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Merge pull request #1784 from NOAA-GSD/ejh_h5_par_zip_test
Add a HDF5 only test of writing and reading a file with parallel I/O and the zlib filter
This commit is contained in:
Ward Fisher
GitHub
commit
ed241d740b
@ -7,6 +7,7 @@ This file contains a high-level description of this package's evolution. Release
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## 4.8.0 - TBD
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* [Enhancement] Added new test for using compression with parallel I/O: nc_test4/tst_h_par_compress.c. See [https://github.com/Unidata/netcdf-c/pull/1784].
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* [Bug Fix] Now allow szip to be used on variables with unlimited dimension [https://github.com/Unidata/netcdf-c/issues/1774].
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* [Enhancement] Add support for cloud storage using a variant of the Zarr storage format. Warning: this feature is highly experimental and is subject to rapid evolution [https://www.unidata.ucar.edu/blogs/developer/en/entry/overview-of-zarr-support-in].
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* [Bug Fix] Fix nccopy to properly set default chunking parameters when not otherwise specified. This can significantly improve performance in selected cases. Note that if seeing slow performance with nccopy, then, as a work-around, specifically set the chunking parameters. [https://github.com/Unidata/netcdf-c/issues/1763].
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@ -22,5 +22,6 @@ ENDFOREACH()
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IF(TEST_PARALLEL4)
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build_bin_test(tst_h_par)
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build_bin_test(tst_h_par_compress)
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add_sh_test(h5_test run_par_tests)
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ENDIF()
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@ -34,7 +34,7 @@ TESTS = $(H5TESTS)
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# The parallel program is run from a script.
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if TEST_PARALLEL4
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check_PROGRAMS += tst_h_par
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check_PROGRAMS += tst_h_par tst_h_par_compress
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TESTS += run_par_tests.sh
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endif
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@ -17,4 +17,10 @@ echo "Testing parallel I/O with HDF5..."
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@MPIEXEC@ -n 4 ./tst_h_par
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echo "SUCCESS!!!"
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echo "Testing parallel I/O with HDF5 and compression..."
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@MPIEXEC@ -n 1 ./tst_h_par_compress
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@MPIEXEC@ -n 2 ./tst_h_par_compress
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@MPIEXEC@ -n 4 ./tst_h_par_compress
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echo "SUCCESS!!!"
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exit 0
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210
h5_test/tst_h_par_compress.c
Normal file
210
h5_test/tst_h_par_compress.c
Normal file
@ -0,0 +1,210 @@
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/* This is part of the netCDF package. Copyright 2020 University
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Corporation for Atmospheric Research/Unidata See COPYRIGHT file for
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conditions of use.
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Test HDF5 file code. These are not intended to be exhaustive tests,
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but they use HDF5 the same way that netCDF-4 does, so if these
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tests don't work, than netCDF-4 won't work either.
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This files tests parallel I/O using compression filters. This
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functionality is only available in HDF5-1.10.3 and later versions.
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Ed Hartnett
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*/
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#include <nc_tests.h>
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#include "err_macros.h"
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#include <hdf5.h>
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#define FILE_NAME "tst_h_par_compress.h5"
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#define VAR_NAME "HALs_memory"
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#define NDIMS 1
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#define MILLION 1000000
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#define DIM2_LEN 16000000
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#define SC1 100000 /* slice count. */
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/* The following code, when uncommented, adds szip testing for
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* parallel I/O. However, this currently fails. I have a support
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* request in to HDF5 about this. Ed 7/8/20 */
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/* #ifdef USE_SZIP */
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/* #define NUM_COMPRESS_FILTERS 2 */
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/* #else */
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/* #define NUM_COMPRESS_FILTERS 1 */
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/* #endif /\* USE_SZIP *\/ */
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#define NUM_COMPRESS_FILTERS 1
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int
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main(int argc, char **argv)
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{
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int p, my_rank;
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MPI_Init(&argc, &argv);
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MPI_Comm_rank(MPI_COMM_WORLD, &my_rank);
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MPI_Comm_size(MPI_COMM_WORLD, &p);
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/* For builds with HDF5 prior to 1.10.3, just return success. */
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#ifdef HDF5_SUPPORTS_PAR_FILTERS
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for (int cf = 0; cf < NUM_COMPRESS_FILTERS; cf++)
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{
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if (!my_rank)
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printf("*** Testing parallel I/O with %s compression...", cf ? "szip" : "zlib");
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{
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hid_t fapl_id, fileid, whole_spaceid, dsid, slice_spaceid, whole_spaceid1, xferid;
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hid_t plistid;
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hsize_t start[NDIMS], count[NDIMS];
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hsize_t dims[1], chunksize = SC1;
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int data[SC1], data_in[SC1];
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int num_steps;
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int deflate_level = 4;
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int i, s;
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/* We will write the same slice of random data over and over to
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* fill the file. */
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for (i = 0; i < SC1; i++)
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data[i] = rand();
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/* Create file. */
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if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR;
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if (H5Pset_fapl_mpio(fapl_id, MPI_COMM_WORLD, MPI_INFO_NULL) < 0) ERR;
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if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT,
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fapl_id)) < 0) ERR;
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/* Create a space to deal with one slice in memory. */
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dims[0] = SC1;
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if ((slice_spaceid = H5Screate_simple(NDIMS, dims, NULL)) < 0) ERR;
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/* Create a space to write all slices. */
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dims[0] = DIM2_LEN;
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if ((whole_spaceid = H5Screate_simple(NDIMS, dims, NULL)) < 0) ERR;
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/* Create property list for dataset. */
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if ((plistid = H5Pcreate(H5P_DATASET_CREATE)) < 0) ERR;
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/* Turn off object tracking times in HDF5 (as is done in nc4hdf.c). */
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if (H5Pset_obj_track_times(plistid, 0) < 0) ERR;
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/* Required to truly turn HDF5 fill values off */
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if (H5Pset_fill_time(plistid, H5D_FILL_TIME_NEVER) < 0) ERR;
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/* Set compression, either deflate or szip. */
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if (cf == 0)
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{
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if (H5Pset_deflate(plistid, deflate_level) < 0) ERR;
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}
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else
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{
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int options_mask = 32;
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int bits_per_pixel = 32;
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if (H5Pset_szip(plistid, options_mask, bits_per_pixel)) ERR;
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}
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/* Set chunking. */
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if (H5Pset_chunk(plistid, NDIMS, &chunksize) < 0) ERR;
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/* Turn on creation order tracking. */
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if (H5Pset_attr_creation_order(plistid, H5P_CRT_ORDER_TRACKED|
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H5P_CRT_ORDER_INDEXED) < 0) ERR;
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/* Create dataset. */
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if ((dsid = H5Dcreate2(fileid, VAR_NAME, H5T_NATIVE_INT,
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whole_spaceid, H5P_DEFAULT, plistid, H5P_DEFAULT)) < 0) ERR;
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/* Use collective write operations. */
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if ((xferid = H5Pcreate(H5P_DATASET_XFER)) < 0) ERR;
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if (H5Pset_dxpl_mpio(xferid, H5FD_MPIO_COLLECTIVE) < 0) ERR;
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/* Write the data in num_step steps. */
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num_steps = (DIM2_LEN/SC1) / p;
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for (s = 0; s < num_steps; s++)
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{
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/* Select hyperslab for write of one slice. */
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start[0] = s * SC1 * p + my_rank * SC1;
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count[0] = SC1;
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if (H5Sselect_hyperslab(whole_spaceid, H5S_SELECT_SET,
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start, NULL, count, NULL) < 0) ERR;
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if (H5Dwrite(dsid, H5T_NATIVE_INT, slice_spaceid, whole_spaceid,
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xferid, data) < 0) ERR;
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}
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/* Close. These collective operations will allow every process
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* to catch up. */
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if (H5Dclose(dsid) < 0 ||
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H5Sclose(whole_spaceid) < 0 ||
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H5Sclose(slice_spaceid) < 0 ||
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H5Pclose(fapl_id) < 0 ||
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H5Pclose(plistid) < 0 ||
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H5Fclose(fileid) < 0)
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ERR;
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/* Open the file. */
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if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR;
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if (H5Pset_fapl_mpio(fapl_id, MPI_COMM_WORLD, MPI_INFO_NULL) < 0) ERR;
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if (H5Pset_libver_bounds(fapl_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) ERR;
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if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDONLY, fapl_id)) < 0) ERR;
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/* Create a space to deal with one slice in memory. */
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dims[0] = SC1;
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if ((slice_spaceid = H5Screate_simple(NDIMS, dims, NULL)) < 0) ERR;
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/* Open the dataset. */
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if ((dsid = H5Dopen(fileid, VAR_NAME)) < 0) ERR;
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if ((whole_spaceid1 = H5Dget_space(dsid)) < 0) ERR;
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/* Read the data, a slice at a time. */
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for (s = 0; s < num_steps; s++)
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{
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/* Select hyperslab for read of one slice. */
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start[0] = s * SC1 * p + my_rank * SC1;
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count[0] = SC1;
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if (H5Sselect_hyperslab(whole_spaceid1, H5S_SELECT_SET,
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start, NULL, count, NULL) < 0)
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{
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ERR;
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return 2;
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}
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if (H5Dread(dsid, H5T_NATIVE_INT, slice_spaceid, whole_spaceid1,
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H5P_DEFAULT, data_in) < 0)
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{
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ERR;
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return 2;
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}
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/* Check the slice of data. */
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for (i = 0; i < SC1; i++)
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if (data[i] != data_in[i])
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{
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ERR;
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return 2;
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}
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}
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/* Close down. */
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if (H5Dclose(dsid) < 0 ||
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H5Sclose(slice_spaceid) < 0 ||
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H5Sclose(whole_spaceid1) < 0 ||
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H5Pclose(fapl_id) < 0 ||
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H5Fclose(fileid) < 0)
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ERR;
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}
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if (!my_rank)
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SUMMARIZE_ERR;
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} /* next cf */
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#else
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{
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if (!my_rank)
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printf("*** HDF5 1.10.3 or greater required for this test.\n");
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}
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#endif /* HDF5_SUPPORTS_PAR_FILTERS */
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MPI_Finalize();
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if (!my_rank)
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FINAL_RESULTS;
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return 0;
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}
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@ -322,8 +322,7 @@ main(int argc, char **argv)
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{
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/* This test is related to
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* https://github.com/Unidata/netcdf-c/issues/1715. */
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int ncid, varid;
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int test_data_in, test_data = 42;
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int ncid;
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size_t size, nelems;
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float preemption;
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