diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md index 48a8b2fcb4..0ab86f7443 100644 --- a/RELEASE_NOTES.md +++ b/RELEASE_NOTES.md @@ -7,6 +7,7 @@ This file contains a high-level description of this package's evolution. Release ## 4.8.0 - TBD +* [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]. * [Bug Fix] Now allow szip to be used on variables with unlimited dimension [https://github.com/Unidata/netcdf-c/issues/1774]. * [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]. * [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]. diff --git a/h5_test/CMakeLists.txt b/h5_test/CMakeLists.txt index 40702e9ddb..3f040c9cbc 100644 --- a/h5_test/CMakeLists.txt +++ b/h5_test/CMakeLists.txt @@ -22,5 +22,6 @@ ENDFOREACH() IF(TEST_PARALLEL4) build_bin_test(tst_h_par) + build_bin_test(tst_h_par_compress) add_sh_test(h5_test run_par_tests) ENDIF() diff --git a/h5_test/Makefile.am b/h5_test/Makefile.am index dfea153bb4..115709c0b7 100644 --- a/h5_test/Makefile.am +++ b/h5_test/Makefile.am @@ -34,7 +34,7 @@ TESTS = $(H5TESTS) # The parallel program is run from a script. if TEST_PARALLEL4 -check_PROGRAMS += tst_h_par +check_PROGRAMS += tst_h_par tst_h_par_compress TESTS += run_par_tests.sh endif diff --git a/h5_test/run_par_tests.sh.in b/h5_test/run_par_tests.sh.in index 70716aec80..d8f6297a86 100644 --- a/h5_test/run_par_tests.sh.in +++ b/h5_test/run_par_tests.sh.in @@ -17,4 +17,10 @@ echo "Testing parallel I/O with HDF5..." @MPIEXEC@ -n 4 ./tst_h_par echo "SUCCESS!!!" +echo "Testing parallel I/O with HDF5 and compression..." +@MPIEXEC@ -n 1 ./tst_h_par_compress +@MPIEXEC@ -n 2 ./tst_h_par_compress +@MPIEXEC@ -n 4 ./tst_h_par_compress +echo "SUCCESS!!!" + exit 0 diff --git a/h5_test/tst_h_par_compress.c b/h5_test/tst_h_par_compress.c new file mode 100644 index 0000000000..e24313ab7a --- /dev/null +++ b/h5_test/tst_h_par_compress.c @@ -0,0 +1,210 @@ +/* This is part of the netCDF package. Copyright 2020 University + Corporation for Atmospheric Research/Unidata See COPYRIGHT file for + conditions of use. + + Test HDF5 file code. These are not intended to be exhaustive tests, + but they use HDF5 the same way that netCDF-4 does, so if these + tests don't work, than netCDF-4 won't work either. + + This files tests parallel I/O using compression filters. This + functionality is only available in HDF5-1.10.3 and later versions. + + Ed Hartnett +*/ +#include +#include "err_macros.h" +#include + +#define FILE_NAME "tst_h_par_compress.h5" +#define VAR_NAME "HALs_memory" +#define NDIMS 1 +#define MILLION 1000000 +#define DIM2_LEN 16000000 +#define SC1 100000 /* slice count. */ + +/* The following code, when uncommented, adds szip testing for + * parallel I/O. However, this currently fails. I have a support + * request in to HDF5 about this. Ed 7/8/20 */ +/* #ifdef USE_SZIP */ +/* #define NUM_COMPRESS_FILTERS 2 */ +/* #else */ +/* #define NUM_COMPRESS_FILTERS 1 */ +/* #endif /\* USE_SZIP *\/ */ +#define NUM_COMPRESS_FILTERS 1 + +int +main(int argc, char **argv) +{ + int p, my_rank; + + MPI_Init(&argc, &argv); + MPI_Comm_rank(MPI_COMM_WORLD, &my_rank); + MPI_Comm_size(MPI_COMM_WORLD, &p); + + /* For builds with HDF5 prior to 1.10.3, just return success. */ +#ifdef HDF5_SUPPORTS_PAR_FILTERS + for (int cf = 0; cf < NUM_COMPRESS_FILTERS; cf++) + { + if (!my_rank) + printf("*** Testing parallel I/O with %s compression...", cf ? "szip" : "zlib"); + { + hid_t fapl_id, fileid, whole_spaceid, dsid, slice_spaceid, whole_spaceid1, xferid; + hid_t plistid; + hsize_t start[NDIMS], count[NDIMS]; + hsize_t dims[1], chunksize = SC1; + int data[SC1], data_in[SC1]; + int num_steps; + int deflate_level = 4; + int i, s; + + /* We will write the same slice of random data over and over to + * fill the file. */ + for (i = 0; i < SC1; i++) + data[i] = rand(); + + /* Create file. */ + if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR; + if (H5Pset_fapl_mpio(fapl_id, MPI_COMM_WORLD, MPI_INFO_NULL) < 0) ERR; + if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT, + fapl_id)) < 0) ERR; + + /* Create a space to deal with one slice in memory. */ + dims[0] = SC1; + if ((slice_spaceid = H5Screate_simple(NDIMS, dims, NULL)) < 0) ERR; + + /* Create a space to write all slices. */ + dims[0] = DIM2_LEN; + if ((whole_spaceid = H5Screate_simple(NDIMS, dims, NULL)) < 0) ERR; + + /* Create property list for dataset. */ + if ((plistid = H5Pcreate(H5P_DATASET_CREATE)) < 0) ERR; + + /* Turn off object tracking times in HDF5 (as is done in nc4hdf.c). */ + if (H5Pset_obj_track_times(plistid, 0) < 0) ERR; + + /* Required to truly turn HDF5 fill values off */ + if (H5Pset_fill_time(plistid, H5D_FILL_TIME_NEVER) < 0) ERR; + + /* Set compression, either deflate or szip. */ + if (cf == 0) + { + if (H5Pset_deflate(plistid, deflate_level) < 0) ERR; + } + else + { + int options_mask = 32; + int bits_per_pixel = 32; + if (H5Pset_szip(plistid, options_mask, bits_per_pixel)) ERR; + } + + /* Set chunking. */ + if (H5Pset_chunk(plistid, NDIMS, &chunksize) < 0) ERR; + + /* Turn on creation order tracking. */ + if (H5Pset_attr_creation_order(plistid, H5P_CRT_ORDER_TRACKED| + H5P_CRT_ORDER_INDEXED) < 0) ERR; + + /* Create dataset. */ + if ((dsid = H5Dcreate2(fileid, VAR_NAME, H5T_NATIVE_INT, + whole_spaceid, H5P_DEFAULT, plistid, H5P_DEFAULT)) < 0) ERR; + + /* Use collective write operations. */ + if ((xferid = H5Pcreate(H5P_DATASET_XFER)) < 0) ERR; + if (H5Pset_dxpl_mpio(xferid, H5FD_MPIO_COLLECTIVE) < 0) ERR; + + /* Write the data in num_step steps. */ + num_steps = (DIM2_LEN/SC1) / p; + for (s = 0; s < num_steps; s++) + { + /* Select hyperslab for write of one slice. */ + start[0] = s * SC1 * p + my_rank * SC1; + count[0] = SC1; + if (H5Sselect_hyperslab(whole_spaceid, H5S_SELECT_SET, + start, NULL, count, NULL) < 0) ERR; + + if (H5Dwrite(dsid, H5T_NATIVE_INT, slice_spaceid, whole_spaceid, + xferid, data) < 0) ERR; + + } + + /* Close. These collective operations will allow every process + * to catch up. */ + if (H5Dclose(dsid) < 0 || + H5Sclose(whole_spaceid) < 0 || + H5Sclose(slice_spaceid) < 0 || + H5Pclose(fapl_id) < 0 || + H5Pclose(plistid) < 0 || + H5Fclose(fileid) < 0) + ERR; + + /* Open the file. */ + if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR; + if (H5Pset_fapl_mpio(fapl_id, MPI_COMM_WORLD, MPI_INFO_NULL) < 0) ERR; + + + if (H5Pset_libver_bounds(fapl_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) ERR; + if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDONLY, fapl_id)) < 0) ERR; + + /* Create a space to deal with one slice in memory. */ + dims[0] = SC1; + if ((slice_spaceid = H5Screate_simple(NDIMS, dims, NULL)) < 0) ERR; + + /* Open the dataset. */ + if ((dsid = H5Dopen(fileid, VAR_NAME)) < 0) ERR; + if ((whole_spaceid1 = H5Dget_space(dsid)) < 0) ERR; + + /* Read the data, a slice at a time. */ + for (s = 0; s < num_steps; s++) + { + /* Select hyperslab for read of one slice. */ + start[0] = s * SC1 * p + my_rank * SC1; + count[0] = SC1; + if (H5Sselect_hyperslab(whole_spaceid1, H5S_SELECT_SET, + start, NULL, count, NULL) < 0) + { + ERR; + return 2; + } + + if (H5Dread(dsid, H5T_NATIVE_INT, slice_spaceid, whole_spaceid1, + H5P_DEFAULT, data_in) < 0) + { + ERR; + return 2; + } + + /* Check the slice of data. */ + for (i = 0; i < SC1; i++) + if (data[i] != data_in[i]) + { + ERR; + return 2; + } + } + + /* Close down. */ + if (H5Dclose(dsid) < 0 || + H5Sclose(slice_spaceid) < 0 || + H5Sclose(whole_spaceid1) < 0 || + H5Pclose(fapl_id) < 0 || + H5Fclose(fileid) < 0) + ERR; + } + if (!my_rank) + SUMMARIZE_ERR; + + } /* next cf */ +#else + { + if (!my_rank) + printf("*** HDF5 1.10.3 or greater required for this test.\n"); + } + +#endif /* HDF5_SUPPORTS_PAR_FILTERS */ + + MPI_Finalize(); + + if (!my_rank) + FINAL_RESULTS; + return 0; +} diff --git a/nc_test4/tst_parallel5.c b/nc_test4/tst_parallel5.c index ba9cf5242b..9c2e490548 100644 --- a/nc_test4/tst_parallel5.c +++ b/nc_test4/tst_parallel5.c @@ -322,8 +322,7 @@ main(int argc, char **argv) { /* This test is related to * https://github.com/Unidata/netcdf-c/issues/1715. */ - int ncid, varid; - int test_data_in, test_data = 42; + int ncid; size_t size, nelems; float preemption;