I want to write a function that will append a buffer to an extendible HDF5 dataset. The buffer will always have the same size (NXN) during the program execution. Following this brilliant answer https://stackoverflow.com/questions/15379399/writing-appending-arrays-of-float-to-the-only-dataset-in-hdf5-file-in-c I have written the following code.
MAIN
#include <iostream>
#include <H5Cpp.h>
#include "Myclass.hpp"
const char saveFilePath[] = "test.h5";
int main()
{
const hsize_t nrows = 2;
const hsize_t ncols = 2;
const hsize_t nghost = 1;
Myclass hfield(ncols,nrows,nghost); // the dimension of the buffer is 4X4
hfield(0,0) = 1;
hfield(1,0) = 2;
hfield(0,1) = 3;
hfield(1,1) = 4;
hid_t file = H5Fcreate(saveFilePath, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
std::cout << "- File created" << std::endl;
write_to_extendible_H5("test.h5", hfield);
write_to_extendible_H5("test.h5", hfield);
return 0;
}
FUNCTION
void write_to_extendible_H5(const char* FILENAME, Myclass& hfield)
{
hsize_t ndims = 2;
hsize_t nrows = hfield.getrows() + 2*hfield.getnghost();
hsize_t ncols = hfield.getcols() + 2*hfield.getnghost();
/* Create a memory dataspace to indicate the
size of our buffer to be written in memory. */
hsize_t mbuff_dims[ndims];
mbuff_dims[0] = nrows;
mbuff_dims[1] = ncols;
hid_t mem_space = H5Screate_simple(ndims, mbuff_dims, NULL);
std::cout << "- Memory dataspace created" << std::endl;
/* Open the file. */
hid_t file = H5Fopen(FILENAME, H5F_ACC_RDWR, H5P_DEFAULT);
/* Check if there is a dataset. */
if ( !H5Lexists(file,"dset1",H5P_DEFAULT) )
{
/* Dataset does not exist. Create it and
write the first buffer. */
// Create a 2D dataspace.
hsize_t dims[ndims] = {nrows, ncols};
hsize_t max_dims[ndims] = {H5S_UNLIMITED, ncols};
hid_t file_space = H5Screate_simple(ndims, dims, max_dims);
std::cout << "- Dataspace created" << std::endl;
// Then create a dataset creation property list.
hid_t plist = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_layout(plist, H5D_CHUNKED);
hsize_t chunk_dims[ndims] = {nrows, ncols};
H5Pset_chunk(plist, ndims, chunk_dims);
std::cout << "- Property list created" << std::endl;
// Create the dataset.
hid_t dset = H5Dcreate(file, "dset1", H5T_NATIVE_DOUBLE,
file_space, H5P_DEFAULT, plist, H5P_DEFAULT);
std::cout << "- Dataset 'dset1' created" << std::endl;
/* Close resources. */
H5Pclose(plist);
H5Sclose(file_space);
/* Write the first buffer */
// Select hyperslab on file dataset.
file_space = H5Dget_space(dset);
hsize_t start[2] = {0, 0};
hsize_t count[2] = {nrows, ncols};
H5Sselect_hyperslab(file_space, H5S_SELECT_SET, start,
NULL, count, NULL);
std::cout << "- First hyperslab selected" << std::endl;
/* Write buffer to dataset. */
H5Dwrite(dset, H5T_NATIVE_DOUBLE, mem_space, file_space,
H5P_DEFAULT, hfield.getmemory());
std::cout << "- First buffer written" << std::endl;
/*We can now close the file dataspace. */
H5Sclose(file_space);
}
else
{
/* Dataset already exists. Extend it and write
the next buffer. */
// Open the dataset and get the dimensions of the existing dataset.
hid_t dset = H5Dopen(file,"dset1",H5P_DEFAULT);
hid_t file_space = H5Dget_space(dset);
hsize_t dims[ndims];
H5Sget_simple_extent_dims(file_space, dims, NULL);
std::cout << "- The dataset dimensions before extension are:" << std::endl;
std::cout << "No of rows: " << dims[0] << std::endl;
std::cout << "No of cols: " << dims[1] << std::endl;
// Extend the dimensions.
dims[0] += nrows;
dims[1] = ncols;
H5Dset_extent(dset, dims);
std::cout << "- Dataset extended" << std::endl;
// Select hyperslab
hsize_t start[2] = {dims[0]-nrows, 0};
hsize_t count[2] = {nrows, ncols};
H5Sselect_hyperslab(file_space, H5S_SELECT_SET, start,
NULL, count, NULL);
std::cout << "- Next hyperslab selected" << std::endl;
// Write buffer
H5Dwrite(dset, H5T_NATIVE_DOUBLE, mem_space, file_space,
H5P_DEFAULT, hfield.getmemory());
std::cout << "- Next buffer written" << std::endl;
/*We can now close the file dataspace. */
H5Sclose(file_space);
}
}
The output from h5dump is:
HDF5 "test.h5" {
GROUP "/" {
DATASET "dset1" {
DATATYPE H5T_IEEE_F64LE
DATASPACE SIMPLE { ( 8, 4 ) / ( H5S_UNLIMITED, 4 ) }
DATA {
(0,0): 0, 0, 0, 0,
(1,0): 0, 1, 2, 0,
(2,0): 0, 3, 4, 0,
(3,0): 0, 0, 0, 0,
(4,0): 0, 0, 0, 0,
(5,0): 0, 0, 0, 0,
(6,0): 0, 0, 0, 0,
(7,0): 0, 0, 0, 0
}
}
}
}
And the console gives:
- File created
- Memory dataspace created
- Dataspace created
- Property list created
- Dataset 'dset1' created
- First hyperslab selected
- First buffer written
- Memory dataspace created
- The dataset dimensions before extension are:
No of rows: 4
No of cols: 4
- Dataset extended
- Next hyperslab selected
HDF5-DIAG: Error detected in HDF5 (1.12.0) thread 0:
#000: H5Dio.c line 314 in H5Dwrite(): can't write data
major: Dataset
minor: Write failed
#001: H5VLcallback.c line 2186 in H5VL_dataset_write(): dataset write failed
major: Virtual Object Layer
minor: Write failed
#002: H5VLcallback.c line 2152 in H5VL__dataset_write(): dataset write failed
major: Virtual Object Layer
minor: Write failed
#003: H5VLnative_dataset.c line 203 in H5VL__native_dataset_write(): could not get a validated dataspace from file_space_id
major: Invalid arguments to routine
minor: Bad value
#004: H5S.c line 279 in H5S_get_validated_dataspace(): selection + offset not within extent
major: Dataspace
minor: Out of range
- Next buffer written
Can you please tell me why is the second buffer not written?