void hdf5_save_float<float>(hid_t loc_id,
const string& dataset_name, float f) {
hsize_t one = 1;
herr_t status = \
H5LTmake_dataset_float(loc_id, dataset_name.c_str(), 1, &one, &f);
CHECK_GE(status, 0)
<< "Failed to save int dataset with name " << dataset_name;
}
void hdf5_save_nd_dataset<float>(
const hid_t file_id, const string dataset_name, const Blob<float>& blob) {
hsize_t dims[HDF5_NUM_DIMS];
dims[0] = blob.num();
dims[1] = blob.channels();
dims[2] = blob.height();
dims[3] = blob.width();
herr_t status = H5LTmake_dataset_float(
file_id, dataset_name.c_str(), HDF5_NUM_DIMS, dims, blob.cpu_data());
CHECK_GE(status, 0) << "Failed to make float dataset " << dataset_name;
}
/**
* Write data into a dataset.
*
* @param [in] DatasetName
* @param [in] DimensionSizes
* @param [in] Data
* @throw ios::failure
*/
void THDF5_File::WriteCompleteDataset(const char * DatasetName, const TDimensionSizes & DimensionSizes, const float * Data){
const int rank = 3;
const hsize_t dims[]={DimensionSizes.Z, DimensionSizes.Y,DimensionSizes.X};
// write to dataset
herr_t status = H5LTmake_dataset_float(HDF5_FileId,DatasetName,rank,dims, Data);
if (status < 0) {
char ErrorMessage[256];
sprintf(ErrorMessage,HDF5_ERR_FMT_CouldNotWriteTo,DatasetName);
throw ios::failure(ErrorMessage);
}
}// end of WriteDataset (float)
static void
psc_fields_single_write(struct psc_fields *flds, struct mrc_io *io)
{
int ierr;
long h5_file;
mrc_io_get_h5_file(io, &h5_file);
hid_t group = H5Gopen(h5_file, mrc_io_obj_path(io, flds), H5P_DEFAULT); H5_CHK(group);
ierr = H5LTset_attribute_int(group, ".", "p", &flds->p, 1); CE;
ierr = H5LTset_attribute_int(group, ".", "ib", flds->ib, 3); CE;
ierr = H5LTset_attribute_int(group, ".", "im", flds->im, 3); CE;
ierr = H5LTset_attribute_int(group, ".", "nr_comp", &flds->nr_comp, 1); CE;
// write components separately instead?
hsize_t hdims[4] = { flds->nr_comp, flds->im[2], flds->im[1], flds->im[0] };
ierr = H5LTmake_dataset_float(group, "fields_single", 4, hdims, flds->data); CE;
ierr = H5Gclose(group); CE;
}
void hdf5_save_nd_dataset<float>(
const hid_t file_id, const string& dataset_name, const Blob<float>& blob,
bool write_diff) {
int num_axes = blob.num_axes();
hsize_t *dims = new hsize_t[num_axes];
for (int i = 0; i < num_axes; ++i) {
dims[i] = blob.shape(i);
}
const float* data;
if (write_diff) {
data = blob.cpu_diff();
} else {
data = blob.cpu_data();
}
herr_t status = H5LTmake_dataset_float(
file_id, dataset_name.c_str(), num_axes, dims, data);
CHECK_GE(status, 0) << "Failed to make float dataset " << dataset_name;
delete[] dims;
}
/*+++++++++++++++++++++++++ Main Program or Function +++++++++++++++*/
void SCIA_LV1_WR_H5_BASE( struct param_record param,
const struct base_scia *base )
{
hid_t gads_id;
hsize_t adim;
/*
* open/create group /GADS
*/
gads_id = NADC_OPEN_HDF5_Group( param.hdf_file_id, "/GADS" );
if ( gads_id < 0 ) NADC_RETURN_ERROR( NADC_ERR_HDF_GRP, "/GADS" );
/*
* write datasets
*/
adim = SCIENCE_PIXELS;
(void) H5LTmake_dataset_float( gads_id, "SPECTRAL_BASE", 1, &adim,
base->wvlen_det_pix );
/*
* close interface
*/
(void) H5Gclose( gads_id );
}
int
main (int argc, char **argv)
{
extern char* optarg;
extern int optind, optopt;
int c, errflg, backflg, incrflg, nopagflg, pagflg, rank, nranks;
hid_t fapl, file, group, group1, dset;
size_t incr, page;
unsigned iter, level, igroup, idset, maxiter;
char name[MAX_LEN];
char g1name[MAX_LEN];
char g2name[MAX_LEN];
hsize_t dims[3] = { X, Y, Z };
float *buf;
double start, stop;
double t1, t2;
char cdum[MAX_LEN];
int i, memtotal, memfree, buffers, cached, swapcached, active, inactive;
float fdum;
assert (MPI_Init (&argc, &argv) >= 0);
assert (MPI_Comm_rank (MPI_COMM_WORLD, &rank) >= 0);
assert (MPI_Comm_size (MPI_COMM_WORLD, &nranks) >= 0);
/* parse arguments */
backflg = errflg = incrflg = nopagflg = pagflg = 0;
incr = INCREMENT;
page = PAGE_SIZE;
maxiter = MAX_ITER;
while ((c = getopt(argc, argv, ":bni:t:p:")) != -1)
{
switch (c)
{
case 'b':
backflg++;
break;
case 'i':
incrflg++;
incr = (size_t)atol(optarg);
if (incr == 0)
{
fprintf(stderr,
"Option -%c requires a positive integer argument\n", optopt);
errflg++;
}
break;
case 'n':
nopagflg++;
break;
case 'p':
pagflg++;
page = (size_t)atol(optarg);
if (page == 0)
{
fprintf(stderr,
"Option -%c requires a positive integer argument\n", optopt);
errflg++;
}
break;
case 't':
maxiter = (unsigned)atol(optarg);
if (maxiter == 0)
{
fprintf(stderr,
"Option -%c requires a positive integer argument\n", optopt);
errflg++;
}
break;
case ':': /* -i or -p without operand */
fprintf(stderr,
"Option -%c requires an operand\n", optopt);
errflg++;
break;
case '?':
fprintf(stderr, "Unrecognized option: -%c\n", optopt);
errflg++;
break;
default:
errflg++;
break;
}
}
if (errflg)
{
if (rank == 0)
{
fprintf(stderr, "usage: . . . ");
fprintf(stderr, "usage: h5core [OPTIONS]\n");
fprintf(stderr, " OPTIONS\n");
fprintf(stderr, " -b Write file to disk on exit\n");
fprintf(stderr, " -i I Memory buffer increment size in bytes [default: 512 MB]\n");
fprintf(stderr, " -n Disable write (to disk) paging\n");
fprintf(stderr, " -p P Page size in bytes [default: 64 MB]\n");
fprintf(stderr, " -t T Number of iterations [default: 5]\n");
fprintf(stderr, "\n");
fflush(stderr);
}
exit(2);
}
if ((backflg == 0) && (pagflg > 0))
{
if (rank == 0)
{
fprintf(stderr, "The -p has no effect without the -b option");
fflush(stderr);
}
}
if (pagflg && nopagflg)
{
if (rank == 0)
{
fprintf(stderr, "The -n and -p options are mutually exclusive.");
fflush(stderr);
}
exit(3);
}
/* Let's go! */
fapl = H5Pcreate (H5P_FILE_ACCESS);
assert (fapl >= 0);
assert (H5Pset_libver_bounds (fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0);
assert (H5Pset_fapl_core (fapl, incr, (hbool_t) backflg) >= 0);
if (nopagflg == 0) /* the user didn't disable paging */
{
assert (H5Pset_core_write_tracking (fapl, 1, page) >= 0);
}
if (rank == 0)
{
printf("\n");
printf("Write to disk: %s\n", (backflg > 0) ? "YES" : "NO");
printf("Increment size: %ld [bytes]\n", incr);
if (nopagflg == 0)
{
printf("Page size: %ld [bytes]\n", page);
}
else
{
printf("Page size: PAGING DISABLED!\n");
}
printf("Iterations: %d\n", maxiter);
printf("\n");
fflush(stdout);
}
buf = (float *) malloc (X * Y * Z * sizeof (float));
// Get basic memory info on each node, see how memory usage changes
// after flushing to disk; do we end up back where we started?
getmemory (&memtotal, &memfree, &buffers, &cached, &swapcached, &active,
&inactive);
if (rank == 0)
{
fprintf (stdout, "BEFORE RUNNING:\n");
fflush (stdout);
}
for (i = 0; i < nranks; i++)
{
if (rank == i)
{
printmemory (rank, memtotal, memfree, buffers, cached, swapcached,
active, inactive);
}
MPI_Barrier (MPI_COMM_WORLD);
}
start = MPI_Wtime ();
/* outer loop - simulated time */
for (iter = 0; iter < maxiter; ++iter)
{
if (rank == 0)
{
printf ("Iteration: %u\n", iter);
assert (fflush (stdout) == 0);
}
assert (sprintf (name, "rank%05dtime%04u.h5", rank, iter) > 0);
file = H5Fcreate (name, H5F_ACC_TRUNC, H5P_DEFAULT, fapl);
assert (file >= 0);
t1 = MPI_Wtime ();
/* time level */
for (level = 0; level < MAX_TIME_LEVEL; ++level)
{
assert (sprintf (g1name, "level%03d", level) > 0);
group = H5Gcreate2 (file, g1name, H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT);
assert (group >= 0);
/* group level */
for (igroup = 0; igroup < MAX_GROUPS; ++igroup)
{
assert (sprintf (g2name, "group%02d", igroup) > 0);
group1 = H5Gcreate2 (group, g2name, H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT);
assert (group1 >= 0);
/* dataset level */
for (idset = 0; idset < MAX_DATASETS; ++idset)
{
assert (sprintf (name, "dataset%02d", idset) > 0);
assert (H5LTmake_dataset_float (group1, name, RANK, dims, buf) >= 0);
#ifdef DEBUG
assert (fprintf (stderr,
"rank %i time %i Wrote dataset %s/%s/%s\n",
rank, level, g1name, g2name, name));
assert (fflush (stderr) == 0);
#endif
}
assert (H5Gclose (group1) >= 0);
}
assert (H5Gclose (group) >= 0);
}
t2 = MPI_Wtime ();
assert (fprintf (stdout,
"rank %04i Total time for buffering chunks to memory:\t %f seconds\n",
rank, t2 - t1));
assert (fflush (stdout) == 0);
MPI_Barrier (MPI_COMM_WORLD); // To keep output less jumbled
getmemory (&memtotal, &memfree, &buffers, &cached, &swapcached, &active,
&inactive);
if (rank == 0)
{
fprintf (stdout, "BEFORE FLUSHING:\n");
fflush (stdout);
}
for (i = 0; i < nranks; i++)
{
if (rank == i)
{
printmemory (rank, memtotal, memfree, buffers, cached, swapcached,
active, inactive);
}
MPI_Barrier (MPI_COMM_WORLD);
}
/* close the file */
t1 = MPI_Wtime ();
assert (H5Fclose (file) >= 0);
t2 = MPI_Wtime ();
getmemory (&memtotal, &memfree, &buffers, &cached, &swapcached, &active,
&inactive);
if (rank == 0)
{
fprintf (stdout, "AFTER FLUSHING:\n");
fflush (stdout);
}
for (i = 0; i < nranks; i++)
{
if (rank == i)
{
printmemory (rank, memtotal, memfree, buffers, cached, swapcached,
active, inactive);
assert (fprintf (stdout, "rank %04i Total time for flushing to disk:\t\t %10.2f seconds\n", rank, t2 - t1));
assert (fflush (stderr) == 0);
}
MPI_Barrier (MPI_COMM_WORLD);
}
}
stop = MPI_Wtime ();
MPI_Barrier (MPI_COMM_WORLD);
if (rank == 0)
{
printf ("Total time: %f s\n", stop - start);
printf ("Aggregate bandwidth per process: %f GB/s\n",
((float) X * Y * Z * sizeof (float)) *
((float) MAX_DATASETS * MAX_GROUPS * MAX_TIME_LEVEL * MAX_ITER) /
(1024.0 * 1024.0 * 1024.0 * (stop - start)));
}
free ((void *) buf);
assert (H5Pclose (fapl) >= 0);
assert (MPI_Finalize () >= 0);
return 0;
}
static int test_dsets( void )
{
int rank = 2;
hsize_t dims[2] = {2,3};
hid_t file_id;
hid_t dataset_id;
char data_char_in[DIM] = {1,2,3,4,5,6};
char data_char_out[DIM];
short data_short_in[DIM] = {1,2,3,4,5,6};
short data_short_out[DIM];
int data_int_in[DIM] = {1,2,3,4,5,6};
int data_int_out[DIM];
long data_long_in[DIM] = {1,2,3,4,5,6};
long data_long_out[DIM];
float data_float_in[DIM] = {1,2,3,4,5,6};
float data_float_out[DIM];
double data_double_in[DIM] = {1,2,3,4,5,6};
double data_double_out[DIM];
const char *data_string_in = "This is a string";
char data_string_out[20];
int i;
/* Create a new file using default properties. */
file_id = H5Fcreate( FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT );
/*-------------------------------------------------------------------------
* H5LTmake_dataset test
*-------------------------------------------------------------------------
*/
TESTING("H5LTmake_dataset");
/* Make dataset */
if ( H5LTmake_dataset( file_id, DSET0_NAME, rank, dims, H5T_NATIVE_INT, data_int_in ) < 0 )
goto out;
/* Read dataset using the basic HDF5 API */
if ( ( dataset_id = H5Dopen2(file_id, DSET0_NAME, H5P_DEFAULT) ) < 0 )
goto out;
if ( H5Dread ( dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, data_int_out ) < 0 )
goto out;
if ( H5Dclose( dataset_id ) < 0 )
goto out;
for (i = 0; i < DIM; i++)
{
if ( data_int_in[i] != data_int_out[i] ) {
goto out;
}
}
PASSED();
/*-------------------------------------------------------------------------
* read using the LT function H5LTread_dataset
*-------------------------------------------------------------------------
*/
TESTING("H5LTread_dataset");
if ( H5LTread_dataset( file_id, DSET0_NAME, H5T_NATIVE_INT, data_int_out ) < 0 )
goto out;
for (i = 0; i < DIM; i++)
{
if ( data_int_in[i] != data_int_out[i] ) {
goto out;
}
}
PASSED();
/*-------------------------------------------------------------------------
* test the H5LTmake_dataset_ functions
*-------------------------------------------------------------------------
*/
/*-------------------------------------------------------------------------
* H5LTmake_dataset_char
*-------------------------------------------------------------------------
*/
TESTING("H5LTmake_dataset_char");
/* Make dataset char */
if ( H5LTmake_dataset_char( file_id, DSET1_NAME, rank, dims, data_char_in ) < 0 )
goto out;
/* Read dataset */
if ( H5LTread_dataset( file_id, DSET1_NAME, H5T_NATIVE_CHAR, data_char_out ) < 0 )
goto out;
for (i = 0; i < DIM; i++)
{
if ( data_char_in[i] != data_char_out[i] ) {
goto out;
}
}
/* Read dataset */
if ( H5LTread_dataset_char( file_id, DSET1_NAME, data_char_out ) < 0 )
goto out;
for (i = 0; i < DIM; i++)
{
if ( data_char_in[i] != data_char_out[i] ) {
goto out;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTmake_dataset_short
*-------------------------------------------------------------------------
*/
TESTING("H5LTmake_dataset_short");
/* Make dataset short */
if ( H5LTmake_dataset_short( file_id, DSET2_NAME, rank, dims, data_short_in ) < 0 )
goto out;
/* Read dataset */
if ( H5LTread_dataset( file_id, DSET2_NAME, H5T_NATIVE_SHORT, data_short_out ) < 0 )
goto out;
for (i = 0; i < DIM; i++)
{
if ( data_short_in[i] != data_short_out[i] ) {
goto out;
}
}
/* Read dataset */
if ( H5LTread_dataset_short( file_id, DSET2_NAME, data_short_out ) < 0 )
goto out;
for (i = 0; i < DIM; i++)
{
if ( data_short_in[i] != data_short_out[i] ) {
goto out;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTmake_dataset_int
*-------------------------------------------------------------------------
*/
TESTING("H5LTmake_dataset_int");
/* Make dataset int */
if ( H5LTmake_dataset_int( file_id, DSET3_NAME, rank, dims, data_int_in ) < 0 )
goto out;
/* Read dataset */
if ( H5LTread_dataset( file_id, DSET3_NAME, H5T_NATIVE_INT, data_int_out ) < 0 )
goto out;
for (i = 0; i < DIM; i++)
{
if ( data_int_in[i] != data_int_out[i] ) {
goto out;
}
}
/* Read dataset */
if ( H5LTread_dataset_int( file_id, DSET3_NAME, data_int_out ) < 0 )
goto out;
for (i = 0; i < DIM; i++)
{
if ( data_int_in[i] != data_int_out[i] ) {
goto out;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTmake_dataset_long
*-------------------------------------------------------------------------
*/
TESTING("H5LTmake_dataset_long");
/* Make dataset long */
if ( H5LTmake_dataset_long( file_id, DSET4_NAME, rank, dims, data_long_in ) < 0 )
goto out;
/* Read dataset */
if ( H5LTread_dataset( file_id, DSET4_NAME, H5T_NATIVE_LONG, data_long_out ) < 0 )
goto out;
for (i = 0; i < DIM; i++)
{
if ( data_long_in[i] != data_long_out[i] ) {
goto out;
}
}
/* Read dataset */
if ( H5LTread_dataset_long( file_id, DSET4_NAME, data_long_out ) < 0 )
goto out;
for (i = 0; i < DIM; i++)
{
if ( data_long_in[i] != data_long_out[i] ) {
goto out;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTmake_dataset_float
*-------------------------------------------------------------------------
*/
TESTING("H5LTmake_dataset_float");
/* Make dataset float */
if ( H5LTmake_dataset_float( file_id, DSET5_NAME, rank, dims, data_float_in ) < 0 )
goto out;
/* Read dataset */
if ( H5LTread_dataset( file_id, DSET5_NAME, H5T_NATIVE_FLOAT, data_float_out ) < 0 )
goto out;
for (i = 0; i < DIM; i++)
{
if ( data_float_in[i] != data_float_out[i] ) {
goto out;
}
}
/* Read dataset */
if ( H5LTread_dataset_float( file_id, DSET5_NAME, data_float_out ) < 0 )
goto out;
for (i = 0; i < DIM; i++)
{
if ( data_float_in[i] != data_float_out[i] ) {
goto out;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTmake_dataset_double
*-------------------------------------------------------------------------
*/
TESTING("H5LTmake_dataset_double");
/* Make dataset double */
if ( H5LTmake_dataset_double( file_id, DSET6_NAME, rank, dims, data_double_in ) < 0 )
goto out;
/* Read dataset */
if ( H5LTread_dataset( file_id, DSET6_NAME, H5T_NATIVE_DOUBLE, data_double_out ) < 0 )
goto out;
for (i = 0; i < DIM; i++)
{
if ( data_double_in[i] != data_double_out[i] ) {
goto out;
}
}
/* Read dataset */
if ( H5LTread_dataset_double( file_id, DSET6_NAME, data_double_out ) < 0 )
goto out;
for (i = 0; i < DIM; i++)
{
if ( data_double_in[i] != data_double_out[i] ) {
goto out;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTmake_dataset_string
*-------------------------------------------------------------------------
*/
TESTING("H5LTmake_dataset_string");
/* Make dataset string */
if ( H5LTmake_dataset_string(file_id,DSET7_NAME,data_string_in) < 0 )
goto out;
/* Read dataset */
if ( H5LTread_dataset_string(file_id,DSET7_NAME,data_string_out) < 0 )
goto out;
if ( strcmp(data_string_in,data_string_out) != 0 )
goto out;
/*-------------------------------------------------------------------------
* end tests
*-------------------------------------------------------------------------
*/
/* Close the file. */
H5Fclose( file_id );
PASSED();
return 0;
out:
/* Close the file. */
H5_FAILED();
return -1;
}
int main(void)
{
hid_t fid; /* file ID */
hid_t did; /* dataset ID */
hid_t dsid; /* DS dataset ID */
int rank = RANK; /* rank of data dataset */
int rankds = 1; /* rank of DS dataset */
hsize_t dims[RANK] = {DIM1_SIZE,DIM2_SIZE}; /* size of data dataset */
int buf[DIM_DATA] = {1,2,3,4,5,6,7,8,9,10,11,12}; /* data of data dataset */
hsize_t s1_dim[1] = {DIM1_SIZE}; /* size of DS 1 dataset */
hsize_t s2_dim[1] = {DIM2_SIZE}; /* size of DS 2 dataset */
float s1_wbuf[DIM1_SIZE] = {10,20,30}; /* data of DS 1 dataset */
int s2_wbuf[DIM2_SIZE] = {10,20,50,100}; /* data of DS 2 dataset */
/* create a file using default properties */
if ((fid=H5Fcreate("ex_ds1.h5",H5F_ACC_TRUNC,H5P_DEFAULT,H5P_DEFAULT))<0)
goto out;
/* make a dataset */
if (H5LTmake_dataset_int(fid,DSET_NAME,rank,dims,buf)<0)
goto out;
/* make a DS dataset for the first dimension */
if (H5LTmake_dataset_float(fid,DS_1_NAME,rankds,s1_dim,s1_wbuf)<0)
goto out;
/* make a DS dataset for the second dimension */
if (H5LTmake_dataset_int(fid,DS_2_NAME,rankds,s2_dim,s2_wbuf)<0)
goto out;
/*-------------------------------------------------------------------------
* attach the DS_1_NAME dimension scale to DSET_NAME at dimension 0
*-------------------------------------------------------------------------
*/
/* get the dataset id for DSET_NAME */
if ((did = H5Dopen2(fid,DSET_NAME, H5P_DEFAULT))<0)
goto out;
/* get the DS dataset id */
if ((dsid = H5Dopen2(fid,DS_1_NAME, H5P_DEFAULT))<0)
goto out;
/* attach the DS_1_NAME dimension scale to DSET_NAME at dimension index 0 */
if (H5DSattach_scale(did,dsid,DIM0)<0)
goto out;
/* close DS id */
if (H5Dclose(dsid)<0)
goto out;
/*-------------------------------------------------------------------------
* attach the DS_2_NAME dimension scale to DSET_NAME
*-------------------------------------------------------------------------
*/
/* get the DS dataset id */
if ((dsid = H5Dopen2(fid,DS_2_NAME, H5P_DEFAULT))<0)
goto out;
/* attach the DS_2_NAME dimension scale to DSET_NAME as the 2nd dimension (index 1) */
if (H5DSattach_scale(did,dsid,DIM1)<0)
goto out;
/* close DS id */
if (H5Dclose(dsid)<0)
goto out;
/* close file */
H5Fclose(fid);
return 0;
out:
printf("Error on return function...Exiting\n");
return 1;
}
