Here is the error message I get, after compiling and running
'attr_for_empty_dset_prll.c'
( see the attachment and also the previous letter ). Can somebody
confirm it?
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: ../../../src/H5D.c line 426 in H5Dclose(): can't decrement
count on dataset ID
major: Dataset
minor: Unable to decrement reference count
#001: ../../../src/H5I.c line 1533 in
H5I_dec_app_ref_always_close(): can't decrement ID ref count
major: Object atom
minor: Unable to decrement reference count
#002: ../../../src/H5I.c line 1475 in H5I_dec_app_ref(): can't
decrement ID ref count
major: Object atom
minor: Unable to decrement reference count
#003: ../../../src/H5Dint.c line 1386 in H5D_close(): unable to
flush cached dataset info
major: Dataset
minor: Write failed
#004: ../../../src/H5Dint.c line 2316 in H5D__flush_real(): unable
to update layout/pline/efl info
major: Dataset
minor: Write failed
#005: ../../../src/H5Dlayout.c line 479 in H5D__layout_oh_write():
unable to update layout message
major: Dataset
minor: Write failed
#006: ../../../src/H5Omessage.c line 335 in H5O_msg_write_oh():
unable to write object header message
major: Object header
minor: Write failed
#007: ../../../src/H5Omessage.c line 389 in H5O_msg_write_real():
unable to modify constant message
major: Object header
minor: Write failed
On 11/24/2015 06:46 PM, A.B. wrote:
Hello.
I've run into the following problem while using HDF5: I can't create
an attribute for an empty dataset when application is executed in
parallel.
I have some dataset with total number of elements N. I'm writing it to
a file as 1d dataset.
When application is executed in parallel, each process writes it's own
piece of data.
After saving the dataset to the file, I want to attach some attributes
to it.
And here is the problem emerges: if total number of elements N is
zero, i.e. dataset is empty,
my attemp to create an attribute results in an error and program
termination.
It doesn't happen if the dataset is nonempty.
Besides, serial version of the program works fine it both cases.
I must be doing something wrong, but I can't figure out what exactly.
What is the correct way to create an attribute for a dataset in parallel?
Attached is the source code for the parallel and the serial versions
of the program.
I'm using Debian with libhdf5-1.8.13.
#include <hdf5.h>
#include <stdlib.h>
#include <mpi.h>
#define FILE "empty_dset.h5"
#define DSET "/dset"
void distribute_elements_between_processes( hsize_t *subset_dims,
hsize_t *subset_offset,
int total_elements );
int main(){
MPI_Init(NULL, NULL);
int mpi_process_rank;
MPI_Comm_rank( MPI_COMM_WORLD, &mpi_process_rank );
hid_t file_id, dataset_id, dataspace_id, attribute_id; /* identifiers */
hid_t plist_id, memspace, filespace;
herr_t status;
int dset_rank = 1;
int total_elements = 0;
hsize_t dims[dset_rank];
dims[0] = total_elements;
/* Create a new file collectively. */
plist_id = H5Pcreate( H5P_FILE_ACCESS );
H5Pset_fapl_mpio( plist_id, MPI_COMM_WORLD, MPI_INFO_NULL );
file_id = H5Fcreate( FILE, H5F_ACC_TRUNC, H5P_DEFAULT, plist_id );
H5Pclose(plist_id);
hsize_t subset_dims[dset_rank], subset_offset[dset_rank];
distribute_elements_between_processes( subset_dims, subset_offset, total_elements );
int *data = (int *) malloc( subset_dims[0] * sizeof(int) );
for( int i = 0; i < subset_dims[0]; i++ ){
data[i] = mpi_process_rank;
}
plist_id = H5Pcreate( H5P_DATASET_XFER );
status = H5Pset_dxpl_mpio( plist_id, H5FD_MPIO_COLLECTIVE );
memspace = H5Screate_simple( dset_rank, subset_dims, NULL );
filespace = H5Screate_simple( dset_rank, dims, NULL );
status = H5Sselect_hyperslab( filespace, H5S_SELECT_SET,
subset_offset, NULL, subset_dims, NULL );
/* Create a dataset. */
dataset_id = H5Dcreate2(file_id, DSET, H5T_STD_I32BE, filespace,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
status = H5Dwrite( dataset_id, H5T_NATIVE_INT,
memspace, filespace, plist_id, data );
H5Dclose( dataset_id );
H5Sclose( filespace );
H5Sclose( memspace );
H5Pclose( plist_id );
free(data);
/* Create an attribute */
hsize_t attr_dspace_rank = 1;
hsize_t single_element = 1;
double attr = 3.0;
dataset_id = H5Dopen2(file_id, DSET, H5P_DEFAULT);
dataspace_id = H5Screate_simple( attr_dspace_rank, &single_element, NULL);
attribute_id = H5Acreate2( dataset_id, "attr", H5T_IEEE_F64BE, dataspace_id,
H5P_DEFAULT, H5P_DEFAULT );
status = H5Awrite(attribute_id, H5T_NATIVE_DOUBLE, &attr);
status = H5Aclose(attribute_id);
status = H5Sclose(dataspace_id);
status = H5Dclose(dataset_id);
/* Close the file. */
status = H5Fclose(file_id);
MPI_Finalize();
}
void distribute_elements_between_processes( hsize_t *subset_dims,
hsize_t *subset_offset,
int total_elements )
{
int rest;
int mpi_n_of_proc, mpi_process_rank;
MPI_Comm_size( MPI_COMM_WORLD, &mpi_n_of_proc );
MPI_Comm_rank( MPI_COMM_WORLD, &mpi_process_rank );
subset_dims[0] = total_elements / mpi_n_of_proc;
rest = total_elements % mpi_n_of_proc;
if( mpi_process_rank < rest )
subset_dims[0]++;
subset_offset[0] = subset_dims[0] * mpi_process_rank;
if( mpi_process_rank > rest )
subset_offset[0] += rest;
/* printf( "proc = %d, dims = %d, offset = %d \n", */
/* mpi_process_rank, subset_dims[0], subset_offset[0] ); */
return;
}
#include <hdf5.h>
#include <stdlib.h>
#define FILE "empty_dset.h5"
#define DSET "/dset"
int main(){
hid_t file_id, dataset_id, dataspace_id, attribute_id; /* identifiers */
hid_t plist_id, memspace, filespace;
herr_t status;
int dset_rank = 1;
int total_elements = 10;
hsize_t dims[dset_rank];
dims[0] = total_elements;
int *data = (int *) malloc( dims[0] * sizeof(int) );
for( int i = 0; i < dims[0]; i++ ){
data[i] = i;
}
/* Create a new file. */
file_id = H5Fcreate( FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT );
/* Create a dataset. */
dataspace_id = H5Screate_simple( dset_rank, dims, NULL);
dataset_id = H5Dcreate2(file_id, DSET, H5T_STD_I32BE, dataspace_id,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
status = H5Dwrite( dataset_id, H5T_NATIVE_INT,
H5S_ALL, H5S_ALL, H5P_DEFAULT, data );
H5Dclose( dataset_id );
H5Sclose( dataspace_id );
free(data);
/* Create an attribute */
hsize_t attr_dim = 1;
hsize_t single_element = 1;
double attr = 3.0;
dataset_id = H5Dopen2(file_id, DSET, H5P_DEFAULT);
dataspace_id = H5Screate_simple( attr_dim, &single_element, NULL);
attribute_id = H5Acreate2( dataset_id, "attr", H5T_IEEE_F64BE, dataspace_id,
H5P_DEFAULT, H5P_DEFAULT );
status = H5Awrite(attribute_id, H5T_NATIVE_DOUBLE, &attr);
status = H5Aclose(attribute_id);
status = H5Sclose(dataspace_id);
status = H5Dclose(dataset_id);
/* Close the file. */
status = H5Fclose(file_id);
}
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