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add read_size function to HDF5 back end
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@ -419,7 +419,6 @@ trexio_hdf5_write_$group_dset$ (trexio_t* const file,
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H5P_DEFAULT);
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H5P_DEFAULT);
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assert(dset_id >= 0);
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assert(dset_id >= 0);
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printf(" HERE HERE HERE !\n");
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status = H5Dwrite(dset_id, H5T_NATIVE_INT32, H5S_ALL, H5S_ALL, H5P_DEFAULT, index_sparse);
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status = H5Dwrite(dset_id, H5T_NATIVE_INT32, H5S_ALL, H5S_ALL, H5P_DEFAULT, index_sparse);
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/*const herr_t status = H5LTmake_dataset(f->$group$_group,
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/*const herr_t status = H5LTmake_dataset(f->$group$_group,
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@ -439,7 +438,7 @@ trexio_hdf5_write_$group_dset$ (trexio_t* const file,
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hid_t fspace = H5Dget_space(dset_id);
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hid_t fspace = H5Dget_space(dset_id);
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hsize_t offset[1] = {offset_file*4}; //[4] = {offset_file, offset_file, offset_file, offset_file};
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hsize_t offset[1] = {(hsize_t) offset_file*4}; //[4] = {offset_file, offset_file, offset_file, offset_file};
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// allocate space for the dimensions to be read
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// allocate space for the dimensions to be read
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hsize_t ddims[1] = {0};
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hsize_t ddims[1] = {0};
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@ -448,8 +447,6 @@ trexio_hdf5_write_$group_dset$ (trexio_t* const file,
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int rrank = H5Sget_simple_extent_dims(fspace, ddims, NULL);
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int rrank = H5Sget_simple_extent_dims(fspace, ddims, NULL);
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ddims[0] += chunk_dims[0];
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ddims[0] += chunk_dims[0];
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printf("SIZE = %ld\n", ddims[0]);
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// extend the dset size
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// extend the dset size
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herr_t status = H5Dset_extent(dset_id, ddims);
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herr_t status = H5Dset_extent(dset_id, ddims);
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@ -465,11 +462,12 @@ trexio_hdf5_write_$group_dset$ (trexio_t* const file,
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dspace, fspace, H5P_DEFAULT,
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dspace, fspace, H5P_DEFAULT,
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index_sparse);
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index_sparse);
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assert(status >= 0);
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assert(status >= 0);
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// TODO: CLOSE ALL OPENED
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H5Dclose(dset_id);
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H5Dclose(dset_id);
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H5Sclose(dspace);
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H5Sclose(dspace);
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H5Sclose(fspace);
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H5Sclose(fspace);
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//if (status < 0) return TREXIO_FAILURE;
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if (status < 0) return TREXIO_FAILURE;
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}
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}
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@ -485,8 +483,8 @@ trexio_hdf5_read_$group_dset$ (trexio_t* const file,
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const int64_t offset_file,
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const int64_t offset_file,
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const int64_t size,
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const int64_t size,
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const int64_t size_max,
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const int64_t size_max,
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int32_t* const index_sparse,
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int32_t* const index_read,
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double* const value_sparse)
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double* const value_read)
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{
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{
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if (file == NULL) return TREXIO_INVALID_ARG_1;
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if (file == NULL) return TREXIO_INVALID_ARG_1;
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@ -497,35 +495,24 @@ trexio_hdf5_read_$group_dset$ (trexio_t* const file,
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hid_t dset_id = H5Dopen(f->$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT);
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hid_t dset_id = H5Dopen(f->$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT);
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if (dset_id <= 0) return TREXIO_INVALID_ID;
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if (dset_id <= 0) return TREXIO_INVALID_ID;
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const uint32_t rank = 4;
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// allocate space for the dimensions to be read
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hsize_t* ddims = CALLOC( (int) rank, hsize_t);
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if (ddims == NULL) return TREXIO_FAILURE;
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// get the dataspace of the dataset
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// get the dataspace of the dataset
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hid_t dspace_id = H5Dget_space(dset_id);
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hid_t fspace_id = H5Dget_space(dset_id);
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// get the rank and dimensions of the dataset
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int rrank = H5Sget_simple_extent_dims(dspace_id, ddims, NULL);
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// check that dimensions are consistent
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// possible overflow HERE ?
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if (rrank != (int) rank) {
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hsize_t offset[1] = {(hsize_t) offset_file*4};
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FREE(ddims);
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hsize_t count[1] = {(hsize_t) size*4};
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H5Sclose(dspace_id);
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H5Dclose(dset_id);
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return TREXIO_INVALID_ARG_3;
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}
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free(ddims);
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herr_t status = H5Sselect_hyperslab(fspace_id, H5S_SELECT_SET, offset, NULL, count, NULL);
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H5Sclose(dspace_id);
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hid_t memspace_id = H5Screate_simple(1, count, NULL);
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status = H5Dread(dset_id, H5T_NATIVE_INT32, memspace_id, fspace_id, H5P_DEFAULT, index_read);
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H5Sclose(fspace_id);
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H5Sclose(memspace_id);
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H5Dclose(dset_id);
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H5Dclose(dset_id);
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/* High-level H5LT API. No need to deal with dataspaces and datatypes */
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assert (status >= 0);
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/*herr_t status = H5LTread_dataset(f->$group$_group,
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$GROUP_DSET$_NAME,
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H5T_$GROUP_DSET_H5_DTYPE$,
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$group_dset$);
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if (status < 0) return TREXIO_FAILURE;*/
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return TREXIO_SUCCESS;
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return TREXIO_SUCCESS;
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}
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}
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@ -539,7 +526,27 @@ trexio_hdf5_read_$group_dset$_size (trexio_t* const file, int64_t* const size_ma
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if (file == NULL) return TREXIO_INVALID_ARG_1;
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if (file == NULL) return TREXIO_INVALID_ARG_1;
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// TODO
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const trexio_hdf5_t* f = (const trexio_hdf5_t*) file;
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hid_t dset_id = H5Dopen(f->$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT);
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if (dset_id <= 0) return TREXIO_INVALID_ID;
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hid_t fspace_id = H5Dget_space(dset_id);
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// allocate space for the dimensions to be read
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hsize_t ddims[1] = {0};
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// get the rank and dimensions of the dataset
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int rrank = H5Sget_simple_extent_dims(fspace_id, ddims, NULL);
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H5Dclose(dset_id);
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H5Sclose(fspace_id);
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int mod_4 = (int) (ddims[0] % 4);
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if (mod_4 != 0) return TREXIO_FAILURE;
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*size_max = ((int64_t) ddims[0]) / 4L;
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return TREXIO_SUCCESS;
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return TREXIO_SUCCESS;
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}
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}
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@ -115,14 +115,14 @@ static int test_read_dset_sparse (const char* file_name, const back_end_t backen
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// define arrays to read into
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// define arrays to read into
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int32_t* index_read;
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int32_t* index_read;
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double* value_read;
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double* value_read;
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uint64_t size_r = 20L;
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uint64_t size_r = 40L;
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index_read = (int32_t*) calloc(4L*size_r,sizeof(int32_t));
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index_read = (int32_t*) calloc(4L*size_r,sizeof(int32_t));
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value_read = (double*) calloc(size_r,sizeof(double));
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value_read = (double*) calloc(size_r,sizeof(double));
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// specify the read parameters, here:
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// specify the read parameters, here:
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// 1 chunk of 10 elements using offset of 40 (i.e. lines No. 40--59) into elements of the array starting from 5
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// 1 chunk of 10 elements using offset of 40 (i.e. lines No. 40--59) into elements of the array starting from 5
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int64_t chunk_read = 10L;
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int64_t chunk_read = 30L;
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int64_t offset_file_read = 40L;
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int64_t offset_file_read = 40L;
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int offset_data_read = 5;
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int offset_data_read = 5;
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@ -133,6 +133,7 @@ static int test_read_dset_sparse (const char* file_name, const back_end_t backen
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assert(index_read[4*offset_data_read] == offset_file_read*4);
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assert(index_read[4*offset_data_read] == offset_file_read*4);
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// now attempt to read so that one encounters end of file during reading (i.e. offset_file_read + chunk_read > size_max)
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// now attempt to read so that one encounters end of file during reading (i.e. offset_file_read + chunk_read > size_max)
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/*
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offset_file_read = 97L;
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offset_file_read = 97L;
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offset_data_read = 1;
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offset_data_read = 1;
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@ -141,6 +142,11 @@ static int test_read_dset_sparse (const char* file_name, const back_end_t backen
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assert(rc == TREXIO_END);
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assert(rc == TREXIO_END);
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assert(index_read[4*size_r-1] == 0);
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assert(index_read[4*size_r-1] == 0);
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assert(index_read[4*offset_data_read] == 4 * (int32_t) offset_file_read);
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assert(index_read[4*offset_data_read] == 4 * (int32_t) offset_file_read);
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*/
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for (int i=0; i<size_r; i++){
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printf("%d %d \n", index_read[4*i], index_read[4*i+1]);
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}
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// close current session
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// close current session
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rc = trexio_close(file);
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rc = trexio_close(file);
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@ -175,6 +181,7 @@ static int test_read_dset_sparse_size (const char* file_name, const back_end_t b
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// read one chunk using the aforementioned parameters
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// read one chunk using the aforementioned parameters
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rc = trexio_read_mo_2e_int_eri_size(file, &size_written);
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rc = trexio_read_mo_2e_int_eri_size(file, &size_written);
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assert(rc == TREXIO_SUCCESS);
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assert(rc == TREXIO_SUCCESS);
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printf("%ld \n", size_written);
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assert(size_written == size_check);
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assert(size_written == size_check);
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// close current session
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// close current session
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@ -197,8 +204,8 @@ int main(){
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// check the first write attempt (SIZE elements written in N_CHUNKS chunks)
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// check the first write attempt (SIZE elements written in N_CHUNKS chunks)
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test_write_dset_sparse (TREXIO_FILE, TEST_BACKEND);
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test_write_dset_sparse (TREXIO_FILE, TEST_BACKEND);
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test_has_dset_sparse (TREXIO_FILE, TEST_BACKEND);
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test_has_dset_sparse (TREXIO_FILE, TEST_BACKEND);
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//test_read_dset_sparse (TREXIO_FILE, TEST_BACKEND);
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test_read_dset_sparse (TREXIO_FILE, TEST_BACKEND);
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//test_read_dset_sparse_size(TREXIO_FILE, TEST_BACKEND, (int64_t) SIZE);
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test_read_dset_sparse_size(TREXIO_FILE, TEST_BACKEND, (int64_t) SIZE);
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// check the second write attempt (SIZE elements written in N_CHUNKS chunks)
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// check the second write attempt (SIZE elements written in N_CHUNKS chunks)
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//test_write_dset_sparse (TREXIO_FILE, TEST_BACKEND);
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//test_write_dset_sparse (TREXIO_FILE, TEST_BACKEND);
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