diff options
Diffstat (limited to 'examples')
| -rw-r--r-- | examples/CMakeLists.txt | 8 | ||||
| -rw-r--r-- | examples/CMakeTests.cmake | 12 | ||||
| -rw-r--r-- | examples/Makefile.am | 16 | ||||
| -rw-r--r-- | examples/Makefile.in | 1395 | ||||
| -rw-r--r-- | examples/h5_vds-eiger.c | 177 | ||||
| -rw-r--r-- | examples/h5_vds-exc.c | 226 | ||||
| -rw-r--r-- | examples/h5_vds-exclim.c | 222 | ||||
| -rw-r--r-- | examples/h5_vds-percival-unlim-maxmin.c | 309 | ||||
| -rw-r--r-- | examples/h5_vds-percival-unlim.c | 352 | ||||
| -rw-r--r-- | examples/h5_vds-percival.c | 242 | ||||
| -rw-r--r-- | examples/h5_vds-simpleIO.c | 184 | ||||
| -rw-r--r-- | examples/h5_vds.c | 267 | ||||
| -rw-r--r-- | examples/run-c-ex.sh.in | 18 |
13 files changed, 3425 insertions, 3 deletions
diff --git a/examples/CMakeLists.txt b/examples/CMakeLists.txt index 7953161..8849ce7 100644 --- a/examples/CMakeLists.txt +++ b/examples/CMakeLists.txt @@ -34,6 +34,14 @@ set (examples h5_extlink h5_elink_unix2win h5_shared_mesg + 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 ) foreach (example ${examples}) diff --git a/examples/CMakeTests.cmake b/examples/CMakeTests.cmake index 42b42b3..2cf82b8 100644 --- a/examples/CMakeTests.cmake +++ b/examples/CMakeTests.cmake @@ -46,6 +46,18 @@ blue/prefix_target.h5 red/prefix_target.h5 u2w/u2w_target.h5 + vds.h5 + vds-excalibur.h5 + vds-exclim.h5 + vds-percival.h5 + vds-percival-unlim.h5 + vds-percival-unlim-maxmin.h5 + a.h5 + b.h5 + c.h5 + d.h5 + vds-simpleIO.h5 + vds-eiger.h5 ) if (NOT "${last_test}" STREQUAL "") set_tests_properties (EXAMPLES-clear-objects PROPERTIES DEPENDS ${last_test}) diff --git a/examples/Makefile.am b/examples/Makefile.am index 5d0da93..883b99d 100644 --- a/examples/Makefile.am +++ b/examples/Makefile.am @@ -37,7 +37,9 @@ EXAMPLE_PROG = h5_write h5_read h5_extend_write h5_chunk_read h5_compound \ h5_crtgrpd h5_subset h5_cmprss h5_rdwt h5_crtgrpar h5_extend \ h5_crtatt h5_crtgrp h5_crtdat \ h5_group h5_select h5_attribute h5_mount h5_reference h5_drivers \ - h5_ref2reg h5_extlink h5_elink_unix2win h5_shared_mesg + h5_ref2reg h5_extlink h5_elink_unix2win h5_shared_mesg h5_vds h5_vds-exc \ + h5_vds-exclim h5_vds-eiger h5_vds-simpleIO h5_vds-percival \ + h5_vds-percival-unlim h5_vds-percival-unlim-maxmin TEST_SCRIPT=testh5cc.sh TEST_EXAMPLES_SCRIPT=$(INSTALL_SCRIPT_FILES) @@ -48,7 +50,9 @@ INSTALL_FILES = h5_write.c h5_read.c h5_extend_write.c h5_chunk_read.c \ h5_extend.c h5_crtatt.c h5_crtgrp.c h5_crtdat.c \ h5_compound.c h5_group.c h5_select.c h5_attribute.c h5_mount.c \ h5_reference.c h5_drivers.c h5_extlink.c h5_elink_unix2win.c \ - h5_ref2reg.c h5_shared_mesg.c ph5example.c + h5_ref2reg.c h5_shared_mesg.c ph5example.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 @@ -117,6 +121,14 @@ 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/Makefile.in b/examples/Makefile.in new file mode 100644 index 0000000..1b3520b --- /dev/null +++ b/examples/Makefile.in @@ -0,0 +1,1395 @@ +# Makefile.in generated by automake 1.15 from Makefile.am. +# @configure_input@ + +# Copyright (C) 1994-2014 Free Software Foundation, Inc. + +# This Makefile.in is free software; the Free Software Foundation +# gives unlimited permission to copy and/or distribute it, +# with or without modifications, as long as this notice is preserved. + +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY, to the extent permitted by law; without +# even the implied warranty of MERCHANTABILITY or FITNESS FOR A +# PARTICULAR PURPOSE. + +@SET_MAKE@ + +# +# Copyright by The HDF Group. +# Copyright by the Board of Trustees of the University of Illinois. +# All rights reserved. +# +# This file is part of HDF5. 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Serialize them. +h5_rdwt.chkexe_: h5_crtdat.chkexe_ +h5_crtatt.chkexe_: h5_rdwt.chkexe_ + +$(EXTLINK_DIRS): + echo $(mkdir_p) $@ + $(mkdir_p) $@ + +# List dependencies for each program. Normally, automake would take +# care of this for us, but if we tell automake about the programs it +# will try to build them with the normal C compiler, not h5cc. This is +# an inelegant way of solving the problem. +# All programs share the same build rule and a dependency on the main hdf5 +# library above. +h5_chunk_read: $(srcdir)/h5_chunk_read.c +h5_compound: $(srcdir)/h5_compound.c +h5_crtgrpd: $(srcdir)/h5_crtgrpd.c +h5_subset: $(srcdir)/h5_subset.c +h5_cmprss: $(srcdir)/h5_cmprss.c +h5_rdwt: $(srcdir)/h5_rdwt.c +h5_crtgrpar: $(srcdir)/h5_crtgrpar.c +h5_extend: $(srcdir)/h5_extend.c +h5_crtatt: $(srcdir)/h5_crtatt.c +h5_crtgrp: $(srcdir)/h5_crtgrp.c +h5_crtdat: $(srcdir)/h5_crtdat.c +h5_extend_write: $(srcdir)/h5_extend_write.c +h5_group: $(srcdir)/h5_group.c +h5_write: $(srcdir)/h5_write.c +h5_read: $(srcdir)/h5_read.c +h5_select: $(srcdir)/h5_select.c +h5_attribute: $(srcdir)/h5_attribute.c +h5_mount: $(srcdir)/h5_mount.c +h5_reference: $(srcdir)/h5_reference.c +h5_ref2reg: $(srcdir)/h5_ref2reg.c +h5_drivers: $(srcdir)/h5_drivers.c +ph5example: $(srcdir)/ph5example.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: $(srcdir)/h5_vds-percival-unlim-maxmin.c + +# How to create EXAMPLEDIR if it doesn't already exist +$(EXAMPLEDIR): + -$(top_srcdir)/bin/mkdirs $@ +$(EXAMPLETOPDIR): + -$(top_srcdir)/bin/mkdirs $@ + +# Install and uninstall rules. We install the source files, not the +# example programs themselves. +install-data-local: + @$(MAKE) $(AM_MAKEFLAGS) install-examples +uninstall-local: + @$(MAKE) $(AM_MAKEFLAGS) uninstall-examples + +install-examples: $(EXAMPLEDIR) $(INSTALL_FILES) + @for f in X $(INSTALL_FILES); do \ + if test $$f != X; then \ + (set -x; $(INSTALL) $(srcdir)/$$f $(EXAMPLEDIR)/. || exit 1); \ + chmod a-x $(EXAMPLEDIR)/$$f; \ + fi; \ + done + @for f in X $(INSTALL_SCRIPT_FILES); do \ + if test $$f != X; then \ + (set -x; $(INSTALL) $$f $(EXAMPLEDIR)/. || exit 1);\ + fi; \ + done + @for f in X $(INSTALL_TOP_FILES); do \ + if test $$f != X; then \ + (set -x; $(INSTALL) $(srcdir)/$$f $(EXAMPLETOPDIR)/. || exit 1); \ + chmod a-x $(EXAMPLETOPDIR)/$$f;\ + fi; \ + done + @for f in X $(INSTALL_TOP_SCRIPT_FILES); do \ + if test $$f != X; then \ + (set -x; $(INSTALL) $(srcdir)/$$f $(EXAMPLETOPDIR)/. || exit 1); \ + fi; \ + done + +uninstall-examples: + @if test -n "$(INSTALL_FILES)" -a -d $(EXAMPLEDIR); then \ + set -x; cd $(EXAMPLEDIR) && $(RM) $(INSTALL_FILES); \ + fi + @if test -n "$(INSTALL_SCRIPT_FILES)" -a -d $(EXAMPLEDIR); then \ + set -x; cd $(EXAMPLEDIR) && $(RM) $(INSTALL_SCRIPT_FILES); \ + fi + @if test -n "$(INSTALL_TOP_FILES)" -a -d $(EXAMPLETOPDIR); then \ + set -x; cd $(EXAMPLETOPDIR) && $(RM) $(INSTALL_TOP_FILES); \ + fi + @if test -n "$(INSTALL_TOP_SCRIPT_FILES)" -a -d $(EXAMPLETOPDIR); then \ + set -x; cd $(EXAMPLETOPDIR) && $(RM) $(INSTALL_TOP_SCRIPT_FILES); \ + fi + +installcheck-local: + @if test "$(STATIC_SHARED)" = "static, shared"; then \ + H5CCFLAGS="-shlib" $(MAKE) $(AM_MAKEFLAGS) check; \ + $(MAKE) $(AM_MAKEFLAGS) clean; \ + H5CCFLAGS="" $(MAKE) $(AM_MAKEFLAGS) check; \ + elif test "$(STATIC_SHARED)" = "shared"; then \ + H5CCFLAGS="-shlib" $(MAKE) $(AM_MAKEFLAGS) check; \ + else \ + $(MAKE) $(AM_MAKEFLAGS) check; \ + fi + @if test "$(INSTALL_FILES)" -a $(TEST_EXAMPLES_SCRIPT) -a -d $(EXAMPLEDIR); then \ + echo "============================"; \ + echo "Testing $(TEST_EXAMPLES_SCRIPT)"; \ + echo "============================"; \ + (cd $(EXAMPLEDIR); \ + /bin/sh ./$(TEST_EXAMPLES_SCRIPT);) \ + fi + +# lib/progs/tests targets recurse into subdirectories. build-* targets +# build files in this directory. +build-lib: $(LIB) +build-progs: $(LIB) $(PROGS) +build-tests: $(LIB) $(PROGS) $(chk_TESTS) + +# General rule for recursive building targets. +# BUILT_SOURCES contain targets that need to be built before anything else +# in the directory (e.g., for Fortran type detection) +lib progs tests check-s check-p :: $(BUILT_SOURCES) + @$(MAKE) $(AM_MAKEFLAGS) build-$@ || exit 1; + @for d in X $(SUBDIRS); do \ + if test $$d != X && test $$d != .; then \ + (set -x; cd $$d && $(MAKE) $(AM_MAKEFLAGS) $@) || exit 1; \ + fi; \ + done + +# General rule for recursive cleaning targets. Like the rule above, +# but doesn't require building BUILT_SOURCES. +check-clean :: + @$(MAKE) $(AM_MAKEFLAGS) build-$@ || exit 1; + @for d in X $(SUBDIRS); do \ + if test $$d != X && test $$d != .; then \ + (set -x; cd $$d && $(MAKE) $(AM_MAKEFLAGS) $@) || exit 1; \ + fi; \ + done + +# Tell Automake to build tests when the user types `make all' (this is +# not its default behavior). Also build EXTRA_LIB and EXTRA_PROG since +# Automake won't build them automatically, either. +all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS) + +# make install-doc doesn't do anything outside of doc directory, but +# Makefiles should recognize it. +# UPDATE: docs no longer reside in this build tree, so this target +# is depreciated. +install-doc uninstall-doc: + @echo "Nothing to be done." + +# clean up files generated by tests so they can be re-run. +build-check-clean: + $(RM) -rf $(CHECK_CLEANFILES) + +# run check-clean whenever mostlyclean is run +mostlyclean-local: build-check-clean + +# check-install is just a synonym for installcheck +check-install: installcheck + +# Run each test in order, passing $(TEST_FLAGS) to the program. +# Since tests are done in a shell loop, "make -i" does apply inside it. +# Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop. +# The timestamps give a rough idea how much time the tests use. +# +# Note that targets in chk_TESTS (defined above) will be built when the user +# types 'make tests' or 'make check', but only programs in TEST_PROG, +# TEST_PROG_PARA, or TEST_SCRIPT will actually be executed. +check-TESTS: test + +test _test: + @$(MAKE) build-check-s + @$(MAKE) build-check-p + +# Actual execution of check-s. +build-check-s: $(LIB) $(PROGS) $(chk_TESTS) + @if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then \ + echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \ + fi + @$(MAKE) $(AM_MAKEFLAGS) _exec_check-s + @if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then \ + echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` ended `date`===";\ + fi + +_exec_check-s: $(TEST_PROG_CHKEXE) $(TEST_SCRIPT_CHKSH) + +# The dummy.chkexe here prevents the target from being +# empty if there are no tests in the current directory. +# $${log} is the log file. +# $${tname} is the name of test. +$(TEST_PROG_CHKEXE) $(TEST_PROG_PARA_CHKEXE) dummy.chkexe_: + @if test "X$@" != "X.chkexe_" && test "X$@" != "Xdummy.chkexe_"; then \ + tname=$(@:.chkexe_=)$(EXEEXT);\ + log=$(@:.chkexe_=.chklog); \ + echo "============================"; \ + if $(top_srcdir)/bin/newer $(@:.chkexe_=.chkexe) $${tname}; then \ + echo "No need to test $${tname} again."; \ + else \ + echo "============================" > $${log}; \ + if test "X$(FORTRAN_API)" = "Xyes"; then \ + echo "Fortran API: Testing $(HDF5_DRIVER) $${tname} $(TEST_FLAGS)"; 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then \ + cmd=$(@:.chkexe_=);\ + tname=`basename $$cmd`;\ + chkname=`basename $(@:.chkexe_=.chkexe)`;\ + log=`basename $(@:.chkexe_=.chklog)`; \ + echo "============================"; \ + if $(top_srcdir)/bin/newer $${chkname} $$cmd $(SCRIPT_DEPEND); then \ + echo "No need to test $${tname} again."; \ + else \ + echo "============================" > $${log}; \ + if test "X$(FORTRAN_API)" = "Xyes"; then \ + echo "Fortran API: Testing $${tname} $(TEST_FLAGS)"; \ + echo "Fortran API: $${tname} $(TEST_FLAGS) Test Log" >> $${log}; \ + elif test "X$(CXX_API)" = "Xyes"; then \ + echo "C++ API: Testing $${tname} $(TEST_FLAGS)"; \ + echo "C++ API: $${tname} $(TEST_FLAGS) Test Log" >> $${log}; \ + else \ + echo "Testing $${tname} $(TEST_FLAGS)"; \ + echo "$${tname} $(TEST_FLAGS) Test Log" >> $${log}; \ + fi; \ + echo "============================" >> $${log}; \ + RUNSERIAL="$(RUNSERIAL)" RUNPARALLEL="$(RUNPARALLEL)" \ + srcdir="$(srcdir)" \ + $(TIME) $(SHELL) $$cmd $(TEST_FLAGS) >> $${log} 2>&1 \ + && touch $${chkname} || \ + (test $$HDF5_Make_Ignore && echo "*** Error ignored") || \ + (cat $${log} && false) || exit 1; 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E.g.,"; \ + echo " HDF5_PARAPREFIX=/PFS/user/me"; \ + echo " export HDF5_PARAPREFIX"; \ + echo " make check"; \ + echo "**** end of Hint ****"; \ + fi + @for test in $(TEST_PROG_PARA) dummy; do \ + if test $$test != dummy; then \ + $(MAKE) $(AM_MAKEFLAGS) $$test.chkexe_ \ + RUNEXEC="$(RUNPARALLEL)" || exit 1; \ + fi; \ + done + @for test in $(TEST_SCRIPT_PARA) dummy; do \ + if test $$test != dummy; then \ + $(MAKE) $(AM_MAKEFLAGS) $$test.chkexe_ || exit 1; \ + fi; \ + done + @if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then \ + echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` ended `date`===";\ + fi + +# Run test with different Virtual File Driver +check-vfd: $(LIB) $(PROGS) $(chk_TESTS) + @for vfd in $(VFD_LIST) dummy; do \ + if test $$vfd != dummy; then \ + echo "============================"; \ + echo "Testing Virtual File Driver $$vfd"; \ + echo "============================"; \ + $(MAKE) $(AM_MAKEFLAGS) check-clean || exit 1; \ + HDF5_DRIVER=$$vfd $(MAKE) $(AM_MAKEFLAGS) check || exit 1; \ + fi; \ + done + +# Tell versions [3.59,3.63) of GNU make to not export all variables. +# Otherwise a system limit (for SysV at least) may be exceeded. +.NOEXPORT: diff --git a/examples/h5_vds-eiger.c b/examples/h5_vds-eiger.c new file mode 100644 index 0000000..ea22243 --- /dev/null +++ b/examples/h5_vds-eiger.c @@ -0,0 +1,177 @@ +/************************************************************ + + 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 virttual 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 new file mode 100644 index 0000000..039cdb8 --- /dev/null +++ b/examples/h5_vds-exc.c @@ -0,0 +1,226 @@ +/************************************************************ + + 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 */ + stride[3], + 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 virttual 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 new file mode 100644 index 0000000..4933471 --- /dev/null +++ b/examples/h5_vds-exclim.c @@ -0,0 +1,222 @@ +/************************************************************ + + 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 */ + stride[3], + 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 virttual 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 new file mode 100644 index 0000000..a6eecfb --- /dev/null +++ b/examples/h5_vds-percival-unlim-maxmin.c @@ -0,0 +1,309 @@ +/************************************************************ + + 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. Appen 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 virttual 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 new file mode 100644 index 0000000..b5f3ebd --- /dev/null +++ b/examples/h5_vds-percival-unlim.c @@ -0,0 +1,352 @@ +/************************************************************ + + 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 virttual 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 new file mode 100644 index 0000000..757bb69 --- /dev/null +++ b/examples/h5_vds-percival.c @@ -0,0 +1,242 @@ +/************************************************************ + + 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 virttual 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 new file mode 100644 index 0000000..b707ae4 --- /dev/null +++ b/examples/h5_vds-simpleIO.c @@ -0,0 +1,184 @@ +/************************************************************ + + 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 dimesnion 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 virttual 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 new file mode 100644 index 0000000..1e502c6 --- /dev/null +++ b/examples/h5_vds.c @@ -0,0 +1,267 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * Copyright by The HDF Group. * + * Copyright by the Board of Trustees of the University of Illinois. * + * 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 files COPYING and Copyright.html. COPYING can be found at the root * + * of the source code distribution tree; Copyright.html can be found at the * + * root level of an installed copy of the electronic HDF5 document set and * + * is linked from the top-level documents page. It can also be found at * + * http://hdfgroup.org/HDF5/doc/Copyright.html. 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 */ + stride[2], + 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; + 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 virttual 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++) { + printf("("); + for (k=0; k<RANK2-1; k++) + printf("%d,", (int)buf[k]); + printf("%d ) - (", (int)buf[k]); + for (k=0; k<RANK2-1; k++) + printf("%d,", (int)buf[RANK2+k]); + printf("%d)\n", (int)buf[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/run-c-ex.sh.in b/examples/run-c-ex.sh.in index 6b5d0f7..1661344 100644 --- a/examples/run-c-ex.sh.in +++ b/examples/run-c-ex.sh.in @@ -125,7 +125,23 @@ then RunTest h5_elink_unix2win &&\ rm h5_elink_unix2win &&\ RunTest h5_shared_mesg &&\ - rm h5_shared_mesg); then + 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 EXIT_VALUE=${EXIT_SUCCESS} else EXIT_VALUE=${EXIT_FAILURE} |