//--------------------------------------------------------------------------
// Function: H5Library::termH5cpp (static)
///\brief Sends request for the C layer to terminate.
///\par Description
/// If the C library fails to terminate, exit with a failure.
// Programmer Binh-Minh Ribler - September, 2015
//--------------------------------------------------------------------------
void H5Library::termH5cpp()
{
// Close the C library
herr_t ret_value = H5close();
if (ret_value == -1)
exit(-1);
}
/*-------------------------------------------------------------------------
* Function: main
*
* Purpose:
*
* Return: Success:
*
* Failure:
*
* Programmer: Robb Matzke
* Tuesday, June 16, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
int
main (void)
{
int nerrors=0;
/*
* Open the library explicitly for thread-safe builds, so per-thread
* things are initialized correctly.
*/
#ifdef H5_HAVE_THREADSAFE
H5open();
#endif /* H5_HAVE_THREADSAFE */
nerrors += test_find ()<0?1:0;
nerrors += test_set ()<0?1:0;
nerrors += test_clear()<0?1:0;
nerrors += test_copy ()<0?1:0;
nerrors += test_shift()<0?1:0;
nerrors += test_increment ()<0?1:0;
nerrors += test_decrement ()<0?1:0;
nerrors += test_negate ()<0?1:0;
if (nerrors) {
printf("***** %u FAILURE%s! *****\n",
nerrors, 1==nerrors?"":"S");
exit(1);
}
printf("All bit tests passed.\n");
#ifdef H5_HAVE_THREADSAFE
H5close();
#endif /* H5_HAVE_THREADSAFE */
return 0;
}
/*-------------------------------------------------------------------------
* Function: main
*
* Purpose:
*
* Return: Success:
*
* Failure:
*
* Programmer: Robb Matzke
* Tuesday, June 16, 1998
*
*-------------------------------------------------------------------------
*/
int
main(void)
{
int nerrors = 0;
/*
* Open the library explicitly.
*/
H5open();
nerrors += test_find() < 0 ? 1 : 0;
nerrors += test_set() < 0 ? 1 : 0;
nerrors += test_clear() < 0 ? 1 : 0;
nerrors += test_copy() < 0 ? 1 : 0;
nerrors += test_shift() < 0 ? 1 : 0;
nerrors += test_increment() < 0 ? 1 : 0;
nerrors += test_decrement() < 0 ? 1 : 0;
nerrors += test_negate() < 0 ? 1 : 0;
if(nerrors) {
printf("***** %u FAILURE%s! *****\n",
nerrors, 1 == nerrors ? "" : "S");
exit(1);
}
printf("All bit tests passed.\n");
H5close();
return 0;
}
//--------------------------------------------------------------------------
// Function: H5Library::close (static)
///\brief Flushes all data to disk, closes files, and cleans up memory.
///
///\exception H5::LibraryIException
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
void H5Library::close()
{
herr_t ret_value = H5close();
if (ret_value < 0)
{
throw LibraryIException("H5Library::close", "H5close failed");
}
}
/*---------------------------------------------------------------------------
* Name: h5close_c
* Purpose: Calls H5close call to close C HDF5 library
* Returns: 0 on success, -1 on failure
* Programmer: Elena Pourmal
* Friday, November 17, 2000
* Modifications:
*---------------------------------------------------------------------------*/
int_f
nh5close_c()
{
int ret_value = -1;
if (H5close() < 0) return ret_value;
ret_value = 0;
return ret_value;
}
int main ( int argc, char *argv[] )
{
char *prog_name = "mat2hdf";
int c;
scats_mat_t *mat;
SCATS_MATVAR *matvar;
hid_t hdf_id;
if ( argc > 1 && !strcmp(argv[1],"--version")) {
printf("mat2hdf v%d.%d.%d (compiled %s, %s for %s)\n",
SCATS_MAJOR_VERSION, SCATS_MINOR_VERSION, SCATS_RELEASE_LEVEL,
__DATE__, __TIME__, SCATS_PLATFORM );
exit(0);
} else if ( argc > 1 && !strcmp(argv[1],"--help") ) {
Scats_Help(helpstr);
exit(0);
} else if ( argc < 3 )
Scats_Help(helpstr);
Scats_LogInit(prog_name);
while ((c = getopt(argc, argv, "v")) != EOF) {
switch (c) {
case 'v':
Scats_SetVerbose(1,0);
break;
default:
Scats_Warning("%c not a valid option\n", c);
break;
}
}
mat = Scats_MatOpen( argv[optind],SCATS_ACC_RDONLY );
if ( !mat )
Scats_Error("Error opening %s\n", argv[1]);
H5open();
hdf_id = Scats_HDFOpen(argv[optind+1], SCATS_ACC_RDWR);
if ( hdf_id < 0 ) {
printf("Error opening HDF file %s\n", argv[2]);
Scats_MatClose(mat);
return 1;
}
while ( (matvar = Scats_MatVarReadNext(mat)) != NULL ) {
write_mat(hdf_id,matvar);
Scats_MatVarFree(matvar);
matvar = NULL;
}
Scats_MatClose(mat);
Scats_HDFClose(hdf_id);
H5close();
return 0;
}
/****if* H5_f/h5close_c
* NAME
* h5close_c
* PURPOSE
* Calls H5close call to close C HDF5 library
* RETURNS
* 0 on success, -1 on failure
* AUTHOR
* Elena Pourmal
* SOURCE
*/
int_f
nh5close_c(void)
/******/
{
int ret_value = -1;
if (H5close() < 0) return ret_value;
ret_value = 0;
return ret_value;
}
/*
* Class: hdf_hdf5lib_H5
* Method: H5close
* Signature: ()I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5close
(JNIEnv *env, jclass clss)
{
herr_t retVal = H5close();
if (retVal < 0)
h5libraryError(env);
return (jint)retVal;
} /* end Java_hdf_hdf5lib_H5_H5close */
med_err
MEDlibraryClose(void)
{
med_err _ret = -1;
_MEDmodeErreurVerrouiller();
if ( H5close() < 0) {
MED_ERR_(_ret,MED_ERR_CLOSE,MED_ERR_LIBRARY,"");
goto ERROR;
}
_ret = 0;
ERROR:
return _ret;
}
bool dump_hdf5(const char *file_name, Mesh *mesh) {
herr_t status;
// init HDF5
H5open();
// create a file
hid_t file_id = H5Fcreate(file_name, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
// create main group
hid_t mesh_group_id = H5Gcreate(file_id, "/mesh3d", 0);
// version
hsize_t dims = 2;
hid_t dataspace_id = H5Screate_simple(1, &dims, NULL);
hid_t attr_ver = H5Acreate(mesh_group_id, "version", H5T_STD_I8BE, dataspace_id, H5P_DEFAULT);
char attr_data[2] = { 1, 0 };
status = H5Awrite(attr_ver, H5T_NATIVE_CHAR, attr_data);
H5Aclose(attr_ver);
H5Sclose(dataspace_id);
// description
hid_t type = H5Tcopy(H5T_C_S1);
status = H5Tset_size(type, H5T_VARIABLE);
const char *descr = "Test mesh";
hid_t dataspace_id2 = H5Screate(H5S_SCALAR);
hid_t attr_descr = H5Acreate(mesh_group_id, "description", type, dataspace_id2, H5P_DEFAULT);
status = H5Awrite(attr_descr, type, &descr);
H5Aclose(attr_descr);
H5Tclose(type);
H5Sclose(dataspace_id2);
save_vertices(mesh_group_id, mesh);
save_elements(mesh_group_id, mesh);
save_bc(mesh_group_id, mesh);
status = H5Gclose(mesh_group_id); // close the group
status = H5Fclose(file_id); // close the file
// deinit HDF5
H5close();
return 0;
}
/*-------------------------------------------------------------------------
* Function: h5_reset
*
* Purpose: Reset the library by closing it.
*
* Return: void
*
* Programmer: Robb Matzke
* Friday, November 20, 1998
*
*-------------------------------------------------------------------------
*/
void
h5_reset(void)
{
HDfflush(stdout);
HDfflush(stderr);
H5close();
/* Save current error stack reporting routine and redirect to our local one */
HDassert(err_func == NULL);
H5Eget_auto2(H5E_DEFAULT, &err_func, NULL);
H5Eset_auto2(H5E_DEFAULT, h5_errors, NULL);
/*
* I commented this chunk of code out because it's not clear what diagnostics
* were being output and under what circumstances, and creating this file
* is throwing off debugging some of the tests. I can't see any _direct_
* harm in keeping this section of code, but I can't see any _direct_
* benefit right now either. If we figure out under which circumstances
* diagnostics are being output, we should enable this behavior based on
* appropriate configure flags/macros. QAK - 2007/12/20
*/
#ifdef OLD_WAY
{
char filename[1024];
/*
* Cause the library to emit some diagnostics early so they don't
* interfere with other formatted output.
*/
sprintf(filename, "/tmp/h5emit-%05d.h5", HDgetpid());
H5E_BEGIN_TRY {
hid_t file = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT,
H5P_DEFAULT);
hid_t grp = H5Gcreate2(file, "emit", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Gclose(grp);
H5Fclose(file);
HDunlink(filename);
} H5E_END_TRY;
}
#endif /* OLD_WAY */
}
extern void profile_fini(void)
{
H5close(); /* make sure all H5 Objects are closed */
return;
}
/* ****************************************************************************************************************************** */
int main(int argc, char *argv[]) {
hid_t fileID, datasetID, dataspaceID;
hsize_t dims[3] = {MAX_X, MAX_Y, MAX_T};
herr_t hErrVal;
float floatDataPoint[10];
int id, i, j, k;
float temp[MAX_X][MAX_Y][MAX_T];
char *strPerDim[3];
float valPerDim[3];
/* Create phony data. */
for(i=0,id=0; i<MAX_X; i++)
for(j=0; j<MAX_Y; j++)
for(k=0; k<MAX_T; k++)
temp[i][j][k] = id++;
/* Load the library -- not required on most platforms. */
hErrVal = H5open();
mjrHDF5_chkError(hErrVal);
/* Create a new file using default properties. */
fileID = H5Fcreate(TST_FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
mjrHDF5_chkError(fileID);
hErrVal = mjrHDF5_put_gblAtt_oneFCstr(fileID, "Author", "Mitch Richling");
mjrHDF5_chkError(hErrVal);
hErrVal = mjrHDF5_put_gblAtt_oneFCstr(fileID, "title", "Example File");
mjrHDF5_chkError(hErrVal);
/* Create the data space for the dataset. */
dataspaceID = H5Screate_simple(3, dims, NULL);
mjrHDF5_chkError(dataspaceID);
/* Create the dataset. */
datasetID = H5Dcreate(fileID, "/dset", H5T_IEEE_F32BE, dataspaceID, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
mjrHDF5_chkError(datasetID);
/* Try to use standard unit names and formats... */
hErrVal = mjrHDF5_put_att_oneFCstr(datasetID, "units", "Celsius");
mjrHDF5_chkError(hErrVal);
/* Use this value for labeling plots and the like by programs that
also support netCDF */
hErrVal = mjrHDF5_put_att_oneFCstr(datasetID, "long_name", "Some Name For Plots");
mjrHDF5_chkError(hErrVal);
/* Add an array of strings to name each dim.*/
strPerDim[0] = "lat";
strPerDim[1] = "lon";
strPerDim[2] = "temp";
hErrVal = mjrHDF5_put_att_arrVCstr(datasetID, "dimNames", strPerDim, 3);
mjrHDF5_chkError(hErrVal);
/* Add an array of strings to to give units for each dim.*/
strPerDim[0] = "degrees";
strPerDim[1] = "degrees";
strPerDim[2] = "hours";
hErrVal = mjrHDF5_put_att_arrVCstr(datasetID, "dimUnits", strPerDim, 3);
mjrHDF5_chkError(hErrVal);
/* Add annotation describing minimum values for each dim. */
valPerDim[0] = 0.0;
valPerDim[1] = 0.0;
valPerDim[2] = 0.0;
hErrVal = mjrHDF5_put_att_arry(datasetID, H5T_IEEE_F32BE, "dimStart", valPerDim, H5T_NATIVE_FLOAT, 3);
mjrHDF5_chkError(hErrVal);
/* Add annotation describing the "step" between values on each dim. */
valPerDim[0] = 10.0;
valPerDim[1] = 20.0;
valPerDim[2] = 24.0;
hErrVal = mjrHDF5_put_att_arry(datasetID, H5T_IEEE_F32BE, "dimStep", valPerDim, H5T_NATIVE_FLOAT, 3);
mjrHDF5_chkError(hErrVal);
/* Just for fun, create a floating point attribute! */
floatDataPoint[0] = 1.234;
mjrHDF5_put_att_sclr(datasetID, H5T_IEEE_F32BE, "Pressure", floatDataPoint, H5T_NATIVE_FLOAT);
/* Write some data into our dataset. */
hErrVal = H5Dwrite(datasetID, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, H5P_DEFAULT, temp);
mjrHDF5_chkError(hErrVal);
/* End access to the dataset and release resources used by it. */
hErrVal = H5Dclose(datasetID);
mjrHDF5_chkError(hErrVal);
/* Terminate access to the data space. */
hErrVal = H5Sclose(dataspaceID);
mjrHDF5_chkError(hErrVal);
/* Close the file. */
hErrVal = H5Fclose(fileID);
mjrHDF5_chkError(hErrVal);
/* Unload the library and free any remaining resources. */
hErrVal = H5close();
mjrHDF5_chkError(hErrVal);
return 0;
} /* end func main */
int main(int argc, char **argv)
{
int mpi_size, mpi_rank; /* mpi variables */
H5Ptest_param_t ndsets_params, ngroups_params;
H5Ptest_param_t collngroups_params;
H5Ptest_param_t io_mode_confusion_params;
/* Un-buffer the stdout and stderr */
setbuf(stderr, NULL);
setbuf(stdout, NULL);
MPI_Init(&argc, &argv);
MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
dim0 = ROW_FACTOR*mpi_size;
dim1 = COL_FACTOR*mpi_size;
if (MAINPROCESS) {
printf("===================================\n");
printf("PHDF5 TESTS START\n");
printf("===================================\n");
}
H5open();
h5_show_hostname();
/* Initialize testing framework */
TestInit(argv[0], usage, parse_options);
/* Tests are generally arranged from least to most complexity... */
AddTest("mpiodup", test_fapl_mpio_dup, NULL,
"fapl_mpio duplicate", NULL);
AddTest("posixdup", test_fapl_mpiposix_dup, NULL,
"fapl_mpiposix duplicate", NULL);
AddTest("split", test_split_comm_access, NULL,
"dataset using split communicators", PARATESTFILE);
AddTest("idsetw", dataset_writeInd, NULL,
"dataset independent write", PARATESTFILE);
AddTest("idsetr", dataset_readInd, NULL,
"dataset independent read", PARATESTFILE);
AddTest("cdsetw", dataset_writeAll, NULL,
"dataset collective write", PARATESTFILE);
AddTest("cdsetr", dataset_readAll, NULL,
"dataset collective read", PARATESTFILE);
AddTest("eidsetw", extend_writeInd, NULL,
"extendible dataset independent write", PARATESTFILE);
AddTest("eidsetr", extend_readInd, NULL,
"extendible dataset independent read", PARATESTFILE);
AddTest("ecdsetw", extend_writeAll, NULL,
"extendible dataset collective write", PARATESTFILE);
AddTest("ecdsetr", extend_readAll, NULL,
"extendible dataset collective read", PARATESTFILE);
AddTest("eidsetw2", extend_writeInd2, NULL,
"extendible dataset independent write #2", PARATESTFILE);
AddTest("selnone", none_selection_chunk, NULL,
"chunked dataset with none-selection", PARATESTFILE);
AddTest("calloc", test_chunk_alloc, NULL,
"parallel extend Chunked allocation on serial file", PARATESTFILE);
AddTest("fltread", test_filter_read, NULL,
"parallel read of dataset written serially with filters", PARATESTFILE);
#ifdef H5_HAVE_FILTER_DEFLATE
AddTest("cmpdsetr", compress_readAll, NULL,
"compressed dataset collective read", PARATESTFILE);
#endif /* H5_HAVE_FILTER_DEFLATE */
ndsets_params.name = PARATESTFILE;
ndsets_params.count = ndatasets;
AddTest("ndsetw", multiple_dset_write, NULL,
"multiple datasets write", &ndsets_params);
ngroups_params.name = PARATESTFILE;
ngroups_params.count = ngroups;
AddTest("ngrpw", multiple_group_write, NULL,
"multiple groups write", &ngroups_params);
AddTest("ngrpr", multiple_group_read, NULL,
"multiple groups read", &ngroups_params);
AddTest("compact", compact_dataset, NULL,
"compact dataset test", PARATESTFILE);
collngroups_params.name = PARATESTFILE;
collngroups_params.count = ngroups;
AddTest("cngrpw", collective_group_write, NULL,
"collective group and dataset write", &collngroups_params);
AddTest("ingrpr", independent_group_read, NULL,
"independent group and dataset read", &collngroups_params);
AddTest("bigdset", big_dataset, NULL,
"big dataset test", PARATESTFILE);
AddTest("fill", dataset_fillvalue, NULL,
"dataset fill value", PARATESTFILE);
AddTest("cchunk1",
coll_chunk1,NULL, "simple collective chunk io",PARATESTFILE);
AddTest("cchunk2",
coll_chunk2,NULL, "noncontiguous collective chunk io",PARATESTFILE);
AddTest("cchunk3",
coll_chunk3,NULL, "multi-chunk collective chunk io",PARATESTFILE);
AddTest("cchunk4",
coll_chunk4,NULL, "collective chunk io with partial non-selection ",PARATESTFILE);
if((mpi_size < 3)&& MAINPROCESS ) {
printf("Collective chunk IO optimization APIs ");
printf("needs at least 3 processes to participate\n");
printf("Collective chunk IO API tests will be skipped \n");
}
AddTest((mpi_size <3)? "-cchunk5":"cchunk5" ,
coll_chunk5,NULL,
"linked chunk collective IO without optimization",PARATESTFILE);
AddTest((mpi_size < 3)? "-cchunk6" : "cchunk6",
coll_chunk6,NULL,
"multi-chunk collective IO without optimization",PARATESTFILE);
AddTest((mpi_size < 3)? "-cchunk7" : "cchunk7",
coll_chunk7,NULL,
"linked chunk collective IO with optimization",PARATESTFILE);
AddTest((mpi_size < 3)? "-cchunk8" : "cchunk8",
coll_chunk8,NULL,
"linked chunk collective IO transferring to multi-chunk",PARATESTFILE);
AddTest((mpi_size < 3)? "-cchunk9" : "cchunk9",
coll_chunk9,NULL,
"multiple chunk collective IO with optimization",PARATESTFILE);
AddTest((mpi_size < 3)? "-cchunk10" : "cchunk10",
coll_chunk10,NULL,
"multiple chunk collective IO transferring to independent IO",PARATESTFILE);
/* irregular collective IO tests*/
AddTest("ccontw",
coll_irregular_cont_write,NULL,
"collective irregular contiguous write",PARATESTFILE);
AddTest("ccontr",
coll_irregular_cont_read,NULL,
"collective irregular contiguous read",PARATESTFILE);
AddTest("cschunkw",
coll_irregular_simple_chunk_write,NULL,
"collective irregular simple chunk write",PARATESTFILE);
AddTest("cschunkr",
coll_irregular_simple_chunk_read,NULL,
"collective irregular simple chunk read",PARATESTFILE);
AddTest("ccchunkw",
coll_irregular_complex_chunk_write,NULL,
"collective irregular complex chunk write",PARATESTFILE);
AddTest("ccchunkr",
coll_irregular_complex_chunk_read,NULL,
"collective irregular complex chunk read",PARATESTFILE);
#if 0
if((mpi_size > 3) && MAINPROCESS) {
printf("Collective irregular chunk IO tests haven't been tested \n");
printf(" for the number of process greater than 3.\n");
printf("Please try with the number of process \n");
printf(" no greater than 3 for collective irregular chunk IO test.\n");
printf("Collective irregular chunk tests will be skipped \n");
}
AddTest((mpi_size > 3) ? "-ccontw" : "ccontw",
coll_irregular_cont_write,NULL,
"collective irregular contiguous write",PARATESTFILE);
AddTest((mpi_size > 3) ? "-ccontr" : "ccontr",
coll_irregular_cont_read,NULL,
"collective irregular contiguous read",PARATESTFILE);
AddTest((mpi_size > 3) ? "-cschunkw" : "cschunkw",
coll_irregular_simple_chunk_write,NULL,
"collective irregular simple chunk write",PARATESTFILE);
AddTest((mpi_size > 3) ? "-cschunkr" : "cschunkr",
coll_irregular_simple_chunk_read,NULL,
"collective irregular simple chunk read",PARATESTFILE);
AddTest((mpi_size > 3) ? "-ccchunkw" : "ccchunkw",
coll_irregular_complex_chunk_write,NULL,
"collective irregular complex chunk write",PARATESTFILE);
AddTest((mpi_size > 3) ? "-ccchunkr" : "ccchunkr",
coll_irregular_complex_chunk_read,NULL,
"collective irregular complex chunk read",PARATESTFILE);
#endif
AddTest("null", null_dataset, NULL,
"null dataset test", PARATESTFILE);
io_mode_confusion_params.name = PARATESTFILE;
io_mode_confusion_params.count = 0; /* value not used */
AddTest("I/Omodeconf", io_mode_confusion, NULL,
"I/O mode confusion test -- hangs quickly on failure",
&io_mode_confusion_params);
/* Display testing information */
TestInfo(argv[0]);
/* setup file access property list */
fapl = H5Pcreate (H5P_FILE_ACCESS);
H5Pset_fapl_mpio(fapl, MPI_COMM_WORLD, MPI_INFO_NULL);
/* Parse command line arguments */
TestParseCmdLine(argc, argv);
if (facc_type == FACC_MPIPOSIX && MAINPROCESS) {
printf("===================================\n"
" Using MPIPOSIX driver\n"
"===================================\n");
}
if (dxfer_coll_type == DXFER_INDEPENDENT_IO && MAINPROCESS) {
printf("===================================\n"
" Using Independent I/O with file set view to replace collective I/O \n"
"===================================\n");
}
/* Perform requested testing */
PerformTests();
/* make sure all processes are finished before final report, cleanup
* and exit.
*/
MPI_Barrier(MPI_COMM_WORLD);
/* Display test summary, if requested */
if (MAINPROCESS && GetTestSummary())
TestSummary();
/* Clean up test files */
h5_cleanup(FILENAME, fapl);
nerrors += GetTestNumErrs();
/* Gather errors from all processes */
{
int temp;
MPI_Allreduce(&nerrors, &temp, 1, MPI_INT, MPI_MAX, MPI_COMM_WORLD);
nerrors=temp;
}
if (MAINPROCESS) { /* only process 0 reports */
printf("===================================\n");
if (nerrors)
printf("***PHDF5 tests detected %d errors***\n", nerrors);
else
printf("PHDF5 tests finished with no errors\n");
printf("===================================\n");
}
/* close HDF5 library */
H5close();
/* MPI_Finalize must be called AFTER H5close which may use MPI calls */
MPI_Finalize();
/* cannot just return (nerrors) because exit code is limited to 1byte */
return(nerrors!=0);
}
int
main(int argc, char **argv)
{
int mpi_size, mpi_rank; /* mpi variables */
int ret_code;
MPI_Init(&argc, &argv);
MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
/* Attempt to turn off atexit post processing so that in case errors
* happen during the test and the process is aborted, it will not get
* hang in the atexit post processing in which it may try to make MPI
* calls. By then, MPI calls may not work.
*/
if (H5dont_atexit() < 0){
printf("Failed to turn off atexit processing. Continue.\n", mpi_rank);
};
H5open();
if (parse_options(argc, argv) != 0){
if (MAINPROCESS)
usage();
goto finish;
}
if (MAINPROCESS){
printf("===================================\n");
printf("MPI functionality tests\n");
printf("===================================\n");
}
if (VERBOSE_MED)
h5_show_hostname();
fapl = H5Pcreate (H5P_FILE_ACCESS);
H5Pset_fapl_mpio(fapl, MPI_COMM_WORLD, MPI_INFO_NULL);
/* set alarm. */
ALARM_ON;
/*=======================================
* MPIO 1 write Many read test
*=======================================*/
MPI_BANNER("MPIO 1 write Many read test...");
ret_code = test_mpio_1wMr(filenames[0], USENONE);
ret_code = errors_sum(ret_code);
if (mpi_rank==0 && ret_code > 0){
printf("***FAILED with %d total errors\n", ret_code);
nerrors += ret_code;
}
/* test atomicity and file sync in high verbose mode only */
/* since they often hang when broken and PHDF5 does not use them. */
if (VERBOSE_HI){
MPI_BANNER("MPIO 1 write Many read test with atomicity...");
ret_code = test_mpio_1wMr(filenames[0], USEATOM);
ret_code = errors_sum(ret_code);
if (mpi_rank==0 && ret_code > 0){
printf("***FAILED with %d total errors\n", ret_code);
nerrors += ret_code;
}
MPI_BANNER("MPIO 1 write Many read test with file sync...");
ret_code = test_mpio_1wMr(filenames[0], USEFSYNC);
ret_code = errors_sum(ret_code);
if (mpi_rank==0 && ret_code > 0){
printf("***FAILED with %d total errors\n", ret_code);
nerrors += ret_code;
}
}
/*=======================================
* MPIO MPIO File size range test
*=======================================*/
MPI_BANNER("MPIO File size range test...");
#ifndef H5_HAVE_WIN32_API
ret_code = test_mpio_gb_file(filenames[0]);
ret_code = errors_sum(ret_code);
if (mpi_rank==0 && ret_code > 0){
printf("***FAILED with %d total errors\n", ret_code);
nerrors += ret_code;
}
#else
if (mpi_rank==0)
printf(" will be skipped on Windows (JIRA HDDFV-8064)\n");
#endif
/*=======================================
* MPIO independent overlapping writes
*=======================================*/
MPI_BANNER("MPIO independent overlapping writes...");
ret_code = test_mpio_overlap_writes(filenames[0]);
ret_code = errors_sum(ret_code);
if (mpi_rank==0 && ret_code > 0){
printf("***FAILED with %d total errors\n", ret_code);
nerrors += ret_code;
}
/*=======================================
* MPIO complicated derived datatype test
*=======================================*/
MPI_BANNER("MPIO complicated derived datatype test...");
ret_code = test_mpio_derived_dtype(filenames[0]);
ret_code = errors_sum(ret_code);
if (mpi_rank==0 && ret_code > 0){
printf("***FAILED with %d total errors\n", ret_code);
nerrors += ret_code;
}
/*=======================================
* MPIO special collective IO test
*=======================================*/
if (mpi_size < 4) {
MPI_BANNER("MPIO special collective io test SKIPPED.");
if (mpi_rank == 0)
printf("This test needs at least four processes to run.\n");
ret_code = 0;
goto sc_finish;
} /* end if */
MPI_BANNER("MPIO special collective io test...");
ret_code = test_mpio_special_collective(filenames[0]);
sc_finish:
ret_code = errors_sum(ret_code);
if (mpi_rank==0 && ret_code > 0){
printf("***FAILED with %d total errors\n", ret_code);
nerrors += ret_code;
}
finish:
/* make sure all processes are finished before final report, cleanup
* and exit.
*/
MPI_Barrier(MPI_COMM_WORLD);
if (MAINPROCESS){ /* only process 0 reports */
printf("===================================\n");
if (nerrors){
printf("***MPI tests detected %d errors***\n", nerrors);
}
else{
printf("MPI tests finished with no errors\n");
}
printf("===================================\n");
}
/* turn off alarm */
ALARM_OFF;
h5_cleanup(FILENAME, fapl);
H5close();
/* MPI_Finalize must be called AFTER H5close which may use MPI calls */
MPI_Finalize();
/* cannot just return (nerrors) because exit code is limited to 1byte */
return(nerrors!=0);
}
/* Get the size of the type */
dataSize = H5Tget_size(dataTypeID);
if(dataSize == 0) {
printf("ERROR: Failure in H5Tget_size().\n");
exit(1);
} /* end if */
printf(" Size: %3lu ", (unsigned long)dataSize);
hErrVal = H5Tclose(dataTypeID);
mjrHDF5_chkError(hErrVal);
printf(" Name: %s \n", attrName);
hErrVal = H5Aclose(attrID);
mjrHDF5_chkError(hErrVal);
} /* end for */
} /* end if */
/* Close the dataset. */
hErrVal = H5Dclose(dataSetID);
/* Close the file. */
hErrVal = H5Fclose(fileID);
/* Unload the library and free any remaining resources. */
hErrVal = H5close();
mjrHDF5_chkError(hErrVal);
return 0;
} /* end func main */
void stfio::importHDF5File(const std::string& fName, Recording& ReturnData, ProgressInfo& progDlg) {
/* Create a new file using default properties. */
hid_t file_id = H5Fopen(fName.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
/* H5TBread_table
const int NRECORDS = 1;*/
const int NFIELDS = 3;
/* Calculate the size and the offsets of our struct members in memory */
size_t rt_offset[NFIELDS] = { HOFFSET( rt, channels ),
HOFFSET( rt, date ),
HOFFSET( rt, time )};
rt rt_buf[1];
size_t rt_sizes[NFIELDS] = { sizeof( rt_buf[0].channels),
sizeof( rt_buf[0].date),
sizeof( rt_buf[0].time)};
herr_t status=H5TBread_table( file_id, "description", sizeof(rt), rt_offset, rt_sizes, rt_buf );
if (status < 0) {
std::string errorMsg("Exception while reading description in stfio::importHDF5File");
throw std::runtime_error(errorMsg);
}
int numberChannels =rt_buf[0].channels;
if ( ReturnData.SetDate(rt_buf[0].date)
|| ReturnData.SetTime(rt_buf[0].time) ) {
std::cout << "Warning HDF5: could not decode date/time " << rt_buf[0].date << " " << rt_buf[0].time << std::endl;
}
/* Create the data space for the dataset. */
hsize_t dims;
H5T_class_t class_id;
size_t type_size;
std::string description, comment;
hid_t group_id = H5Gopen2(file_id, "/comment", H5P_DEFAULT);
status = H5Lexists(group_id, "/comment/description", 0);
if (status==1) {
status = H5LTget_dataset_info( file_id, "/comment/description", &dims, &class_id, &type_size );
if (status >= 0) {
description.resize( type_size );
status = H5LTread_dataset_string (file_id, "/comment/description", &description[0]);
if (status < 0) {
std::string errorMsg("Exception while reading description in stfio::importHDF5File");
throw std::runtime_error(errorMsg);
}
}
}
ReturnData.SetFileDescription(description);
status = H5Lexists(group_id, "/comment/comment", 0);
if (status==1) {
status = H5LTget_dataset_info( file_id, "/comment/comment", &dims, &class_id, &type_size );
if (status >= 0) {
comment.resize( type_size );
status = H5LTread_dataset_string (file_id, "/comment/comment", &comment[0]);
if (status < 0) {
std::string errorMsg("Exception while reading comment in stfio::importHDF5File");
throw std::runtime_error(errorMsg);
}
}
}
ReturnData.SetComment(comment);
double dt = 1.0;
std::string yunits = "";
for (int n_c=0;n_c<numberChannels;++n_c) {
/* Calculate the size and the offsets of our struct members in memory */
size_t ct_offset[NFIELDS] = { HOFFSET( ct, n_sections ) };
ct ct_buf[1];
size_t ct_sizes[NFIELDS] = { sizeof( ct_buf[0].n_sections) };
/* Read channel name */
hsize_t cdims;
H5T_class_t cclass_id;
size_t ctype_size;
std::ostringstream desc_path;
desc_path << "/channels/ch" << (n_c);
status = H5LTget_dataset_info( file_id, desc_path.str().c_str(), &cdims, &cclass_id, &ctype_size );
if (status < 0) {
std::string errorMsg("Exception while reading channel in stfio::importHDF5File");
throw std::runtime_error(errorMsg);
}
hid_t string_typec= H5Tcopy( H5T_C_S1 );
H5Tset_size( string_typec, ctype_size );
std::vector<char> szchannel_name(ctype_size);
// szchannel_name.reset( new char[ctype_size] );
status = H5LTread_dataset(file_id, desc_path.str().c_str(), string_typec, &szchannel_name[0] );
if (status < 0) {
std::string errorMsg("Exception while reading channel name in stfio::importHDF5File");
throw std::runtime_error(errorMsg);
}
std::ostringstream channel_name;
for (std::size_t c=0; c<ctype_size; ++c) {
channel_name << szchannel_name[c];
}
std::ostringstream channel_path;
channel_path << "/" << channel_name.str();
hid_t channel_group = H5Gopen2(file_id, channel_path.str().c_str(), H5P_DEFAULT );
status=H5TBread_table( channel_group, "description", sizeof(ct), ct_offset, ct_sizes, ct_buf );
if (status < 0) {
std::string errorMsg("Exception while reading channel description in stfio::importHDF5File");
throw std::runtime_error(errorMsg);
}
Channel TempChannel(ct_buf[0].n_sections);
TempChannel.SetChannelName( channel_name.str() );
int max_log10 = 0;
if (ct_buf[0].n_sections > 1) {
max_log10 = int(log10((double)ct_buf[0].n_sections-1.0));
}
for (int n_s=0; n_s < ct_buf[0].n_sections; ++n_s) {
int progbar =
// Channel contribution:
(int)(((double)n_c/(double)numberChannels)*100.0+
// Section contribution:
(double)(n_s)/(double)ct_buf[0].n_sections*(100.0/numberChannels));
std::ostringstream progStr;
progStr << "Reading channel #" << n_c + 1 << " of " << numberChannels
<< ", Section #" << n_s+1 << " of " << ct_buf[0].n_sections;
progDlg.Update(progbar, progStr.str());
// construct a number with leading zeros:
int n10 = 0;
if (n_s > 0) {
n10 = int(log10((double)n_s));
}
std::ostringstream strZero; strZero << "";
for (int n_z=n10; n_z < max_log10; ++n_z) {
strZero << "0";
}
// construct a section name:
std::ostringstream section_name;
section_name << "sec" << n_s;
// create a child group in the channel:
std::ostringstream section_path;
section_path << channel_path.str() << "/" << "section_" << strZero.str() << n_s;
hid_t section_group = H5Gopen2(file_id, section_path.str().c_str(), H5P_DEFAULT );
std::ostringstream data_path; data_path << section_path.str() << "/data";
hsize_t sdims;
H5T_class_t sclass_id;
size_t stype_size;
status = H5LTget_dataset_info( file_id, data_path.str().c_str(), &sdims, &sclass_id, &stype_size );
if (status < 0) {
std::string errorMsg("Exception while reading data information in stfio::importHDF5File");
throw std::runtime_error(errorMsg);
}
Vector_float TempSection(sdims);
status = H5LTread_dataset(file_id, data_path.str().c_str(), H5T_IEEE_F32LE, &TempSection[0]);
if (status < 0) {
std::string errorMsg("Exception while reading data in stfio::importHDF5File");
throw std::runtime_error(errorMsg);
}
Section TempSectionT(TempSection.size(), section_name.str());
for (std::size_t cp = 0; cp < TempSectionT.size(); ++cp) {
TempSectionT[cp] = double(TempSection[cp]);
}
// std::copy(TempSection.begin(),TempSection.end(),&TempSectionT[0]);
try {
TempChannel.InsertSection(TempSectionT,n_s);
}
catch (...) {
throw;
}
/* H5TBread_table
const int NSRECORDS = 1; */
const int NSFIELDS = 3;
/* Calculate the size and the offsets of our struct members in memory */
size_t st_offset[NSFIELDS] = { HOFFSET( st, dt ),
HOFFSET( st, xunits ),
HOFFSET( st, yunits )};
st st_buf[1];
size_t st_sizes[NSFIELDS] = { sizeof( st_buf[0].dt),
sizeof( st_buf[0].xunits),
sizeof( st_buf[0].yunits)};
status=H5TBread_table( section_group, "description", sizeof(st), st_offset, st_sizes, st_buf );
if (status < 0) {
std::string errorMsg("Exception while reading data description in stfio::importHDF5File");
throw std::runtime_error(errorMsg);
}
dt = st_buf[0].dt;
yunits = st_buf[0].yunits;
H5Gclose( section_group );
}
try {
if ((int)ReturnData.size()<numberChannels) {
ReturnData.resize(numberChannels);
}
ReturnData.InsertChannel(TempChannel,n_c);
ReturnData[n_c].SetYUnits( yunits );
}
catch (...) {
ReturnData.resize(0);
throw;
}
H5Gclose( channel_group );
}
ReturnData.SetXScale(dt);
/* Terminate access to the file. */
status = H5Fclose(file_id);
if (status < 0) {
std::string errorMsg("Exception while closing file in stfio::importHDF5File");
throw std::runtime_error(errorMsg);
}
/* Release all hdf5 resources */
status = H5close();
if (status < 0) {
std::string errorMsg("Exception while closing file in stfio::exportHDF5File");
throw std::runtime_error(errorMsg);
}
}
bool stfio::exportHDF5File(const std::string& fName, const Recording& WData, ProgressInfo& progDlg) {
hid_t file_id = H5Fcreate(fName.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
const int NRECORDS = 1;
const int NFIELDS = 3;
/* Calculate the size and the offsets of our struct members in memory */
size_t rt_offset[NFIELDS] = { HOFFSET( rt, channels ),
HOFFSET( rt, date ),
HOFFSET( rt, time )};
/* Define an array of root tables */
rt p_data;
p_data.channels = WData.size();
struct tm t = WData.GetDateTime();
std::size_t date_length = snprintf(p_data.date, DATELEN, "%04i-%02i-%02i", t.tm_year+1900, t.tm_mon+1, t.tm_mday);
std::size_t time_length = snprintf(p_data.time, TIMELEN, "%02i:%02i:%02i", t.tm_hour, t.tm_min, t.tm_sec);
// ensure that an undefine string is set to "\0", and that the terminating \0 is counted in string length
p_data.date[date_length++] = 0;
p_data.time[time_length++] = 0;
/* Define field information */
const char *field_names[NFIELDS] = { "channels", "date", "time" };
hid_t field_type[NFIELDS];
/* Initialize the field field_type */
hid_t string_type1 = H5Tcopy( H5T_C_S1 );
hid_t string_type2 = H5Tcopy( H5T_C_S1 );
H5Tset_size( string_type1, date_length);
H5Tset_size( string_type2, time_length);
field_type[0] = H5T_NATIVE_INT;
field_type[1] = string_type1;
field_type[2] = string_type2;
std::ostringstream desc;
desc << "Description of " << fName;
herr_t status = H5TBmake_table( desc.str().c_str(), file_id, "description", (hsize_t)NFIELDS, (hsize_t)NRECORDS, sizeof(rt),
field_names, rt_offset, field_type, 10, NULL, 0, &p_data );
if (status < 0) {
std::string errorMsg("Exception while writing description in stfio::exportHDF5File");
H5Fclose(file_id);
H5close();
throw std::runtime_error(errorMsg);
}
hid_t comment_group = H5Gcreate2( file_id,"/comment", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
/* File comment. */
std::string description(WData.GetFileDescription());
if (description.length() <= 0) {
description = "No description";
}
status = H5LTmake_dataset_string(file_id, "/comment/description", description.c_str());
if (status < 0) {
std::string errorMsg("Exception while writing description in stfio::exportHDF5File");
H5Fclose(file_id);
H5close();
throw std::runtime_error(errorMsg);
}
std::string comment(WData.GetComment());
if (comment.length() <= 0) {
comment = "No comment";
}
status = H5LTmake_dataset_string(file_id, "/comment/comment", comment.c_str());
if (status < 0) {
std::string errorMsg("Exception while writing comment in stfio::exportHDF5File");
H5Fclose(file_id);
H5close();
throw std::runtime_error(errorMsg);
}
H5Gclose(comment_group);
std::vector<std::string> channel_name(WData.size());
hid_t channels_group = H5Gcreate2( file_id,"/channels", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
for ( std::size_t n_c=0; n_c < WData.size(); ++n_c) {
/* Channel descriptions. */
std::ostringstream ossname;
ossname << WData[n_c].GetChannelName();
if ( ossname.str() == "" ) {
ossname << "ch" << (n_c);
}
channel_name[n_c] = ossname.str();
hsize_t dimsc[1] = { 1 };
hid_t string_typec = H5Tcopy( H5T_C_S1 );
std::size_t cn_length = channel_name[n_c].length();
if (cn_length <= 0) cn_length = 1;
H5Tset_size( string_typec, cn_length );
std::vector<char> datac(channel_name[n_c].length());
std::copy(channel_name[n_c].begin(),channel_name[n_c].end(), datac.begin());
std::ostringstream desc_path; desc_path << "/channels/ch" << (n_c);
status = H5LTmake_dataset(file_id, desc_path.str().c_str(), 1, dimsc, string_typec, &datac[0]);
if (status < 0) {
std::string errorMsg("Exception while writing channel name in stfio::exportHDF5File");
H5Fclose(file_id);
H5close();
throw std::runtime_error(errorMsg);
}
std::ostringstream channel_path; channel_path << "/" << channel_name[n_c];
hid_t channel_group = H5Gcreate2( file_id, channel_path.str().c_str(), H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (channel_group < 0) {
std::ostringstream errorMsg;
errorMsg << "Exception while creating channel group for "
<< channel_path.str().c_str();
H5Fclose(file_id);
H5close();
throw std::runtime_error(errorMsg.str());
}
/* Calculate the size and the offsets of our struct members in memory */
size_t ct_size = sizeof( ct );
size_t ct_offset[1] = { HOFFSET( rt, channels ) };
/* Define an array of channel tables */
ct c_data = { (int)WData[n_c].size() };
/* Define field information */
const char *cfield_names[1] = { "n_sections" };
hid_t cfield_type[1] = {H5T_NATIVE_INT};
std::ostringstream c_desc;
c_desc << "Description of channel " << n_c;
status = H5TBmake_table( c_desc.str().c_str(), channel_group, "description", (hsize_t)1, (hsize_t)1, ct_size,
cfield_names, ct_offset, cfield_type, 10, NULL, 0, &c_data );
if (status < 0) {
std::string errorMsg("Exception while writing channel description in stfio::exportHDF5File");
H5Fclose(file_id);
H5close();
throw std::runtime_error(errorMsg);
}
int max_log10 = 0;
if (WData[n_c].size() > 1) {
max_log10 = int(log10((double)WData[n_c].size()-1.0));
}
for (std::size_t n_s=0; n_s < WData[n_c].size(); ++n_s) {
int progbar =
// Channel contribution:
(int)(((double)n_c/(double)WData.size())*100.0+
// Section contribution:
(double)(n_s)/(double)WData[n_c].size()*(100.0/WData.size()));
std::ostringstream progStr;
progStr << "Writing channel #" << n_c + 1 << " of " << WData.size()
<< ", Section #" << n_s << " of " << WData[n_c].size();
progDlg.Update(progbar, progStr.str());
// construct a number with leading zeros:
int n10 = 0;
if (n_s > 0) {
n10 = int(log10((double)n_s));
}
std::ostringstream strZero; strZero << "";
for (int n_z=n10; n_z < max_log10; ++n_z) {
strZero << "0";
}
// construct a section name:
std::ostringstream section_name; section_name << WData[n_c][n_s].GetSectionDescription();
if ( section_name.str() == "" ) {
section_name << "sec" << n_s;
}
// create a child group in the channel:
std::ostringstream section_path;
section_path << channel_path.str() << "/" << "section_" << strZero.str() << n_s;
hid_t section_group = H5Gcreate2( file_id, section_path.str().c_str(), H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
// add data and description, store as 32 bit little endian independent of machine:
hsize_t dims[1] = { WData[n_c][n_s].size() };
std::ostringstream data_path;
data_path << section_path.str() << "/data";
Vector_float data_cp(WData[n_c][n_s].get().size()); /* 32 bit */
for (std::size_t n_cp = 0; n_cp < WData[n_c][n_s].get().size(); ++n_cp) {
data_cp[n_cp] = float(WData[n_c][n_s][n_cp]);
}
status = H5LTmake_dataset(file_id, data_path.str().c_str(), 1, dims, H5T_IEEE_F32LE, &data_cp[0]);
if (status < 0) {
std::string errorMsg("Exception while writing data in stfio::exportHDF5File");
H5Fclose(file_id);
H5close();
throw std::runtime_error(errorMsg);
}
const int NSRECORDS = 1;
const int NSFIELDS = 3;
/* Calculate the size and the offsets of our struct members in memory */
size_t st_size = sizeof( st );
size_t st_offset[NSFIELDS] = { HOFFSET( st, dt ),
HOFFSET( st, xunits ),
HOFFSET( st, yunits )};
/* Define an array of root tables */
st s_data;
s_data.dt = WData.GetXScale();
if (WData.GetXUnits().length() < UNITLEN)
strcpy( s_data.xunits, WData.GetXUnits().c_str() );
if (WData[n_c].GetYUnits().length() < UNITLEN)
strcpy( s_data.yunits, WData[n_c].GetYUnits().c_str() );
/* Define field information */
const char *sfield_names[NSFIELDS] = { "dt", "xunits", "yunits" };
hid_t sfield_type[NSFIELDS];
/* Initialize the field field_type */
hid_t string_type4 = H5Tcopy( H5T_C_S1 );
hid_t string_type5 = H5Tcopy( H5T_C_S1 );
H5Tset_size( string_type4, 2);
std::size_t yu_length = WData[n_c].GetYUnits().length();
if (yu_length <= 0) yu_length = 1;
H5Tset_size( string_type5, yu_length );
sfield_type[0] = H5T_NATIVE_DOUBLE;
sfield_type[1] = string_type4;
sfield_type[2] = string_type5;
std::ostringstream sdesc;
sdesc << "Description of " << section_name.str();
status = H5TBmake_table( sdesc.str().c_str(), section_group, "description", (hsize_t)NSFIELDS, (hsize_t)NSRECORDS, st_size,
sfield_names, st_offset, sfield_type, 10, NULL, 0, &s_data );
if (status < 0) {
std::string errorMsg("Exception while writing section description in stfio::exportHDF5File");
H5Fclose(file_id);
H5close();
throw std::runtime_error(errorMsg);
}
H5Gclose(section_group);
}
H5Gclose(channel_group);
}
H5Gclose(channels_group);
/* Terminate access to the file. */
status = H5Fclose(file_id);
if (status < 0) {
std::string errorMsg("Exception while closing file in stfio::exportHDF5File");
throw std::runtime_error(errorMsg);
}
/* Release all hdf5 resources */
status = H5close();
if (status < 0) {
std::string errorMsg("Exception while closing file in stfio::exportHDF5File");
throw std::runtime_error(errorMsg);
}
return (status >= 0);
}
int main (int argc, char* argv[])
{
// Library initilization.
MPI_Init(&argc, &argv);
herr_t H5open();
std::string filename = argv[1];
// We determine the size and ranks of our process.
int rank, size;
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
MPI_Comm_size(MPI_COMM_WORLD, &size);
// We distribute the indices among the processors.
// For proper load balancing, we should have size % 6 = 0.
std::vector<std::vector<unsigned int> > indices;
indices.resize(size);
for (unsigned int i=0; i<6; i++)
{
int idx = user_mod(i,size);
indices[idx].push_back(i);
}
// Open existing file.
hid_t plist_id;
plist_id = H5Pcreate(H5P_FILE_ACCESS);
H5Pset_fapl_mpio(plist_id,MPI_COMM_WORLD,MPI_INFO_NULL);
hid_t file_id = H5Fopen(filename.c_str(), H5F_ACC_RDONLY, plist_id);
// We store the name of the datasets we want to open.
std::vector<std::string> dataset_names;
dataset_names.push_back(std::string("/besselJ"));
dataset_names.push_back(std::string("/besselY"));
dataset_names.push_back(std::string("/besselI"));
dataset_names.push_back(std::string("/besselK"));
dataset_names.push_back(std::string("/hankelH1"));
dataset_names.push_back(std::string("/hankelH2"));
// We store the appropriate functions pointers in an array.
std::vector<std::complex<double> (*) (double, std::complex<double>, int)> f_ptr;
f_ptr.push_back(sp_bessel::besselJp);
f_ptr.push_back(sp_bessel::besselYp);
f_ptr.push_back(sp_bessel::besselIp);
f_ptr.push_back(sp_bessel::besselKp);
f_ptr.push_back(sp_bessel::hankelH1p);
f_ptr.push_back(sp_bessel::hankelH2p);
// We loop over the datasets.
for (auto iter = indices[rank].begin(); iter != indices[rank].end(); iter++)
{
// Open dataset.
hid_t dataset_id = H5Dopen(file_id, dataset_names[*iter].c_str(), H5P_DEFAULT);
// Obtain the dataspace
hid_t dspace = H5Dget_space(dataset_id);
// We obtain the dimensions of the dataset.
const int ndims = H5Sget_simple_extent_ndims(dspace);
hsize_t dims[ndims];
H5Sget_simple_extent_dims(dspace, dims, NULL);
// We read the dataset.
std::complex<double> values[dims[0]][dims[1]][dims[2]][dims[3]];
hid_t complex_id = H5Dget_type(dataset_id);
H5Dread(dataset_id, complex_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, values);
// We now open/read the attributes.
double vmax, zimin, zimax, zrmin, zrmax;
hid_t vmax_id = H5Aopen(dataset_id, "vmax", H5P_DEFAULT);
hid_t zimin_id = H5Aopen(dataset_id, "zimin", H5P_DEFAULT);
hid_t zimax_id = H5Aopen(dataset_id, "zrmax", H5P_DEFAULT);
hid_t zrmin_id = H5Aopen(dataset_id, "zrmin", H5P_DEFAULT);
hid_t zrmax_id = H5Aopen(dataset_id, "zrmax", H5P_DEFAULT);
H5Aread(vmax_id, H5T_NATIVE_DOUBLE, &vmax);
H5Aread(zimin_id, H5T_NATIVE_DOUBLE, &zimin);
H5Aread(zimax_id, H5T_NATIVE_DOUBLE, &zimax);
H5Aread(zrmin_id, H5T_NATIVE_DOUBLE, &zrmin);
H5Aread(zrmax_id, H5T_NATIVE_DOUBLE, &zrmax);
// We now evaluate the Bessel functions at the computed values.
arma::vec orders = arma::linspace(-vmax, vmax, dims[1]);
arma::vec realZ = arma::linspace(zrmin, zrmax, dims[2]);
arma::vec imagZ = arma::linspace(zimin, zimax, dims[3]);
unsigned int count = 0;
for (int i=0; i<dims[0]; i++)
{
for (int j=0; j<dims[1]; j++)
{
for (int k=0; k<dims[2]; k++)
{
for (int l=0; l<dims[3]; l++)
{
double eps = std::abs(f_ptr[*iter](orders(j), std::complex<double>(realZ(k), imagZ(l)), i)
- values[i][j][k][l]);
if (eps > 1.0e-13)
{
std::cout << "Issue in " << dataset_names[*iter].c_str()
<< " at nu = " << orders(j)
<< " z = " << realZ(k) << " + i" << imagZ(l) << "."
<< " and p = " << i << std::endl;
std::cout << "Epsilon is " << eps << std::endl;
count++;
}
}
}
}
}
}
// Library closures
herr_t H5close();
MPI_Finalize();
return 0;
}
int main(int argc, char *argv[])
{
(void)argc;
(void)argv;
typedef struct rt {
int channels;
char date[DATELEN];
char time[TIMELEN];
} rt;
// H5Fis_hdf5("/dev/null");
/*
* Create a new file using H5ACC_TRUNC access,
* default file creation properties, and default file
* access properties.
* Then close the file.
*/
const int NRECORDS = 1;
const int NFIELDS = 3;
char fName[] = "tmp.h5";
/* Calculate the size and the offsets of our struct members in memory */
size_t rt_offset[NFIELDS] = { HOFFSET( rt, channels ),
HOFFSET( rt, date ),
HOFFSET( rt, time )};
rt p_data;
p_data.channels = 1;
strcpy( p_data.date, "1234-Dec-31");
strcpy( p_data.time, "12:34:56");
hid_t file_id = H5Fcreate(fName, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/* Define field information */
const char *field_names[NFIELDS] = { "channels", "date", "time" };
hid_t field_type[NFIELDS];
/* Initialize the field field_type */
hid_t string_type1 = H5Tcopy( H5T_C_S1 );
hid_t string_type2 = H5Tcopy( H5T_C_S1 );
H5Tset_size( string_type1, strlen(p_data.date));
H5Tset_size( string_type2, strlen(p_data.time));
field_type[0] = H5T_NATIVE_INT;
field_type[1] = string_type1;
field_type[2] = string_type2;
std::ostringstream desc;
desc << "Description of " << fName;
herr_t status = H5TBmake_table( desc.str().c_str(), file_id, "description", (hsize_t)NFIELDS, (hsize_t)NRECORDS, sizeof(rt),
field_names, rt_offset, field_type, 10, NULL, 0, &p_data );
if (status < 0) {
perror("Exception while writing description in stfio::exportHDF5File");
H5Fclose(file_id);
H5close();
exit(-1);
}
H5Fclose(file_id);
return(0);
}
int
main(int argc, char **argv)
{
int mpi_size, mpi_rank; /* mpi variables */
int ret_code;
MPI_Init(&argc, &argv);
MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
H5open();
if (parse_options(argc, argv) != 0){
if (MAINPROCESS)
usage();
goto finish;
}
if (MAINPROCESS){
printf("===================================\n");
printf("MPI functionality tests\n");
printf("===================================\n");
}
if (VERBOSE_MED)
h5_show_hostname();
fapl = H5Pcreate (H5P_FILE_ACCESS);
H5Pset_fapl_mpio(fapl, MPI_COMM_WORLD, MPI_INFO_NULL);
MPI_BANNER("MPIO 1 write Many read test...");
ret_code = test_mpio_1wMr(filenames[0], USENONE);
ret_code = errors_sum(ret_code);
if (mpi_rank==0 && ret_code > 0){
printf("***FAILED with %d total errors\n", ret_code);
nerrors += ret_code;
}
/* test atomicity and file sync in high verbose mode only */
/* since they often hang when broken and PHDF5 does not use them. */
if (VERBOSE_HI){
MPI_BANNER("MPIO 1 write Many read test with atomicity...");
ret_code = test_mpio_1wMr(filenames[0], USEATOM);
ret_code = errors_sum(ret_code);
if (mpi_rank==0 && ret_code > 0){
printf("***FAILED with %d total errors\n", ret_code);
nerrors += ret_code;
}
MPI_BANNER("MPIO 1 write Many read test with file sync...");
ret_code = test_mpio_1wMr(filenames[0], USEFSYNC);
ret_code = errors_sum(ret_code);
if (mpi_rank==0 && ret_code > 0){
printf("***FAILED with %d total errors\n", ret_code);
nerrors += ret_code;
}
}
MPI_BANNER("MPIO File size range test...");
ret_code = test_mpio_gb_file(filenames[0]);
ret_code = errors_sum(ret_code);
if (mpi_rank==0 && ret_code > 0){
printf("***FAILED with %d total errors\n", ret_code);
nerrors += ret_code;
}
MPI_BANNER("MPIO independent overlapping writes...");
ret_code = test_mpio_overlap_writes(filenames[0]);
ret_code = errors_sum(ret_code);
if (mpi_rank==0 && ret_code > 0){
printf("***FAILED with %d total errors\n", ret_code);
nerrors += ret_code;
}
finish:
/* make sure all processes are finished before final report, cleanup
* and exit.
*/
MPI_Barrier(MPI_COMM_WORLD);
if (MAINPROCESS){ /* only process 0 reports */
printf("===================================\n");
if (nerrors){
printf("***MPI tests detected %d errors***\n", nerrors);
}
else{
printf("MPI tests finished with no errors\n");
}
printf("===================================\n");
}
h5_cleanup(FILENAME, fapl);
H5close();
/* MPI_Finalize must be called AFTER H5close which may use MPI calls */
MPI_Finalize();
/* cannot just return (nerrors) because exit code is limited to 1byte */
return(nerrors!=0);
}