diff options
| -rw-r--r-- | HDF5Examples/C/H5PAR/ph5example.c (renamed from examples/ph5example.c) | 0 | ||||
| -rw-r--r-- | HDF5Examples/CTestConfig.cmake | 24 | ||||
| -rw-r--r-- | examples/CMakeLists.txt | 42 | ||||
| -rw-r--r-- | examples/CMakeTests.cmake | 43 | ||||
| -rw-r--r-- | examples/Makefile.am | 33 | ||||
| -rw-r--r-- | examples/h5_vds-eiger.c | 179 | ||||
| -rw-r--r-- | examples/h5_vds-exc.c | 217 | ||||
| -rw-r--r-- | examples/h5_vds-exclim.c | 214 | ||||
| -rw-r--r-- | examples/h5_vds-percival-unlim-maxmin.c | 304 | ||||
| -rw-r--r-- | examples/h5_vds-percival-unlim.c | 346 | ||||
| -rw-r--r-- | examples/h5_vds-percival.c | 241 | ||||
| -rw-r--r-- | examples/h5_vds-simpleIO.c | 190 | ||||
| -rw-r--r-- | examples/h5_vds.c | 252 | ||||
| -rw-r--r-- | examples/ph5_filtered_writes.c | 488 | ||||
| -rw-r--r-- | examples/ph5_filtered_writes_no_sel.c | 369 | ||||
| -rw-r--r-- | examples/ph5_subfiling.c | 551 | ||||
| -rw-r--r-- | examples/run-c-ex.sh.in | 18 |
17 files changed, 22 insertions, 3489 deletions
diff --git a/examples/ph5example.c b/HDF5Examples/C/H5PAR/ph5example.c index 5ec2cdc..5ec2cdc 100644 --- a/examples/ph5example.c +++ b/HDF5Examples/C/H5PAR/ph5example.c diff --git a/HDF5Examples/CTestConfig.cmake b/HDF5Examples/CTestConfig.cmake index 44e26e2..aef6da8 100644 --- a/HDF5Examples/CTestConfig.cmake +++ b/HDF5Examples/CTestConfig.cmake @@ -1,18 +1,32 @@ +# +# Copyright by The HDF Group. +# All rights reserved. +# +# This file is part of HDF5. The full HDF5 copyright notice, including +# terms governing use, modification, and redistribution, is contained in +# the COPYING file, which can be found at the root of the source code +# distribution tree, or in https://www.hdfgroup.org/licenses. +# If you do not have access to either file, you may request a copy from +# help@hdfgroup.org. +# ## This file should be placed in the root directory of your project. ## Then modify the CMakeLists.txt file in the root directory of your ## project to incorporate the testing dashboard. -## # The following are required to uses Dart and the Cdash dashboard +## # The following are required to use Dart and the CDash dashboard ## ENABLE_TESTING() ## INCLUDE(CTest) -set (CTEST_NIGHTLY_START_TIME "18:00:00 CST") set (CTEST_PROJECT_NAME "HDF5Examples") +set (CTEST_NIGHTLY_START_TIME "18:00:00 CST") set (CTEST_DROP_METHOD "https") -if (CDASH_LOCAL) - set (CTEST_DROP_SITE "cdash-internal.hdfgroup.org") - set (CTEST_DROP_LOCATION "/submit.php?project=HDF5Examples") +if (CTEST_DROP_SITE_INIT) + set (CTEST_DROP_SITE "${CTEST_DROP_SITE_INIT}") else () set (CTEST_DROP_SITE "cdash.hdfgroup.org") +endif () +if (CTEST_DROP_LOCATION_INIT) + set (CTEST_DROP_LOCATION "${CTEST_DROP_LOCATION_INIT}") +else () set (CTEST_DROP_LOCATION "/submit.php?project=HDF5Examples") endif () set (CTEST_DROP_SITE_CDASH TRUE) diff --git a/examples/CMakeLists.txt b/examples/CMakeLists.txt index 10c6ede..43d7af2 100644 --- a/examples/CMakeLists.txt +++ b/examples/CMakeLists.txt @@ -32,28 +32,8 @@ set (examples h5_elink_unix2win h5_shared_mesg h5_debug_trace - h5_vds - h5_vds-exc - h5_vds-exclim - h5_vds-eiger - h5_vds-simpleIO - h5_vds-percival - h5_vds-percival-unlim - h5_vds-percival-unlim-maxmin ) -if (H5_HAVE_PARALLEL) - set (parallel_examples - ph5example - ph5_filtered_writes - ph5_filtered_writes_no_sel - ) - - if (HDF5_ENABLE_SUBFILING_VFD) - list (APPEND parallel_examples ph5_subfiling) - endif () -endif () - foreach (example ${examples}) add_executable (${example} ${HDF5_EXAMPLES_SOURCE_DIR}/${example}.c) target_include_directories (${example} PRIVATE "${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") @@ -74,28 +54,6 @@ foreach (example ${examples}) endif () endforeach () -if (H5_HAVE_PARALLEL) - foreach (parallel_example ${parallel_examples}) - add_executable (${parallel_example} ${HDF5_EXAMPLES_SOURCE_DIR}/${parallel_example}.c) - target_include_directories (${parallel_example} PRIVATE "${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") - if (NOT BUILD_SHARED_LIBS) - TARGET_C_PROPERTIES (${parallel_example} STATIC) - target_link_libraries (${parallel_example} PRIVATE ${HDF5_LIB_TARGET} MPI::MPI_C) - else () - TARGET_C_PROPERTIES (${parallel_example} SHARED) - target_link_libraries (${parallel_example} PRIVATE ${HDF5_LIBSH_TARGET} MPI::MPI_C) - endif () - set_target_properties (${parallel_example} PROPERTIES FOLDER examples) - - #----------------------------------------------------------------------------- - # Add Target to clang-format - #----------------------------------------------------------------------------- - if (HDF5_ENABLE_FORMATTERS) - clang_format (HDF5_EXAMPLES_${parallel_example}_FORMAT ${parallel_example}) - endif () - endforeach () -endif () - if (BUILD_TESTING AND HDF5_TEST_EXAMPLES) include (CMakeTests.cmake) endif () diff --git a/examples/CMakeTests.cmake b/examples/CMakeTests.cmake index 449bc44..09f9060 100644 --- a/examples/CMakeTests.cmake +++ b/examples/CMakeTests.cmake @@ -30,8 +30,6 @@ set (test_ex_CLEANFILES group.h5 groups.h5 hard_link.h5 - h5_subfiling_default_example.h5 - h5_subfiling_custom_example.h5 mount1.h5 mount2.h5 one_index_file.h5 @@ -54,19 +52,6 @@ set (test_ex_CLEANFILES blue/prefix_target.h5 red/prefix_target.h5 u2w/u2w_target.h5 - vds.h5 - vds-exc.h5 - vds-excalibur.h5 - vds-exclim.h5 - vds-percival.h5 - vds-percival-unlim.h5 - vds-percival-unlim-maxmin.h5 - a.h5 - b.h5 - c.h5 - d.h5 - vds-simpleIO.h5 - vds-eiger.h5 ) if (HDF5_TEST_SERIAL) @@ -110,31 +95,3 @@ if (HDF5_TEST_SERIAL) set (last_test "EXAMPLES-${example}") endforeach () endif () - -### Windows pops up a modal permission dialog on this test -if (H5_HAVE_PARALLEL AND HDF5_TEST_PARALLEL AND NOT WIN32) - # Ensure that 24 is a multiple of the number of processes. - # The number 24 corresponds to SPACE1_DIM1 and SPACE1_DIM2 defined in ph5example.c - math(EXPR NUMPROCS "24 / ((24 + ${MPIEXEC_MAX_NUMPROCS} - 1) / ${MPIEXEC_MAX_NUMPROCS})") - - foreach (parallel_example ${parallel_examples}) - if (HDF5_ENABLE_USING_MEMCHECKER) - add_test (NAME MPI_TEST_EXAMPLES-${parallel_example} COMMAND ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${NUMPROCS} ${MPIEXEC_PREFLAGS} $<TARGET_FILE:${parallel_example}> ${MPIEXEC_POSTFLAGS}) - else () - add_test (NAME MPI_TEST_EXAMPLES-${parallel_example} COMMAND "${CMAKE_COMMAND}" - -D "TEST_PROGRAM=${MPIEXEC_EXECUTABLE}" - -D "TEST_ARGS:STRING=${MPIEXEC_NUMPROC_FLAG};${NUMPROCS};${MPIEXEC_PREFLAGS};$<TARGET_FILE:${parallel_example}>;${MPIEXEC_POSTFLAGS}" - -D "TEST_EXPECT=0" - -D "TEST_SKIP_COMPARE=TRUE" - -D "TEST_OUTPUT=${parallel_example}.out" - -D "TEST_REFERENCE:STRING=PHDF5 example finished with no errors" - -D "TEST_FOLDER=${PROJECT_BINARY_DIR}" - -P "${HDF_RESOURCES_DIR}/grepTest.cmake" - ) - endif () - if (last_test) - set_tests_properties (MPI_TEST_EXAMPLES-${parallel_example} PROPERTIES DEPENDS ${last_test}) - endif () - set (last_test "MPI_TEST_EXAMPLES-${parallel_example}") - endforeach () -endif () diff --git a/examples/Makefile.am b/examples/Makefile.am index a09042c..508664b 100644 --- a/examples/Makefile.am +++ b/examples/Makefile.am @@ -18,15 +18,6 @@ include $(top_srcdir)/config/commence.am -if BUILD_PARALLEL_CONDITIONAL - EXAMPLE_PROG_PARA = ph5example ph5_filtered_writes ph5_filtered_writes_no_sel - -if SUBFILING_VFD_CONDITIONAL - EXAMPLE_PROG_PARA += ph5_subfiling -endif - -endif - INSTALL_SCRIPT_FILES = run-c-ex.sh INSTALL_TOP_SCRIPT_FILES = run-all-ex.sh INSTALL_TOP_FILES = README @@ -40,9 +31,7 @@ EXAMPLE_PROG = h5_write h5_read h5_extend_write h5_chunk_read h5_compound \ h5_crtatt h5_crtgrp h5_crtdat \ h5_group h5_select h5_attribute h5_mount h5_drivers \ h5_reference_deprec h5_ref_extern h5_ref_compat h5_ref2reg_deprec \ - h5_extlink h5_elink_unix2win h5_shared_mesg h5_debug_trace \ - h5_vds h5_vds-exc h5_vds-exclim h5_vds-eiger h5_vds-simpleIO \ - h5_vds-percival h5_vds-percival-unlim h5_vds-percival-unlim-maxmin + h5_extlink h5_elink_unix2win h5_shared_mesg h5_debug_trace TEST_SCRIPT=testh5cc.sh TEST_EXAMPLES_SCRIPT=$(INSTALL_SCRIPT_FILES) @@ -53,13 +42,7 @@ INSTALL_FILES = h5_write.c h5_read.c h5_extend_write.c h5_chunk_read.c h5_compou h5_crtatt.c h5_crtgrp.c h5_crtdat.c \ h5_group.c h5_select.c h5_attribute.c h5_mount.c h5_drivers.c \ h5_reference_deprec.c h5_ref_extern.c h5_ref_compat.c h5_ref2reg_deprec.c \ - h5_extlink.c h5_elink_unix2win.c h5_shared_mesg.c h5_debug_trace.c \ - ph5example.c ph5_filtered_writes.c ph5_filtered_writes_no_sel.c \ - ph5_subfiling.c h5_vds.c h5_vds-exc.c h5_vds-exclim.c h5_vds-eiger.c \ - h5_vds-simpleIO.c h5_vds-percival.c h5_vds-percival-unlim.c \ - h5_vds-percival-unlim-maxmin.c - - + h5_extlink.c h5_elink_unix2win.c h5_shared_mesg.c h5_debug_trace.c # How to build examples, using installed version of h5cc if BUILD_PARALLEL_CONDITIONAL @@ -123,22 +106,10 @@ h5_ref_extern: $(srcdir)/h5_ref_extern.c h5_reference_deprec: $(srcdir)/h5_reference_deprec.c h5_ref2reg_deprec: $(srcdir)/h5_ref2reg_deprec.c h5_drivers: $(srcdir)/h5_drivers.c -ph5example: $(srcdir)/ph5example.c -ph5_filtered_writes: $(srcdir)/ph5_filtered_writes.c -ph5_filtered_writes_no_sel: $(srcdir)/ph5_filtered_writes_no_sel.c -ph5_subfiling: $(srcdir)/ph5_subfiling.c h5_dtransform: $(srcdir)/h5_dtransform.c h5_extlink: $(srcdir)/h5_extlink.c $(EXTLINK_DIRS) h5_elink_unix2win: $(srcdir)/h5_elink_unix2win.c $(EXTLINK_DIRS) h5_shared_mesg: $(srcdir)/h5_shared_mesg.c -h5_vds: $(srcdir)/h5_vds.c -h5_vds-exc: $(srcdir)/h5_vds-exc.c -h5_vds-exclim: $(srcdir)/h5_vds-exclim.c -h5_vds-eiger: $(srcdir)/h5_vds-eiger.c -h5_vds-simpleIO: $(srcdir)/h5_vds-simpleIO.c -h5_vds-percival: $(srcdir)/h5_vds-percival.c -h5_vds-percival-unlim: $(srcdir)/h5_vds-percival-unlim.c -h5_vds-percival-unlim-maxmin: $(srcdir)/h5_vds-percival-unlim-maxmin.c if BUILD_SHARED_SZIP_CONDITIONAL LD_LIBRARY_PATH=$(LL_PATH) diff --git a/examples/h5_vds-eiger.c b/examples/h5_vds-eiger.c deleted file mode 100644 index fcde490..0000000 --- a/examples/h5_vds-eiger.c +++ /dev/null @@ -1,179 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * Copyright by The HDF Group. * - * All rights reserved. * - * * - * This file is part of HDF5. The full HDF5 copyright notice, including * - * terms governing use, modification, and redistribution, is contained in * - * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://www.hdfgroup.org/licenses. * - * If you do not have access to either file, you may request a copy from * - * help@hdfgroup.org. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ -/************************************************************ - - This example illustrates the concept of the virtual dataset. - Eiger use case. Every 5 frames 10x10 are in the source - dataset "/A" in file with the name f-<#>.h5 - This file is intended for use with HDF5 Library version 1.10 - - ************************************************************/ -/* EIP Add link to the picture */ - -#include "hdf5.h" -#include <stdio.h> -#include <stdlib.h> - -#define FILE "vds-eiger.h5" -#define DATASET "VDS-Eiger" -#define VDSDIM0 5 -#define VDSDIM1 10 -#define VDSDIM2 10 -#define DIM0 5 -#define DIM1 10 -#define DIM2 10 -#define RANK 3 - -int -main(void) -{ - hid_t file, src_space, vspace, dset; /* Handles */ - hid_t dcpl; - herr_t status; - hsize_t vdsdims[3] = {VDSDIM0, VDSDIM1, VDSDIM2}, vdsdims_max[3] = {H5S_UNLIMITED, VDSDIM1, VDSDIM1}, - dims[3] = {DIM0, DIM1, DIM2}, start[3], /* Hyperslab parameters */ - stride[3], count[3], block[3]; - hsize_t start_out[3], /* Hyperslab parameter out */ - stride_out[3], count_out[3], block_out[3]; - int i; - H5D_layout_t layout; /* Storage layout */ - size_t num_map; /* Number of mappings */ - ssize_t len; /* Length of the string; also a return value */ - char *filename; - char *dsetname; - - file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); - - /* Create VDS dataspace. */ - vspace = H5Screate_simple(RANK, vdsdims, vdsdims_max); - - /* Create dataspaces for the source dataset. */ - src_space = H5Screate_simple(RANK, dims, NULL); - - /* Create VDS creation property */ - dcpl = H5Pcreate(H5P_DATASET_CREATE); - - /* Initialize hyperslab values */ - - start[0] = 0; - start[1] = 0; - start[2] = 0; - stride[0] = DIM0; - stride[1] = 1; - stride[2] = 1; - count[0] = H5S_UNLIMITED; - count[1] = 1; - count[2] = 1; - block[0] = DIM0; - block[1] = DIM1; - block[2] = DIM2; - - /* - * Build the mappings - * - */ - status = H5Sselect_hyperslab(vspace, H5S_SELECT_SET, start, stride, count, block); - status = H5Pset_virtual(dcpl, vspace, "f-%b.h5", "/A", src_space); - - /* Create a virtual dataset */ - dset = H5Dcreate2(file, DATASET, H5T_NATIVE_INT, vspace, H5P_DEFAULT, dcpl, H5P_DEFAULT); - status = H5Sclose(vspace); - status = H5Sclose(src_space); - status = H5Dclose(dset); - status = H5Fclose(file); - - /* - * Now we begin the read section of this example. - */ - - /* - * Open file and dataset using the default properties. - */ - file = H5Fopen(FILE, H5F_ACC_RDONLY, H5P_DEFAULT); - dset = H5Dopen2(file, DATASET, H5P_DEFAULT); - - /* - * Get creation property list and mapping properties. - */ - dcpl = H5Dget_create_plist(dset); - - /* - * Get storage layout. - */ - layout = H5Pget_layout(dcpl); - - if (H5D_VIRTUAL == layout) - printf(" Dataset has a virtual layout \n"); - else - printf(" Wrong layout found \n"); - - /* - * Find number of mappings. - */ - status = H5Pget_virtual_count(dcpl, &num_map); - printf(" Number of mappings is %d\n", (int)num_map); - - /* - * Get mapping parameters for each mapping. - */ - for (i = 0; i < (int)num_map; i++) { - printf(" Mapping %d \n", i); - printf(" Selection in the virtual dataset \n"); - /* Get selection in the virtual dataset */ - vspace = H5Pget_virtual_vspace(dcpl, (size_t)i); - if (H5Sget_select_type(vspace) == H5S_SEL_HYPERSLABS) { - if (H5Sis_regular_hyperslab(vspace)) { - status = H5Sget_regular_hyperslab(vspace, start_out, stride_out, count_out, block_out); - printf(" start = [%llu, %llu, %llu] \n", (unsigned long long)start_out[0], - (unsigned long long)start_out[1], (unsigned long long)start_out[2]); - printf(" stride = [%llu, %llu, %llu] \n", (unsigned long long)stride_out[0], - (unsigned long long)stride_out[1], (unsigned long long)stride_out[2]); - printf(" count = [%llu, %llu, %llu] \n", (unsigned long long)count_out[0], - (unsigned long long)count_out[1], (unsigned long long)count_out[2]); - printf(" block = [%llu, %llu, %llu] \n", (unsigned long long)block_out[0], - (unsigned long long)block_out[1], (unsigned long long)block_out[2]); - } - } - /* Get source file name */ - len = H5Pget_virtual_filename(dcpl, (size_t)i, NULL, 0); - filename = (char *)malloc((size_t)len * sizeof(char) + 1); - H5Pget_virtual_filename(dcpl, (size_t)i, filename, len + 1); - printf(" Source filename %s\n", filename); - - /* Get source dataset name */ - len = H5Pget_virtual_dsetname(dcpl, (size_t)i, NULL, 0); - dsetname = (char *)malloc((size_t)len * sizeof(char) + 1); - H5Pget_virtual_dsetname(dcpl, (size_t)i, dsetname, len + 1); - printf(" Source dataset name %s\n", dsetname); - - /* Get selection in the source dataset */ - printf(" Selection in the source dataset "); - src_space = H5Pget_virtual_srcspace(dcpl, (size_t)i); - if (H5Sget_select_type(src_space) == H5S_SEL_ALL) { - printf("H5S_ALL \n"); - } - /* EIP read data back */ - H5Sclose(vspace); - H5Sclose(src_space); - free(filename); - free(dsetname); - } - - /* - * Close and release resources. - */ - status = H5Pclose(dcpl); - status = H5Dclose(dset); - status = H5Fclose(file); - - return 0; -} diff --git a/examples/h5_vds-exc.c b/examples/h5_vds-exc.c deleted file mode 100644 index 01597cc..0000000 --- a/examples/h5_vds-exc.c +++ /dev/null @@ -1,217 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * Copyright by The HDF Group. * - * All rights reserved. * - * * - * This file is part of HDF5. The full HDF5 copyright notice, including * - * terms governing use, modification, and redistribution, is contained in * - * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://www.hdfgroup.org/licenses. * - * If you do not have access to either file, you may request a copy from * - * help@hdfgroup.org. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ -/************************************************************ - - This example illustrates the concept of the virtual dataset. - Excalibur use case with k=2 and m=3. - This file is intended for use with HDF5 Library version 1.10 - - ************************************************************/ -/* EIP Add link to the picture */ - -#include "hdf5.h" -#include <stdio.h> -#include <stdlib.h> - -#define FILE "vds-exc.h5" -#define DATASET "VDS-Excalibur" -#define VDSDIM0 0 -#define VDSDIM1 15 -#define VDSDIM2 6 -#define KDIM0 0 -#define KDIM1 2 -#define KDIM2 6 -#define NDIM0 0 -#define NDIM1 3 -#define NDIM2 6 -#define RANK 3 - -const char *SRC_FILE[] = {"a.h5", "b.h5", "c.h5", "d.h5", "e.h5", "f.h5"}; - -const char *SRC_DATASET[] = {"A", "B", "C", "D", "E", "F"}; - -int -main(void) -{ - hid_t file, space, ksrc_space, nsrc_space, vspace, src_space, dset; /* Handles */ - hid_t dcpl; - herr_t status; - hsize_t vdsdims[3] = {VDSDIM0, VDSDIM1, VDSDIM2}, vdsdims_max[3] = {H5S_UNLIMITED, VDSDIM1, VDSDIM2}, - kdims[3] = {KDIM0, KDIM1, KDIM2}, kdims_max[3] = {H5S_UNLIMITED, KDIM1, KDIM2}, - ndims[3] = {NDIM0, NDIM1, NDIM2}, ndims_max[3] = {H5S_UNLIMITED, NDIM1, NDIM2}, - start[3], /* Hyperslab parameters */ - count[3], block[3]; - hsize_t start_out[3], stride_out[3], count_out[3], block_out[3]; - int k = 2; - int n = 3; - int i; - H5D_layout_t layout; /* Storage layout */ - size_t num_map; /* Number of mappings */ - ssize_t len; /* Length of the string; also a return value */ - char *filename; - char *dsetname; - - file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); - - /* Create VDS dataspace. */ - space = H5Screate_simple(RANK, vdsdims, vdsdims_max); - /* Create dataspaces for A, C, and E datasets. */ - ksrc_space = H5Screate_simple(RANK, kdims, kdims_max); - /* Create dataspaces for B, D, and F datasets. */ - nsrc_space = H5Screate_simple(RANK, ndims, ndims_max); - - /* Create VDS creation property */ - dcpl = H5Pcreate(H5P_DATASET_CREATE); - - /* Initialize hyperslab values */ - - start[0] = 0; - start[1] = 0; - start[2] = 0; - count[0] = H5S_UNLIMITED; - count[1] = 1; - count[2] = 1; - block[0] = 1; - block[1] = k; - block[2] = VDSDIM2; - - /* - * Build the mappings for A, C and E source datasets. - * Unlimited hyperslab selection is the same in the source datasets. - * Unlimited hyperslab selections in the virtual dataset have different offsets. - */ - status = H5Sselect_hyperslab(ksrc_space, H5S_SELECT_SET, start, NULL, count, block); - for (i = 0; i < 3; i++) { - start[1] = (hsize_t)((k + n) * i); - status = H5Sselect_hyperslab(space, H5S_SELECT_SET, start, NULL, count, block); - status = H5Pset_virtual(dcpl, space, SRC_FILE[2 * i], SRC_DATASET[2 * i], ksrc_space); - } - - /* Reinitialize start[1] and block[1] to build the second set of mappings. */ - start[1] = 0; - block[1] = n; - /* - * Build the mappings for B, D and F source datasets. - * Unlimited hyperslab selection is the same in the source datasets. - * Unlimited hyperslab selections in the virtual dataset have different offsets. - */ - status = H5Sselect_hyperslab(nsrc_space, H5S_SELECT_SET, start, NULL, count, block); - for (i = 0; i < 3; i++) { - start[1] = (hsize_t)(k + (k + n) * i); - status = H5Sselect_hyperslab(space, H5S_SELECT_SET, start, NULL, count, block); - status = H5Pset_virtual(dcpl, space, SRC_FILE[2 * i + 1], SRC_DATASET[2 * i + 1], nsrc_space); - } - - /* Create a virtual dataset */ - dset = H5Dcreate2(file, DATASET, H5T_NATIVE_INT, space, H5P_DEFAULT, dcpl, H5P_DEFAULT); - status = H5Sclose(space); - status = H5Sclose(nsrc_space); - status = H5Sclose(ksrc_space); - status = H5Dclose(dset); - status = H5Fclose(file); - - /* - * Now we begin the read section of this example. - */ - - /* - * Open file and dataset using the default properties. - */ - file = H5Fopen(FILE, H5F_ACC_RDONLY, H5P_DEFAULT); - dset = H5Dopen2(file, DATASET, H5P_DEFAULT); - - /* - * Get creation property list and mapping properties. - */ - dcpl = H5Dget_create_plist(dset); - - /* - * Get storage layout. - */ - layout = H5Pget_layout(dcpl); - - if (H5D_VIRTUAL == layout) - printf(" Dataset has a virtual layout \n"); - else - printf("Wrong layout found \n"); - - /* - * Find number of mappings. - */ - status = H5Pget_virtual_count(dcpl, &num_map); - printf(" Number of mappings is %lu\n", (unsigned long)num_map); - - /* - * Get mapping parameters for each mapping. - */ - for (i = 0; i < (int)num_map; i++) { - printf(" Mapping %d \n", i); - printf(" Selection in the virtual dataset \n"); - /* Get selection in the virtual dataset */ - vspace = H5Pget_virtual_vspace(dcpl, (size_t)i); - if (H5Sget_select_type(vspace) == H5S_SEL_HYPERSLABS) { - if (H5Sis_regular_hyperslab(vspace)) { - status = H5Sget_regular_hyperslab(vspace, start_out, stride_out, count_out, block_out); - printf(" start = [%llu, %llu, %llu] \n", (unsigned long long)start_out[0], - (unsigned long long)start_out[1], (unsigned long long)start_out[2]); - printf(" stride = [%llu, %llu, %llu] \n", (unsigned long long)stride_out[0], - (unsigned long long)stride_out[1], (unsigned long long)stride_out[2]); - printf(" count = [%llu, %llu, %llu] \n", (unsigned long long)count_out[0], - (unsigned long long)count_out[1], (unsigned long long)count_out[2]); - printf(" block = [%llu, %llu, %llu] \n", (unsigned long long)block_out[0], - (unsigned long long)block_out[1], (unsigned long long)block_out[2]); - } - } - /* Get source file name */ - len = H5Pget_virtual_filename(dcpl, (size_t)i, NULL, 0); - filename = (char *)malloc((size_t)len * sizeof(char) + 1); - H5Pget_virtual_filename(dcpl, (size_t)i, filename, len + 1); - printf(" Source filename %s\n", filename); - - /* Get source dataset name */ - len = H5Pget_virtual_dsetname(dcpl, (size_t)i, NULL, 0); - dsetname = (char *)malloc((size_t)len * sizeof(char) + 1); - H5Pget_virtual_dsetname(dcpl, (size_t)i, dsetname, len + 1); - printf(" Source dataset name %s\n", dsetname); - - /* Get selection in the source dataset */ - printf(" Selection in the source dataset \n"); - src_space = H5Pget_virtual_srcspace(dcpl, (size_t)i); - if (H5Sget_select_type(src_space) == H5S_SEL_HYPERSLABS) { - if (H5Sis_regular_hyperslab(vspace)) { - status = H5Sget_regular_hyperslab(src_space, start_out, stride_out, count_out, block_out); - printf(" start = [%llu, %llu, %llu] \n", (unsigned long long)start_out[0], - (unsigned long long)start_out[1], (unsigned long long)start_out[2]); - printf(" stride = [%llu, %llu, %llu] \n", (unsigned long long)stride_out[0], - (unsigned long long)stride_out[1], (unsigned long long)stride_out[2]); - printf(" count = [%llu, %llu, %llu] \n", (unsigned long long)count_out[0], - (unsigned long long)count_out[1], (unsigned long long)count_out[2]); - printf(" block = [%llu, %llu, %llu] \n", (unsigned long long)block_out[0], - (unsigned long long)block_out[1], (unsigned long long)block_out[2]); - } - } - H5Sclose(vspace); - H5Sclose(src_space); - free(filename); - free(dsetname); - } - /* EIP read data back */ - - /* - * Close and release resources. - */ - status = H5Pclose(dcpl); - status = H5Dclose(dset); - status = H5Fclose(file); - - return 0; -} diff --git a/examples/h5_vds-exclim.c b/examples/h5_vds-exclim.c deleted file mode 100644 index 4fb5536..0000000 --- a/examples/h5_vds-exclim.c +++ /dev/null @@ -1,214 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * Copyright by The HDF Group. * - * All rights reserved. * - * * - * This file is part of HDF5. The full HDF5 copyright notice, including * - * terms governing use, modification, and redistribution, is contained in * - * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://www.hdfgroup.org/licenses. * - * If you do not have access to either file, you may request a copy from * - * help@hdfgroup.org. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ -/************************************************************ - - This example illustrates the concept of the virtual dataset. - Excalibur use case with k=2 and m=3 and only 3 planes in - Z-direction (i.e., not unlimited). - This file is intended for use with HDF5 Library version 1.10 - - ************************************************************/ -/* EIP Add link to the picture */ - -#include "hdf5.h" -#include <stdio.h> -#include <stdlib.h> - -#define FILE "vds-exclim.h5" -#define DATASET "VDS-Excaliburlim" -#define VDSDIM0 3 -#define VDSDIM1 15 -#define VDSDIM2 6 -#define KDIM0 3 -#define KDIM1 2 -#define KDIM2 6 -#define NDIM0 3 -#define NDIM1 3 -#define NDIM2 6 -#define RANK 3 - -const char *SRC_FILE[] = {"a.h5", "b.h5", "c.h5", "d.h5", "e.h5", "f.h5"}; - -const char *SRC_DATASET[] = {"A", "B", "C", "D", "E", "F"}; - -int -main(void) -{ - hid_t file, space, ksrc_space, nsrc_space, vspace, src_space, dset; /* Handles */ - hid_t dcpl; - herr_t status; - hsize_t vdsdims[3] = {VDSDIM0, VDSDIM1, VDSDIM2}, kdims[3] = {KDIM0, KDIM1, KDIM2}, - ndims[3] = {NDIM0, NDIM1, NDIM2}, start[3], /* Hyperslab parameters */ - count[3], block[3]; - hsize_t start_out[3], stride_out[3], count_out[3], block_out[3]; - int k = 2; - int n = 3; - int i; - H5D_layout_t layout; /* Storage layout */ - size_t num_map; /* Number of mappings */ - ssize_t len; /* Length of the string; also a return value */ - char *filename; - char *dsetname; - - file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); - - /* Create VDS dataspace. */ - space = H5Screate_simple(RANK, vdsdims, NULL); - /* Create dataspaces for A, C, and E datasets. */ - ksrc_space = H5Screate_simple(RANK, kdims, NULL); - /* Create dataspaces for B, D, and F datasets. */ - nsrc_space = H5Screate_simple(RANK, ndims, NULL); - - /* Create VDS creation property */ - dcpl = H5Pcreate(H5P_DATASET_CREATE); - - /* Initialize hyperslab values */ - - start[0] = 0; - start[1] = 0; - start[2] = 0; - count[0] = VDSDIM0; - count[1] = 1; - count[2] = 1; - block[0] = 1; - block[1] = k; - block[2] = VDSDIM2; - - /* - * Build the mappings for A, C and E source datasets. - * - */ - status = H5Sselect_hyperslab(ksrc_space, H5S_SELECT_SET, start, NULL, count, block); - for (i = 0; i < 3; i++) { - start[1] = (hsize_t)((k + n) * i); - status = H5Sselect_hyperslab(space, H5S_SELECT_SET, start, NULL, count, block); - status = H5Pset_virtual(dcpl, space, SRC_FILE[2 * i], SRC_DATASET[2 * i], ksrc_space); - } - - /* Reinitialize start[0] and block[1] */ - start[0] = 0; - block[1] = n; - /* - * Build the mappings for B, D and F source datasets. - * - */ - status = H5Sselect_hyperslab(nsrc_space, H5S_SELECT_SET, start, NULL, count, block); - for (i = 0; i < 3; i++) { - start[1] = (hsize_t)(k + (k + n) * i); - status = H5Sselect_hyperslab(space, H5S_SELECT_SET, start, NULL, count, block); - status = H5Pset_virtual(dcpl, space, SRC_FILE[2 * i + 1], SRC_DATASET[2 * i + 1], nsrc_space); - } - - /* Create a virtual dataset */ - dset = H5Dcreate2(file, DATASET, H5T_NATIVE_INT, space, H5P_DEFAULT, dcpl, H5P_DEFAULT); - status = H5Sclose(space); - status = H5Sclose(nsrc_space); - status = H5Sclose(ksrc_space); - status = H5Dclose(dset); - status = H5Fclose(file); - - /* - * Now we begin the read section of this example. - */ - - /* - * Open file and dataset using the default properties. - */ - file = H5Fopen(FILE, H5F_ACC_RDONLY, H5P_DEFAULT); - dset = H5Dopen2(file, DATASET, H5P_DEFAULT); - - /* - * Get creation property list and mapping properties. - */ - dcpl = H5Dget_create_plist(dset); - - /* - * Get storage layout. - */ - layout = H5Pget_layout(dcpl); - - if (H5D_VIRTUAL == layout) - printf(" Dataset has a virtual layout \n"); - else - printf("Wrong layout found \n"); - - /* - * Find number of mappings. - */ - status = H5Pget_virtual_count(dcpl, &num_map); - printf(" Number of mappings is %lu\n", (unsigned long)num_map); - - /* - * Get mapping parameters for each mapping. - */ - for (i = 0; i < (int)num_map; i++) { - printf(" Mapping %d \n", i); - printf(" Selection in the virtual dataset \n"); - /* Get selection in the virtual dataset */ - vspace = H5Pget_virtual_vspace(dcpl, (size_t)i); - if (H5Sget_select_type(vspace) == H5S_SEL_HYPERSLABS) { - if (H5Sis_regular_hyperslab(vspace)) { - status = H5Sget_regular_hyperslab(vspace, start_out, stride_out, count_out, block_out); - printf(" start = [%llu, %llu, %llu] \n", (unsigned long long)start_out[0], - (unsigned long long)start_out[1], (unsigned long long)start_out[2]); - printf(" stride = [%llu, %llu, %llu] \n", (unsigned long long)stride_out[0], - (unsigned long long)stride_out[1], (unsigned long long)stride_out[2]); - printf(" count = [%llu, %llu, %llu] \n", (unsigned long long)count_out[0], - (unsigned long long)count_out[1], (unsigned long long)count_out[2]); - printf(" block = [%llu, %llu, %llu] \n", (unsigned long long)block_out[0], - (unsigned long long)block_out[1], (unsigned long long)block_out[2]); - } - } - /* Get source file name */ - len = H5Pget_virtual_filename(dcpl, (size_t)i, NULL, 0); - filename = (char *)malloc((size_t)len * sizeof(char) + 1); - H5Pget_virtual_filename(dcpl, (size_t)i, filename, len + 1); - printf(" Source filename %s\n", filename); - - /* Get source dataset name */ - len = H5Pget_virtual_dsetname(dcpl, (size_t)i, NULL, 0); - dsetname = (char *)malloc((size_t)len * sizeof(char) + 1); - H5Pget_virtual_dsetname(dcpl, (size_t)i, dsetname, len + 1); - printf(" Source dataset name %s\n", dsetname); - - /* Get selection in the source dataset */ - printf(" Selection in the source dataset \n"); - src_space = H5Pget_virtual_srcspace(dcpl, (size_t)i); - if (H5Sget_select_type(src_space) == H5S_SEL_HYPERSLABS) { - if (H5Sis_regular_hyperslab(vspace)) { - status = H5Sget_regular_hyperslab(vspace, start_out, stride_out, count_out, block_out); - printf(" start = [%d, %d, %d] \n", (int)start_out[0], (int)start_out[1], - (int)start_out[2]); - printf(" stride = [%d, %d, %d] \n", (int)stride_out[0], (int)stride_out[1], - (int)stride_out[2]); - printf(" count = [%d, %d, %d] \n", (int)count_out[0], (int)count_out[1], - (int)count_out[2]); - printf(" block = [%d, %d, %d] \n", (int)block_out[0], (int)block_out[1], - (int)block_out[2]); - } - } - H5Sclose(vspace); - H5Sclose(src_space); - free(filename); - free(dsetname); - } - /* EIP read data back */ - - /* - * Close and release resources. - */ - status = H5Pclose(dcpl); - status = H5Dclose(dset); - status = H5Fclose(file); - - return 0; -} diff --git a/examples/h5_vds-percival-unlim-maxmin.c b/examples/h5_vds-percival-unlim-maxmin.c deleted file mode 100644 index 9ef514d..0000000 --- a/examples/h5_vds-percival-unlim-maxmin.c +++ /dev/null @@ -1,304 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * Copyright by The HDF Group. * - * All rights reserved. * - * * - * This file is part of HDF5. The full HDF5 copyright notice, including * - * terms governing use, modification, and redistribution, is contained in * - * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://www.hdfgroup.org/licenses. * - * If you do not have access to either file, you may request a copy from * - * help@hdfgroup.org. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ -/************************************************************ - - This example illustrates the concept of the virtual dataset. - Percival use case. Every fifth 10x10 plane in VDS is stored in - the corresponding 3D unlimited dataset. - There are 4 source datasets total. - Each of the source datasets is extended to different sizes. - VDS access property can be used to get max and min extent. - This file is intended for use with HDF5 Library version 1.10 - - ************************************************************/ -/* EIP Add link to the picture */ - -#include "hdf5.h" -#include <stdio.h> -#include <stdlib.h> - -#define VFILE "vds-percival-unlim-maxmin.h5" -#define DATASET "VDS-Percival-unlim-maxmin" -#define VDSDIM0 H5S_UNLIMITED -#define VDSDIM1 10 -#define VDSDIM2 10 - -#define DIM0 H5S_UNLIMITED -#define DIM0_1 4 /* Initial size of the source datasets */ -#define DIM1 10 -#define DIM2 10 -#define RANK 3 -#define PLANE_STRIDE 4 - -const char *SRC_FILE[] = {"a.h5", "b.h5", "c.h5", "d.h5"}; - -const char *SRC_DATASET[] = {"A", "B", "C", "D"}; - -int -main(void) -{ - hid_t vfile, file, src_space, mem_space, vspace, vdset, dset; /* Handles */ - hid_t dcpl, dapl; - herr_t status; - hsize_t vdsdims[3] = {4 * DIM0_1, VDSDIM1, VDSDIM2}, vdsdims_max[3] = {VDSDIM0, VDSDIM1, VDSDIM2}, - dims[3] = {DIM0_1, DIM1, DIM2}, memdims[3] = {DIM0_1, DIM1, DIM2}, - extdims[3] = {0, DIM1, DIM2}, /* Dimensions of the extended source datasets */ - chunk_dims[3] = {DIM0_1, DIM1, DIM2}, dims_max[3] = {DIM0, DIM1, DIM2}, vdsdims_out[3], - vdsdims_max_out[3], start[3], /* Hyperslab parameters */ - stride[3], count[3], src_count[3], block[3]; - hsize_t start_out[3], /* Hyperslab parameter out */ - stride_out[3], count_out[3], block_out[3]; - int i, j; - H5D_layout_t layout; /* Storage layout */ - size_t num_map; /* Number of mappings */ - ssize_t len; /* Length of the string; also a return value */ - char *filename; - char *dsetname; - int wdata[DIM0_1 * DIM1 * DIM2]; - - /* - * Create source files and datasets. This step is optional. - */ - for (i = 0; i < PLANE_STRIDE; i++) { - /* - * Initialize data for i-th source dataset. - */ - for (j = 0; j < DIM0_1 * DIM1 * DIM2; j++) - wdata[j] = i + 1; - - /* - * Create the source files and datasets. Write data to each dataset and - * close all resources. - */ - - file = H5Fcreate(SRC_FILE[i], H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); - src_space = H5Screate_simple(RANK, dims, dims_max); - dcpl = H5Pcreate(H5P_DATASET_CREATE); - status = H5Pset_chunk(dcpl, RANK, chunk_dims); - dset = H5Dcreate2(file, SRC_DATASET[i], H5T_NATIVE_INT, src_space, H5P_DEFAULT, dcpl, H5P_DEFAULT); - status = H5Dwrite(dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, wdata); - status = H5Sclose(src_space); - status = H5Pclose(dcpl); - status = H5Dclose(dset); - status = H5Fclose(file); - } - - vfile = H5Fcreate(VFILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); - - /* Create VDS dataspace. */ - vspace = H5Screate_simple(RANK, vdsdims, vdsdims_max); - - /* Create dataspaces for the source dataset. */ - src_space = H5Screate_simple(RANK, dims, dims_max); - - /* Create VDS creation property */ - dcpl = H5Pcreate(H5P_DATASET_CREATE); - - /* Initialize hyperslab values */ - - start[0] = 0; - start[1] = 0; - start[2] = 0; - stride[0] = PLANE_STRIDE; /* we will select every fifth plane in VDS */ - stride[1] = 1; - stride[2] = 1; - count[0] = H5S_UNLIMITED; - count[1] = 1; - count[2] = 1; - src_count[0] = H5S_UNLIMITED; - src_count[1] = 1; - src_count[2] = 1; - block[0] = 1; - block[1] = DIM1; - block[2] = DIM2; - - /* - * Build the mappings - * - */ - status = H5Sselect_hyperslab(src_space, H5S_SELECT_SET, start, NULL, src_count, block); - for (i = 0; i < PLANE_STRIDE; i++) { - status = H5Sselect_hyperslab(vspace, H5S_SELECT_SET, start, stride, count, block); - status = H5Pset_virtual(dcpl, vspace, SRC_FILE[i], SRC_DATASET[i], src_space); - start[0]++; - } - - H5Sselect_none(vspace); - - /* Create a virtual dataset */ - vdset = H5Dcreate2(vfile, DATASET, H5T_NATIVE_INT, vspace, H5P_DEFAULT, dcpl, H5P_DEFAULT); - status = H5Sclose(vspace); - status = H5Sclose(src_space); - status = H5Pclose(dcpl); - - /* Let's add data to the source datasets and check new dimensions for VDS */ - /* We will add only one plane to the first source dataset, two planes to the - second one, three to the third, and four to the forth. */ - - for (i = 0; i < PLANE_STRIDE; i++) { - /* - * Initialize data for i-th source dataset. - */ - for (j = 0; j < (i + 1) * DIM1 * DIM2; j++) - wdata[j] = 10 * (i + 1); - - /* - * Open the source files and datasets. Append data to each dataset and - * close all resources. - */ - - file = H5Fopen(SRC_FILE[i], H5F_ACC_RDWR, H5P_DEFAULT); - dset = H5Dopen2(file, SRC_DATASET[i], H5P_DEFAULT); - extdims[0] = DIM0_1 + i + 1; - status = H5Dset_extent(dset, extdims); - src_space = H5Dget_space(dset); - start[0] = DIM0_1; - start[1] = 0; - start[2] = 0; - count[0] = 1; - count[1] = 1; - count[2] = 1; - block[0] = i + 1; - block[1] = DIM1; - block[2] = DIM2; - - memdims[0] = i + 1; - mem_space = H5Screate_simple(RANK, memdims, NULL); - status = H5Sselect_hyperslab(src_space, H5S_SELECT_SET, start, NULL, count, block); - status = H5Dwrite(dset, H5T_NATIVE_INT, mem_space, src_space, H5P_DEFAULT, wdata); - status = H5Sclose(src_space); - status = H5Dclose(dset); - status = H5Fclose(file); - } - - status = H5Dclose(vdset); - status = H5Fclose(vfile); - - /* - * Now we begin the read section of this example. - */ - - /* - * Open file and dataset using the default properties. - */ - vfile = H5Fopen(VFILE, H5F_ACC_RDONLY, H5P_DEFAULT); - - /* - * Open VDS using different access properties to use max or - * min extents depending on the sizes of the underlying datasets - */ - dapl = H5Pcreate(H5P_DATASET_ACCESS); - - for (i = 0; i < 2; i++) { - status = H5Pset_virtual_view(dapl, i ? H5D_VDS_LAST_AVAILABLE : H5D_VDS_FIRST_MISSING); - vdset = H5Dopen2(vfile, DATASET, dapl); - - /* Let's get space of the VDS and its dimension; we should get 32(or 20)x10x10 */ - vspace = H5Dget_space(vdset); - H5Sget_simple_extent_dims(vspace, vdsdims_out, vdsdims_max_out); - printf("VDS dimensions, bounds = H5D_VDS_%s: ", i ? "LAST_AVAILABLE" : "FIRST_MISSING"); - for (j = 0; j < RANK; j++) - printf(" %d ", (int)vdsdims_out[j]); - printf("\n"); - - /* Close */ - status = H5Dclose(vdset); - status = H5Sclose(vspace); - } - - status = H5Pclose(dapl); - - vdset = H5Dopen2(vfile, DATASET, H5P_DEFAULT); - - /* - * Get creation property list and mapping properties. - */ - dcpl = H5Dget_create_plist(vdset); - - /* - * Get storage layout. - */ - layout = H5Pget_layout(dcpl); - - if (H5D_VIRTUAL == layout) - printf(" Dataset has a virtual layout \n"); - else - printf(" Wrong layout found \n"); - - /* - * Find number of mappings. - */ - status = H5Pget_virtual_count(dcpl, &num_map); - printf(" Number of mappings is %lu\n", (unsigned long)num_map); - - /* - * Get mapping parameters for each mapping. - */ - for (i = 0; i < (int)num_map; i++) { - printf(" Mapping %d \n", i); - printf(" Selection in the virtual dataset \n"); - /* Get selection in the virtual dataset */ - vspace = H5Pget_virtual_vspace(dcpl, (size_t)i); - if (H5Sget_select_type(vspace) == H5S_SEL_HYPERSLABS) { - if (H5Sis_regular_hyperslab(vspace)) { - status = H5Sget_regular_hyperslab(vspace, start_out, stride_out, count_out, block_out); - printf(" start = [%llu, %llu, %llu] \n", (unsigned long long)start_out[0], - (unsigned long long)start_out[1], (unsigned long long)start_out[2]); - printf(" stride = [%llu, %llu, %llu] \n", (unsigned long long)stride_out[0], - (unsigned long long)stride_out[1], (unsigned long long)stride_out[2]); - printf(" count = [%llu, %llu, %llu] \n", (unsigned long long)count_out[0], - (unsigned long long)count_out[1], (unsigned long long)count_out[2]); - printf(" block = [%llu, %llu, %llu] \n", (unsigned long long)block_out[0], - (unsigned long long)block_out[1], (unsigned long long)block_out[2]); - } - } - /* Get source file name */ - len = H5Pget_virtual_filename(dcpl, (size_t)i, NULL, 0); - filename = (char *)malloc((size_t)len * sizeof(char) + 1); - H5Pget_virtual_filename(dcpl, (size_t)i, filename, len + 1); - printf(" Source filename %s\n", filename); - - /* Get source dataset name */ - len = H5Pget_virtual_dsetname(dcpl, (size_t)i, NULL, 0); - dsetname = (char *)malloc((size_t)len * sizeof(char) + 1); - H5Pget_virtual_dsetname(dcpl, (size_t)i, dsetname, len + 1); - printf(" Source dataset name %s\n", dsetname); - - /* Get selection in the source dataset */ - printf(" Selection in the source dataset \n"); - src_space = H5Pget_virtual_srcspace(dcpl, (size_t)i); - if (H5Sget_select_type(src_space) == H5S_SEL_HYPERSLABS) { - if (H5Sis_regular_hyperslab(src_space)) { - status = H5Sget_regular_hyperslab(src_space, start_out, stride_out, count_out, block_out); - printf(" start = [%llu, %llu, %llu] \n", (unsigned long long)start_out[0], - (unsigned long long)start_out[1], (unsigned long long)start_out[2]); - printf(" stride = [%llu, %llu, %llu] \n", (unsigned long long)stride_out[0], - (unsigned long long)stride_out[1], (unsigned long long)stride_out[2]); - printf(" count = [%llu, %llu, %llu] \n", (unsigned long long)count_out[0], - (unsigned long long)count_out[1], (unsigned long long)count_out[2]); - printf(" block = [%llu, %llu, %llu] \n", (unsigned long long)block_out[0], - (unsigned long long)block_out[1], (unsigned long long)block_out[2]); - } - } - H5Sclose(vspace); - H5Sclose(src_space); - free(filename); - free(dsetname); - } - /* - * Close and release resources. - */ - status = H5Pclose(dcpl); - status = H5Dclose(vdset); - status = H5Fclose(vfile); - return 0; -} diff --git a/examples/h5_vds-percival-unlim.c b/examples/h5_vds-percival-unlim.c deleted file mode 100644 index ddbcdec..0000000 --- a/examples/h5_vds-percival-unlim.c +++ /dev/null @@ -1,346 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * Copyright by The HDF Group. * - * All rights reserved. * - * * - * This file is part of HDF5. The full HDF5 copyright notice, including * - * terms governing use, modification, and redistribution, is contained in * - * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://www.hdfgroup.org/licenses. * - * If you do not have access to either file, you may request a copy from * - * help@hdfgroup.org. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ -/************************************************************ - - This example illustrates the concept of the virtual dataset. - Percival use case. Every fifth 10x10 plane in VDS is stored in - the corresponding 3D unlimited dataset. - There are 4 source datasets total. - This file is intended for use with HDF5 Library version 1.10 - - ************************************************************/ -/* EIP Add link to the picture */ - -#include "hdf5.h" -#include <stdio.h> -#include <stdlib.h> - -#define VFILE "vds-percival-unlim.h5" -#define DATASET "VDS-Percival-unlim" -#define VDSDIM0 H5S_UNLIMITED -#define VDSDIM1 10 -#define VDSDIM2 10 - -#define DIM0 H5S_UNLIMITED -#define DIM0_1 10 /* Initial size of the datasets */ -#define DIM1 10 -#define DIM2 10 -#define RANK 3 -#define PLANE_STRIDE 4 - -const char *SRC_FILE[] = {"a.h5", "b.h5", "c.h5", "d.h5"}; - -const char *SRC_DATASET[] = {"A", "B", "C", "D"}; - -int -main(void) -{ - hid_t vfile, file, src_space, mem_space, vspace, vdset, dset; /* Handles */ - hid_t dcpl; - herr_t status; - hsize_t vdsdims[3] = {4 * DIM0_1, VDSDIM1, VDSDIM2}, vdsdims_max[3] = {VDSDIM0, VDSDIM1, VDSDIM2}, - dims[3] = {DIM0_1, DIM1, DIM2}, extdims[3] = {2 * DIM0_1, DIM1, DIM2}, - chunk_dims[3] = {DIM0_1, DIM1, DIM2}, dims_max[3] = {DIM0, DIM1, DIM2}, vdsdims_out[3], - vdsdims_max_out[3], start[3], /* Hyperslab parameters */ - stride[3], count[3], src_count[3], block[3]; - hsize_t start_out[3], /* Hyperslab parameter out */ - stride_out[3], count_out[3], block_out[3]; - int i, j, k; - H5D_layout_t layout; /* Storage layout */ - size_t num_map; /* Number of mappings */ - ssize_t len; /* Length of the string; also a return value */ - char *filename; - char *dsetname; - int wdata[DIM0_1 * DIM1 * DIM2]; - int rdata[80][10][10]; - int a_rdata[20][10][10]; - - /* - * Create source files and datasets. This step is optional. - */ - for (i = 0; i < PLANE_STRIDE; i++) { - /* - * Initialize data for i-th source dataset. - */ - for (j = 0; j < DIM0_1 * DIM1 * DIM2; j++) - wdata[j] = i + 1; - - /* - * Create the source files and datasets. Write data to each dataset and - * close all resources. - */ - - file = H5Fcreate(SRC_FILE[i], H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); - src_space = H5Screate_simple(RANK, dims, dims_max); - dcpl = H5Pcreate(H5P_DATASET_CREATE); - status = H5Pset_chunk(dcpl, RANK, chunk_dims); - dset = H5Dcreate2(file, SRC_DATASET[i], H5T_NATIVE_INT, src_space, H5P_DEFAULT, dcpl, H5P_DEFAULT); - status = H5Dwrite(dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, wdata); - status = H5Sclose(src_space); - status = H5Pclose(dcpl); - status = H5Dclose(dset); - status = H5Fclose(file); - } - - vfile = H5Fcreate(VFILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); - - /* Create VDS dataspace. */ - vspace = H5Screate_simple(RANK, vdsdims, vdsdims_max); - - /* Create dataspaces for the source dataset. */ - src_space = H5Screate_simple(RANK, dims, dims_max); - - /* Create VDS creation property */ - dcpl = H5Pcreate(H5P_DATASET_CREATE); - - /* Initialize hyperslab values */ - - start[0] = 0; - start[1] = 0; - start[2] = 0; - stride[0] = PLANE_STRIDE; /* we will select every fifth plane in VDS */ - stride[1] = 1; - stride[2] = 1; - count[0] = H5S_UNLIMITED; - count[1] = 1; - count[2] = 1; - src_count[0] = H5S_UNLIMITED; - src_count[1] = 1; - src_count[2] = 1; - block[0] = 1; - block[1] = DIM1; - block[2] = DIM2; - - /* - * Build the mappings - * - */ - status = H5Sselect_hyperslab(src_space, H5S_SELECT_SET, start, NULL, src_count, block); - for (i = 0; i < PLANE_STRIDE; i++) { - status = H5Sselect_hyperslab(vspace, H5S_SELECT_SET, start, stride, count, block); - status = H5Pset_virtual(dcpl, vspace, SRC_FILE[i], SRC_DATASET[i], src_space); - start[0]++; - } - - H5Sselect_none(vspace); - - /* Create a virtual dataset */ - vdset = H5Dcreate2(vfile, DATASET, H5T_NATIVE_INT, vspace, H5P_DEFAULT, dcpl, H5P_DEFAULT); - status = H5Sclose(vspace); - status = H5Sclose(src_space); - status = H5Pclose(dcpl); - /* Let's get space of the VDS and its dimension; we should get 40x10x10 */ - vspace = H5Dget_space(vdset); - H5Sget_simple_extent_dims(vspace, vdsdims_out, vdsdims_max_out); - printf("VDS dimensions first time \n"); - printf(" Current: "); - for (i = 0; i < RANK; i++) - printf(" %d ", (int)vdsdims_out[i]); - printf("\n"); - - /* Let's add data to the source datasets and check new dimensions for VDS */ - - for (i = 0; i < PLANE_STRIDE; i++) { - /* - * Initialize data for i-th source dataset. - */ - for (j = 0; j < DIM0_1 * DIM1 * DIM2; j++) - wdata[j] = 10 * (i + 1); - - /* - * Create the source files and datasets. Write data to each dataset and - * close all resources. - */ - - file = H5Fopen(SRC_FILE[i], H5F_ACC_RDWR, H5P_DEFAULT); - dset = H5Dopen2(file, SRC_DATASET[i], H5P_DEFAULT); - status = H5Dset_extent(dset, extdims); - src_space = H5Dget_space(dset); - start[0] = DIM0_1; - start[1] = 0; - start[2] = 0; - count[0] = 1; - count[1] = 1; - count[2] = 1; - block[0] = DIM0_1; - block[1] = DIM1; - block[2] = DIM2; - - mem_space = H5Screate_simple(RANK, dims, NULL); - status = H5Sselect_hyperslab(src_space, H5S_SELECT_SET, start, NULL, count, block); - status = H5Dwrite(dset, H5T_NATIVE_INT, mem_space, src_space, H5P_DEFAULT, wdata); - status = H5Sclose(src_space); - status = H5Dclose(dset); - status = H5Fclose(file); - } - - status = H5Dclose(vdset); - status = H5Fclose(vfile); - - /* - * Now we begin the read section of this example. - */ - - /* - * Open file and dataset using the default properties. - */ - vfile = H5Fopen(VFILE, H5F_ACC_RDONLY, H5P_DEFAULT); - vdset = H5Dopen2(vfile, DATASET, H5P_DEFAULT); - - /* - * Get creation property list and mapping properties. - */ - dcpl = H5Dget_create_plist(vdset); - - /* - * Get storage layout. - */ - layout = H5Pget_layout(dcpl); - - if (H5D_VIRTUAL == layout) - printf(" Dataset has a virtual layout \n"); - else - printf(" Wrong layout found \n"); - - /* - * Find number of mappings. - */ - status = H5Pget_virtual_count(dcpl, &num_map); - printf(" Number of mappings is %lu\n", (unsigned long)num_map); - - /* - * Get mapping parameters for each mapping. - */ - for (i = 0; i < (int)num_map; i++) { - printf(" Mapping %d \n", i); - printf(" Selection in the virtual dataset \n"); - /* Get selection in the virtual dataset */ - vspace = H5Pget_virtual_vspace(dcpl, (size_t)i); - if (H5Sget_select_type(vspace) == H5S_SEL_HYPERSLABS) { - if (H5Sis_regular_hyperslab(vspace)) { - status = H5Sget_regular_hyperslab(vspace, start_out, stride_out, count_out, block_out); - printf(" start = [%llu, %llu, %llu] \n", (unsigned long long)start_out[0], - (unsigned long long)start_out[1], (unsigned long long)start_out[2]); - printf(" stride = [%llu, %llu, %llu] \n", (unsigned long long)stride_out[0], - (unsigned long long)stride_out[1], (unsigned long long)stride_out[2]); - printf(" count = [%llu, %llu, %llu] \n", (unsigned long long)count_out[0], - (unsigned long long)count_out[1], (unsigned long long)count_out[2]); - printf(" block = [%llu, %llu, %llu] \n", (unsigned long long)block_out[0], - (unsigned long long)block_out[1], (unsigned long long)block_out[2]); - } - } - /* Get source file name */ - len = H5Pget_virtual_filename(dcpl, (size_t)i, NULL, 0); - filename = (char *)malloc((size_t)len * sizeof(char) + 1); - H5Pget_virtual_filename(dcpl, (size_t)i, filename, len + 1); - printf(" Source filename %s\n", filename); - - /* Get source dataset name */ - len = H5Pget_virtual_dsetname(dcpl, (size_t)i, NULL, 0); - dsetname = (char *)malloc((size_t)len * sizeof(char) + 1); - H5Pget_virtual_dsetname(dcpl, (size_t)i, dsetname, len + 1); - printf(" Source dataset name %s\n", dsetname); - - /* Get selection in the source dataset */ - printf(" Selection in the source dataset \n"); - src_space = H5Pget_virtual_srcspace(dcpl, (size_t)i); - if (H5Sget_select_type(src_space) == H5S_SEL_HYPERSLABS) { - if (H5Sis_regular_hyperslab(src_space)) { - status = H5Sget_regular_hyperslab(src_space, start_out, stride_out, count_out, block_out); - printf(" start = [%llu, %llu, %llu] \n", (unsigned long long)start_out[0], - (unsigned long long)start_out[1], (unsigned long long)start_out[2]); - printf(" stride = [%llu, %llu, %llu] \n", (unsigned long long)stride_out[0], - (unsigned long long)stride_out[1], (unsigned long long)stride_out[2]); - printf(" count = [%llu, %llu, %llu] \n", (unsigned long long)count_out[0], - (unsigned long long)count_out[1], (unsigned long long)count_out[2]); - printf(" block = [%llu, %llu, %llu] \n", (unsigned long long)block_out[0], - (unsigned long long)block_out[1], (unsigned long long)block_out[2]); - } - } - H5Sclose(vspace); - H5Sclose(src_space); - free(filename); - free(dsetname); - } - /* - * Read data from VDS. - */ - vspace = H5Dget_space(vdset); - H5Sget_simple_extent_dims(vspace, vdsdims_out, vdsdims_max_out); - printf("VDS dimensions second time \n"); - printf(" Current: "); - for (i = 0; i < RANK; i++) - printf(" %d ", (int)vdsdims_out[i]); - printf("\n"); - - /* Read all VDS data */ - - /* EIP We should be able to do it by using H5S_ALL instead of making selection - * or using H5Sselect_all from vspace. - */ - start[0] = 0; - start[1] = 0; - start[2] = 0; - count[0] = 1; - count[1] = 1; - count[2] = 1; - block[0] = vdsdims_out[0]; - block[1] = vdsdims_out[1]; - block[2] = vdsdims_out[2]; - - status = H5Sselect_hyperslab(vspace, H5S_SELECT_SET, start, NULL, count, block); - mem_space = H5Screate_simple(RANK, vdsdims_out, NULL); - status = H5Dread(vdset, H5T_NATIVE_INT, mem_space, vspace, H5P_DEFAULT, rdata); - printf(" All data: \n"); - for (i = 0; i < (int)vdsdims_out[0]; i++) { - for (j = 0; j < (int)vdsdims_out[1]; j++) { - printf("(%d, %d, 0)", i, j); - for (k = 0; k < (int)vdsdims_out[2]; k++) - printf(" %d ", rdata[i][j][k]); - printf("\n"); - } - } - /* Read VDS, but only data mapeed to dataset a.h5 */ - start[0] = 0; - start[1] = 0; - start[2] = 0; - stride[0] = PLANE_STRIDE; - stride[1] = 1; - stride[2] = 1; - count[0] = 2 * DIM0_1; - count[1] = 1; - count[2] = 1; - block[0] = 1; - block[1] = vdsdims_out[1]; - block[2] = vdsdims_out[2]; - dims[0] = 2 * DIM0_1; - status = H5Sselect_hyperslab(vspace, H5S_SELECT_SET, start, stride, count, block); - mem_space = H5Screate_simple(RANK, dims, NULL); - status = H5Dread(vdset, H5T_NATIVE_INT, mem_space, vspace, H5P_DEFAULT, a_rdata); - printf(" All data: \n"); - for (i = 0; i < 2 * DIM0_1; i++) { - for (j = 0; j < (int)vdsdims_out[1]; j++) { - printf("(%d, %d, 0)", i, j); - for (k = 0; k < (int)vdsdims_out[2]; k++) - printf(" %d ", a_rdata[i][j][k]); - printf("\n"); - } - } - /* - * Close and release resources. - */ - status = H5Sclose(mem_space); - status = H5Pclose(dcpl); - status = H5Dclose(vdset); - status = H5Fclose(vfile); - return 0; -} diff --git a/examples/h5_vds-percival.c b/examples/h5_vds-percival.c deleted file mode 100644 index 82c8ef4..0000000 --- a/examples/h5_vds-percival.c +++ /dev/null @@ -1,241 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * Copyright by The HDF Group. * - * All rights reserved. * - * * - * This file is part of HDF5. The full HDF5 copyright notice, including * - * terms governing use, modification, and redistribution, is contained in * - * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://www.hdfgroup.org/licenses. * - * If you do not have access to either file, you may request a copy from * - * help@hdfgroup.org. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ -/************************************************************ - - This example illustrates the concept of the virtual dataset. - Percival use case. Every fifth 10x10 plane in VDS is stored in - the corresponding 3D unlimited dataset. - EIP: For now we will use finite dimension. - There are 4 source datasets total. - This file is intended for use with HDF5 Library version 1.10 - - ************************************************************/ -/* EIP Add link to the picture */ - -#include "hdf5.h" -#include <stdio.h> -#include <stdlib.h> - -#define FILE "vds-percival.h5" -#define DATASET "VDS-Percival" -/* later -#define VDSDIM0 H5S_UNLIMITED -*/ -#define VDSDIM0 40 -#define VDSDIM1 10 -#define VDSDIM2 10 -/* later -#define DIM0 H5S_UNLIMITED -*/ -#define DIM0 10 -#define DIM1 10 -#define DIM2 10 -#define RANK 3 -#define PLANE_STRIDE 4 - -const char *SRC_FILE[] = {"a.h5", "b.h5", "c.h5", "d.h5"}; - -const char *SRC_DATASET[] = {"A", "B", "C", "D"}; - -int -main(void) -{ - hid_t file, src_space, vspace, dset; /* Handles */ - hid_t dcpl; - herr_t status; - hsize_t vdsdims[3] = {VDSDIM0, VDSDIM1, VDSDIM2}, vdsdims_max[3] = {VDSDIM0, VDSDIM1, VDSDIM2}, - dims[3] = {DIM0, DIM1, DIM2}, dims_max[3] = {DIM0, DIM1, DIM2}, - start[3], /* Hyperslab start parameter for VDS */ - stride[3], count[3], src_count[3], block[3]; - hsize_t start_out[3], /* Hyperslab parameter out */ - stride_out[3], count_out[3], block_out[3]; - int i, j; - H5D_layout_t layout; /* Storage layout */ - size_t num_map; /* Number of mappings */ - ssize_t len; /* Length of the string; also a return value */ - char *filename; - char *dsetname; - int wdata[DIM0 * DIM1 * DIM2]; - - /* - * Create source files and datasets. This step is optional. - */ - for (i = 0; i < PLANE_STRIDE; i++) { - /* - * Initialize data for i-th source dataset. - */ - for (j = 0; j < DIM0 * DIM1 * DIM2; j++) - wdata[j] = i + 1; - - /* - * Create the source files and datasets. Write data to each dataset and - * close all resources. - */ - - file = H5Fcreate(SRC_FILE[i], H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); - src_space = H5Screate_simple(RANK, dims, NULL); - dset = H5Dcreate2(file, SRC_DATASET[i], H5T_NATIVE_INT, src_space, H5P_DEFAULT, H5P_DEFAULT, - H5P_DEFAULT); - status = H5Dwrite(dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, wdata); - status = H5Sclose(src_space); - status = H5Dclose(dset); - status = H5Fclose(file); - } - - file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); - - /* Create VDS dataspace. */ - vspace = H5Screate_simple(RANK, vdsdims, vdsdims_max); - - /* Create dataspaces for the source dataset. */ - src_space = H5Screate_simple(RANK, dims, dims_max); - - /* Create VDS creation property */ - dcpl = H5Pcreate(H5P_DATASET_CREATE); - - /* Initialize hyperslab values */ - - start[0] = 0; - start[1] = 0; - start[2] = 0; - stride[0] = PLANE_STRIDE; /* we will select every fifth plane in VDS */ - stride[1] = 1; - stride[2] = 1; - /* later - count[0] = H5S_UNLIMITED; - */ - count[0] = VDSDIM0 / 4; - count[1] = 1; - count[2] = 1; - /* later - src_count[0] = H5S_UNLIMITED; - */ - src_count[0] = DIM0; - src_count[1] = 1; - src_count[2] = 1; - block[0] = 1; - block[1] = DIM1; - block[2] = DIM2; - - /* - * Build the mappings - * - */ - status = H5Sselect_hyperslab(src_space, H5S_SELECT_SET, start, NULL, src_count, block); - for (i = 0; i < PLANE_STRIDE; i++) { - status = H5Sselect_hyperslab(vspace, H5S_SELECT_SET, start, stride, count, block); - status = H5Pset_virtual(dcpl, vspace, SRC_FILE[i], SRC_DATASET[i], src_space); - start[0]++; - } - - H5Sselect_none(vspace); - - /* Create a virtual dataset */ - dset = H5Dcreate2(file, DATASET, H5T_NATIVE_INT, vspace, H5P_DEFAULT, dcpl, H5P_DEFAULT); - status = H5Sclose(vspace); - status = H5Sclose(src_space); - status = H5Dclose(dset); - status = H5Fclose(file); - - /* - * Now we begin the read section of this example. - */ - - /* - * Open file and dataset using the default properties. - */ - file = H5Fopen(FILE, H5F_ACC_RDONLY, H5P_DEFAULT); - dset = H5Dopen2(file, DATASET, H5P_DEFAULT); - - /* - * Get creation property list and mapping properties. - */ - dcpl = H5Dget_create_plist(dset); - - /* - * Get storage layout. - */ - layout = H5Pget_layout(dcpl); - - if (H5D_VIRTUAL == layout) - printf(" Dataset has a virtual layout \n"); - else - printf(" Wrong layout found \n"); - - /* - * Find number of mappings. - */ - status = H5Pget_virtual_count(dcpl, &num_map); - printf(" Number of mappings is %lu\n", (unsigned long)num_map); - - /* - * Get mapping parameters for each mapping. - */ - for (i = 0; i < (int)num_map; i++) { - printf(" Mapping %d \n", i); - printf(" Selection in the virtual dataset \n"); - /* Get selection in the virtual dataset */ - vspace = H5Pget_virtual_vspace(dcpl, (size_t)i); - if (H5Sget_select_type(vspace) == H5S_SEL_HYPERSLABS) { - if (H5Sis_regular_hyperslab(vspace)) { - status = H5Sget_regular_hyperslab(vspace, start_out, stride_out, count_out, block_out); - printf(" start = [%llu, %llu, %llu] \n", (unsigned long long)start_out[0], - (unsigned long long)start_out[1], (unsigned long long)start_out[2]); - printf(" stride = [%llu, %llu, %llu] \n", (unsigned long long)stride_out[0], - (unsigned long long)stride_out[1], (unsigned long long)stride_out[2]); - printf(" count = [%llu, %llu, %llu] \n", (unsigned long long)count_out[0], - (unsigned long long)count_out[1], (unsigned long long)count_out[2]); - printf(" block = [%llu, %llu, %llu] \n", (unsigned long long)block_out[0], - (unsigned long long)block_out[1], (unsigned long long)block_out[2]); - } - } - /* Get source file name */ - len = H5Pget_virtual_filename(dcpl, (size_t)i, NULL, 0); - filename = (char *)malloc((size_t)len * sizeof(char) + 1); - H5Pget_virtual_filename(dcpl, (size_t)i, filename, len + 1); - printf(" Source filename %s\n", filename); - - /* Get source dataset name */ - len = H5Pget_virtual_dsetname(dcpl, (size_t)i, NULL, 0); - dsetname = (char *)malloc((size_t)len * sizeof(char) + 1); - H5Pget_virtual_dsetname(dcpl, (size_t)i, dsetname, len + 1); - printf(" Source dataset name %s\n", dsetname); - - /* Get selection in the source dataset */ - printf(" Selection in the source dataset \n"); - src_space = H5Pget_virtual_srcspace(dcpl, (size_t)i); - if (H5Sget_select_type(src_space) == H5S_SEL_HYPERSLABS) { - if (H5Sis_regular_hyperslab(src_space)) { - status = H5Sget_regular_hyperslab(src_space, start_out, stride_out, count_out, block_out); - printf(" start = [%llu, %llu, %llu] \n", (unsigned long long)start_out[0], - (unsigned long long)start_out[1], (unsigned long long)start_out[2]); - printf(" stride = [%llu, %llu, %llu] \n", (unsigned long long)stride_out[0], - (unsigned long long)stride_out[1], (unsigned long long)stride_out[2]); - printf(" count = [%llu, %llu, %llu] \n", (unsigned long long)count_out[0], - (unsigned long long)count_out[1], (unsigned long long)count_out[2]); - printf(" block = [%llu, %llu, %llu] \n", (unsigned long long)block_out[0], - (unsigned long long)block_out[1], (unsigned long long)block_out[2]); - } - } - H5Sclose(vspace); - H5Sclose(src_space); - free(filename); - free(dsetname); - } - /* - * Close and release resources. - */ - status = H5Pclose(dcpl); - status = H5Dclose(dset); - status = H5Fclose(file); - return 0; -} diff --git a/examples/h5_vds-simpleIO.c b/examples/h5_vds-simpleIO.c deleted file mode 100644 index f516af9..0000000 --- a/examples/h5_vds-simpleIO.c +++ /dev/null @@ -1,190 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * Copyright by The HDF Group. * - * All rights reserved. * - * * - * This file is part of HDF5. The full HDF5 copyright notice, including * - * terms governing use, modification, and redistribution, is contained in * - * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://www.hdfgroup.org/licenses. * - * If you do not have access to either file, you may request a copy from * - * help@hdfgroup.org. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ -/************************************************************ - - This example illustrates the concept of virtual dataset I/O - The program creates 2-dim source dataset and writes - data to it. Then it creates 2-dim virtual dataset that has - the same dimension sizes and maps the all elements of the - virtual dataset to all elements of the source dataset. - Then VDS is read back. - - This file is intended for use with HDF5 Library version 1.10 - - ************************************************************/ -/* EIP Add link to the picture */ - -#include "hdf5.h" -#include <stdio.h> -#include <stdlib.h> - -#define FILE "vds-simpleIO.h5" -#define DATASET "VDS" -#define DIM1 6 -#define DIM0 4 -#define RANK 2 - -#define SRC_FILE "a.h5" -#define SRC_DATASET "/A" - -int -main(void) -{ - hid_t file, space, src_space, vspace, dset; /* Handles */ - hid_t dcpl; - herr_t status; - hsize_t vdsdims[2] = {DIM0, DIM1}, /* Virtual dataset dimension */ - dims[2] = {DIM0, DIM1}; /* Source dataset dimensions */ - int wdata[DIM0][DIM1], /* Write buffer for source dataset */ - rdata[DIM0][DIM1], /* Read buffer for virtual dataset */ - i, j; - H5D_layout_t layout; /* Storage layout */ - size_t num_map; /* Number of mappings */ - ssize_t len; /* Length of the string; also a return value */ - char *filename; - char *dsetname; - /* - * Initialize data. - */ - for (i = 0; i < DIM0; i++) - for (j = 0; j < DIM1; j++) - wdata[i][j] = i + 1; - - /* - * Create the source file and the dataset. Write data to the source dataset - * and close all resources. - */ - - file = H5Fcreate(SRC_FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); - space = H5Screate_simple(RANK, dims, NULL); - dset = H5Dcreate2(file, SRC_DATASET, H5T_NATIVE_INT, space, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); - status = H5Dwrite(dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, wdata[0]); - status = H5Sclose(space); - status = H5Dclose(dset); - status = H5Fclose(file); - - /* Create file in which virtual dataset will be stored. */ - file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); - - /* Create VDS dataspace. */ - vspace = H5Screate_simple(RANK, vdsdims, NULL); - - /* Set VDS creation property. */ - dcpl = H5Pcreate(H5P_DATASET_CREATE); - - /* - * Build the mappings. - * Selections in the source datasets are H5S_ALL. - * In the virtual dataset we select the first, the second and the third rows - * and map each row to the data in the corresponding source dataset. - */ - src_space = H5Screate_simple(RANK, dims, NULL); - status = H5Pset_virtual(dcpl, vspace, SRC_FILE, SRC_DATASET, src_space); - - /* Create a virtual dataset. */ - dset = H5Dcreate2(file, DATASET, H5T_NATIVE_INT, vspace, H5P_DEFAULT, dcpl, H5P_DEFAULT); - status = H5Sclose(vspace); - status = H5Sclose(src_space); - status = H5Dclose(dset); - status = H5Fclose(file); - - /* - * Now we begin the read section of this example. - */ - - /* - * Open the file and virtual dataset. - */ - file = H5Fopen(FILE, H5F_ACC_RDONLY, H5P_DEFAULT); - dset = H5Dopen2(file, DATASET, H5P_DEFAULT); - /* - * Get creation property list and mapping properties. - */ - dcpl = H5Dget_create_plist(dset); - - /* - * Get storage layout. - */ - layout = H5Pget_layout(dcpl); - if (H5D_VIRTUAL == layout) - printf(" Dataset has a virtual layout \n"); - else - printf(" Wrong layout found \n"); - - /* - * Find the number of mappings. - */ - status = H5Pget_virtual_count(dcpl, &num_map); - printf(" Number of mappings is %lu\n", (unsigned long)num_map); - - /* - * Get mapping parameters for each mapping. - */ - for (i = 0; i < (int)num_map; i++) { - printf(" Mapping %d \n", i); - printf(" Selection in the virtual dataset "); - /* Get selection in the virtual dataset */ - vspace = H5Pget_virtual_vspace(dcpl, (size_t)i); - - /* Make sure it is ALL selection and then print selection. */ - if (H5Sget_select_type(vspace) == H5S_SEL_ALL) { - printf("Selection is H5S_ALL \n"); - } - /* Get source file name. */ - len = H5Pget_virtual_filename(dcpl, (size_t)i, NULL, 0); - filename = (char *)malloc((size_t)len * sizeof(char) + 1); - H5Pget_virtual_filename(dcpl, (size_t)i, filename, len + 1); - printf(" Source filename %s\n", filename); - - /* Get source dataset name. */ - len = H5Pget_virtual_dsetname(dcpl, (size_t)i, NULL, 0); - dsetname = (char *)malloc((size_t)len * sizeof(char) + 1); - H5Pget_virtual_dsetname(dcpl, (size_t)i, dsetname, len + 1); - printf(" Source dataset name %s\n", dsetname); - - /* Get selection in the source dataset. */ - printf(" Selection in the source dataset "); - src_space = H5Pget_virtual_srcspace(dcpl, (size_t)i); - - /* Make sure it is ALL selection and then print selection. */ - if (H5Sget_select_type(src_space) == H5S_SEL_ALL) { - printf("Selection is H5S_ALL \n"); - } - H5Sclose(vspace); - H5Sclose(src_space); - free(filename); - free(dsetname); - } - /* - * Read the data using the default properties. - */ - status = H5Dread(dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, rdata[0]); - - /* - * Output the data to the screen. - */ - printf(" VDS Data:\n"); - for (i = 0; i < DIM0; i++) { - printf(" ["); - for (j = 0; j < DIM1; j++) - printf(" %3d", rdata[i][j]); - printf("]\n"); - } - /* - * Close and release resources. - */ - status = H5Pclose(dcpl); - status = H5Dclose(dset); - status = H5Fclose(file); - - return 0; -} diff --git a/examples/h5_vds.c b/examples/h5_vds.c deleted file mode 100644 index 96bd8a2..0000000 --- a/examples/h5_vds.c +++ /dev/null @@ -1,252 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * Copyright by The HDF Group. * - * All rights reserved. * - * * - * This file is part of HDF5. The full HDF5 copyright notice, including * - * terms governing use, modification, and redistribution, is contained in * - * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://www.hdfgroup.org/licenses. * - * If you do not have access to either file, you may request a copy from * - * help@hdfgroup.org. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - - This example illustrates the concept of virtual dataset. - The program creates three 1-dim source datasets and writes - data to them. Then it creates a 2-dim virtual dataset and - maps the first three rows of the virtual dataset to the data - in the source datasets. Elements of a row are mapped to all - elements of the corresponding source dataset. - The fourth row is not mapped and will be filled with the fill - values when virtual dataset is read back. - - The program closes all datasets, and then reopens the virtual - dataset, and finds and prints its creation properties. - Then it reads the values. - - This file is intended for use with HDF5 Library version 1.10 - - ************************************************************/ -/* EIP Add link to the picture */ - -#include "hdf5.h" -#include <stdio.h> -#include <stdlib.h> - -#define FILE "vds.h5" -#define DATASET "VDS" -#define VDSDIM1 6 -#define VDSDIM0 4 -#define DIM0 6 -#define RANK1 1 -#define RANK2 2 - -const char *SRC_FILE[] = {"a.h5", "b.h5", "c.h5"}; - -const char *SRC_DATASET[] = {"A", "B", "C"}; - -int -main(void) -{ - hid_t file, space, src_space, vspace, dset; /* Handles */ - hid_t dcpl; - herr_t status; - hsize_t vdsdims[2] = {VDSDIM0, VDSDIM1}, /* Virtual datasets dimension */ - dims[1] = {DIM0}, /* Source datasets dimensions */ - start[2], /* Hyperslab parameters */ - count[2], block[2]; - hsize_t start_out[2], stride_out[2], count_out[2], block_out[2]; - int wdata[DIM0], /* Write buffer for source dataset */ - rdata[VDSDIM0][VDSDIM1], /* Read buffer for virtual dataset */ - i, j, k, l, block_inc; - int fill_value = -1; /* Fill value for VDS */ - H5D_layout_t layout; /* Storage layout */ - size_t num_map; /* Number of mappings */ - ssize_t len; /* Length of the string; also a return value */ - char *filename; - char *dsetname; - hsize_t nblocks; - hsize_t *buf; /* Buffer to hold hyperslab coordinates */ - - /* - * Create source files and datasets. This step is optional. - */ - for (i = 0; i < 3; i++) { - /* - * Initialize data for i-th source dataset. - */ - for (j = 0; j < DIM0; j++) - wdata[j] = i + 1; - - /* - * Create the source files and datasets. Write data to each dataset and - * close all resources. - */ - - file = H5Fcreate(SRC_FILE[i], H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); - space = H5Screate_simple(RANK1, dims, NULL); - dset = H5Dcreate2(file, SRC_DATASET[i], H5T_NATIVE_INT, space, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); - status = H5Dwrite(dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, wdata); - status = H5Sclose(space); - status = H5Dclose(dset); - status = H5Fclose(file); - } - - /* Create file in which virtual dataset will be stored. */ - file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); - - /* Create VDS dataspace. */ - space = H5Screate_simple(RANK2, vdsdims, NULL); - - /* Set VDS creation property. */ - dcpl = H5Pcreate(H5P_DATASET_CREATE); - status = H5Pset_fill_value(dcpl, H5T_NATIVE_INT, &fill_value); - - /* Initialize hyperslab values. */ - start[0] = 0; - start[1] = 0; - count[0] = 1; - count[1] = 1; - block[0] = 1; - block[1] = VDSDIM1; - - /* - * Build the mappings. - * Selections in the source datasets are H5S_ALL. - * In the virtual dataset we select the first, the second and the third rows - * and map each row to the data in the corresponding source dataset. - */ - src_space = H5Screate_simple(RANK1, dims, NULL); - for (i = 0; i < 3; i++) { - start[0] = (hsize_t)i; - /* Select i-th row in the virtual dataset; selection in the source datasets is the same. */ - status = H5Sselect_hyperslab(space, H5S_SELECT_SET, start, NULL, count, block); - status = H5Pset_virtual(dcpl, space, SRC_FILE[i], SRC_DATASET[i], src_space); - } - - /* Create a virtual dataset. */ - dset = H5Dcreate2(file, DATASET, H5T_NATIVE_INT, space, H5P_DEFAULT, dcpl, H5P_DEFAULT); - status = H5Sclose(space); - status = H5Sclose(src_space); - status = H5Dclose(dset); - status = H5Fclose(file); - - /* - * Now we begin the read section of this example. - */ - - /* - * Open the file and virtual dataset. - */ - file = H5Fopen(FILE, H5F_ACC_RDONLY, H5P_DEFAULT); - dset = H5Dopen2(file, DATASET, H5P_DEFAULT); - - /* - * Get creation property list and mapping properties. - */ - dcpl = H5Dget_create_plist(dset); - - /* - * Get storage layout. - */ - layout = H5Pget_layout(dcpl); - if (H5D_VIRTUAL == layout) - printf(" Dataset has a virtual layout \n"); - else - printf(" Wrong layout found \n"); - - /* - * Find the number of mappings. - */ - status = H5Pget_virtual_count(dcpl, &num_map); - printf(" Number of mappings is %lu\n", (unsigned long)num_map); - - /* - * Get mapping parameters for each mapping. - */ - for (i = 0; i < (int)num_map; i++) { - printf(" Mapping %d \n", i); - printf(" Selection in the virtual dataset "); - /* Get selection in the virtual dataset */ - vspace = H5Pget_virtual_vspace(dcpl, (size_t)i); - - /* Make sure that this is a hyperslab selection and then print information. */ - if (H5Sget_select_type(vspace) == H5S_SEL_HYPERSLABS) { - nblocks = H5Sget_select_hyper_nblocks(vspace); - buf = (hsize_t *)malloc(sizeof(hsize_t) * 2 * RANK2 * nblocks); - status = H5Sget_select_hyper_blocklist(vspace, (hsize_t)0, nblocks, buf); - for (l = 0; l < nblocks; l++) { - block_inc = 2 * RANK2 * l; - printf("("); - for (k = 0; k < RANK2 - 1; k++) - printf("%d,", (int)buf[block_inc + k]); - printf("%d) - (", (int)buf[block_inc + k]); - for (k = 0; k < RANK2 - 1; k++) - printf("%d,", (int)buf[block_inc + RANK2 + k]); - printf("%d)\n", (int)buf[block_inc + RANK2 + k]); - } - /* We also can use new APIs to get start, stride, count and block */ - if (H5Sis_regular_hyperslab(vspace)) { - status = H5Sget_regular_hyperslab(vspace, start_out, stride_out, count_out, block_out); - printf(" start = [%llu, %llu] \n", (unsigned long long)start_out[0], - (unsigned long long)start_out[1]); - printf(" stride = [%llu, %llu] \n", (unsigned long long)stride_out[0], - (unsigned long long)stride_out[1]); - printf(" count = [%llu, %llu] \n", (unsigned long long)count_out[0], - (unsigned long long)count_out[1]); - printf(" block = [%llu, %llu] \n", (unsigned long long)block_out[0], - (unsigned long long)block_out[1]); - } - } - /* Get source file name. */ - len = H5Pget_virtual_filename(dcpl, (size_t)i, NULL, 0); - filename = (char *)malloc((size_t)len * sizeof(char) + 1); - H5Pget_virtual_filename(dcpl, (size_t)i, filename, len + 1); - printf(" Source filename %s\n", filename); - - /* Get source dataset name. */ - len = H5Pget_virtual_dsetname(dcpl, (size_t)i, NULL, 0); - dsetname = (char *)malloc((size_t)len * sizeof(char) + 1); - H5Pget_virtual_dsetname(dcpl, (size_t)i, dsetname, len + 1); - printf(" Source dataset name %s\n", dsetname); - - /* Get selection in the source dataset. */ - printf(" Selection in the source dataset "); - src_space = H5Pget_virtual_srcspace(dcpl, (size_t)i); - - /* Make sure it is ALL selection and then print the coordinates. */ - if (H5Sget_select_type(src_space) == H5S_SEL_ALL) { - printf("(0) - (%d) \n", DIM0 - 1); - } - H5Sclose(vspace); - H5Sclose(src_space); - free(filename); - free(dsetname); - free(buf); - } - - /* - * Read the data using the default properties. - */ - status = H5Dread(dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, rdata[0]); - - /* - * Output the data to the screen. - */ - printf(" VDS Data:\n"); - for (i = 0; i < VDSDIM0; i++) { - printf(" ["); - for (j = 0; j < VDSDIM1; j++) - printf(" %3d", rdata[i][j]); - printf("]\n"); - } - /* - * Close and release resources. - */ - status = H5Pclose(dcpl); - status = H5Dclose(dset); - status = H5Fclose(file); - - return 0; -} diff --git a/examples/ph5_filtered_writes.c b/examples/ph5_filtered_writes.c deleted file mode 100644 index f4ddae9..0000000 --- a/examples/ph5_filtered_writes.c +++ /dev/null @@ -1,488 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * Copyright by The HDF Group. * - * All rights reserved. * - * * - * This file is part of HDF5. The full HDF5 copyright notice, including * - * terms governing use, modification, and redistribution, is contained in * - * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://www.hdfgroup.org/licenses. * - * If you do not have access to either file, you may request a copy from * - * help@hdfgroup.org. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/* - * Example of using the parallel HDF5 library to write to datasets - * with filters applied to them. - * - * If the HDF5_NOCLEANUP environment variable is set, the file that - * this example creates will not be removed as the example finishes. - * - * The need of requirement of parallel file prefix is that in general - * the current working directory in which compiling is done, is not suitable - * for parallel I/O and there is no standard pathname for parallel file - * systems. In some cases, the parallel file name may even need some - * parallel file type prefix such as: "pfs:/GF/...". Therefore, this - * example parses the HDF5_PARAPREFIX environment variable for a prefix, - * if one is needed. - */ - -#include <stdlib.h> - -#include "hdf5.h" - -#if defined(H5_HAVE_PARALLEL) && defined(H5_HAVE_PARALLEL_FILTERED_WRITES) - -#define EXAMPLE_FILE "ph5_filtered_writes.h5" -#define EXAMPLE_DSET1_NAME "DSET1" -#define EXAMPLE_DSET2_NAME "DSET2" - -#define EXAMPLE_DSET_DIMS 2 -#define EXAMPLE_DSET_CHUNK_DIM_SIZE 10 - -/* Dataset datatype */ -#define HDF5_DATATYPE H5T_NATIVE_INT -typedef int C_DATATYPE; - -#ifndef PATH_MAX -#define PATH_MAX 512 -#endif - -/* Global variables */ -int mpi_rank, mpi_size; - -/* - * Routine to set an HDF5 filter on the given DCPL - */ -static void -set_filter(hid_t dcpl_id) -{ - htri_t filter_avail; - - /* - * Check if 'deflate' filter is available - */ - filter_avail = H5Zfilter_avail(H5Z_FILTER_DEFLATE); - if (filter_avail < 0) - return; - else if (filter_avail) { - /* - * Set 'deflate' filter with reasonable - * compression level on DCPL - */ - H5Pset_deflate(dcpl_id, 6); - } - else { - /* - * Set Fletcher32 checksum filter on DCPL - * since it is always available in HDF5 - */ - H5Pset_fletcher32(dcpl_id); - } -} - -/* - * Routine to fill a data buffer with data. Assumes - * dimension rank is 2 and data is stored contiguous. - */ -void -fill_databuf(hsize_t start[], hsize_t count[], hsize_t stride[], C_DATATYPE *data) -{ - C_DATATYPE *dataptr = data; - hsize_t i, j; - - /* Use MPI rank value for data */ - for (i = 0; i < count[0]; i++) { - for (j = 0; j < count[1]; j++) { - *dataptr++ = mpi_rank; - } - } -} - -/* Cleanup created file */ -static void -cleanup(char *filename) -{ - bool do_cleanup = getenv(HDF5_NOCLEANUP) ? false : true; - - if (do_cleanup) - MPI_File_delete(filename, MPI_INFO_NULL); -} - -/* - * Routine to write to a dataset in a fashion - * where no chunks in the dataset are written - * to by more than 1 MPI rank. This will - * generally give the best performance as the - * MPI ranks will need the least amount of - * inter-process communication. - */ -static void -write_dataset_no_overlap(hid_t file_id, hid_t dxpl_id) -{ - C_DATATYPE data[EXAMPLE_DSET_CHUNK_DIM_SIZE][4 * EXAMPLE_DSET_CHUNK_DIM_SIZE]; - hsize_t dataset_dims[EXAMPLE_DSET_DIMS]; - hsize_t chunk_dims[EXAMPLE_DSET_DIMS]; - hsize_t start[EXAMPLE_DSET_DIMS]; - hsize_t stride[EXAMPLE_DSET_DIMS]; - hsize_t count[EXAMPLE_DSET_DIMS]; - hid_t dset_id = H5I_INVALID_HID; - hid_t dcpl_id = H5I_INVALID_HID; - hid_t file_dataspace = H5I_INVALID_HID; - - /* - * ------------------------------------ - * Setup Dataset Creation Property List - * ------------------------------------ - */ - - dcpl_id = H5Pcreate(H5P_DATASET_CREATE); - - /* - * REQUIRED: Dataset chunking must be enabled to - * apply a data filter to the dataset. - * Chunks in the dataset are of size - * EXAMPLE_DSET_CHUNK_DIM_SIZE x EXAMPLE_DSET_CHUNK_DIM_SIZE. - */ - chunk_dims[0] = EXAMPLE_DSET_CHUNK_DIM_SIZE; - chunk_dims[1] = EXAMPLE_DSET_CHUNK_DIM_SIZE; - H5Pset_chunk(dcpl_id, EXAMPLE_DSET_DIMS, chunk_dims); - - /* Set filter to be applied to created datasets */ - set_filter(dcpl_id); - - /* - * ------------------------------------ - * Define the dimensions of the dataset - * and create it - * ------------------------------------ - */ - - /* - * Create a dataset composed of 4 chunks - * per MPI rank. The first dataset dimension - * scales according to the number of MPI ranks. - * The second dataset dimension stays fixed - * according to the chunk size. - */ - dataset_dims[0] = EXAMPLE_DSET_CHUNK_DIM_SIZE * mpi_size; - dataset_dims[1] = 4 * EXAMPLE_DSET_CHUNK_DIM_SIZE; - - file_dataspace = H5Screate_simple(EXAMPLE_DSET_DIMS, dataset_dims, NULL); - - /* Create the dataset */ - dset_id = H5Dcreate2(file_id, EXAMPLE_DSET1_NAME, HDF5_DATATYPE, file_dataspace, H5P_DEFAULT, dcpl_id, - H5P_DEFAULT); - - /* - * ------------------------------------ - * Setup selection in the dataset for - * each MPI rank - * ------------------------------------ - */ - - /* - * Each MPI rank's selection covers a - * single chunk in the first dataset - * dimension. Each MPI rank's selection - * covers 4 chunks in the second dataset - * dimension. This leads to each MPI rank - * writing to 4 chunks of the dataset. - */ - start[0] = mpi_rank * EXAMPLE_DSET_CHUNK_DIM_SIZE; - start[1] = 0; - stride[0] = 1; - stride[1] = 1; - count[0] = EXAMPLE_DSET_CHUNK_DIM_SIZE; - count[1] = 4 * EXAMPLE_DSET_CHUNK_DIM_SIZE; - - H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, NULL); - - /* - * -------------------------------------- - * Fill data buffer with MPI rank's rank - * value to make it easy to see which - * part of the dataset each rank wrote to - * -------------------------------------- - */ - - fill_databuf(start, count, stride, &data[0][0]); - - /* - * --------------------------------- - * Write to the dataset collectively - * --------------------------------- - */ - - H5Dwrite(dset_id, HDF5_DATATYPE, H5S_BLOCK, file_dataspace, dxpl_id, data); - - /* - * -------------- - * Close HDF5 IDs - * -------------- - */ - - H5Sclose(file_dataspace); - H5Pclose(dcpl_id); - H5Dclose(dset_id); -} - -/* - * Routine to write to a dataset in a fashion - * where every chunk in the dataset is written - * to by every MPI rank. This will generally - * give the worst performance as the MPI ranks - * will need the most amount of inter-process - * communication. - */ -static void -write_dataset_overlap(hid_t file_id, hid_t dxpl_id) -{ - C_DATATYPE *data = NULL; - hsize_t dataset_dims[EXAMPLE_DSET_DIMS]; - hsize_t chunk_dims[EXAMPLE_DSET_DIMS]; - hsize_t start[EXAMPLE_DSET_DIMS]; - hsize_t stride[EXAMPLE_DSET_DIMS]; - hsize_t count[EXAMPLE_DSET_DIMS]; - hid_t dset_id = H5I_INVALID_HID; - hid_t dcpl_id = H5I_INVALID_HID; - hid_t file_dataspace = H5I_INVALID_HID; - - /* - * ------------------------------------ - * Setup Dataset Creation Property List - * ------------------------------------ - */ - - dcpl_id = H5Pcreate(H5P_DATASET_CREATE); - - /* - * REQUIRED: Dataset chunking must be enabled to - * apply a data filter to the dataset. - * Chunks in the dataset are of size - * mpi_size x EXAMPLE_DSET_CHUNK_DIM_SIZE. - */ - chunk_dims[0] = mpi_size; - chunk_dims[1] = EXAMPLE_DSET_CHUNK_DIM_SIZE; - H5Pset_chunk(dcpl_id, EXAMPLE_DSET_DIMS, chunk_dims); - - /* Set filter to be applied to created datasets */ - set_filter(dcpl_id); - - /* - * ------------------------------------ - * Define the dimensions of the dataset - * and create it - * ------------------------------------ - */ - - /* - * Create a dataset composed of N chunks, - * where N is the number of MPI ranks. The - * first dataset dimension scales according - * to the number of MPI ranks. The second - * dataset dimension stays fixed according - * to the chunk size. - */ - dataset_dims[0] = mpi_size * chunk_dims[0]; - dataset_dims[1] = EXAMPLE_DSET_CHUNK_DIM_SIZE; - - file_dataspace = H5Screate_simple(EXAMPLE_DSET_DIMS, dataset_dims, NULL); - - /* Create the dataset */ - dset_id = H5Dcreate2(file_id, EXAMPLE_DSET2_NAME, HDF5_DATATYPE, file_dataspace, H5P_DEFAULT, dcpl_id, - H5P_DEFAULT); - - /* - * ------------------------------------ - * Setup selection in the dataset for - * each MPI rank - * ------------------------------------ - */ - - /* - * Each MPI rank's selection covers - * part of every chunk in the first - * dimension. Each MPI rank's selection - * covers all of every chunk in the - * second dimension. This leads to - * each MPI rank writing an equal - * amount of data to every chunk - * in the dataset. - */ - start[0] = mpi_rank; - start[1] = 0; - stride[0] = chunk_dims[0]; - stride[1] = 1; - count[0] = mpi_size; - count[1] = EXAMPLE_DSET_CHUNK_DIM_SIZE; - - H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, NULL); - - /* - * -------------------------------------- - * Fill data buffer with MPI rank's rank - * value to make it easy to see which - * part of the dataset each rank wrote to - * -------------------------------------- - */ - - data = malloc(mpi_size * EXAMPLE_DSET_CHUNK_DIM_SIZE * sizeof(C_DATATYPE)); - - fill_databuf(start, count, stride, data); - - /* - * --------------------------------- - * Write to the dataset collectively - * --------------------------------- - */ - - H5Dwrite(dset_id, HDF5_DATATYPE, H5S_BLOCK, file_dataspace, dxpl_id, data); - - free(data); - - /* - * -------------- - * Close HDF5 IDs - * -------------- - */ - - H5Sclose(file_dataspace); - H5Pclose(dcpl_id); - H5Dclose(dset_id); -} - -int -main(int argc, char **argv) -{ - MPI_Comm comm = MPI_COMM_WORLD; - MPI_Info info = MPI_INFO_NULL; - hid_t file_id = H5I_INVALID_HID; - hid_t fapl_id = H5I_INVALID_HID; - hid_t dxpl_id = H5I_INVALID_HID; - char *par_prefix = NULL; - char filename[PATH_MAX]; - - MPI_Init(&argc, &argv); - MPI_Comm_size(comm, &mpi_size); - MPI_Comm_rank(comm, &mpi_rank); - - /* - * ---------------------------------- - * Start parallel access to HDF5 file - * ---------------------------------- - */ - - /* Setup File Access Property List with parallel I/O access */ - fapl_id = H5Pcreate(H5P_FILE_ACCESS); - H5Pset_fapl_mpio(fapl_id, comm, info); - - /* - * OPTIONAL: Set collective metadata reads on FAPL to allow - * parallel writes to filtered datasets to perform - * better at scale. While not strictly necessary, - * this is generally recommended. - */ - H5Pset_all_coll_metadata_ops(fapl_id, true); - - /* - * OPTIONAL: Set the latest file format version for HDF5 in - * order to gain access to different dataset chunk - * index types and better data encoding methods. - * While not strictly necessary, this is generally - * recommended. - */ - H5Pset_libver_bounds(fapl_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST); - - /* Parse any parallel prefix and create filename */ - par_prefix = getenv("HDF5_PARAPREFIX"); - - snprintf(filename, PATH_MAX, "%s%s%s", par_prefix ? par_prefix : "", par_prefix ? "/" : "", EXAMPLE_FILE); - - /* Create HDF5 file */ - file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id); - - /* - * -------------------------------------- - * Setup Dataset Transfer Property List - * with collective I/O - * -------------------------------------- - */ - - dxpl_id = H5Pcreate(H5P_DATASET_XFER); - - /* - * REQUIRED: Setup collective I/O for the dataset - * write operations. Parallel writes to - * filtered datasets MUST be collective, - * even if some ranks have no data to - * contribute to the write operation. - * - * Refer to the 'ph5_filtered_writes_no_sel' - * example to see how to setup a dataset - * write when one or more MPI ranks have - * no data to contribute to the write - * operation. - */ - H5Pset_dxpl_mpio(dxpl_id, H5FD_MPIO_COLLECTIVE); - - /* - * -------------------------------- - * Create and write to each dataset - * -------------------------------- - */ - - /* - * Write to a dataset in a fashion where no - * chunks in the dataset are written to by - * more than 1 MPI rank. This will generally - * give the best performance as the MPI ranks - * will need the least amount of inter-process - * communication. - */ - write_dataset_no_overlap(file_id, dxpl_id); - - /* - * Write to a dataset in a fashion where - * every chunk in the dataset is written - * to by every MPI rank. This will generally - * give the worst performance as the MPI ranks - * will need the most amount of inter-process - * communication. - */ - write_dataset_overlap(file_id, dxpl_id); - - /* - * ------------------ - * Close all HDF5 IDs - * ------------------ - */ - - H5Pclose(dxpl_id); - H5Pclose(fapl_id); - H5Fclose(file_id); - - printf("PHDF5 example finished with no errors\n"); - - /* - * ------------------------------------ - * Cleanup created HDF5 file and finish - * ------------------------------------ - */ - - cleanup(filename); - - MPI_Finalize(); - - return 0; -} - -#else - -int -main(void) -{ - printf("HDF5 not configured with parallel support or parallel filtered writes are disabled!\n"); - return 0; -} - -#endif diff --git a/examples/ph5_filtered_writes_no_sel.c b/examples/ph5_filtered_writes_no_sel.c deleted file mode 100644 index e3ec103..0000000 --- a/examples/ph5_filtered_writes_no_sel.c +++ /dev/null @@ -1,369 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * Copyright by The HDF Group. * - * All rights reserved. * - * * - * This file is part of HDF5. The full HDF5 copyright notice, including * - * terms governing use, modification, and redistribution, is contained in * - * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://www.hdfgroup.org/licenses. * - * If you do not have access to either file, you may request a copy from * - * help@hdfgroup.org. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/* - * Example of using the parallel HDF5 library to collectively write to - * datasets with filters applied to them when one or MPI ranks do not - * have data to contribute to the dataset. - * - * If the HDF5_NOCLEANUP environment variable is set, the file that - * this example creates will not be removed as the example finishes. - * - * The need of requirement of parallel file prefix is that in general - * the current working directory in which compiling is done, is not suitable - * for parallel I/O and there is no standard pathname for parallel file - * systems. In some cases, the parallel file name may even need some - * parallel file type prefix such as: "pfs:/GF/...". Therefore, this - * example parses the HDF5_PARAPREFIX environment variable for a prefix, - * if one is needed. - */ - -#include <stdlib.h> - -#include "hdf5.h" - -#if defined(H5_HAVE_PARALLEL) && defined(H5_HAVE_PARALLEL_FILTERED_WRITES) - -#define EXAMPLE_FILE "ph5_filtered_writes_no_sel.h5" -#define EXAMPLE_DSET_NAME "DSET" - -#define EXAMPLE_DSET_DIMS 2 -#define EXAMPLE_DSET_CHUNK_DIM_SIZE 10 - -/* Dataset datatype */ -#define HDF5_DATATYPE H5T_NATIVE_INT -typedef int C_DATATYPE; - -#ifndef PATH_MAX -#define PATH_MAX 512 -#endif - -/* Global variables */ -int mpi_rank, mpi_size; - -/* - * Routine to set an HDF5 filter on the given DCPL - */ -static void -set_filter(hid_t dcpl_id) -{ - htri_t filter_avail; - - /* - * Check if 'deflate' filter is available - */ - filter_avail = H5Zfilter_avail(H5Z_FILTER_DEFLATE); - if (filter_avail < 0) - return; - else if (filter_avail) { - /* - * Set 'deflate' filter with reasonable - * compression level on DCPL - */ - H5Pset_deflate(dcpl_id, 6); - } - else { - /* - * Set Fletcher32 checksum filter on DCPL - * since it is always available in HDF5 - */ - H5Pset_fletcher32(dcpl_id); - } -} - -/* - * Routine to fill a data buffer with data. Assumes - * dimension rank is 2 and data is stored contiguous. - */ -void -fill_databuf(hsize_t start[], hsize_t count[], hsize_t stride[], C_DATATYPE *data) -{ - C_DATATYPE *dataptr = data; - hsize_t i, j; - - /* Use MPI rank value for data */ - for (i = 0; i < count[0]; i++) { - for (j = 0; j < count[1]; j++) { - *dataptr++ = mpi_rank; - } - } -} - -/* Cleanup created file */ -static void -cleanup(char *filename) -{ - bool do_cleanup = getenv(HDF5_NOCLEANUP) ? false : true; - - if (do_cleanup) - MPI_File_delete(filename, MPI_INFO_NULL); -} - -/* - * Routine to write to a dataset in a fashion - * where no chunks in the dataset are written - * to by more than 1 MPI rank. This will - * generally give the best performance as the - * MPI ranks will need the least amount of - * inter-process communication. - */ -static void -write_dataset_some_no_sel(hid_t file_id, hid_t dxpl_id) -{ - C_DATATYPE data[EXAMPLE_DSET_CHUNK_DIM_SIZE][4 * EXAMPLE_DSET_CHUNK_DIM_SIZE]; - hsize_t dataset_dims[EXAMPLE_DSET_DIMS]; - hsize_t chunk_dims[EXAMPLE_DSET_DIMS]; - hsize_t start[EXAMPLE_DSET_DIMS]; - hsize_t stride[EXAMPLE_DSET_DIMS]; - hsize_t count[EXAMPLE_DSET_DIMS]; - bool no_selection; - hid_t dset_id = H5I_INVALID_HID; - hid_t dcpl_id = H5I_INVALID_HID; - hid_t file_dataspace = H5I_INVALID_HID; - - /* - * ------------------------------------ - * Setup Dataset Creation Property List - * ------------------------------------ - */ - - dcpl_id = H5Pcreate(H5P_DATASET_CREATE); - - /* - * REQUIRED: Dataset chunking must be enabled to - * apply a data filter to the dataset. - * Chunks in the dataset are of size - * EXAMPLE_DSET_CHUNK_DIM_SIZE x EXAMPLE_DSET_CHUNK_DIM_SIZE. - */ - chunk_dims[0] = EXAMPLE_DSET_CHUNK_DIM_SIZE; - chunk_dims[1] = EXAMPLE_DSET_CHUNK_DIM_SIZE; - H5Pset_chunk(dcpl_id, EXAMPLE_DSET_DIMS, chunk_dims); - - /* Set filter to be applied to created datasets */ - set_filter(dcpl_id); - - /* - * ------------------------------------ - * Define the dimensions of the dataset - * and create it - * ------------------------------------ - */ - - /* - * Create a dataset composed of 4 chunks - * per MPI rank. The first dataset dimension - * scales according to the number of MPI ranks. - * The second dataset dimension stays fixed - * according to the chunk size. - */ - dataset_dims[0] = EXAMPLE_DSET_CHUNK_DIM_SIZE * mpi_size; - dataset_dims[1] = 4 * EXAMPLE_DSET_CHUNK_DIM_SIZE; - - file_dataspace = H5Screate_simple(EXAMPLE_DSET_DIMS, dataset_dims, NULL); - - /* Create the dataset */ - dset_id = H5Dcreate2(file_id, EXAMPLE_DSET_NAME, HDF5_DATATYPE, file_dataspace, H5P_DEFAULT, dcpl_id, - H5P_DEFAULT); - - /* - * ------------------------------------ - * Setup selection in the dataset for - * each MPI rank - * ------------------------------------ - */ - - /* - * Odd rank value MPI ranks do not - * contribute any data to the dataset. - */ - no_selection = (mpi_rank % 2) == 1; - - if (no_selection) { - /* - * MPI ranks not contributing data to - * the dataset should call H5Sselect_none - * on the file dataspace that will be - * passed to H5Dwrite. - */ - H5Sselect_none(file_dataspace); - } - else { - /* - * Even MPI ranks contribute data to - * the dataset. Each MPI rank's selection - * covers a single chunk in the first dataset - * dimension. Each MPI rank's selection - * covers 4 chunks in the second dataset - * dimension. This leads to each contributing - * MPI rank writing to 4 chunks of the dataset. - */ - start[0] = mpi_rank * EXAMPLE_DSET_CHUNK_DIM_SIZE; - start[1] = 0; - stride[0] = 1; - stride[1] = 1; - count[0] = EXAMPLE_DSET_CHUNK_DIM_SIZE; - count[1] = 4 * EXAMPLE_DSET_CHUNK_DIM_SIZE; - - H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, NULL); - - /* - * -------------------------------------- - * Fill data buffer with MPI rank's rank - * value to make it easy to see which - * part of the dataset each rank wrote to - * -------------------------------------- - */ - - fill_databuf(start, count, stride, &data[0][0]); - } - - /* - * --------------------------------- - * Write to the dataset collectively - * --------------------------------- - */ - - H5Dwrite(dset_id, HDF5_DATATYPE, no_selection ? H5S_ALL : H5S_BLOCK, file_dataspace, dxpl_id, data); - - /* - * -------------- - * Close HDF5 IDs - * -------------- - */ - - H5Sclose(file_dataspace); - H5Pclose(dcpl_id); - H5Dclose(dset_id); -} - -int -main(int argc, char **argv) -{ - MPI_Comm comm = MPI_COMM_WORLD; - MPI_Info info = MPI_INFO_NULL; - hid_t file_id = H5I_INVALID_HID; - hid_t fapl_id = H5I_INVALID_HID; - hid_t dxpl_id = H5I_INVALID_HID; - char *par_prefix = NULL; - char filename[PATH_MAX]; - - MPI_Init(&argc, &argv); - MPI_Comm_size(comm, &mpi_size); - MPI_Comm_rank(comm, &mpi_rank); - - /* - * ---------------------------------- - * Start parallel access to HDF5 file - * ---------------------------------- - */ - - /* Setup File Access Property List with parallel I/O access */ - fapl_id = H5Pcreate(H5P_FILE_ACCESS); - H5Pset_fapl_mpio(fapl_id, comm, info); - - /* - * OPTIONAL: Set collective metadata reads on FAPL to allow - * parallel writes to filtered datasets to perform - * better at scale. While not strictly necessary, - * this is generally recommended. - */ - H5Pset_all_coll_metadata_ops(fapl_id, true); - - /* - * OPTIONAL: Set the latest file format version for HDF5 in - * order to gain access to different dataset chunk - * index types and better data encoding methods. - * While not strictly necessary, this is generally - * recommended. - */ - H5Pset_libver_bounds(fapl_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST); - - /* Parse any parallel prefix and create filename */ - par_prefix = getenv("HDF5_PARAPREFIX"); - - snprintf(filename, PATH_MAX, "%s%s%s", par_prefix ? par_prefix : "", par_prefix ? "/" : "", EXAMPLE_FILE); - - /* Create HDF5 file */ - file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id); - - /* - * -------------------------------------- - * Setup Dataset Transfer Property List - * with collective I/O - * -------------------------------------- - */ - - dxpl_id = H5Pcreate(H5P_DATASET_XFER); - - /* - * REQUIRED: Setup collective I/O for the dataset - * write operations. Parallel writes to - * filtered datasets MUST be collective, - * even if some ranks have no data to - * contribute to the write operation. - */ - H5Pset_dxpl_mpio(dxpl_id, H5FD_MPIO_COLLECTIVE); - - /* - * -------------------------------- - * Create and write to the dataset - * -------------------------------- - */ - - /* - * Write to a dataset in a fashion where no - * chunks in the dataset are written to by - * more than 1 MPI rank and some MPI ranks - * have nothing to contribute to the dataset. - * In this case, the MPI ranks that have no - * data to contribute must still participate - * in the collective H5Dwrite call, but should - * call H5Sselect_none on the file dataspace - * passed to the H5Dwrite call. - */ - write_dataset_some_no_sel(file_id, dxpl_id); - - /* - * ------------------ - * Close all HDF5 IDs - * ------------------ - */ - - H5Pclose(dxpl_id); - H5Pclose(fapl_id); - H5Fclose(file_id); - - printf("PHDF5 example finished with no errors\n"); - - /* - * ------------------------------------ - * Cleanup created HDF5 file and finish - * ------------------------------------ - */ - - cleanup(filename); - - MPI_Finalize(); - - return 0; -} - -#else - -int -main(void) -{ - printf("HDF5 not configured with parallel support or parallel filtered writes are disabled!\n"); - return 0; -} - -#endif diff --git a/examples/ph5_subfiling.c b/examples/ph5_subfiling.c deleted file mode 100644 index f9c3322..0000000 --- a/examples/ph5_subfiling.c +++ /dev/null @@ -1,551 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * Copyright by The HDF Group. * - * All rights reserved. * - * * - * This file is part of HDF5. The full HDF5 copyright notice, including * - * terms governing use, modification, and redistribution, is contained in * - * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://www.hdfgroup.org/licenses. * - * If you do not have access to either file, you may request a copy from * - * help@hdfgroup.org. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/* - * Example of using HDF5's Subfiling VFD to write to an - * HDF5 file that is striped across multiple subfiles - * - * If the HDF5_NOCLEANUP environment variable is set, the - * files that this example creates will not be removed as - * the example finishes. - * - * In general, the current working directory in which compiling - * is done, is not suitable for parallel I/O and there is no - * standard pathname for parallel file systems. In some cases, - * the parallel file name may even need some parallel file type - * prefix such as: "pfs:/GF/...". Therefore, this example parses - * the HDF5_PARAPREFIX environment variable for a prefix, if one - * is needed. - */ - -#include <stdlib.h> - -#include "hdf5.h" - -#if defined(H5_HAVE_PARALLEL) && defined(H5_HAVE_SUBFILING_VFD) - -#define EXAMPLE_FILE "h5_subfiling_default_example.h5" -#define EXAMPLE_FILE2 "h5_subfiling_custom_example.h5" -#define EXAMPLE_FILE3 "h5_subfiling_precreate_example.h5" - -#define EXAMPLE_DSET_NAME "DSET" -#define EXAMPLE_DSET_DIMS 2 - -/* Have each MPI rank write 16MiB of data */ -#define EXAMPLE_DSET_NY 4194304 - -/* Dataset datatype */ -#define EXAMPLE_DSET_DATATYPE H5T_NATIVE_INT -typedef int EXAMPLE_DSET_C_DATATYPE; - -/* Cleanup created files */ -static void -cleanup(char *filename, hid_t fapl_id) -{ - bool do_cleanup = getenv(HDF5_NOCLEANUP) ? false : true; - - if (do_cleanup) - H5Fdelete(filename, fapl_id); -} - -/* - * An example of using the HDF5 Subfiling VFD with - * its default settings of 1 subfile per node, with - * a stripe size of 32MiB - */ -static void -subfiling_write_default(hid_t fapl_id, int mpi_size, int mpi_rank) -{ - EXAMPLE_DSET_C_DATATYPE *data; - hsize_t dset_dims[EXAMPLE_DSET_DIMS]; - hsize_t start[EXAMPLE_DSET_DIMS]; - hsize_t count[EXAMPLE_DSET_DIMS]; - hid_t file_id; - hid_t subfiling_fapl; - hid_t dset_id; - hid_t filespace; - char filename[512]; - char *par_prefix; - - /* - * Make a copy of the FAPL so we don't disturb - * it for the other examples - */ - subfiling_fapl = H5Pcopy(fapl_id); - - /* - * Set Subfiling VFD on FAPL using default settings - * (use IOC VFD, 1 IOC per node, 32MiB stripe size) - * - * Note that all of Subfiling's configuration settings - * can be adjusted with environment variables as well - * in this case. - */ - H5Pset_fapl_subfiling(subfiling_fapl, NULL); - - /* - * OPTIONAL: Set alignment of objects in HDF5 file to - * be equal to the Subfiling stripe size. - * Choosing a Subfiling stripe size and HDF5 - * object alignment value that are some - * multiple of the disk block size can - * generally help performance by ensuring - * that I/O is well-aligned and doesn't - * excessively cross stripe boundaries. - * - * Note that this option can substantially - * increase the size of the resulting HDF5 - * files, so it is a good idea to keep an eye - * on this. - */ - H5Pset_alignment(subfiling_fapl, 0, 33554432); /* Align to default 32MiB stripe size */ - - /* Parse any parallel prefix and create filename */ - par_prefix = getenv("HDF5_PARAPREFIX"); - - snprintf(filename, sizeof(filename), "%s%s%s", par_prefix ? par_prefix : "", par_prefix ? "/" : "", - EXAMPLE_FILE); - - /* - * Create a new file collectively - */ - file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, subfiling_fapl); - - /* - * Create the dataspace for the dataset. The first - * dimension varies with the number of MPI ranks - * while the second dimension is fixed. - */ - dset_dims[0] = mpi_size; - dset_dims[1] = EXAMPLE_DSET_NY; - filespace = H5Screate_simple(EXAMPLE_DSET_DIMS, dset_dims, NULL); - - /* - * Create the dataset with default properties - */ - dset_id = H5Dcreate2(file_id, EXAMPLE_DSET_NAME, EXAMPLE_DSET_DATATYPE, filespace, H5P_DEFAULT, - H5P_DEFAULT, H5P_DEFAULT); - - /* - * Each MPI rank writes from a contiguous memory - * region to the hyperslab in the file - */ - start[0] = mpi_rank; - start[1] = 0; - count[0] = 1; - count[1] = dset_dims[1]; - H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, NULL, count, NULL); - - /* - * Initialize data buffer - */ - data = malloc(count[0] * count[1] * sizeof(EXAMPLE_DSET_C_DATATYPE)); - for (size_t i = 0; i < count[0] * count[1]; i++) { - data[i] = mpi_rank + i; - } - - /* - * Write to dataset - */ - H5Dwrite(dset_id, EXAMPLE_DSET_DATATYPE, H5S_BLOCK, filespace, H5P_DEFAULT, data); - - /* - * Close/release resources. - */ - - free(data); - - H5Dclose(dset_id); - H5Sclose(filespace); - H5Fclose(file_id); - - cleanup(EXAMPLE_FILE, subfiling_fapl); - - H5Pclose(subfiling_fapl); -} - -/* - * An example of using the HDF5 Subfiling VFD with - * custom settings - */ -static void -subfiling_write_custom(hid_t fapl_id, int mpi_size, int mpi_rank) -{ - EXAMPLE_DSET_C_DATATYPE *data; - H5FD_subfiling_config_t subf_config; - H5FD_ioc_config_t ioc_config; - hsize_t dset_dims[EXAMPLE_DSET_DIMS]; - hsize_t start[EXAMPLE_DSET_DIMS]; - hsize_t count[EXAMPLE_DSET_DIMS]; - hid_t file_id; - hid_t subfiling_fapl; - hid_t dset_id; - hid_t filespace; - char filename[512]; - char *par_prefix; - - /* - * Make a copy of the FAPL so we don't disturb - * it for the other examples - */ - subfiling_fapl = H5Pcopy(fapl_id); - - /* - * Get a default Subfiling and IOC configuration - */ - H5Pget_fapl_subfiling(subfiling_fapl, &subf_config); - H5Pget_fapl_ioc(subfiling_fapl, &ioc_config); - - /* - * Set Subfiling configuration to use a 1MiB - * stripe size and the SELECT_IOC_EVERY_NTH_RANK - * selection method. By default, without a setting - * in the H5FD_SUBFILING_IOC_SELECTION_CRITERIA - * environment variable, this will use every MPI - * rank as an I/O concentrator. - */ - subf_config.shared_cfg.stripe_size = 1048576; - subf_config.shared_cfg.ioc_selection = SELECT_IOC_EVERY_NTH_RANK; - - /* - * Set IOC configuration to use 2 worker threads - * per IOC instead of the default setting and - * update IOC configuration with new subfiling - * configuration. - */ - ioc_config.thread_pool_size = 2; - - /* - * Set our new configuration on the IOC - * FAPL used for Subfiling - */ - H5Pset_fapl_ioc(subf_config.ioc_fapl_id, &ioc_config); - - /* - * Finally, set our new Subfiling configuration - * on the original FAPL - */ - H5Pset_fapl_subfiling(subfiling_fapl, &subf_config); - - /* - * OPTIONAL: Set alignment of objects in HDF5 file to - * be equal to the Subfiling stripe size. - * Choosing a Subfiling stripe size and HDF5 - * object alignment value that are some - * multiple of the disk block size can - * generally help performance by ensuring - * that I/O is well-aligned and doesn't - * excessively cross stripe boundaries. - * - * Note that this option can substantially - * increase the size of the resulting HDF5 - * files, so it is a good idea to keep an eye - * on this. - */ - H5Pset_alignment(subfiling_fapl, 0, 1048576); /* Align to custom 1MiB stripe size */ - - /* Parse any parallel prefix and create filename */ - par_prefix = getenv("HDF5_PARAPREFIX"); - - snprintf(filename, sizeof(filename), "%s%s%s", par_prefix ? par_prefix : "", par_prefix ? "/" : "", - EXAMPLE_FILE2); - - /* - * Create a new file collectively - */ - file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, subfiling_fapl); - - /* - * Create the dataspace for the dataset. The first - * dimension varies with the number of MPI ranks - * while the second dimension is fixed. - */ - dset_dims[0] = mpi_size; - dset_dims[1] = EXAMPLE_DSET_NY; - filespace = H5Screate_simple(EXAMPLE_DSET_DIMS, dset_dims, NULL); - - /* - * Create the dataset with default properties - */ - dset_id = H5Dcreate2(file_id, EXAMPLE_DSET_NAME, EXAMPLE_DSET_DATATYPE, filespace, H5P_DEFAULT, - H5P_DEFAULT, H5P_DEFAULT); - - /* - * Each MPI rank writes from a contiguous memory - * region to the hyperslab in the file - */ - start[0] = mpi_rank; - start[1] = 0; - count[0] = 1; - count[1] = dset_dims[1]; - H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, NULL, count, NULL); - - /* - * Initialize data buffer - */ - data = malloc(count[0] * count[1] * sizeof(EXAMPLE_DSET_C_DATATYPE)); - for (size_t i = 0; i < count[0] * count[1]; i++) { - data[i] = mpi_rank + i; - } - - /* - * Write to dataset - */ - H5Dwrite(dset_id, EXAMPLE_DSET_DATATYPE, H5S_BLOCK, filespace, H5P_DEFAULT, data); - - /* - * Close/release resources. - */ - - free(data); - - H5Dclose(dset_id); - H5Sclose(filespace); - H5Fclose(file_id); - - cleanup(EXAMPLE_FILE2, subfiling_fapl); - - H5Pclose(subfiling_fapl); -} - -/* - * An example of pre-creating an HDF5 file on MPI rank - * 0 when using the HDF5 Subfiling VFD. In this case, - * the subfiling stripe count must be set so that rank - * 0 knows how many subfiles to pre-create. - */ -static void -subfiling_write_precreate(hid_t fapl_id, int mpi_size, int mpi_rank) -{ - EXAMPLE_DSET_C_DATATYPE *data; - H5FD_subfiling_config_t subf_config; - hsize_t dset_dims[EXAMPLE_DSET_DIMS]; - hsize_t start[EXAMPLE_DSET_DIMS]; - hsize_t count[EXAMPLE_DSET_DIMS]; - hid_t file_id; - hid_t subfiling_fapl; - hid_t dset_id; - hid_t filespace; - char filename[512]; - char *par_prefix; - - /* - * Make a copy of the FAPL so we don't disturb - * it for the other examples - */ - subfiling_fapl = H5Pcopy(fapl_id); - - /* - * Get a default Subfiling and IOC configuration - */ - H5Pget_fapl_subfiling(subfiling_fapl, &subf_config); - - /* - * Set the Subfiling stripe count so that rank - * 0 knows how many subfiles the logical HDF5 - * file should consist of. In this case, use - * 5 subfiles with a default stripe size of - * 32MiB. - */ - subf_config.shared_cfg.stripe_count = 5; - - /* - * OPTIONAL: Set alignment of objects in HDF5 file to - * be equal to the Subfiling stripe size. - * Choosing a Subfiling stripe size and HDF5 - * object alignment value that are some - * multiple of the disk block size can - * generally help performance by ensuring - * that I/O is well-aligned and doesn't - * excessively cross stripe boundaries. - * - * Note that this option can substantially - * increase the size of the resulting HDF5 - * files, so it is a good idea to keep an eye - * on this. - */ - H5Pset_alignment(subfiling_fapl, 0, 1048576); /* Align to custom 1MiB stripe size */ - - /* Parse any parallel prefix and create filename */ - par_prefix = getenv("HDF5_PARAPREFIX"); - - snprintf(filename, sizeof(filename), "%s%s%s", par_prefix ? par_prefix : "", par_prefix ? "/" : "", - EXAMPLE_FILE3); - - /* Set dataset dimensionality */ - dset_dims[0] = mpi_size; - dset_dims[1] = EXAMPLE_DSET_NY; - - if (mpi_rank == 0) { - /* - * Make sure only this rank opens the file - */ - H5Pset_mpi_params(subfiling_fapl, MPI_COMM_SELF, MPI_INFO_NULL); - - /* - * Set the Subfiling VFD on our FAPL using - * our custom configuration - */ - H5Pset_fapl_subfiling(subfiling_fapl, &subf_config); - - /* - * Create a new file on rank 0 - */ - file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, subfiling_fapl); - - /* - * Create the dataspace for the dataset. The first - * dimension varies with the number of MPI ranks - * while the second dimension is fixed. - */ - filespace = H5Screate_simple(EXAMPLE_DSET_DIMS, dset_dims, NULL); - - /* - * Create the dataset with default properties - */ - dset_id = H5Dcreate2(file_id, EXAMPLE_DSET_NAME, EXAMPLE_DSET_DATATYPE, filespace, H5P_DEFAULT, - H5P_DEFAULT, H5P_DEFAULT); - - /* - * Initialize data buffer - */ - data = malloc(dset_dims[0] * dset_dims[1] * sizeof(EXAMPLE_DSET_C_DATATYPE)); - for (size_t i = 0; i < dset_dims[0] * dset_dims[1]; i++) { - data[i] = i; - } - - /* - * Rank 0 writes to the whole dataset - */ - H5Dwrite(dset_id, EXAMPLE_DSET_DATATYPE, H5S_BLOCK, filespace, H5P_DEFAULT, data); - - /* - * Close/release resources. - */ - - free(data); - - H5Dclose(dset_id); - H5Sclose(filespace); - H5Fclose(file_id); - } - - MPI_Barrier(MPI_COMM_WORLD); - - /* - * Use all MPI ranks to re-open the file and - * read back the dataset that was created - */ - H5Pset_mpi_params(subfiling_fapl, MPI_COMM_WORLD, MPI_INFO_NULL); - - /* - * Use the same subfiling configuration as rank 0 - * used to create the file - */ - H5Pset_fapl_subfiling(subfiling_fapl, &subf_config); - - /* - * Re-open the file on all ranks - */ - file_id = H5Fopen(filename, H5F_ACC_RDONLY, subfiling_fapl); - - /* - * Open the dataset that was created - */ - dset_id = H5Dopen2(file_id, EXAMPLE_DSET_NAME, H5P_DEFAULT); - - /* - * Initialize data buffer - */ - data = malloc(dset_dims[0] * dset_dims[1] * sizeof(EXAMPLE_DSET_C_DATATYPE)); - - /* - * Read the dataset on all ranks - */ - H5Dread(dset_id, EXAMPLE_DSET_DATATYPE, H5S_BLOCK, H5S_ALL, H5P_DEFAULT, data); - - /* - * Close/release resources. - */ - - free(data); - - H5Dclose(dset_id); - H5Fclose(file_id); - - cleanup(EXAMPLE_FILE3, subfiling_fapl); - - H5Pclose(subfiling_fapl); -} - -int -main(int argc, char **argv) -{ - MPI_Comm comm = MPI_COMM_WORLD; - MPI_Info info = MPI_INFO_NULL; - hid_t fapl_id; - int mpi_size; - int mpi_rank; - int mpi_thread_required = MPI_THREAD_MULTIPLE; - int mpi_thread_provided = 0; - - /* HDF5 Subfiling VFD requires MPI_Init_thread with MPI_THREAD_MULTIPLE */ - MPI_Init_thread(&argc, &argv, mpi_thread_required, &mpi_thread_provided); - if (mpi_thread_provided < mpi_thread_required) { - printf("MPI_THREAD_MULTIPLE not supported\n"); - MPI_Abort(comm, -1); - } - - MPI_Comm_size(comm, &mpi_size); - MPI_Comm_rank(comm, &mpi_rank); - - /* - * Set up File Access Property List with MPI - * parameters for the Subfiling VFD to use - */ - fapl_id = H5Pcreate(H5P_FILE_ACCESS); - H5Pset_mpi_params(fapl_id, comm, info); - - /* Use Subfiling VFD with default settings */ - subfiling_write_default(fapl_id, mpi_size, mpi_rank); - - /* Use Subfiling VFD with custom settings */ - subfiling_write_custom(fapl_id, mpi_size, mpi_rank); - - /* - * Use Subfiling VFD to precreate the HDF5 - * file on MPI rank 0 - */ - subfiling_write_precreate(fapl_id, mpi_size, mpi_rank); - - H5Pclose(fapl_id); - - if (mpi_rank == 0) - printf("PHDF5 example finished with no errors\n"); - - MPI_Finalize(); - - return 0; -} - -#else - -/* dummy program since HDF5 is not parallel-enabled */ -int -main(void) -{ - printf( - "Example program cannot run - HDF5 must be built with parallel support and Subfiling VFD support\n"); - return 0; -} - -#endif /* H5_HAVE_PARALLEL && H5_HAVE_SUBFILING_VFD */ diff --git a/examples/run-c-ex.sh.in b/examples/run-c-ex.sh.in index aae1d34..b51c5d6 100644 --- a/examples/run-c-ex.sh.in +++ b/examples/run-c-ex.sh.in @@ -155,23 +155,7 @@ then HDF5_DEBUG=$OLD_DEBUG_STRING &&\ rm h5_debug_trace &&\ RunTest h5_shared_mesg &&\ - rm h5_shared_mesg &&\ - RunTest h5_vds-eiger &&\ - rm h5_vds-eiger &&\ - RunTest h5_vds-exclim &&\ - rm h5_vds-exclim &&\ - RunTest h5_vds-exc &&\ - rm h5_vds-exc &&\ - RunTest h5_vds-simpleIO &&\ - rm h5_vds-simpleIO &&\ - RunTest h5_vds-percival &&\ - rm h5_vds-percival &&\ - RunTest h5_vds-percival-unlim &&\ - rm h5_vds-percival-unlim &&\ - RunTest h5_vds-percival-unlim-maxmin&&\ - rm h5_vds-percival-unlim-maxmin &&\ - RunTest h5_vds &&\ - rm h5_vds); then + rm h5_shared_mesg); then EXIT_VALUE=${EXIT_SUCCESS} else EXIT_VALUE=${EXIT_FAILURE} |