muz) ) < 0) HERR(routineName);
if (( H5LTmake_dataset(ncid_atmos, "wmu", 1, dims,
H5T_NATIVE_DOUBLE, geometry.wmu) ) < 0) HERR(routineName);
x = (double *) malloc(mpi.nx * sizeof(double));
y = (double *) malloc(mpi.ny * sizeof(double));
for (i=0; i < mpi.nx; i++) x[i] = infile.x[mpi.xnum[i]];
for (i=0; i < mpi.ny; i++) y[i] = infile.y[mpi.ynum[i]];
dims[0] = mpi.nx;
if (( H5LTmake_dataset(ncid_atmos, "x", 1, dims,
H5T_NATIVE_DOUBLE, x) ) < 0) HERR(routineName);
dims[0] = mpi.ny;
if (( H5LTmake_dataset(ncid_atmos, "y", 1, dims,
H5T_NATIVE_DOUBLE, y) ) < 0) HERR(routineName);
free(x);
free(y);
/* attributes */
if (( H5LTset_attribute_uchar(ncid_atmos, ".", "moving",
(unsigned char *) &atmos.moving, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_uchar(ncid_atmos, ".", "stokes",
(unsigned char *) &atmos.Stokes, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_atmos, "temperature", "units",
"K") ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_atmos, "velocity_z", "units",
"m s^-1") ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_atmos, "height", "units",
"m") ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_atmos, "element_weight", "units",
"atomic_mass_units") ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_atmos, "x", "units",
"m") ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_atmos, "y", "units",
"m") ) < 0) HERR(routineName);
/* --- Definitions for the MPI group --- */
/* dimensions */
if (( H5LTset_attribute_int(ncid_mpi, ".", "nprocesses",
&mpi.size, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_mpi, ".", "niterations",
&NMaxIter, 1) ) < 0) HERR(routineName);
/* variables*/
dims[0] = mpi.nx;
if (( H5LTmake_dataset(ncid_mpi, XNUM_NAME, 1, dims,
H5T_NATIVE_INT, mpi.xnum) ) < 0) HERR(routineName);
dims[0] = mpi.ny;
if (( H5LTmake_dataset(ncid_mpi, YNUM_NAME, 1, dims,
H5T_NATIVE_INT, mpi.ynum) ) < 0) HERR(routineName);
dims[0] = mpi.nx;
dims[1] = mpi.ny;
if (( file_dspace = H5Screate_simple(2, dims, NULL) ) < 0) HERR(routineName);
if (( plist = H5Pcreate(H5P_DATASET_CREATE) ) < 0) HERR(routineName);
if (( H5Pset_fill_value(plist, H5T_NATIVE_FLOAT, &FILLVALUE) ) < 0)
HERR(routineName);
if (( H5Pset_alloc_time(plist, H5D_ALLOC_TIME_EARLY) ) < 0) HERR(routineName);
if (( H5Pset_fill_time(plist, H5D_FILL_TIME_ALLOC) ) < 0) HERR(routineName);
if (( io.in_mpi_tm = H5Dcreate(ncid_mpi, TASK_MAP, H5T_NATIVE_LONG,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( io.in_mpi_tn = H5Dcreate(ncid_mpi, TASK_NUMBER, H5T_NATIVE_LONG,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( io.in_mpi_it = H5Dcreate(ncid_mpi, ITER_NAME, H5T_NATIVE_LONG,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( io.in_mpi_conv = H5Dcreate(ncid_mpi, CONV_NAME, H5T_NATIVE_LONG,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( io.in_mpi_dm = H5Dcreate(ncid_mpi, DM_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( io.in_mpi_zc = H5Dcreate(ncid_mpi, ZC_NAME, H5T_NATIVE_INT,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5Pclose(plist) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
dims[0] = mpi.nx;
dims[1] = mpi.ny;
dims[2] = NMaxIter;
if (( file_dspace = H5Screate_simple(3, dims, NULL) ) < 0) HERR(routineName);
if (( plist = H5Pcreate(H5P_DATASET_CREATE) ) < 0) HERR(routineName);
if (( H5Pset_fill_value(plist, H5T_NATIVE_FLOAT, &FILLVALUE) ) < 0)
HERR(routineName);
if (( H5Pset_alloc_time(plist, H5D_ALLOC_TIME_EARLY) ) < 0) HERR(routineName);
if (( H5Pset_fill_time(plist, H5D_FILL_TIME_ALLOC) ) < 0) HERR(routineName);
if (( io.in_mpi_dmh = H5Dcreate(ncid_mpi, DMH_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5Pclose(plist) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
/* attributes */
if (( H5LTset_attribute_int(ncid_mpi, ".", "x_start",
&input.p15d_x0, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_mpi, ".", "x_end",
&input.p15d_x1, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_mpi, ".", "x_step",
&input.p15d_xst, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_mpi, ".", "y_start",
&input.p15d_y0, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_mpi, ".", "y_end",
&input.p15d_y1, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_mpi, ".", "y_step",
&input.p15d_yst, 1) ) < 0) HERR(routineName);
/* Tiago: most of the arrays involving Ntasks or rank as index are not
currently being written. They should eventually be migrated into
arrays of [ix, iy] and be written for each task. This is to
avoid causing problems with pool mode, where these quantities are
not known from the start.
*/
/* Flush ensures file is created in case of crash */
if (( H5Fflush(ncid, H5F_SCOPE_LOCAL) ) < 0) HERR(routineName);
/* --- Copy stuff to the IO data struct --- */
io.in_ncid = ncid;
io.in_input_ncid = ncid_input;
io.in_atmos_ncid = ncid_atmos;
io.in_mpi_ncid = ncid_mpi;
return;
}
int
main(void)
{
hid_t src_sid = -1; /* source dataset's dataspace ID */
hid_t src_dcplid = -1; /* source dataset property list ID */
hid_t vds_sid = -1; /* VDS dataspace ID */
hid_t vds_dcplid = -1; /* VDS dataset property list ID */
hid_t fid = -1; /* HDF5 file ID */
hid_t did = -1; /* dataset ID */
hid_t msid = -1; /* memory dataspace ID */
hid_t fsid = -1; /* file dataspace ID */
hsize_t extent[RANK]; /* source dataset extents */
hsize_t start[RANK]; /* starting point for hyperslab */
hsize_t stride[RANK]; /* hypserslab stride */
hsize_t count[RANK]; /* hypserslab count */
int map_start = -1; /* starting point in the VDS map */
int *buffer = NULL; /* data buffer */
int value = -1; /* value written to datasets */
hsize_t n = 0; /* number of elements in a plane */
int i; /* iterator */
int j; /* iterator */
int k; /* iterator */
/* Start by creating the virtual dataset (VDS) dataspace and creation
* property list. The individual source datasets are then created
* and the VDS map (stored in the VDS property list) is updated.
*/
/* Create VDS dcpl */
if((vds_dcplid = H5Pcreate(H5P_DATASET_CREATE)) < 0)
UC_ERROR
if(H5Pset_fill_value(vds_dcplid, UC_5_VDS_DATATYPE,
&UC_5_VDS_FILL_VALUE) < 0)
UC_ERROR
/* Create VDS dataspace */
if((vds_sid = H5Screate_simple(RANK, UC_5_VDS_DIMS,
UC_5_VDS_MAX_DIMS)) < 0)
UC_ERROR
/*********************************
* Map source files and datasets *
*********************************/
/* Hyperslab array setup */
start[0] = 0;
start[1] = 0;
start[2] = 0;
map_start = 0;
stride[0] = UC_5_N_SOURCES;
stride[1] = 1;
stride[2] = 1;
count[0] = H5S_UNLIMITED;
count[1] = 1;
count[2] = 1;
extent[0] = UC_5_SRC_PLANES;
extent[1] = UC_5_HEIGHT;
extent[2] = UC_5_WIDTH;
for(i = 0; i < UC_5_N_SOURCES; i++) {
/* source dataset dcpl */
if((src_dcplid = H5Pcreate(H5P_DATASET_CREATE)) < 0)
UC_ERROR
if(H5Pset_chunk(src_dcplid, RANK, UC_5_PLANE) < 0)
UC_ERROR
if(H5Pset_fill_value(src_dcplid, UC_5_SOURCE_DATATYPE,
&UC_5_FILL_VALUES[i]) < 0)
UC_ERROR
if(H5Pset_deflate(src_dcplid, COMPRESSION_LEVEL) < 0)
UC_ERROR
/* Create source file, dataspace, and dataset */
if((fid = H5Fcreate(UC_5_FILE_NAMES[i], H5F_ACC_TRUNC,
H5P_DEFAULT, H5P_DEFAULT)) < 0)
UC_ERROR
if((src_sid = H5Screate_simple(RANK, UC_5_SOURCE_DIMS,
UC_5_SOURCE_MAX_DIMS)) < 0)
UC_ERROR
if((did = H5Dcreate2(fid, UC_5_SOURCE_DSET_NAME,
UC_5_SOURCE_DATATYPE, src_sid,
H5P_DEFAULT, src_dcplid, H5P_DEFAULT)) < 0)
UC_ERROR
/* Set the dataset's extent */
if(H5Dset_extent(did, extent) < 0)
UC_ERROR
/* Create a data buffer that represents a plane */
n = UC_5_PLANE[1] * UC_5_PLANE[2];
if(NULL == (buffer = (int *)malloc(n * sizeof(int))))
UC_ERROR
/* Create the memory dataspace */
if((msid = H5Screate_simple(RANK, UC_5_PLANE, NULL)) < 0)
UC_ERROR
/* Get the file dataspace */
if((fsid = H5Dget_space(did)) < 0)
UC_ERROR
/* Write planes to the dataset */
for(j = 0; j < UC_5_SRC_PLANES; j++) {
value = ((i + 1) * 10) + j;
for(k = 0; k < n; k++)
buffer[k] = value;
start[0] = j;
start[1] = 0;
start[2] = 0;
if(H5Sselect_hyperslab(fsid, H5S_SELECT_SET, start, NULL, UC_5_PLANE, NULL) < 0)
UC_ERROR
if(H5Dwrite(did, H5T_NATIVE_INT, msid, fsid, H5P_DEFAULT, buffer) < 0)
UC_ERROR
} /* end for */
/* set up hyperslabs for source and destination datasets */
start[0] = 0;
start[1] = 0;
start[2] = 0;
if(H5Sselect_hyperslab(src_sid, H5S_SELECT_SET, start, NULL,
UC_5_SOURCE_MAX_DIMS, NULL) < 0)
UC_ERROR
start[0] = map_start;
if(H5Sselect_hyperslab(vds_sid, H5S_SELECT_SET, start, stride,
count, UC_5_PLANE) < 0)
UC_ERROR
map_start += 1;
/* Add VDS mapping */
if(H5Pset_virtual(vds_dcplid, vds_sid, UC_5_FILE_NAMES[i],
UC_5_SOURCE_DSET_PATH, src_sid) < 0)
UC_ERROR
/* close */
if(H5Sclose(msid) < 0)
UC_ERROR
if(H5Sclose(fsid) < 0)
UC_ERROR
if(H5Sclose(src_sid) < 0)
UC_ERROR
if(H5Pclose(src_dcplid) < 0)
UC_ERROR
if(H5Dclose(did) < 0)
UC_ERROR
if(H5Fclose(fid) < 0)
UC_ERROR
free(buffer);
} /* end for */
/*******************
* Create VDS file *
*******************/
/* file */
if((fid = H5Fcreate(UC_5_VDS_FILE_NAME, H5F_ACC_TRUNC,
H5P_DEFAULT, H5P_DEFAULT)) < 0)
UC_ERROR
/* dataset */
if((did = H5Dcreate2(fid, UC_5_VDS_DSET_NAME, UC_5_VDS_DATATYPE, vds_sid,
H5P_DEFAULT, vds_dcplid, H5P_DEFAULT)) < 0)
UC_ERROR
/* close */
if(H5Pclose(vds_dcplid) < 0)
UC_ERROR
if(H5Sclose(vds_sid) < 0)
UC_ERROR
if(H5Dclose(did) < 0)
UC_ERROR
if(H5Fclose(fid) < 0)
UC_ERROR
return EXIT_SUCCESS;
error:
H5E_BEGIN_TRY {
if(src_sid >= 0)
(void)H5Sclose(src_sid);
if(src_dcplid >= 0)
(void)H5Pclose(src_dcplid);
if(vds_sid >= 0)
(void)H5Sclose(vds_sid);
if(vds_dcplid >= 0)
(void)H5Pclose(vds_dcplid);
if(fid >= 0)
(void)H5Fclose(fid);
if(did >= 0)
(void)H5Dclose(did);
if(msid >= 0)
(void)H5Sclose(msid);
if(fsid >= 0)
(void)H5Sclose(fsid);
if(buffer != NULL)
free(buffer);
} H5E_END_TRY
return EXIT_FAILURE;
} /* end main() */
void pyne::Material::write_hdf5(std::string filename, std::string datapath,
std::string nucpath, float row, int chunksize) {
int row_num = (int) row;
// Turn off annoying HDF5 errors
H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
//Set file access properties so it closes cleanly
hid_t fapl;
fapl = H5Pcreate(H5P_FILE_ACCESS);
H5Pset_fclose_degree(fapl,H5F_CLOSE_STRONG);
// Create new/open datafile.
hid_t db;
if (pyne::file_exists(filename)) {
bool ish5 = H5Fis_hdf5(filename.c_str());
if (!ish5)
throw h5wrap::FileNotHDF5(filename);
db = H5Fopen(filename.c_str(), H5F_ACC_RDWR, fapl);
}
else
db = H5Fcreate(filename.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, fapl);
//
// Read in nuclist if available, write it out if not
//
bool nucpath_exists = h5wrap::path_exists(db, nucpath);
std::vector<int> nuclides;
int nuc_size;
hsize_t nuc_dims[1];
if (nucpath_exists) {
nuclides = h5wrap::h5_array_to_cpp_vector_1d<int>(db, nucpath, H5T_NATIVE_INT);
nuc_size = nuclides.size();
nuc_dims[0] = nuc_size;
} else {
nuclides = std::vector<int>();
for (pyne::comp_iter i = comp.begin(); i != comp.end(); i++)
nuclides.push_back(i->first);
nuc_size = nuclides.size();
// Create the data if it doesn't exist
int nuc_data [nuc_size];
for (int n = 0; n != nuc_size; n++)
nuc_data[n] = nuclides[n];
nuc_dims[0] = nuc_size;
hid_t nuc_space = H5Screate_simple(1, nuc_dims, NULL);
hid_t nuc_set = H5Dcreate2(db, nucpath.c_str(), H5T_NATIVE_INT, nuc_space,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Dwrite(nuc_set, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, nuc_data);
H5Fflush(db, H5F_SCOPE_GLOBAL);
};
//
// Write out the data itself to the file
//
hid_t data_set, data_space, data_hyperslab;
int data_rank = 1;
hsize_t data_dims[1] = {1};
hsize_t data_max_dims[1] = {H5S_UNLIMITED};
hsize_t data_offset[1] = {0};
size_t material_struct_size = sizeof(pyne::material_struct) + sizeof(double)*nuc_size;
hid_t desc = H5Tcreate(H5T_COMPOUND, material_struct_size);
hid_t comp_values_array_type = H5Tarray_create2(H5T_NATIVE_DOUBLE, 1, nuc_dims);
// make the data table type
H5Tinsert(desc, "mass", HOFFSET(pyne::material_struct, mass), H5T_NATIVE_DOUBLE);
H5Tinsert(desc, "density", HOFFSET(pyne::material_struct, density),
H5T_NATIVE_DOUBLE);
H5Tinsert(desc, "atoms_per_molecule", HOFFSET(pyne::material_struct, atoms_per_mol),
H5T_NATIVE_DOUBLE);
H5Tinsert(desc, "comp", HOFFSET(pyne::material_struct, comp),
comp_values_array_type);
material_struct * mat_data = new material_struct[material_struct_size];
(*mat_data).mass = mass;
(*mat_data).density = density;
(*mat_data).atoms_per_mol = atoms_per_molecule;
for (int n = 0; n != nuc_size; n++) {
if (0 < comp.count(nuclides[n]))
(*mat_data).comp[n] = comp[nuclides[n]];
else
(*mat_data).comp[n] = 0.0;
};
// get / make the data set
bool datapath_exists = h5wrap::path_exists(db, datapath);
if (datapath_exists) {
data_set = H5Dopen2(db, datapath.c_str(), H5P_DEFAULT);
data_space = H5Dget_space(data_set);
data_rank = H5Sget_simple_extent_dims(data_space, data_dims, data_max_dims);
// Determine the row size.
if (std::signbit(row))
row_num = data_dims[0] + row; // careful, row is negative
if (data_dims[0] <= row_num) {
// row == -0, extend to data set so that we can append, or
// row_num is larger than current dimension, resize to accomodate.
data_dims[0] = row_num + 1;
H5Dset_extent(data_set, data_dims);
}
data_offset[0] = row_num;
} else {
// Get full space
data_space = H5Screate_simple(1, data_dims, data_max_dims);
// Make data set properties to enable chunking
hid_t data_set_params = H5Pcreate(H5P_DATASET_CREATE);
hsize_t chunk_dims[1] ={chunksize};
H5Pset_chunk(data_set_params, 1, chunk_dims);
H5Pset_deflate(data_set_params, 1);
material_struct * data_fill_value = new material_struct[material_struct_size];
(*data_fill_value).mass = -1.0;
(*data_fill_value).density= -1.0;
(*data_fill_value).atoms_per_mol = -1.0;
for (int n = 0; n != nuc_size; n++)
(*data_fill_value).comp[n] = 0.0;
H5Pset_fill_value(data_set_params, desc, &data_fill_value);
// Create the data set
data_set = H5Dcreate2(db, datapath.c_str(), desc, data_space, H5P_DEFAULT,
data_set_params, H5P_DEFAULT);
H5Dset_extent(data_set, data_dims);
// Add attribute pointing to nuc path
hid_t nuc_attr_type = H5Tcopy(H5T_C_S1);
H5Tset_size(nuc_attr_type, nucpath.length());
hid_t nuc_attr_space = H5Screate(H5S_SCALAR);
hid_t nuc_attr = H5Acreate2(data_set, "nucpath", nuc_attr_type, nuc_attr_space,
H5P_DEFAULT, H5P_DEFAULT);
H5Awrite(nuc_attr, nuc_attr_type, nucpath.c_str());
H5Fflush(db, H5F_SCOPE_GLOBAL);
// Remember to de-allocate
delete[] data_fill_value;
};
// Get the data hyperslab
data_hyperslab = H5Dget_space(data_set);
hsize_t data_count[1] = {1};
H5Sselect_hyperslab(data_hyperslab, H5S_SELECT_SET, data_offset, NULL, data_count, NULL);
// Get a memory space for writing
hid_t mem_space = H5Screate_simple(1, data_count, data_max_dims);
// Write the row...
H5Dwrite(data_set, desc, mem_space, data_hyperslab, H5P_DEFAULT, mat_data);
// Close out the Dataset
H5Fflush(db, H5F_SCOPE_GLOBAL);
H5Dclose(data_set);
H5Sclose(data_space);
H5Tclose(desc);
//
// Write out the metadata to the file
//
std::string attrpath = datapath + "_metadata";
hid_t metadatapace, attrtype, metadataet, metadatalab, attrmemspace;
int attrrank;
attrtype = H5Tvlen_create(H5T_NATIVE_CHAR);
// get / make the data set
bool attrpath_exists = h5wrap::path_exists(db, attrpath);
if (attrpath_exists) {
metadataet = H5Dopen2(db, attrpath.c_str(), H5P_DEFAULT);
metadatapace = H5Dget_space(metadataet);
attrrank = H5Sget_simple_extent_dims(metadatapace, data_dims, data_max_dims);
if (data_dims[0] <= row_num) {
// row == -0, extend to data set so that we can append, or
// row_num is larger than current dimension, resize to accomodate.
data_dims[0] = row_num + 1;
H5Dset_extent(metadataet, data_dims);
}
data_offset[0] = row_num;
} else {
hid_t metadataetparams;
hsize_t attrchunkdims [1];
// Make data set properties to enable chunking
metadataetparams = H5Pcreate(H5P_DATASET_CREATE);
attrchunkdims[0] = chunksize;
H5Pset_chunk(metadataetparams, 1, attrchunkdims);
H5Pset_deflate(metadataetparams, 1);
hvl_t attrfillvalue [1];
attrfillvalue[0].len = 3;
attrfillvalue[0].p = (char *) "{}\n";
H5Pset_fill_value(metadataetparams, attrtype, &attrfillvalue);
// make dataset
metadatapace = H5Screate_simple(1, data_dims, data_max_dims);
metadataet = H5Dcreate2(db, attrpath.c_str(), attrtype, metadatapace,
H5P_DEFAULT, metadataetparams, H5P_DEFAULT);
H5Dset_extent(metadataet, data_dims);
};
// set the attr string
hvl_t attrdata [1];
Json::FastWriter writer;
std::string metadatatr = writer.write(metadata);
attrdata[0].p = (char *) metadatatr.c_str();
attrdata[0].len = metadatatr.length();
// write the attr
metadatalab = H5Dget_space(metadataet);
H5Sselect_hyperslab(metadatalab, H5S_SELECT_SET, data_offset, NULL, data_count, NULL);
attrmemspace = H5Screate_simple(1, data_count, data_max_dims);
H5Dwrite(metadataet, attrtype, attrmemspace, metadatalab, H5P_DEFAULT, attrdata);
// close attr data objects
H5Fflush(db, H5F_SCOPE_GLOBAL);
H5Dclose(metadataet);
H5Sclose(metadatapace);
H5Tclose(attrtype);
// Close out the HDF5 file
H5Fclose(db);
// Remember the milk!
// ...by which I mean to deallocate
delete[] mat_data;
};
int
main(void)
{
hid_t faplid = -1; /* file access property list ID (all files) */
hid_t src_sid = -1; /* source dataset's dataspace ID */
hid_t src_dcplid = -1; /* source dataset property list ID */
hid_t vds_sid = -1; /* VDS dataspace ID */
hid_t vds_dcplid = -1; /* VDS dataset property list ID */
hid_t fid = -1; /* HDF5 file ID */
hid_t did = -1; /* dataset ID */
hsize_t start[RANK]; /* starting point for hyperslab */
int map_start = -1; /* starting point in the VDS map */
int i; /* iterator */
/* Start by creating the virtual dataset (VDS) dataspace and creation
* property list. The individual source datasets are then created
* and the VDS map (stored in the VDS property list) is updated.
*/
/* Create VDS dcpl */
if((vds_dcplid = H5Pcreate(H5P_DATASET_CREATE)) < 0)
TEST_ERROR
if(H5Pset_fill_value(vds_dcplid, VDS_DATATYPE,
&VDS_FILL_VALUE) < 0)
TEST_ERROR
/* Create VDS dataspace */
if((vds_sid = H5Screate_simple(RANK, VDS_DIMS,
VDS_MAX_DIMS)) < 0)
TEST_ERROR
/************************************
* Create source files and datasets *
************************************/
start[0] = 0;
start[1] = 0;
start[2] = 0;
map_start = 0;
/* All SWMR files need to use the latest file format */
if((faplid = H5Pcreate(H5P_FILE_ACCESS)) < 0)
TEST_ERROR
if(H5Pset_libver_bounds(faplid, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0)
TEST_ERROR
for(i = 0; i < N_SOURCES; i++) {
/* source dataset dcpl */
if((src_dcplid = H5Pcreate(H5P_DATASET_CREATE)) < 0)
TEST_ERROR
if(H5Pset_chunk(src_dcplid, RANK, PLANES[i]) < 0)
TEST_ERROR
if(H5Pset_fill_value(src_dcplid, SOURCE_DATATYPE,
&FILL_VALUES[i]) < 0)
TEST_ERROR
/* Use a mix of compressed and uncompressed datasets */
if(0 != i % 2)
if(H5Pset_deflate(src_dcplid, COMPRESSION_LEVEL) < 0)
TEST_ERROR
/* Create source file, dataspace, and dataset */
if((fid = H5Fcreate(FILE_NAMES[i], H5F_ACC_TRUNC,
H5P_DEFAULT, faplid)) < 0)
TEST_ERROR
if((src_sid = H5Screate_simple(RANK, DIMS[i],
MAX_DIMS[i])) < 0)
TEST_ERROR
if((did = H5Dcreate2(fid, SOURCE_DSET_NAME,
SOURCE_DATATYPE, src_sid,
H5P_DEFAULT, src_dcplid, H5P_DEFAULT)) < 0)
TEST_ERROR
/* set up hyperslabs for source and destination datasets */
start[1] = 0;
if(H5Sselect_hyperslab(src_sid, H5S_SELECT_SET, start, NULL,
MAX_DIMS[i], NULL) < 0)
TEST_ERROR
start[1] = map_start;
if(H5Sselect_hyperslab(vds_sid, H5S_SELECT_SET, start, NULL,
MAX_DIMS[i], NULL) < 0)
TEST_ERROR
map_start += PLANES[i][1];
/* Add VDS mapping */
if(H5Pset_virtual(vds_dcplid, vds_sid, FILE_NAMES[i],
SOURCE_DSET_PATH, src_sid) < 0)
TEST_ERROR
/* close */
if(H5Sclose(src_sid) < 0)
TEST_ERROR
if(H5Pclose(src_dcplid) < 0)
TEST_ERROR
if(H5Dclose(did) < 0)
TEST_ERROR
if(H5Fclose(fid) < 0)
TEST_ERROR
} /* end for */
/*******************
* Create VDS file *
*******************/
/* file */
if((fid = H5Fcreate(VDS_FILE_NAME, H5F_ACC_TRUNC,
H5P_DEFAULT, faplid)) < 0)
TEST_ERROR
/* dataset */
if((did = H5Dcreate2(fid, VDS_DSET_NAME, VDS_DATATYPE, vds_sid,
H5P_DEFAULT, vds_dcplid, H5P_DEFAULT)) < 0)
TEST_ERROR
/* close */
if(H5Pclose(faplid) < 0)
TEST_ERROR
if(H5Pclose(vds_dcplid) < 0)
TEST_ERROR
if(H5Sclose(vds_sid) < 0)
TEST_ERROR
if(H5Dclose(did) < 0)
TEST_ERROR
if(H5Fclose(fid) < 0)
TEST_ERROR
return EXIT_SUCCESS;
error:
H5E_BEGIN_TRY {
if(faplid >= 0)
(void)H5Pclose(faplid);
if(src_sid >= 0)
(void)H5Sclose(src_sid);
if(src_dcplid >= 0)
(void)H5Pclose(src_dcplid);
if(vds_sid >= 0)
(void)H5Sclose(vds_sid);
if(vds_dcplid >= 0)
(void)H5Pclose(vds_dcplid);
if(fid >= 0)
(void)H5Fclose(fid);
if(did >= 0)
(void)H5Dclose(did);
} H5E_END_TRY
return EXIT_FAILURE;
} /* end main */
int
main (void)
{
hid_t file; /* handles */
hid_t dataspace, dataset;
hid_t filespace;
hid_t cparms;
hsize_t dims[2] = { 3, 3}; /*
* dataset dimensions
* at the creation time
*/
hsize_t dims1[2] = { 3, 3}; /* data1 dimensions */
hsize_t dims2[2] = { 7, 1}; /* data2 dimensions */
hsize_t dims3[2] = { 2, 2}; /* data3 dimensions */
hsize_t maxdims[2] = {H5S_UNLIMITED, H5S_UNLIMITED};
hsize_t chunk_dims[2] ={2, 5};
hsize_t size[2];
hsize_t offset[2];
herr_t status;
int data1[3][3] = { {1, 1, 1}, /* data to write */
{1, 1, 1},
{1, 1, 1} };
int data2[7] = { 2, 2, 2, 2, 2, 2, 2};
int data3[2][2] = { {3, 3},
{3, 3} };
int fillvalue = 0;
/*
* Create the data space with unlimited dimensions.
*/
dataspace = H5Screate_simple(RANK, dims, maxdims);
/*
* Create a new file. If file exists its contents will be overwritten.
*/
file = H5Fcreate(H5FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Modify dataset creation properties, i.e. enable chunking.
*/
cparms = H5Pcreate(H5P_DATASET_CREATE);
status = H5Pset_chunk( cparms, RANK, chunk_dims);
status = H5Pset_fill_value (cparms, H5T_NATIVE_INT, &fillvalue );
/*
* Create a new dataset within the file using cparms
* creation properties.
*/
dataset = H5Dcreate2(file, DATASETNAME, H5T_NATIVE_INT, dataspace, H5P_DEFAULT,
cparms, H5P_DEFAULT);
/*
* Extend the dataset. This call assures that dataset is at least 3 x 3.
*/
size[0] = 3;
size[1] = 3;
status = H5Dset_extent(dataset, size);
/*
* Select a hyperslab.
*/
filespace = H5Dget_space(dataset);
offset[0] = 0;
offset[1] = 0;
status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL,
dims1, NULL);
/*
* Write the data to the hyperslab.
*/
status = H5Dwrite(dataset, H5T_NATIVE_INT, dataspace, filespace,
H5P_DEFAULT, data1);
/*
* Extend the dataset. Dataset becomes 10 x 3.
*/
dims[0] = dims1[0] + dims2[0];
size[0] = dims[0];
size[1] = dims[1];
status = H5Dset_extent(dataset, size);
/*
* Select a hyperslab.
*/
filespace = H5Dget_space(dataset);
offset[0] = 3;
offset[1] = 0;
status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL,
dims2, NULL);
/*
* Define memory space
*/
dataspace = H5Screate_simple(RANK, dims2, NULL);
/*
* Write the data to the hyperslab.
*/
status = H5Dwrite(dataset, H5T_NATIVE_INT, dataspace, filespace,
H5P_DEFAULT, data2);
/*
* Extend the dataset. Dataset becomes 10 x 5.
*/
dims[1] = dims1[1] + dims3[1];
size[0] = dims[0];
size[1] = dims[1];
status = H5Dset_extent(dataset, size);
/*
* Select a hyperslab
*/
filespace = H5Dget_space(dataset);
offset[0] = 0;
offset[1] = 3;
status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL,
dims3, NULL);
/*
* Define memory space.
*/
dataspace = H5Screate_simple(RANK, dims3, NULL);
/*
* Write the data to the hyperslab.
*/
status = H5Dwrite(dataset, H5T_NATIVE_INT, dataspace, filespace,
H5P_DEFAULT, data3);
/*
* Resulting dataset
*
* 1 1 1 3 3
* 1 1 1 3 3
* 1 1 1 0 0
* 2 0 0 0 0
* 2 0 0 0 0
* 2 0 0 0 0
* 2 0 0 0 0
* 2 0 0 0 0
* 2 0 0 0 0
* 2 0 0 0 0
*/
/*
* Close/release resources.
*/
H5Dclose(dataset);
H5Sclose(dataspace);
H5Sclose(filespace);
H5Pclose(cparms);
H5Fclose(file);
return 0;
}
herr_t H5TBOmake_table( const char *table_title,
hid_t loc_id,
const char *dset_name,
char *version,
const char *class_,
hid_t type_id,
hsize_t nrecords,
hsize_t chunk_size,
void *fill_data,
int compress,
char *complib,
int shuffle,
int fletcher32,
const void *data )
{
hid_t dataset_id;
hid_t space_id;
hid_t plist_id;
hsize_t dims[1];
hsize_t dims_chunk[1];
hsize_t maxdims[1] = { H5S_UNLIMITED };
unsigned int cd_values[7];
int blosc_compcode;
char *blosc_compname = NULL;
dims[0] = nrecords;
dims_chunk[0] = chunk_size;
/* Create a simple data space with unlimited size */
if ( (space_id = H5Screate_simple( 1, dims, maxdims )) < 0 )
return -1;
/* Modify dataset creation properties, i.e. enable chunking */
plist_id = H5Pcreate (H5P_DATASET_CREATE);
if ( H5Pset_chunk ( plist_id, 1, dims_chunk ) < 0 )
return -1;
/* Set the fill value using a struct as the data type. */
if ( fill_data)
{
if ( H5Pset_fill_value( plist_id, type_id, fill_data ) < 0 )
return -1;
}
else {
if ( H5Pset_fill_time(plist_id, H5D_FILL_TIME_ALLOC) < 0 )
return -1;
}
/*
Dataset creation property list is modified to use filters
*/
/* Fletcher must be first */
if (fletcher32) {
if ( H5Pset_fletcher32( plist_id) < 0 )
return -1;
}
/* Then shuffle (blosc shuffles inplace) */
if ((shuffle && compress) && (strncmp(complib, "blosc", 5) != 0)) {
if ( H5Pset_shuffle( plist_id) < 0 )
return -1;
}
/* Finally compression */
if ( compress )
{
cd_values[0] = compress;
cd_values[1] = (int)(atof(version) * 10);
cd_values[2] = Table;
/* The default compressor in HDF5 (zlib) */
if (strcmp(complib, "zlib") == 0) {
if ( H5Pset_deflate( plist_id, compress) < 0 )
return -1;
}
/* The Blosc compressor does accept parameters */
else if (strcmp(complib, "blosc") == 0) {
cd_values[4] = compress;
cd_values[5] = shuffle;
if ( H5Pset_filter( plist_id, FILTER_BLOSC, H5Z_FLAG_OPTIONAL, 6, cd_values) < 0 )
return -1;
}
/* The Blosc compressor can use other compressors */
else if (strncmp(complib, "blosc:", 6) == 0) {
cd_values[4] = compress;
cd_values[5] = shuffle;
blosc_compname = complib + 6;
blosc_compcode = blosc_compname_to_compcode(blosc_compname);
cd_values[6] = blosc_compcode;
if ( H5Pset_filter( plist_id, FILTER_BLOSC, H5Z_FLAG_OPTIONAL, 7, cd_values) < 0 )
return -1;
}
/* The LZO compressor does accept parameters */
else if (strcmp(complib, "lzo") == 0) {
if ( H5Pset_filter( plist_id, FILTER_LZO, H5Z_FLAG_OPTIONAL, 3, cd_values) < 0 )
return -1;
}
/* The bzip2 compress does accept parameters */
else if (strcmp(complib, "bzip2") == 0) {
if ( H5Pset_filter( plist_id, FILTER_BZIP2, H5Z_FLAG_OPTIONAL, 3, cd_values) < 0 )
return -1;
}
else {
/* Compression library not supported */
return -1;
}
}
/* Create the dataset. */
if ( (dataset_id = H5Dcreate( loc_id, dset_name, type_id, space_id,
H5P_DEFAULT, plist_id, H5P_DEFAULT )) < 0 )
goto out;
/* Only write if there is something to write */
if ( data )
{
/* Write data to the dataset. */
if ( H5Dwrite( dataset_id, type_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, data ) < 0 )
goto out;
}
/* Terminate access to the data space. */
if ( H5Sclose( space_id ) < 0 )
goto out;
/* End access to the property list */
if ( H5Pclose( plist_id ) < 0 )
goto out;
/* Return the object unique ID for future references */
return dataset_id;
/* error zone, gracefully close */
out:
H5E_BEGIN_TRY {
H5Dclose(dataset_id);
H5Sclose(space_id);
H5Pclose(plist_id);
} H5E_END_TRY;
return -1;
}
/*-------------------------------------------------------------------------
* Function: create_scale_offset_dset_long_long
*
* Purpose: Create a dataset of LONG LONG datatype with scale-offset
* filter
*
* Return: Success: 0
* Failure: -1
*
* Programmer: Neil Fortner
* 27 January 2011
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
int
create_scale_offset_dsets_long_long(hid_t fid, hid_t fsid, hid_t msid)
{
hid_t dataset = -1; /* dataset handles */
hid_t dcpl = -1;
long long data[NX][NY]; /* data to write */
long long fillvalue = -2;
hsize_t chunk[RANK] = {CHUNK0, CHUNK1};
int i, j;
/*
* Data and output buffer initialization.
*/
for (j = 0; j < NX; j++) {
for (i = 0; i < NY; i++)
data[j][i] = i + j;
}
/*
* 0 1 2 3 4 5
* 1 2 3 4 5 6
* 2 3 4 5 6 7
* 3 4 5 6 7 8
* 4 5 6 7 8 9
* 5 6 7 8 9 10
*/
/*
* Create the dataset creation property list, add the Scale-Offset
* filter, set the chunk size, and set the fill value.
*/
if((dcpl = H5Pcreate(H5P_DATASET_CREATE)) < 0)
TEST_ERROR
if(H5Pset_scaleoffset(dcpl, H5Z_SO_INT, H5Z_SO_INT_MINBITS_DEFAULT) < 0)
TEST_ERROR
if(H5Pset_chunk(dcpl, RANK, chunk) < 0)
TEST_ERROR
if(H5Pset_fill_value(dcpl, H5T_NATIVE_LLONG, &fillvalue) < 0)
TEST_ERROR
/*
* Create a new dataset within the file using defined dataspace, little
* endian datatype and default dataset creation properties.
*/
if((dataset = H5Dcreate2(fid, DATASETNAME12, H5T_STD_I64LE, fsid,
H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
TEST_ERROR
/*
* Write the data to the dataset using default transfer properties.
*/
if(H5Dwrite(dataset, H5T_NATIVE_LLONG, msid, fsid, H5P_DEFAULT, data) < 0)
TEST_ERROR
/* Close dataset */
if(H5Dclose(dataset) < 0)
TEST_ERROR
/* Now create a dataset with a big-endian type */
if((dataset = H5Dcreate2(fid, DATASETNAME13, H5T_STD_I64BE, fsid,
H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
TEST_ERROR
if(H5Dwrite(dataset, H5T_NATIVE_LLONG, msid, fsid, H5P_DEFAULT, data) < 0)
TEST_ERROR
if(H5Dclose(dataset) < 0)
TEST_ERROR
/*
* Close/release resources.
*/
if(H5Pclose(dcpl) < 0)
TEST_ERROR
return 0;
error:
H5E_BEGIN_TRY {
H5Pclose(dcpl);
H5Dclose(dataset);
} H5E_END_TRY;
return -1;
}
/*-------------------------------------------------------------------------
* Function: create_deflate_dsets_float
*
* Purpose: Create a dataset of FLOAT datatype with deflate filter
*
* Return: Success: 0
* Failure: -1
*
* Programmer: Raymond Lu
* 29 March 2011
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
int
create_deflate_dsets_float(hid_t fid, hid_t fsid, hid_t msid)
{
#ifdef H5_HAVE_FILTER_DEFLATE
hid_t dataset = -1; /* dataset handles */
hid_t dcpl = -1;
float data[NX][NY]; /* data to write */
float fillvalue = -2.2f;
hsize_t chunk[RANK] = {CHUNK0, CHUNK1};
int i, j;
/*
* Data and output buffer initialization.
*/
for (j = 0; j < NX; j++) {
for (i = 0; i < NY; i++)
data[j][i] = ((float)(i + j + 1))/3;
}
/*
* Create the dataset creation property list, add the Scale-Offset
* filter, set the chunk size, and set the fill value.
*/
if((dcpl = H5Pcreate(H5P_DATASET_CREATE)) < 0)
TEST_ERROR
if(H5Pset_deflate (dcpl, 6) < 0)
TEST_ERROR
if(H5Pset_chunk(dcpl, RANK, chunk) < 0)
TEST_ERROR
if(H5Pset_fill_value(dcpl, H5T_NATIVE_FLOAT, &fillvalue) < 0)
TEST_ERROR
/*
* Create a new dataset within the file using defined dataspace, little
* endian datatype and default dataset creation properties.
*/
if((dataset = H5Dcreate2(fid, DATASETNAME16, H5T_IEEE_F32LE, fsid,
H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
TEST_ERROR
/*
* Write the data to the dataset using default transfer properties.
*/
if(H5Dwrite(dataset, H5T_NATIVE_FLOAT, msid, fsid, H5P_DEFAULT, data) < 0)
TEST_ERROR
/* Close dataset */
if(H5Dclose(dataset) < 0)
TEST_ERROR
/* Now create a dataset with a big-endian type */
if((dataset = H5Dcreate2(fid, DATASETNAME17, H5T_IEEE_F32BE, fsid,
H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
TEST_ERROR
if(H5Dwrite(dataset, H5T_NATIVE_FLOAT, msid, fsid, H5P_DEFAULT, data) < 0)
TEST_ERROR
if(H5Dclose(dataset) < 0)
TEST_ERROR
/*
* Close/release resources.
*/
if(H5Pclose(dcpl) < 0)
TEST_ERROR
#else /* H5_HAVE_FILTER_DEFLATE */
const char *not_supported= "Deflate filter is not enabled. Can't create the dataset.";
puts(not_supported);
#endif /* H5_HAVE_FILTER_DEFLATE */
return 0;
#ifdef H5_HAVE_FILTER_DEFLATE
error:
H5E_BEGIN_TRY {
H5Pclose(dcpl);
H5Dclose(dataset);
} H5E_END_TRY;
return -1;
#endif /* H5_HAVE_FILTER_DEFLATE */
}
/* ------- begin -------------------------- init_aux_new.c -- --- */
void init_aux_new(void) {
/* Creates the HDF5 file for the auxiliary data */
const char routineName[] = "init_aux_new";
unsigned int *tmp;
double *tmp_double;
int i;
hid_t plist, ncid, file_dspace, ncid_atom, ncid_mol;
hid_t id_x, id_y, id_z, id_n, id_tmp;
hsize_t dims[4];
char group_name[ARR_STRLEN];
Atom *atom;
Molecule *molecule;
/* Create the file */
if (( plist = H5Pcreate(H5P_FILE_ACCESS) ) < 0) HERR(routineName);
if (( H5Pset_fapl_mpio(plist, mpi.comm, mpi.info) ) < 0) HERR(routineName);
if (( ncid = H5Fcreate(AUX_FILE, H5F_ACC_TRUNC, H5P_DEFAULT,
plist) ) < 0) HERR(routineName);
if (( H5Pclose(plist) ) < 0) HERR(routineName);
/* --- Definitions for the root group --- */
/* dimensions as attributes */
if (( H5LTset_attribute_int(ncid, "/", "nx", &mpi.nx, 1) ) < 0)
HERR(routineName);
if (( H5LTset_attribute_int(ncid, "/", "ny", &mpi.ny, 1) ) < 0)
HERR(routineName);
if (( H5LTset_attribute_int(ncid, "/", "nz", (int *) &infile.nz, 1 )) < 0)
HERR(routineName);
/* attributes */
if (( H5LTset_attribute_string(ncid, "/", "atmosID", atmos.ID)) < 0)
HERR(routineName);
if (( H5LTset_attribute_string(ncid, "/", "rev_id", mpi.rev_id) ) < 0)
HERR(routineName);
/* Create arrays for multiple-atom/molecule output */
io.aux_atom_ncid = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_mol_ncid = (hid_t *) malloc(atmos.Nactivemol * sizeof(hid_t));
if (input.p15d_wpop) {
io.aux_atom_pop = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_atom_poplte = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_mol_pop = (hid_t *) malloc(atmos.Nactivemol * sizeof(hid_t));
io.aux_mol_poplte = (hid_t *) malloc(atmos.Nactivemol * sizeof(hid_t));
}
if (input.p15d_wrates) {
io.aux_atom_RijL = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_atom_RjiL = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_atom_RijC = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_atom_RjiC = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
}
/* Fill value */
if (( plist = H5Pcreate(H5P_DATASET_CREATE) ) < 0) HERR(routineName);
if (( H5Pset_fill_value(plist, H5T_NATIVE_FLOAT, &FILLVALUE) ) < 0)
HERR(routineName);
if (( H5Pset_alloc_time(plist, H5D_ALLOC_TIME_EARLY) ) < 0) HERR(routineName);
if (( H5Pset_fill_time(plist, H5D_FILL_TIME_ALLOC) ) < 0) HERR(routineName);
/* --- Group loop over active ATOMS --- */
for (i=0; i < atmos.Nactiveatom; i++) {
atom = atmos.activeatoms[i];
/* Get group name */
sprintf(group_name, (atom->ID[1] == ' ') ? "atom_%.1s" : "atom_%.2s",
atom->ID);
if (( ncid_atom = H5Gcreate(ncid, group_name, H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT) ) < 0) HERR(routineName);
io.aux_atom_ncid[i] = ncid_atom;
/* --- dimensions as attributes --- */
if (( H5LTset_attribute_int(ncid_atom, ".", "nlevel",
&atom->Nlevel, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_atom, ".", "nline",
&atom->Nline, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_atom, ".", "ncontinuum",
&atom->Ncont, 1)) < 0) HERR(routineName);
/* --- dimension datasets --- */
dims[0] = mpi.nx;
if (( H5LTmake_dataset(ncid_atom, X_NAME, 1, dims, H5T_NATIVE_DOUBLE,
geometry.xscale) ) < 0) HERR(routineName);
if (( id_x = H5Dopen2(ncid_atom, X_NAME, H5P_DEFAULT)) < 0) HERR(routineName);
dims[0] = mpi.ny;
if (( H5LTmake_dataset(ncid_atom, Y_NAME, 1, dims, H5T_NATIVE_DOUBLE,
geometry.yscale) ) < 0) HERR(routineName);
if (( id_y = H5Dopen2(ncid_atom, Y_NAME, H5P_DEFAULT)) < 0) HERR(routineName);
dims[0] = infile.nz;
tmp_double = (double *) calloc(infile.nz , sizeof(double));
if (( H5LTmake_dataset(ncid_atom, ZOUT_NAME, 1, dims, H5T_NATIVE_DOUBLE,
tmp_double) ) < 0) HERR(routineName);
free(tmp_double);
if (( id_z = H5Dopen2(ncid_atom, ZOUT_NAME, H5P_DEFAULT)) < 0) HERR(routineName);
dims[0] = atom->Nlevel;
tmp = (unsigned int *) calloc(atom->Nlevel , sizeof(unsigned int));
if (( H5LTmake_dataset(ncid_atom, LEVEL_NAME, 1, dims, H5T_NATIVE_UINT,
tmp) ) < 0) HERR(routineName);
free(tmp);
dims[0] = atom->Nline;
tmp = (unsigned int *) calloc(atom->Nline , sizeof(unsigned int));
if (( H5LTmake_dataset(ncid_atom, LINE_NAME, 1, dims, H5T_NATIVE_UINT,
tmp) ) < 0) HERR(routineName);
free(tmp);
if (atom->Ncont > 0) {
dims[0] = atom->Ncont;
tmp = (unsigned int *) calloc(atom->Ncont , sizeof(unsigned int));
if (( H5LTmake_dataset(ncid_atom, CONT_NAME, 1, dims, H5T_NATIVE_UINT,
tmp) ) < 0) HERR(routineName);
free(tmp);
}
/* For compatibility with netCDF readers, only use dataset as dimension */
if (( H5LTset_attribute_string(ncid_atom, ZOUT_NAME, "NAME",
NETCDF_COMPAT) ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_atom, LEVEL_NAME, "NAME",
NETCDF_COMPAT) ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_atom, LINE_NAME, "NAME",
NETCDF_COMPAT) ) < 0) HERR(routineName);
if (atom->Ncont > 0) {
if (( H5LTset_attribute_string(ncid_atom, CONT_NAME, "NAME",
NETCDF_COMPAT) ) < 0) HERR(routineName);
}
/* --- variables --- */
dims[0] = atom->Nlevel;
dims[1] = mpi.nx;
dims[2] = mpi.ny;
dims[3] = infile.nz;
/* Populations */
if (input.p15d_wpop) {
if (( file_dspace = H5Screate_simple(4, dims, NULL) ) < 0)
HERR(routineName);
if (( id_n = H5Dopen2(ncid_atom, LEVEL_NAME,
H5P_DEFAULT)) < 0) HERR(routineName);
if (atom->n != NULL) {
if (( id_tmp = H5Dcreate(ncid_atom, POP_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT,
plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_n, 0)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_x, 1)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_y, 2)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_z, 3)) < 0) HERR(routineName);
if (( H5LTset_attribute_float(ncid_atom, POP_NAME, "_FillValue",
&FILLVALUE, 1) ) < 0) HERR(routineName);
io.aux_atom_pop[i] = id_tmp;
}
if (atom->nstar != NULL) {
if (( id_tmp = H5Dcreate(ncid_atom, POPLTE_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT,
plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_n, 0)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_x, 1)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_y, 2)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_z, 3)) < 0) HERR(routineName);
if (( H5LTset_attribute_float(ncid_atom, POPLTE_NAME, "_FillValue",
&FILLVALUE, 1) ) < 0) HERR(routineName);
io.aux_atom_poplte[i] = id_tmp;
}
if (( H5Dclose(id_n) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
}
if (input.p15d_wrates) {
/* Radiative rates */
dims[0] = atom->Nline;
dims[1] = mpi.nx;
dims[2] = mpi.ny;
dims[3] = infile.nz;
if (( file_dspace = H5Screate_simple(4, dims, NULL) ) < 0) HERR(routineName);
if (( id_n = H5Dopen2(ncid_atom, LINE_NAME,
H5P_DEFAULT)) < 0) HERR(routineName);
if (( id_tmp = H5Dcreate(ncid_atom, RIJ_L_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist,
H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_n, 0)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_x, 1)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_y, 2)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_z, 3)) < 0) HERR(routineName);
if (( H5LTset_attribute_float(ncid_atom, RIJ_L_NAME, "_FillValue",
&FILLVALUE, 1) ) < 0) HERR(routineName);
io.aux_atom_RijL[i] = id_tmp;
if (( id_tmp = H5Dcreate(ncid_atom, RJI_L_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist,
H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_n, 0)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_x, 1)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_y, 2)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_z, 3)) < 0) HERR(routineName);
if (( H5LTset_attribute_float(ncid_atom, RJI_L_NAME, "_FillValue",
&FILLVALUE, 1) ) < 0) HERR(routineName);
io.aux_atom_RjiL[i] = id_tmp;
if (( H5Dclose(id_n) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
if (atom->Ncont > 0) {
dims[0] = atom->Ncont;
if (( file_dspace = H5Screate_simple(4, dims, NULL) ) < 0)
HERR(routineName);
if (( id_n = H5Dopen2(ncid_atom, CONT_NAME,
H5P_DEFAULT)) < 0) HERR(routineName);
if (( id_tmp = H5Dcreate(ncid_atom, RIJ_C_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist,
H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_n, 0)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_x, 1)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_y, 2)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_z, 3)) < 0) HERR(routineName);
if (( H5LTset_attribute_float(ncid_atom, RIJ_C_NAME, "_FillValue",
&FILLVALUE, 1) ) < 0) HERR(routineName);
io.aux_atom_RijC[i] = id_tmp;
if (( id_tmp = H5Dcreate(ncid_atom, RJI_C_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist,
H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_n, 0)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_x, 1)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_y, 2)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_z, 3)) < 0) HERR(routineName);
if (( H5LTset_attribute_float(ncid_atom, RJI_C_NAME, "_FillValue",
&FILLVALUE, 1) ) < 0) HERR(routineName);
io.aux_atom_RjiC[i] = id_tmp;
if (( H5Dclose(id_n) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
}
}
if (( H5Dclose(id_x) ) < 0) HERR(routineName);
if (( H5Dclose(id_y) ) < 0) HERR(routineName);
if (( H5Dclose(id_z) ) < 0) HERR(routineName);
} /* end active ATOMS loop */
/* --- Group loop over active MOLECULES --- */
for (i=0; i < atmos.Nactivemol; i++) {
molecule = atmos.activemols[i];
/* Get group name */
sprintf( group_name, "molecule_%s", molecule->ID);
if (( ncid_mol = H5Gcreate(ncid, group_name, H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT) ) < 0) HERR(routineName);
io.aux_mol_ncid[i] = ncid_mol;
/* --- dimensions as attributes --- */
if (( H5LTset_attribute_int(ncid_mol, ".", "nlevel_vibr",
&molecule->Nv, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_mol, ".", "nline_molecule",
&molecule->Nrt, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_mol, ".", "nJ",
&molecule->NJ, 1)) < 0) HERR(routineName);
/* --- dimension datasets --- */
dims[0] = mpi.nx;
if (( H5LTmake_dataset(ncid_mol, X_NAME, 1, dims, H5T_NATIVE_DOUBLE,
geometry.xscale) ) < 0) HERR(routineName);
if (( id_x = H5Dopen2(ncid_mol, X_NAME, H5P_DEFAULT)) < 0) HERR(routineName);
dims[0] = mpi.ny;
if (( H5LTmake_dataset(ncid_mol, Y_NAME, 1, dims, H5T_NATIVE_DOUBLE,
geometry.yscale) ) < 0) HERR(routineName);
if (( id_y = H5Dopen2(ncid_mol, Y_NAME, H5P_DEFAULT)) < 0) HERR(routineName);
dims[0] = infile.nz;
tmp_double = (double *) calloc(infile.nz , sizeof(double));
if (( H5LTmake_dataset(ncid_mol, ZOUT_NAME, 1, dims, H5T_NATIVE_DOUBLE,
tmp_double) ) < 0) HERR(routineName);
free(tmp_double);
if (( id_z = H5Dopen2(ncid_mol, ZOUT_NAME, H5P_DEFAULT)) < 0) HERR(routineName);
dims[0] = molecule->Nv;
tmp = (unsigned int *) calloc(molecule->Nv, sizeof(unsigned int));
if (( H5LTmake_dataset(ncid_mol, VLEVEL_NAME, 1, dims, H5T_NATIVE_UINT,
tmp) ) < 0) HERR(routineName);
free(tmp);
dims[0] = molecule->Nrt;
tmp = (unsigned int *) calloc(molecule->Nrt, sizeof(unsigned int));
if (( H5LTmake_dataset(ncid_mol, VLINE_NAME, 1, dims, H5T_NATIVE_UINT,
tmp) ) < 0) HERR(routineName);
free(tmp);
dims[0] = molecule->NJ;
tmp = (unsigned int *) calloc(molecule->NJ, sizeof(unsigned int));
if (( H5LTmake_dataset(ncid_mol, NJ_NAME, 1, dims, H5T_NATIVE_UINT,
tmp) ) < 0) HERR(routineName);
free(tmp);
/* For compatibility with netCDF readers, only use dataset as dimension */
if (( H5LTset_attribute_string(ncid_mol, ZOUT_NAME, "NAME",
NETCDF_COMPAT) ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_mol, VLEVEL_NAME, "NAME",
NETCDF_COMPAT) ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_mol, VLINE_NAME, "NAME",
NETCDF_COMPAT) ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_mol, NJ_NAME, "NAME",
NETCDF_COMPAT) ) < 0) HERR(routineName);
/* --- variables --- */
dims[0] = molecule->Nv;
dims[1] = mpi.nx;
dims[2] = mpi.ny;
dims[3] = infile.nz;
/* Populations */
if (input.p15d_wpop) {
if (( file_dspace = H5Screate_simple(4, dims, NULL) ) < 0)
HERR(routineName);
if (( id_n = H5Dopen2(ncid_mol, VLEVEL_NAME,
H5P_DEFAULT)) < 0) HERR(routineName);
if (molecule->nv != NULL) {
if (( id_tmp = H5Dcreate(ncid_mol, POP_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist,
H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_n, 0)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_x, 1)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_y, 2)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_z, 3)) < 0) HERR(routineName);
io.aux_mol_pop[i] = id_tmp;
}
if (molecule->nvstar != NULL) {
if (( id_tmp = H5Dcreate(ncid_mol, POPLTE_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist,
H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_n, 0)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_x, 1)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_y, 2)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_z, 3)) < 0) HERR(routineName);
io.aux_mol_poplte[i] = id_tmp;
}
if (( H5Dclose(id_n) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
// TODO: molecule->Ediss, molecule->Tmin, molecule->Tmax
}
if (( H5Dclose(id_x) ) < 0) HERR(routineName);
if (( H5Dclose(id_y) ) < 0) HERR(routineName);
if (( H5Dclose(id_z) ) < 0) HERR(routineName);
} /* end active MOLECULES loop */
io.aux_ncid = ncid; /* Copy stuff to the IO data struct */
if (( H5Pclose(plist) ) < 0) HERR(routineName); /* Free hdf5 resources */
/* Flush ensures file is created in case of crash */
if (( H5Fflush(ncid, H5F_SCOPE_LOCAL) ) < 0) HERR(routineName);
return;
}
/*-------------------------------------------------------------------------
* Function: create_szip_dsets_float
*
* Purpose: Create a dataset of FLOAT datatype with szip filter
*
* Return: Success: 0
* Failure: -1
*
* Programmer: Raymond Lu
* 29 March 2011
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
int
create_szip_dsets_float(hid_t fid, hid_t fsid, hid_t msid)
{
hid_t dataset; /* dataset handles */
hid_t dcpl;
float data[NX][NY]; /* data to write */
float fillvalue = -2.2f;
hsize_t chunk[RANK] = {CHUNK0, CHUNK1};
int i, j;
/*
* Data and output buffer initialization.
*/
for (j = 0; j < NX; j++) {
for (i = 0; i < NY; i++)
data[j][i] = ((float)(i + j + 1))/3;
}
/*
* Create the dataset creation property list, add the Scale-Offset
* filter, set the chunk size, and set the fill value.
*/
if((dcpl = H5Pcreate(H5P_DATASET_CREATE)) < 0)
TEST_ERROR
if(H5Pset_szip(dcpl, H5_SZIP_NN_OPTION_MASK, 4) < 0)
TEST_ERROR
if(H5Pset_chunk(dcpl, RANK, chunk) < 0)
TEST_ERROR
if(H5Pset_fill_value(dcpl, H5T_NATIVE_FLOAT, &fillvalue) < 0)
TEST_ERROR
/*
* Create a new dataset within the file using defined dataspace, little
* endian datatype and default dataset creation properties.
*/
if((dataset = H5Dcreate2(fid, DATASETNAME18, H5T_IEEE_F32LE, fsid,
H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
TEST_ERROR
/*
* Write the data to the dataset using default transfer properties.
*/
if(H5Dwrite(dataset, H5T_NATIVE_FLOAT, msid, fsid, H5P_DEFAULT, data) < 0)
TEST_ERROR
/* Close dataset */
if(H5Dclose(dataset) < 0)
TEST_ERROR
/* Now create a dataset with a big-endian type */
if((dataset = H5Dcreate2(fid, DATASETNAME19, H5T_IEEE_F32BE, fsid,
H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
TEST_ERROR
if(H5Dwrite(dataset, H5T_NATIVE_FLOAT, msid, fsid, H5P_DEFAULT, data) < 0)
TEST_ERROR
if(H5Dclose(dataset) < 0)
TEST_ERROR
/*
* Close/release resources.
*/
if(H5Pclose(dcpl) < 0)
TEST_ERROR
return 0;
error:
H5E_BEGIN_TRY {
H5Pclose(dcpl);
H5Dclose(dataset);
} H5E_END_TRY;
return -1;
}
/*+++++++++++++++++++++++++
.IDENTifer PYTABLE_make_array
.PURPOSE create extensible HDF5 dataset
.INPUT/OUTPUT
call as stat = PYTABLE_make_array( locID, dset_name, title, rank, dims,
extdim, typeID, dims_chunk, fill_data,
compress, shuffle, fletcher32, buff );
input:
hid_t locID : HDF5 identifier of file or group
char *dset_name : name of dataset
char *title :
int rank : number of dimensions
hsize_t *dims : size of each dimension
int extdim : index of expendable dimension
hid_t typeID : data type (HDF5 identifier)
hsize_t *dims_chunk : chunk sizes
void *fill_data : Fill value for data
unsigned int compress : compression level (zero for no compression)
bool shuffle : shuffel data for better compression
bool fletcher32 :
void *buffer : buffer with data to write (or NULL)
.RETURNS A negative value is returned on failure.
.COMMENTS none
-------------------------*/
herr_t PYTABLE_make_array( hid_t locID, const char *dset_name,
const char *title, const int rank,
const hsize_t *dims, int extdim, hid_t typeID,
const hsize_t *dims_chunk, void *fill_data,
unsigned int compress, bool shuffle,
bool fletcher32, const void *buffer )
{
register int ni;
hid_t dataID = -1, spaceID = -1;
herr_t stat;
/* check if the array has to be chunked or not */
if ( dims_chunk != NULL ) {
hid_t plistID;
hsize_t *maxdims = (hsize_t *) malloc( rank * sizeof(hsize_t) );
if ( maxdims == NULL )
NADC_GOTO_ERROR( NADC_ERR_ALLOC, "maxdims" );
for ( ni = 0; ni < rank; ni++ ) {
if ( ni == extdim )
maxdims[ni] = H5S_UNLIMITED;
else
maxdims[ni] =
dims[ni] < dims_chunk[ni] ? dims_chunk[ni] : dims[ni];
}
spaceID = H5Screate_simple( rank, dims, maxdims );
free( maxdims );
if ( spaceID < 0 ) NADC_GOTO_ERROR( NADC_ERR_HDF_SPACE, "" );
/* Modify dataset creation properties, i.e. enable chunking */
plistID = H5Pcreate( H5P_DATASET_CREATE );
if ( H5Pset_chunk( plistID, rank, dims_chunk ) < 0 ) goto done;
/* set the fill value using a struct as the data type */
if ( fill_data != NULL
&& H5Pset_fill_value( plistID, typeID, fill_data ) < 0 )
goto done;
/* dataset creation property list is modified to use */
/* fletcher must be first */
if ( fletcher32 ) {
if ( H5Pset_fletcher32( plistID ) < 0 ) goto done;
}
/* then shuffle */
if ( shuffle ) {
if ( H5Pset_shuffle( plistID ) < 0 ) goto done;
}
/* finally compression */
if ( compress > 0 ) {
if ( H5Pset_deflate( plistID, compress ) < 0 ) goto done;
}
/* create the (chunked) dataset */
dataID = H5Dcreate( locID, dset_name, typeID, spaceID,
H5P_DEFAULT, plistID, H5P_DEFAULT );
if ( dataID < 0 )
NADC_GOTO_ERROR( NADC_ERR_HDF_DATA, dset_name );
/* end access to the property list */
if ( H5Pclose( plistID ) < 0 ) goto done;
} else {
spaceID = H5Screate_simple( rank, dims, NULL );
if ( spaceID < 0 ) return -1;
/* create the dataset (not chunked) */
dataID = H5Dcreate( locID, dset_name, typeID, spaceID,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT );
if ( dataID < 0 )
NADC_GOTO_ERROR( NADC_ERR_HDF_DATA, dset_name );
}
/*
* write the data
*/
stat = H5Dwrite( dataID, typeID, H5S_ALL, H5S_ALL, H5P_DEFAULT, buffer );
if ( stat < 0 ) NADC_GOTO_ERROR( NADC_ERR_HDF_WR, "" );
(void) H5Dclose( dataID );
(void) H5Sclose( spaceID );
/*
* Set the conforming array attributes
*
* attach the CLASS attribute
*/
(void) H5LTset_attribute_string( locID, dset_name, "CLASS",
PY_ARRAY_CLASS );
/* attach the EXTDIM attribute in case of enlargeable arrays */
(void) H5LTset_attribute_int( locID, dset_name, "EXTDIM", &extdim, 1 );
/* attach the FLAVOR attribute */
(void) H5LTset_attribute_string( locID, dset_name, "FLAVOR",
PY_ARRAY_FLAVOR );
/* attach the VERSION attribute */
(void) H5LTset_attribute_string( locID, dset_name, "VERSION",
PY_ARRAY_VERSION );
/* attach the TITLE attribute */
(void) H5LTset_attribute_string( locID, dset_name, "TITLE", title );
return 0;
done:
if ( dataID > 0 ) (void) H5Dclose( dataID );
if ( spaceID > 0 ) (void) H5Sclose( spaceID );
return -1;
}
/* We will read dataset back from the file
to the dataset in memory with these
dataspace parameters. */
#define MSPACE_RANK 2
#define MSPACE_DIM1 8
#define MSPACE_DIM2 9
#define NPOINTS 4 /* Number of points that will be selected
and overwritten */
int
main (void)
{
hid_t file, dataset; /* File and dataset identifiers */
hid_t mid1, mid2, mid, fid; /* Dataspace identifiers */
hid_t plist; /* Dataset property list identifier */
hsize_t dim1[] = {MSPACE1_DIM}; /* Dimension size of the first dataset
(in memory) */
hsize_t dim2[] = {MSPACE2_DIM}; /* Dimension size of the second dataset
(in memory */
hsize_t fdim[] = {FSPACE_DIM1, FSPACE_DIM2};
/* Dimension sizes of the dataset (on disk) */
hsize_t mdim[] = {MSPACE_DIM1, MSPACE_DIM2}; /* Dimension sizes of the
dataset in memory when we
read selection from the
dataset on the disk */
hsize_t start[2]; /* Start of hyperslab */
hsize_t stride[2]; /* Stride of hyperslab */
hsize_t count[2]; /* Block count */
hsize_t block[2]; /* Block sizes */
hsize_t coord[NPOINTS][FSPACE_RANK]; /* Array to store selected points
from the file dataspace */
herr_t ret;
unsigned i,j;
int fillvalue = 0; /* Fill value for the dataset */
int matrix_out[MSPACE_DIM1][MSPACE_DIM2]; /* Buffer to read from the
dataset */
int vector[MSPACE1_DIM];
int values[] = {53, 59, 61, 67}; /* New values to be written */
/*
* Buffers' initialization.
*/
vector[0] = vector[MSPACE1_DIM - 1] = -1;
for(i = 1; i < MSPACE1_DIM - 1; i++)
vector[i] = i;
/*
* Create a file.
*/
file = H5Fcreate(H5FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Create property list for a dataset and set up fill values.
*/
plist = H5Pcreate(H5P_DATASET_CREATE);
ret = H5Pset_fill_value(plist, H5T_NATIVE_INT, &fillvalue);
/*
* Create dataspace for the dataset in the file.
*/
fid = H5Screate_simple(FSPACE_RANK, fdim, NULL);
/*
* Create dataset in the file. Notice that creation
* property list plist is used.
*/
dataset = H5Dcreate2(file, "Matrix in file", H5T_NATIVE_INT, fid, H5P_DEFAULT, plist, H5P_DEFAULT);
/*
* Select hyperslab for the dataset in the file, using 3x2 blocks,
* (4,3) stride and (2,4) count starting at the position (0,1).
*/
start[0] = 0; start[1] = 1;
stride[0] = 4; stride[1] = 3;
count[0] = 2; count[1] = 4;
block[0] = 3; block[1] = 2;
ret = H5Sselect_hyperslab(fid, H5S_SELECT_SET, start, stride, count, block);
/*
* Create dataspace for the first dataset.
*/
mid1 = H5Screate_simple(MSPACE1_RANK, dim1, NULL);
/*
* Select hyperslab.
* We will use 48 elements of the vector buffer starting at the second element.
* Selected elements are 1 2 3 . . . 48
*/
start[0] = 1;
stride[0] = 1;
count[0] = 48;
block[0] = 1;
ret = H5Sselect_hyperslab(mid1, H5S_SELECT_SET, start, stride, count, block);
/*
* Write selection from the vector buffer to the dataset in the file.
*
* File dataset should look like this:
* 0 1 2 0 3 4 0 5 6 0 7 8
* 0 9 10 0 11 12 0 13 14 0 15 16
* 0 17 18 0 19 20 0 21 22 0 23 24
* 0 0 0 0 0 0 0 0 0 0 0 0
* 0 25 26 0 27 28 0 29 30 0 31 32
* 0 33 34 0 35 36 0 37 38 0 39 40
* 0 41 42 0 43 44 0 45 46 0 47 48
* 0 0 0 0 0 0 0 0 0 0 0 0
*/
ret = H5Dwrite(dataset, H5T_NATIVE_INT, mid1, fid, H5P_DEFAULT, vector);
/*
* Reset the selection for the file dataspace fid.
*/
ret = H5Sselect_none(fid);
/*
* Create dataspace for the second dataset.
*/
mid2 = H5Screate_simple(MSPACE2_RANK, dim2, NULL);
/*
* Select sequence of NPOINTS points in the file dataspace.
*/
coord[0][0] = 0; coord[0][1] = 0;
coord[1][0] = 3; coord[1][1] = 3;
coord[2][0] = 3; coord[2][1] = 5;
coord[3][0] = 5; coord[3][1] = 6;
ret = H5Sselect_elements(fid, H5S_SELECT_SET, NPOINTS, (const hsize_t *)coord);
/*
* Write new selection of points to the dataset.
*/
ret = H5Dwrite(dataset, H5T_NATIVE_INT, mid2, fid, H5P_DEFAULT, values);
/*
* File dataset should look like this:
* 53 1 2 0 3 4 0 5 6 0 7 8
* 0 9 10 0 11 12 0 13 14 0 15 16
* 0 17 18 0 19 20 0 21 22 0 23 24
* 0 0 0 59 0 61 0 0 0 0 0 0
* 0 25 26 0 27 28 0 29 30 0 31 32
* 0 33 34 0 35 36 67 37 38 0 39 40
* 0 41 42 0 43 44 0 45 46 0 47 48
* 0 0 0 0 0 0 0 0 0 0 0 0
*
*/
/*
* Close memory file and memory dataspaces.
*/
ret = H5Sclose(mid1);
ret = H5Sclose(mid2);
ret = H5Sclose(fid);
/*
* Close dataset.
*/
ret = H5Dclose(dataset);
/*
* Close the file.
*/
ret = H5Fclose(file);
/*
* Open the file.
*/
file = H5Fopen(H5FILE_NAME, H5F_ACC_RDONLY, H5P_DEFAULT);
/*
* Open the dataset.
*/
dataset = H5Dopen2(file, "Matrix in file", H5P_DEFAULT);
/*
* Get dataspace of the open dataset.
*/
fid = H5Dget_space(dataset);
/*
* Select first hyperslab for the dataset in the file. The following
* elements are selected:
* 10 0 11 12
* 18 0 19 20
* 0 59 0 61
*
*/
start[0] = 1; start[1] = 2;
block[0] = 1; block[1] = 1;
stride[0] = 1; stride[1] = 1;
count[0] = 3; count[1] = 4;
ret = H5Sselect_hyperslab(fid, H5S_SELECT_SET, start, stride, count, block);
/*
* Add second selected hyperslab to the selection.
* The following elements are selected:
* 19 20 0 21 22
* 0 61 0 0 0
* 27 28 0 29 30
* 35 36 67 37 38
* 43 44 0 45 46
* 0 0 0 0 0
* Note that two hyperslabs overlap. Common elements are:
* 19 20
* 0 61
*/
start[0] = 2; start[1] = 4;
block[0] = 1; block[1] = 1;
stride[0] = 1; stride[1] = 1;
count[0] = 6; count[1] = 5;
ret = H5Sselect_hyperslab(fid, H5S_SELECT_OR, start, stride, count, block);
/*
* Create memory dataspace.
*/
mid = H5Screate_simple(MSPACE_RANK, mdim, NULL);
/*
* Select two hyperslabs in memory. Hyperslabs has the same
* size and shape as the selected hyperslabs for the file dataspace.
*/
start[0] = 0; start[1] = 0;
block[0] = 1; block[1] = 1;
stride[0] = 1; stride[1] = 1;
count[0] = 3; count[1] = 4;
ret = H5Sselect_hyperslab(mid, H5S_SELECT_SET, start, stride, count, block);
start[0] = 1; start[1] = 2;
block[0] = 1; block[1] = 1;
stride[0] = 1; stride[1] = 1;
count[0] = 6; count[1] = 5;
ret = H5Sselect_hyperslab(mid, H5S_SELECT_OR, start, stride, count, block);
/*
* Initialize data buffer.
*/
for (i = 0; i < MSPACE_DIM1; i++) {
for (j = 0; j < MSPACE_DIM2; j++)
matrix_out[i][j] = 0;
}
/*
* Read data back to the buffer matrix_out.
*/
ret = H5Dread(dataset, H5T_NATIVE_INT, mid, fid,
H5P_DEFAULT, matrix_out);
/*
* Display the result. Memory dataset is:
*
* 10 0 11 12 0 0 0 0 0
* 18 0 19 20 0 21 22 0 0
* 0 59 0 61 0 0 0 0 0
* 0 0 27 28 0 29 30 0 0
* 0 0 35 36 67 37 38 0 0
* 0 0 43 44 0 45 46 0 0
* 0 0 0 0 0 0 0 0 0
* 0 0 0 0 0 0 0 0 0
*/
for(i = 0; i < MSPACE_DIM1; i++) {
for(j = 0; j < MSPACE_DIM2; j++)
printf("%3d ", matrix_out[i][j]);
printf("\n");
}
/*
* Close memory file and memory dataspaces.
*/
ret = H5Sclose(mid);
ret = H5Sclose(fid);
/*
* Close dataset.
*/
ret = H5Dclose(dataset);
/*
* Close property list
*/
ret = H5Pclose(plist);
/*
* Close the file.
*/
ret = H5Fclose(file);
return 0;
}
void
test_plist_ed(void)
{
hid_t dcpl; /* dataset create prop. list */
hid_t dapl; /* dataset access prop. list */
hid_t dxpl; /* dataset transfer prop. list */
hid_t gcpl; /* group create prop. list */
hid_t lcpl; /* link create prop. list */
hid_t lapl; /* link access prop. list */
hid_t ocpypl; /* object copy prop. list */
hid_t ocpl; /* object create prop. list */
hid_t fapl; /* file access prop. list */
hid_t fcpl; /* file create prop. list */
hid_t strcpl; /* string create prop. list */
hid_t acpl; /* attribute create prop. list */
int mpi_size, mpi_rank, recv_proc;
hsize_t chunk_size = 16384; /* chunk size */
double fill = 2.7f; /* Fill value */
size_t nslots = 521*2;
size_t nbytes = 1048576 * 10;
double w0 = 0.5f;
unsigned max_compact;
unsigned min_dense;
hsize_t max_size[1]; /*data space maximum size */
const char* c_to_f = "x+32";
H5AC_cache_config_t my_cache_config = {
H5AC__CURR_CACHE_CONFIG_VERSION,
TRUE,
FALSE,
FALSE,
"temp",
TRUE,
FALSE,
( 2 * 2048 * 1024),
0.3f,
(64 * 1024 * 1024),
(4 * 1024 * 1024),
60000,
H5C_incr__threshold,
0.8f,
3.0f,
TRUE,
(8 * 1024 * 1024),
H5C_flash_incr__add_space,
2.0f,
0.25f,
H5C_decr__age_out_with_threshold,
0.997f,
0.8f,
TRUE,
(3 * 1024 * 1024),
3,
FALSE,
0.2f,
(256 * 2048),
H5AC__DEFAULT_METADATA_WRITE_STRATEGY};
herr_t ret; /* Generic return value */
if(VERBOSE_MED)
printf("Encode/Decode DCPLs\n");
/* set up MPI parameters */
MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
if(mpi_size == 1)
recv_proc = 0;
else
recv_proc = 1;
dcpl = H5Pcreate(H5P_DATASET_CREATE);
VRFY((dcpl >= 0), "H5Pcreate succeeded");
ret = H5Pset_chunk(dcpl, 1, &chunk_size);
VRFY((ret >= 0), "H5Pset_chunk succeeded");
ret = H5Pset_alloc_time(dcpl, H5D_ALLOC_TIME_LATE);
VRFY((ret >= 0), "H5Pset_alloc_time succeeded");
ret = H5Pset_fill_value(dcpl, H5T_NATIVE_DOUBLE, &fill);
VRFY((ret>=0), "set fill-value succeeded");
max_size[0] = 100;
ret = H5Pset_external(dcpl, "ext1.data", (off_t)0,
(hsize_t)(max_size[0] * sizeof(int)/4));
VRFY((ret>=0), "set external succeeded");
ret = H5Pset_external(dcpl, "ext2.data", (off_t)0,
(hsize_t)(max_size[0] * sizeof(int)/4));
VRFY((ret>=0), "set external succeeded");
ret = H5Pset_external(dcpl, "ext3.data", (off_t)0,
(hsize_t)(max_size[0] * sizeof(int)/4));
VRFY((ret>=0), "set external succeeded");
ret = H5Pset_external(dcpl, "ext4.data", (off_t)0,
(hsize_t)(max_size[0] * sizeof(int)/4));
VRFY((ret>=0), "set external succeeded");
ret = test_encode_decode(dcpl, mpi_rank, recv_proc);
VRFY((ret >= 0), "test_encode_decode succeeded");
ret = H5Pclose(dcpl);
VRFY((ret >= 0), "H5Pclose succeeded");
/******* ENCODE/DECODE DAPLS *****/
dapl = H5Pcreate(H5P_DATASET_ACCESS);
VRFY((dapl >= 0), "H5Pcreate succeeded");
ret = H5Pset_chunk_cache(dapl, nslots, nbytes, w0);
VRFY((ret >= 0), "H5Pset_chunk_cache succeeded");
ret = test_encode_decode(dapl, mpi_rank, recv_proc);
VRFY((ret >= 0), "test_encode_decode succeeded");
ret = H5Pclose(dapl);
VRFY((ret >= 0), "H5Pclose succeeded");
/******* ENCODE/DECODE OCPLS *****/
ocpl = H5Pcreate(H5P_OBJECT_CREATE);
VRFY((ocpl >= 0), "H5Pcreate succeeded");
ret = H5Pset_attr_creation_order(ocpl, (H5P_CRT_ORDER_TRACKED | H5P_CRT_ORDER_INDEXED));
VRFY((ret >= 0), "H5Pset_attr_creation_order succeeded");
ret = H5Pset_attr_phase_change(ocpl, 110, 105);
VRFY((ret >= 0), "H5Pset_attr_phase_change succeeded");
ret = H5Pset_filter(ocpl, H5Z_FILTER_FLETCHER32, 0, (size_t)0, NULL);
VRFY((ret >= 0), "H5Pset_filter succeeded");
ret = test_encode_decode(ocpl, mpi_rank, recv_proc);
VRFY((ret >= 0), "test_encode_decode succeeded");
ret = H5Pclose(ocpl);
VRFY((ret >= 0), "H5Pclose succeeded");
/******* ENCODE/DECODE DXPLS *****/
dxpl = H5Pcreate(H5P_DATASET_XFER);
VRFY((dxpl >= 0), "H5Pcreate succeeded");
ret = H5Pset_btree_ratios(dxpl, 0.2f, 0.6f, 0.2f);
VRFY((ret >= 0), "H5Pset_btree_ratios succeeded");
ret = H5Pset_hyper_vector_size(dxpl, 5);
VRFY((ret >= 0), "H5Pset_hyper_vector_size succeeded");
ret = H5Pset_dxpl_mpio(dxpl, H5FD_MPIO_COLLECTIVE);
VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
ret = H5Pset_dxpl_mpio_collective_opt(dxpl, H5FD_MPIO_INDIVIDUAL_IO);
VRFY((ret >= 0), "H5Pset_dxpl_mpio_collective_opt succeeded");
ret = H5Pset_dxpl_mpio_chunk_opt(dxpl, H5FD_MPIO_CHUNK_MULTI_IO);
VRFY((ret >= 0), "H5Pset_dxpl_mpio_chunk_opt succeeded");
ret = H5Pset_dxpl_mpio_chunk_opt_ratio(dxpl, 30);
VRFY((ret >= 0), "H5Pset_dxpl_mpio_chunk_opt_ratio succeeded");
ret = H5Pset_dxpl_mpio_chunk_opt_num(dxpl, 40);
VRFY((ret >= 0), "H5Pset_dxpl_mpio_chunk_opt_num succeeded");
ret = H5Pset_edc_check(dxpl, H5Z_DISABLE_EDC);
VRFY((ret >= 0), "H5Pset_edc_check succeeded");
ret = H5Pset_data_transform(dxpl, c_to_f);
VRFY((ret >= 0), "H5Pset_data_transform succeeded");
ret = test_encode_decode(dxpl, mpi_rank, recv_proc);
VRFY((ret >= 0), "test_encode_decode succeeded");
ret = H5Pclose(dxpl);
VRFY((ret >= 0), "H5Pclose succeeded");
/******* ENCODE/DECODE GCPLS *****/
gcpl = H5Pcreate(H5P_GROUP_CREATE);
VRFY((gcpl >= 0), "H5Pcreate succeeded");
ret = H5Pset_local_heap_size_hint(gcpl, 256);
VRFY((ret >= 0), "H5Pset_local_heap_size_hint succeeded");
ret = H5Pset_link_phase_change(gcpl, 2, 2);
VRFY((ret >= 0), "H5Pset_link_phase_change succeeded");
/* Query the group creation properties */
ret = H5Pget_link_phase_change(gcpl, &max_compact, &min_dense);
VRFY((ret >= 0), "H5Pget_est_link_info succeeded");
ret = H5Pset_est_link_info(gcpl, 3, 9);
VRFY((ret >= 0), "H5Pset_est_link_info succeeded");
ret = H5Pset_link_creation_order(gcpl, (H5P_CRT_ORDER_TRACKED | H5P_CRT_ORDER_INDEXED));
VRFY((ret >= 0), "H5Pset_link_creation_order succeeded");
ret = test_encode_decode(gcpl, mpi_rank, recv_proc);
VRFY((ret >= 0), "test_encode_decode succeeded");
ret = H5Pclose(gcpl);
VRFY((ret >= 0), "H5Pclose succeeded");
/******* ENCODE/DECODE LCPLS *****/
lcpl = H5Pcreate(H5P_LINK_CREATE);
VRFY((lcpl >= 0), "H5Pcreate succeeded");
ret= H5Pset_create_intermediate_group(lcpl, TRUE);
VRFY((ret >= 0), "H5Pset_create_intermediate_group succeeded");
ret = test_encode_decode(lcpl, mpi_rank, recv_proc);
VRFY((ret >= 0), "test_encode_decode succeeded");
ret = H5Pclose(lcpl);
VRFY((ret >= 0), "H5Pclose succeeded");
/******* ENCODE/DECODE LAPLS *****/
lapl = H5Pcreate(H5P_LINK_ACCESS);
VRFY((lapl >= 0), "H5Pcreate succeeded");
ret = H5Pset_nlinks(lapl, (size_t)134);
VRFY((ret >= 0), "H5Pset_nlinks succeeded");
ret = H5Pset_elink_acc_flags(lapl, H5F_ACC_RDONLY);
VRFY((ret >= 0), "H5Pset_elink_acc_flags succeeded");
ret = H5Pset_elink_prefix(lapl, "/tmpasodiasod");
VRFY((ret >= 0), "H5Pset_nlinks succeeded");
/* Create FAPL for the elink FAPL */
fapl = H5Pcreate(H5P_FILE_ACCESS);
VRFY((fapl >= 0), "H5Pcreate succeeded");
ret = H5Pset_alignment(fapl, 2, 1024);
VRFY((ret >= 0), "H5Pset_alignment succeeded");
ret = H5Pset_elink_fapl(lapl, fapl);
VRFY((ret >= 0), "H5Pset_elink_fapl succeeded");
/* Close the elink's FAPL */
ret = H5Pclose(fapl);
VRFY((ret >= 0), "H5Pclose succeeded");
ret = test_encode_decode(lapl, mpi_rank, recv_proc);
VRFY((ret >= 0), "test_encode_decode succeeded");
ret = H5Pclose(lapl);
VRFY((ret >= 0), "H5Pclose succeeded");
/******* ENCODE/DECODE OCPYPLS *****/
ocpypl = H5Pcreate(H5P_OBJECT_COPY);
VRFY((ocpypl >= 0), "H5Pcreate succeeded");
ret = H5Pset_copy_object(ocpypl, H5O_COPY_EXPAND_EXT_LINK_FLAG);
VRFY((ret >= 0), "H5Pset_copy_object succeeded");
ret = H5Padd_merge_committed_dtype_path(ocpypl, "foo");
VRFY((ret >= 0), "H5Padd_merge_committed_dtype_path succeeded");
ret = H5Padd_merge_committed_dtype_path(ocpypl, "bar");
VRFY((ret >= 0), "H5Padd_merge_committed_dtype_path succeeded");
ret = test_encode_decode(ocpypl, mpi_rank, recv_proc);
VRFY((ret >= 0), "test_encode_decode succeeded");
ret = H5Pclose(ocpypl);
VRFY((ret >= 0), "H5Pclose succeeded");
/******* ENCODE/DECODE FAPLS *****/
fapl = H5Pcreate(H5P_FILE_ACCESS);
VRFY((fapl >= 0), "H5Pcreate succeeded");
ret = H5Pset_family_offset(fapl, 1024);
VRFY((ret >= 0), "H5Pset_family_offset succeeded");
ret = H5Pset_meta_block_size(fapl, 2098452);
VRFY((ret >= 0), "H5Pset_meta_block_size succeeded");
ret = H5Pset_sieve_buf_size(fapl, 1048576);
VRFY((ret >= 0), "H5Pset_sieve_buf_size succeeded");
ret = H5Pset_alignment(fapl, 2, 1024);
VRFY((ret >= 0), "H5Pset_alignment succeeded");
ret = H5Pset_cache(fapl, 1024, 128, 10485760, 0.3f);
VRFY((ret >= 0), "H5Pset_cache succeeded");
ret = H5Pset_elink_file_cache_size(fapl, 10485760);
VRFY((ret >= 0), "H5Pset_elink_file_cache_size succeeded");
ret = H5Pset_gc_references(fapl, 1);
VRFY((ret >= 0), "H5Pset_gc_references succeeded");
ret = H5Pset_small_data_block_size(fapl, 2048);
VRFY((ret >= 0), "H5Pset_small_data_block_size succeeded");
ret = H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST);
VRFY((ret >= 0), "H5Pset_libver_bounds succeeded");
ret = H5Pset_fclose_degree(fapl, H5F_CLOSE_WEAK);
VRFY((ret >= 0), "H5Pset_fclose_degree succeeded");
ret = H5Pset_multi_type(fapl, H5FD_MEM_GHEAP);
VRFY((ret >= 0), "H5Pset_multi_type succeeded");
ret = H5Pset_mdc_config(fapl, &my_cache_config);
VRFY((ret >= 0), "H5Pset_mdc_config succeeded");
ret = test_encode_decode(fapl, mpi_rank, recv_proc);
VRFY((ret >= 0), "test_encode_decode succeeded");
ret = H5Pclose(fapl);
VRFY((ret >= 0), "H5Pclose succeeded");
/******* ENCODE/DECODE FCPLS *****/
fcpl = H5Pcreate(H5P_FILE_CREATE);
VRFY((fcpl >= 0), "H5Pcreate succeeded");
ret = H5Pset_userblock(fcpl, 1024);
VRFY((ret >= 0), "H5Pset_userblock succeeded");
ret = H5Pset_istore_k(fcpl, 3);
VRFY((ret >= 0), "H5Pset_istore_k succeeded");
ret = H5Pset_sym_k(fcpl, 4, 5);
VRFY((ret >= 0), "H5Pset_sym_k succeeded");
ret = H5Pset_shared_mesg_nindexes(fcpl, 8);
VRFY((ret >= 0), "H5Pset_shared_mesg_nindexes succeeded");
ret = H5Pset_shared_mesg_index(fcpl, 1, H5O_SHMESG_SDSPACE_FLAG, 32);
VRFY((ret >= 0), "H5Pset_shared_mesg_index succeeded");
ret = H5Pset_shared_mesg_phase_change(fcpl, 60, 20);
VRFY((ret >= 0), "H5Pset_shared_mesg_phase_change succeeded");
ret = H5Pset_sizes(fcpl, 8, 4);
VRFY((ret >= 0), "H5Pset_sizes succeeded");
ret = test_encode_decode(fcpl, mpi_rank, recv_proc);
VRFY((ret >= 0), "test_encode_decode succeeded");
ret = H5Pclose(fcpl);
VRFY((ret >= 0), "H5Pclose succeeded");
/******* ENCODE/DECODE STRCPLS *****/
strcpl = H5Pcreate(H5P_STRING_CREATE);
VRFY((strcpl >= 0), "H5Pcreate succeeded");
ret = H5Pset_char_encoding(strcpl, H5T_CSET_UTF8);
VRFY((ret >= 0), "H5Pset_char_encoding succeeded");
ret = test_encode_decode(strcpl, mpi_rank, recv_proc);
VRFY((ret >= 0), "test_encode_decode succeeded");
ret = H5Pclose(strcpl);
VRFY((ret >= 0), "H5Pclose succeeded");
/******* ENCODE/DECODE ACPLS *****/
acpl = H5Pcreate(H5P_ATTRIBUTE_CREATE);
VRFY((acpl >= 0), "H5Pcreate succeeded");
ret = H5Pset_char_encoding(acpl, H5T_CSET_UTF8);
VRFY((ret >= 0), "H5Pset_char_encoding succeeded");
ret = test_encode_decode(acpl, mpi_rank, recv_proc);
VRFY((ret >= 0), "test_encode_decode succeeded");
ret = H5Pclose(acpl);
VRFY((ret >= 0), "H5Pclose succeeded");
}
int
main(void)
{
hid_t src_sid = -1; /* source dataset's dataspace ID */
hid_t src_dcplid = -1; /* source dataset property list ID */
hid_t vds_sid = -1; /* VDS dataspace ID */
hid_t vds_dcplid = -1; /* VDS dataset property list ID */
hid_t fid = -1; /* HDF5 file ID */
hid_t did = -1; /* dataset ID */
hid_t msid = -1; /* memory dataspace ID */
hid_t fsid = -1; /* file dataspace ID */
/* Hyperslab arrays */
hsize_t start[RANK] = {0, 0, 0};
hsize_t count[RANK] = {H5S_UNLIMITED, 1, 1};
int *buffer = NULL; /* data buffer */
int value = -1; /* value written to datasets */
hsize_t n = 0; /* number of elements in a plane */
int i; /* iterator */
int j; /* iterator */
int k; /* iterator */
/************************************
* Create source files and datasets *
************************************/
/* Create source dataspace ID */
if((src_sid = H5Screate_simple(RANK, UC_4_SOURCE_DIMS,
UC_4_SOURCE_MAX_DIMS)) < 0)
UC_ERROR
if(H5Sselect_hyperslab(src_sid, H5S_SELECT_SET, start, NULL,
UC_4_SOURCE_MAX_DIMS, NULL) < 0)
UC_ERROR
/* Create source files and datasets */
for(i = 0; i < UC_4_N_SOURCES; i++) {
/* source dataset dcpl */
if((src_dcplid = H5Pcreate(H5P_DATASET_CREATE)) < 0)
UC_ERROR
if(H5Pset_chunk(src_dcplid, RANK, UC_4_PLANE) < 0)
UC_ERROR
if(H5Pset_fill_value(src_dcplid, UC_4_SOURCE_DATATYPE,
&UC_4_FILL_VALUES[i]) < 0)
UC_ERROR
if(H5Pset_deflate(src_dcplid, COMPRESSION_LEVEL) < 0)
UC_ERROR
/* Create source file and dataset */
if((fid = H5Fcreate(UC_4_FILE_NAMES[i], H5F_ACC_TRUNC,
H5P_DEFAULT, H5P_DEFAULT)) < 0)
UC_ERROR
if((did = H5Dcreate2(fid, UC_4_SOURCE_DSET_NAME,
UC_4_SOURCE_DATATYPE, src_sid,
H5P_DEFAULT, src_dcplid, H5P_DEFAULT)) < 0)
UC_ERROR
/* Set the dataset's extent */
if(H5Dset_extent(did, UC_4_SOURCE_MAX_DIMS) < 0)
UC_ERROR
/* Create a data buffer that represents a plane */
n = UC_4_PLANE[1] * UC_4_PLANE[2];
if(NULL == (buffer = (int *)malloc(n * sizeof(int))))
UC_ERROR
/* Create the memory dataspace */
if((msid = H5Screate_simple(RANK, UC_4_PLANE, NULL)) < 0)
UC_ERROR
/* Get the file dataspace */
if((fsid = H5Dget_space(did)) < 0)
UC_ERROR
/* Write planes to the dataset */
for(j = 0; j < UC_4_SRC_PLANES; j++) {
value = ((i + 1) * 10) + j;
for(k = 0; k < n; k++)
buffer[k] = value;
start[0] = j;
start[1] = 0;
start[2] = 0;
if(H5Sselect_hyperslab(fsid, H5S_SELECT_SET, start, NULL, UC_4_PLANE, NULL) < 0)
UC_ERROR
if(H5Dwrite(did, H5T_NATIVE_INT, msid, fsid, H5P_DEFAULT, buffer) < 0)
UC_ERROR
} /* end for */
/* close */
if(H5Sclose(msid) < 0)
UC_ERROR
if(H5Sclose(fsid) < 0)
UC_ERROR
if(H5Pclose(src_dcplid) < 0)
UC_ERROR
if(H5Dclose(did) < 0)
UC_ERROR
if(H5Fclose(fid) < 0)
UC_ERROR
free(buffer);
} /* end for */
/*******************
* Create VDS file *
*******************/
/* Create file */
if((fid = H5Fcreate(UC_4_VDS_FILE_NAME, H5F_ACC_TRUNC,
H5P_DEFAULT, H5P_DEFAULT)) < 0)
UC_ERROR
/* Create VDS dcpl */
if((vds_dcplid = H5Pcreate(H5P_DATASET_CREATE)) < 0)
UC_ERROR
if(H5Pset_fill_value(vds_dcplid, UC_4_VDS_DATATYPE,
&UC_4_VDS_FILL_VALUE) < 0)
UC_ERROR
/* Create VDS dataspace */
if((vds_sid = H5Screate_simple(RANK, UC_4_VDS_DIMS,
UC_4_VDS_MAX_DIMS)) < 0)
UC_ERROR
start[0] = 0;
start[1] = 0;
start[2] = 0;
if(H5Sselect_hyperslab(vds_sid, H5S_SELECT_SET, start,
UC_4_SOURCE_MAX_DIMS, count, UC_4_SOURCE_MAX_DIMS) < 0)
UC_ERROR
/* Add VDS mapping - The mapped file name uses a printf-like
* naming scheme that automatically maps new files.
*/
if(H5Pset_virtual(vds_dcplid, vds_sid, UC_4_MAPPING_FILE_NAME,
UC_4_SOURCE_DSET_PATH, src_sid) < 0)
UC_ERROR
/* Create dataset */
if((did = H5Dcreate2(fid, UC_4_VDS_DSET_NAME, UC_4_VDS_DATATYPE, vds_sid,
H5P_DEFAULT, vds_dcplid, H5P_DEFAULT)) < 0)
UC_ERROR
/* close */
if(H5Sclose(src_sid) < 0)
UC_ERROR
if(H5Pclose(vds_dcplid) < 0)
UC_ERROR
if(H5Sclose(vds_sid) < 0)
UC_ERROR
if(H5Dclose(did) < 0)
UC_ERROR
if(H5Fclose(fid) < 0)
UC_ERROR
return EXIT_SUCCESS;
error:
H5E_BEGIN_TRY {
if(src_sid >= 0)
(void)H5Sclose(src_sid);
if(src_dcplid >= 0)
(void)H5Pclose(src_dcplid);
if(vds_sid >= 0)
(void)H5Sclose(vds_sid);
if(vds_dcplid >= 0)
(void)H5Pclose(vds_dcplid);
if(fid >= 0)
(void)H5Fclose(fid);
if(did >= 0)
(void)H5Dclose(did);
if(msid >= 0)
(void)H5Sclose(msid);
if(fsid >= 0)
(void)H5Sclose(fsid);
if(buffer != NULL)
free(buffer);
} H5E_END_TRY
return EXIT_FAILURE;
} /* end main() */
herr_t H5ARRAYmake( hid_t loc_id,
const char *dset_name,
const char *obversion,
const int rank,
const hsize_t *dims,
int extdim,
hid_t type_id,
hsize_t *dims_chunk,
void *fill_data,
int compress,
char *complib,
int shuffle,
int fletcher32,
const void *data)
{
hid_t dataset_id, space_id;
hsize_t *maxdims = NULL;
hid_t plist_id = 0;
unsigned int cd_values[6];
int chunked = 0;
int i;
/* Check whether the array has to be chunked or not */
if (dims_chunk) {
chunked = 1;
}
if(chunked) {
maxdims = malloc(rank*sizeof(hsize_t));
if(!maxdims) return -1;
for(i=0;i<rank;i++) {
if (i == extdim) {
maxdims[i] = H5S_UNLIMITED;
}
else {
maxdims[i] = dims[i] < dims_chunk[i] ? dims_chunk[i] : dims[i];
}
}
}
/* Create the data space for the dataset. */
if ( (space_id = H5Screate_simple( rank, dims, maxdims )) < 0 )
return -1;
if (chunked) {
/* Modify dataset creation properties, i.e. enable chunking */
plist_id = H5Pcreate (H5P_DATASET_CREATE);
if ( H5Pset_chunk ( plist_id, rank, dims_chunk ) < 0 )
return -1;
/* Set the fill value using a struct as the data type. */
if (fill_data) {
if ( H5Pset_fill_value( plist_id, type_id, fill_data ) < 0 )
return -1;
}
else {
if ( H5Pset_fill_time(plist_id, H5D_FILL_TIME_ALLOC) < 0 )
return -1;
}
/*
Dataset creation property list is modified to use
*/
/* Fletcher must be first */
if (fletcher32) {
if ( H5Pset_fletcher32( plist_id) < 0 )
return -1;
}
/* Then shuffle (not if blosc is activated) */
if ((shuffle) && (strcmp(complib, "blosc") != 0)) {
if ( H5Pset_shuffle( plist_id) < 0 )
return -1;
}
/* Finally compression */
if (compress) {
cd_values[0] = compress;
cd_values[1] = (int)(atof(obversion) * 10);
if (extdim <0)
cd_values[2] = CArray;
else
cd_values[2] = EArray;
/* The default compressor in HDF5 (zlib) */
if (strcmp(complib, "zlib") == 0) {
if ( H5Pset_deflate( plist_id, compress) < 0 )
return -1;
}
/* The Blosc compressor does accept parameters */
else if (strcmp(complib, "blosc") == 0) {
cd_values[4] = compress;
cd_values[5] = shuffle;
if ( H5Pset_filter( plist_id, FILTER_BLOSC, H5Z_FLAG_OPTIONAL, 6, cd_values) < 0 )
return -1;
}
/* The LZO compressor does accept parameters */
else if (strcmp(complib, "lzo") == 0) {
if ( H5Pset_filter( plist_id, FILTER_LZO, H5Z_FLAG_OPTIONAL, 3, cd_values) < 0 )
return -1;
}
/* The bzip2 compress does accept parameters */
else if (strcmp(complib, "bzip2") == 0) {
if ( H5Pset_filter( plist_id, FILTER_BZIP2, H5Z_FLAG_OPTIONAL, 3, cd_values) < 0 )
return -1;
}
else {
/* Compression library not supported */
fprintf(stderr, "Compression library not supported\n");
return -1;
}
}
/* Create the (chunked) dataset */
if ((dataset_id = H5Dcreate(loc_id, dset_name, type_id,
space_id, plist_id )) < 0 )
goto out;
}
else { /* Not chunked case */
/* Create the dataset. */
if ((dataset_id = H5Dcreate(loc_id, dset_name, type_id,
space_id, H5P_DEFAULT )) < 0 )
goto out;
}
/* Write the dataset only if there is data to write */
if (data)
{
if ( H5Dwrite( dataset_id, type_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, data ) < 0 )
goto out;
}
/* Terminate access to the data space. */
if ( H5Sclose( space_id ) < 0 )
return -1;
/* End access to the property list */
if (plist_id)
if ( H5Pclose( plist_id ) < 0 )
goto out;
/* Release resources */
if (maxdims)
free(maxdims);
return dataset_id;
out:
H5Dclose( dataset_id );
H5Sclose( space_id );
if (maxdims)
free(maxdims);
if (dims_chunk)
free(dims_chunk);
return -1;
}
/* -----------------------------------------------------------------------------
//
// -------------------------------------------------------------------------- */
void Create2DExpandableDataset(hid_t gid, const QString& dsetName, int lambertSize, hsize_t chunk_dim,
double* north, double* south)
{
hid_t dataspace = -1;
hid_t filespace = -1;
hid_t dataset = -1;
hid_t cparms = -1;
herr_t status = -1;
hsize_t maxdims[2] = { H5S_UNLIMITED, H5S_UNLIMITED }; // Allow for 2D Arrays
hsize_t chunk_dims[2] = { 1, chunk_dim };
hsize_t dims[2] = { 1ULL, static_cast<hsize_t>(lambertSize) };
hsize_t size[2];
hsize_t offset[2];
hsize_t hyperDims[2] = { 1ULL, static_cast<hsize_t>(lambertSize) };
double fillvalue = -1.0;
int rank = 2;
// int i = 0;
// int strSize = 0;
// char buffer[32];
if (lambertSize == 1)
{
rank = 1;
}
/* printf("CPU [%d,%d] Writing '%s' initial value to array. \n", home->myDomain, home->cycle, dsetName);
fflush(stdout);*/
/* Create the data space with unlimited dimensions */
dataspace = H5Screate_simple(rank, dims, maxdims);
/* Modify dataset creation properties, i.e. enable chunking.*/
cparms = H5Pcreate(H5P_DATASET_CREATE);
status = H5Pset_chunk(cparms, rank, chunk_dims);
status = H5Pset_fill_value(cparms, H5T_NATIVE_DOUBLE, &fillvalue);
/* Create a new dataset within the file using cparms creation properties.*/
// dataset = H5Dcreate(gid, dsetName, H5T_NATIVE_DOUBLE, dataspace, cparms, H5P_DEFAULT, H5P_DEFAULT);
dataset = H5Dcreate2(gid, dsetName.toLatin1().data(), H5T_NATIVE_DOUBLE, dataspace, H5P_DEFAULT, cparms, H5P_DEFAULT);
/* Extend the dataset. This call assures that dataset is at least 1 */
size[0] = 1; // Single Row
size[1] = chunk_dim; // N Columns - What ever the user asked for
status = H5Dset_extent(dataset, size);
/* Select a hyperslab. */
filespace = H5Dget_space(dataset);
offset[0] = 0; // Offset 0 row
offset[1] = 0; // Offset 0 Column
status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, hyperDims, NULL);
/*
* Write the data to the hyperslab.
*/
status = H5Dwrite(dataset, H5T_NATIVE_DOUBLE, dataspace, filespace, H5P_DEFAULT, north);
if (status < 0)
{
qDebug() << "Error Writing Chunked Data set to file" ;
}
filespace = H5Dget_space(dataset);
offset[0] = 0; // Offset 0 row
offset[1] = lambertSize; // Offset 0 Column
status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, hyperDims, NULL);
/*
* Write the data to the hyperslab.
*/
status = H5Dwrite(dataset, H5T_NATIVE_DOUBLE, dataspace, filespace, H5P_DEFAULT, south);
if (status < 0)
{
qDebug() << "Error Writing Chunked Data set to file" ;
}
H5Dclose(dataset);
H5Sclose(dataspace);
H5Sclose(filespace);
H5Pclose(cparms);
}
/*-------------------------------------------------------------------------
* Function: create_scale_offset_dset_int
*
* Purpose: Create a dataset of INT datatype with scale-offset filter
*
* Return: Success: 0
* Failure: -1
*
* Programmer: Raymond Lu
* 21 January 2011
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
int
create_scale_offset_dsets_int(hid_t fid, hid_t fsid, hid_t msid)
{
#ifdef H5_HAVE_FILTER_SCALEOFFSET
hid_t dataset; /* dataset handles */
hid_t dcpl;
int data[NX][NY]; /* data to write */
int fillvalue = -2;
hsize_t chunk[RANK] = {CHUNK0, CHUNK1};
int i, j;
/*
* Data and output buffer initialization.
*/
for (j = 0; j < NX; j++) {
for (i = 0; i < NY; i++)
data[j][i] = i + j;
}
/*
* 0 1 2 3 4 5
* 1 2 3 4 5 6
* 2 3 4 5 6 7
* 3 4 5 6 7 8
* 4 5 6 7 8 9
* 5 6 7 8 9 10
*/
/*
* Create the dataset creation property list, add the Scale-Offset
* filter, set the chunk size, and set the fill value.
*/
if((dcpl = H5Pcreate(H5P_DATASET_CREATE)) < 0)
TEST_ERROR
if(H5Pset_scaleoffset(dcpl, H5Z_SO_INT, H5Z_SO_INT_MINBITS_DEFAULT) < 0)
TEST_ERROR
if(H5Pset_chunk(dcpl, RANK, chunk) < 0)
TEST_ERROR
if(H5Pset_fill_value(dcpl, H5T_NATIVE_INT, &fillvalue) < 0)
TEST_ERROR
/*
* Create a new dataset within the file using defined dataspace, little
* endian datatype and default dataset creation properties.
*/
if((dataset = H5Dcreate2(fid, DATASETNAME10, H5T_STD_I32LE, fsid,
H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
TEST_ERROR
/*
* Write the data to the dataset using default transfer properties.
*/
if(H5Dwrite(dataset, H5T_NATIVE_INT, msid, fsid, H5P_DEFAULT, data) < 0)
TEST_ERROR
/* Close dataset */
if(H5Dclose(dataset) < 0)
TEST_ERROR
/* Now create a dataset with a big-endian type */
if((dataset = H5Dcreate2(fid, DATASETNAME11, H5T_STD_I32BE, fsid,
H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
TEST_ERROR
if(H5Dwrite(dataset, H5T_NATIVE_INT, msid, fsid, H5P_DEFAULT, data) < 0)
TEST_ERROR
if(H5Dclose(dataset) < 0)
TEST_ERROR
/*
* Close/release resources.
*/
if(H5Pclose(dcpl) < 0)
TEST_ERROR
#else /* H5_HAVE_FILTER_SCALEOFFSET */
const char *not_supported= "Scaleoffset filter is not enabled. Can't create the dataset.";
puts(not_supported);
#endif /* H5_HAVE_FILTER_SCALEOFFSET */
return 0;
#ifdef H5_HAVE_FILTER_SCALEOFFSET
error:
H5E_BEGIN_TRY {
H5Pclose(dcpl);
H5Dclose(dataset);
} H5E_END_TRY;
return -1;
#endif /* H5_HAVE_FILTER_SCALEOFFSET */
}
