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authorRaymond Lu <songyulu@hdfgroup.org>2013-01-21 22:47:00 (GMT)
committerRaymond Lu <songyulu@hdfgroup.org>2013-01-21 22:47:00 (GMT)
commitbadedee44d8475964c5235a3435c50f45e148d5e (patch)
tree27743f130e9f212092c49a6bc0da9899859a239f
parent17f2fde031155047beaf003c00427e4f9787abc9 (diff)
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[svn-r23182] I'm merging the changes for DECTRIS project from the trunk (r23162).
Tested on koala, jam, ostrich.
Diffstat
-rw-r--r--MANIFEST5
-rw-r--r--hl/src/CMakeLists.txt2
-rw-r--r--hl/src/H5DO.c137
-rw-r--r--hl/src/H5DOprivate.h37
-rw-r--r--hl/src/H5DOpublic.h42
-rw-r--r--hl/src/Makefile.am4
-rw-r--r--hl/src/Makefile.in9
-rw-r--r--hl/src/hdf5_hl.h1
-rw-r--r--hl/test/CMakeLists.txt2
-rw-r--r--hl/test/Makefile.am5
-rw-r--r--hl/test/Makefile.in24
-rw-r--r--hl/test/dectris_hl_perf.c643
-rw-r--r--hl/test/test_dset_opt.c1138
-rw-r--r--hl/test/test_lite.c4
-rw-r--r--src/H5Dchunk.c102
-rw-r--r--src/H5Dio.c169
-rw-r--r--src/H5Dprivate.h3
-rw-r--r--src/H5Dpublic.h6
-rw-r--r--src/H5Pdxpl.c37
-rw-r--r--test/testfiles/err_compat_15
20 files changed, 2321 insertions, 54 deletions
diff --git a/MANIFEST b/MANIFEST
index c0184e0..f646867 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -1992,6 +1992,9 @@
./hl/src/COPYING
./hl/src/Makefile.am
./hl/src/Makefile.in
+./hl/src/H5DO.c
+./hl/src/H5DOprivate.h
+./hl/src/H5DOpublic.h
./hl/src/H5DS.c
./hl/src/H5DSprivate.h
./hl/src/H5DSpublic.h
@@ -2030,8 +2033,10 @@
./hl/test/image24plane.txt
./hl/test/pal_rgb.h
./hl/test/sepia.pal
+./hl/test/dectris_hl_perf.c
./hl/test/gen_test_ds.c
./hl/test/test_ds.c
+./hl/test/test_dset_opt.c
./hl/test/test_file_image.c
./hl/test/test_image.c
./hl/test/test_lite.c
diff --git a/hl/src/CMakeLists.txt b/hl/src/CMakeLists.txt
index 2df2c23..36547f0 100644
--- a/hl/src/CMakeLists.txt
+++ b/hl/src/CMakeLists.txt
@@ -14,6 +14,7 @@ ENDIF (BUILD_SHARED_LIBS)
INCLUDE_DIRECTORIES (${HDF5_HL_SRC_DIR}/src)
SET (HL_SRCS
+ ${HDF5_HL_SRC_SOURCE_DIR}/H5DO.c
${HDF5_HL_SRC_SOURCE_DIR}/H5DS.c
${HDF5_HL_SRC_SOURCE_DIR}/H5IM.c
${HDF5_HL_SRC_SOURCE_DIR}/H5LT.c
@@ -24,6 +25,7 @@ SET (HL_SRCS
)
SET (HL_HEADERS
+ ${HDF5_HL_SRC_SOURCE_DIR}/H5DOpublic.h
${HDF5_HL_SRC_SOURCE_DIR}/H5DSpublic.h
${HDF5_HL_SRC_SOURCE_DIR}/H5IMpublic.h
${HDF5_HL_SRC_SOURCE_DIR}/H5LTparse.h
diff --git a/hl/src/H5DO.c b/hl/src/H5DO.c
new file mode 100644
index 0000000..9cfd8c1
--- /dev/null
+++ b/hl/src/H5DO.c
@@ -0,0 +1,137 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+* 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. *
+* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+#include <string.h>
+#include <stdlib.h>
+#include <assert.h>
+#include <stdio.h>
+
+#include "H5DOprivate.h"
+
+/*-------------------------------------------------------------------------
+ * Function: H5DOwrite_chunk
+ *
+ * Purpose: Writes an entire chunk to the file directly.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Raymond Lu
+ * 30 July 2012
+ *
+ * Modifications:
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5DOwrite_chunk(hid_t dset_id, hid_t dxpl_id, uint32_t filters, const hsize_t *offset,
+ size_t data_size, const void *buf)
+{
+ hbool_t created_dxpl = FALSE;
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ if(dset_id < 0) {
+ ret_value = FAIL;
+ goto done;
+ }
+
+ if(!buf) {
+ ret_value = FAIL;
+ goto done;
+ }
+
+ if(!offset) {
+ ret_value = FAIL;
+ goto done;
+ }
+
+ if(!data_size) {
+ ret_value = FAIL;
+ goto done;
+ }
+
+ if(H5P_DEFAULT == dxpl_id) {
+ if((dxpl_id = H5Pcreate(H5P_DATASET_XFER)) < 0) {
+ ret_value = FAIL;
+ goto done;
+ }
+
+ created_dxpl = TRUE;
+ }
+
+ if(H5DO_write_chunk(dset_id, dxpl_id, filters, offset, data_size, buf) < 0) {
+ ret_value = FAIL;
+ goto done;
+ }
+
+done:
+ if(created_dxpl) {
+ if(H5Pclose(dxpl_id) < 0)
+ ret_value = FAIL;
+ }
+
+ return ret_value;
+}
+
+/*-------------------------------------------------------------------------
+ * Function: H5DO_write_chunk
+ *
+ * Purpose: Private function for H5DOwrite_chunk
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Raymond Lu
+ * 30 July 2012
+ *
+ * Modifications:
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5DO_write_chunk(hid_t dset_id, hid_t dxpl_id, uint32_t filters, const hsize_t *offset,
+ size_t data_size, const void *buf)
+{
+ hbool_t do_direct_write = TRUE;
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ if(H5Pset(dxpl_id, H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_NAME, &do_direct_write) < 0) {
+ ret_value = FAIL;
+ goto done;
+ }
+
+ if(H5Pset(dxpl_id, H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_NAME, &filters) < 0) {
+ ret_value = FAIL;
+ goto done;
+ }
+
+ if(H5Pset(dxpl_id, H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_NAME, &offset) < 0) {
+ ret_value = FAIL;
+ goto done;
+ }
+
+ if(H5Pset(dxpl_id, H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_NAME, &data_size) < 0) {
+ ret_value = FAIL;
+ goto done;
+ }
+
+ if(H5Dwrite(dset_id, 0, H5S_ALL, H5S_ALL, dxpl_id, buf) < 0) {
+ ret_value = FAIL;
+ goto done;
+ }
+
+done:
+ do_direct_write = FALSE;
+ if(H5Pset(dxpl_id, H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_NAME, &do_direct_write) < 0)
+ ret_value = FAIL;
+
+ return ret_value;
+}
diff --git a/hl/src/H5DOprivate.h b/hl/src/H5DOprivate.h
new file mode 100644
index 0000000..fcea585
--- /dev/null
+++ b/hl/src/H5DOprivate.h
@@ -0,0 +1,37 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * 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. *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+#ifndef _H5DOprivate_H
+#define _H5DOprivate_H
+
+/* High-level library internal header file */
+#include "H5HLprivate2.h"
+
+/* public LT prototypes */
+#include "H5DOpublic.h"
+
+/*-------------------------------------------------------------------------
+ * Private functions
+ *-------------------------------------------------------------------------
+ */
+
+H5_HLDLL herr_t H5DO_write_chunk(hid_t dset_id,
+ hid_t dxpl_id,
+ uint32_t filters,
+ const hsize_t *offset,
+ size_t data_size,
+ const void *buf);
+
+#endif
diff --git a/hl/src/H5DOpublic.h b/hl/src/H5DOpublic.h
new file mode 100644
index 0000000..774709e
--- /dev/null
+++ b/hl/src/H5DOpublic.h
@@ -0,0 +1,42 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * 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. *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+#ifndef _H5DOpublic_H
+#define _H5DOpublic_H
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*-------------------------------------------------------------------------
+ *
+ * Direct chunk write function
+ *
+ *-------------------------------------------------------------------------
+ */
+
+H5_HLDLL herr_t H5DOwrite_chunk(hid_t dset_id,
+ hid_t dxpl_id,
+ uint32_t filters,
+ const hsize_t *offset,
+ size_t data_size,
+ const void *buf);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
+
diff --git a/hl/src/Makefile.am b/hl/src/Makefile.am
index f3d09ab..1e781a9 100644
--- a/hl/src/Makefile.am
+++ b/hl/src/Makefile.am
@@ -31,12 +31,12 @@ lib_LTLIBRARIES=libhdf5_hl.la
libhdf5_hl_la_LDFLAGS= -version-info $(LT_VERS_INTERFACE):$(LT_VERS_REVISION):$(LT_VERS_AGE) $(AM_LDFLAGS)
# List sources to include in the HDF5 HL Library.
-libhdf5_hl_la_SOURCES=H5DS.c H5IM.c H5LT.c H5LTanalyze.c H5LTparse.c H5PT.c H5TB.c
+libhdf5_hl_la_SOURCES=H5DO.c H5DS.c H5IM.c H5LT.c H5LTanalyze.c H5LTparse.c H5PT.c H5TB.c
# HDF5 HL library depends on HDF5 Library.
libhdf5_hl_la_LIBADD=$(LIBHDF5)
# Public header files (to be installed)
-include_HEADERS=hdf5_hl.h H5IMpublic.h H5LTpublic.h H5TBpublic.h H5DSpublic.h H5PTpublic.h
+include_HEADERS=hdf5_hl.h H5DOpublic.h H5IMpublic.h H5LTpublic.h H5TBpublic.h H5DSpublic.h H5PTpublic.h
include $(top_srcdir)/config/conclude.am
diff --git a/hl/src/Makefile.in b/hl/src/Makefile.in
index 3818c9b..21d7e00 100644
--- a/hl/src/Makefile.in
+++ b/hl/src/Makefile.in
@@ -114,8 +114,8 @@ am__uninstall_files_from_dir = { \
am__installdirs = "$(DESTDIR)$(libdir)" "$(DESTDIR)$(includedir)"
LTLIBRARIES = $(lib_LTLIBRARIES)
libhdf5_hl_la_DEPENDENCIES = $(LIBHDF5)
-am_libhdf5_hl_la_OBJECTS = H5DS.lo H5IM.lo H5LT.lo H5LTanalyze.lo \
- H5LTparse.lo H5PT.lo H5TB.lo
+am_libhdf5_hl_la_OBJECTS = H5DO.lo H5DS.lo H5IM.lo H5LT.lo \
+ H5LTanalyze.lo H5LTparse.lo H5PT.lo H5TB.lo
libhdf5_hl_la_OBJECTS = $(am_libhdf5_hl_la_OBJECTS)
AM_V_lt = $(am__v_lt_@AM_V@)
am__v_lt_ = $(am__v_lt_@AM_DEFAULT_V@)
@@ -467,13 +467,13 @@ lib_LTLIBRARIES = libhdf5_hl.la
libhdf5_hl_la_LDFLAGS = -version-info $(LT_VERS_INTERFACE):$(LT_VERS_REVISION):$(LT_VERS_AGE) $(AM_LDFLAGS)
# List sources to include in the HDF5 HL Library.
-libhdf5_hl_la_SOURCES = H5DS.c H5IM.c H5LT.c H5LTanalyze.c H5LTparse.c H5PT.c H5TB.c
+libhdf5_hl_la_SOURCES = H5DO.c H5DS.c H5IM.c H5LT.c H5LTanalyze.c H5LTparse.c H5PT.c H5TB.c
# HDF5 HL library depends on HDF5 Library.
libhdf5_hl_la_LIBADD = $(LIBHDF5)
# Public header files (to be installed)
-include_HEADERS = hdf5_hl.h H5IMpublic.h H5LTpublic.h H5TBpublic.h H5DSpublic.h H5PTpublic.h
+include_HEADERS = hdf5_hl.h H5DOpublic.h H5IMpublic.h H5LTpublic.h H5TBpublic.h H5DSpublic.h H5PTpublic.h
# Automake needs to be taught how to build lib, progs, and tests targets.
# These will be filled in automatically for the most part (e.g.,
@@ -572,6 +572,7 @@ mostlyclean-compile:
distclean-compile:
-rm -f *.tab.c
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5DO.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5DS.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5IM.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5LT.Plo@am__quote@
diff --git a/hl/src/hdf5_hl.h b/hl/src/hdf5_hl.h
index 0fff932..4643932 100644
--- a/hl/src/hdf5_hl.h
+++ b/hl/src/hdf5_hl.h
@@ -22,6 +22,7 @@
#ifndef _HDF5_HL_H
#define _HDF5_HL_H
+#include "H5DOpublic.h" /* dataset optimization */
#include "H5DSpublic.h" /* dimension scales */
#include "H5LTpublic.h" /* lite */
#include "H5IMpublic.h" /* image */
diff --git a/hl/test/CMakeLists.txt b/hl/test/CMakeLists.txt
index f3e42af..a85d271 100644
--- a/hl/test/CMakeLists.txt
+++ b/hl/test/CMakeLists.txt
@@ -65,6 +65,7 @@ ADD_TEST (
test_ds7.h5
test_ds8.h5
test_ds9.h5
+ test_dectris.h5
test_image1.h5
test_image2.h5
test_image3.h5
@@ -76,6 +77,7 @@ ADD_TEST (
)
HL_ADD_TEST (test_ds "dsdata.txt;dslat.txt;dslon.txt;test_ds_be.h5;test_ds_le.h5")
+HL_ADD_TEST (test_dset_opt "")
HL_ADD_TEST (test_image "image8.txt;sepia.pal;earth.pal;image24pixel.txt;image24plane.txt;usa.wri")
HL_ADD_TEST (test_lite "dtype_file.txt")
HL_ADD_TEST (test_packet "")
diff --git a/hl/test/Makefile.am b/hl/test/Makefile.am
index 8893b93..0809deb 100644
--- a/hl/test/Makefile.am
+++ b/hl/test/Makefile.am
@@ -29,7 +29,7 @@ LDADD=$(LIBH5_HL) $(LIBH5TEST) $(LIBHDF5)
# Test programs. These are our main targets. They should be listed in the
# order to be executed, generally most specific tests to least specific tests.
-TEST_PROG=test_lite test_image test_file_image test_table test_ds test_packet
+TEST_PROG=test_lite test_image test_file_image test_table test_ds test_packet test_dset_opt
check_PROGRAMS=$(TEST_PROG)
# These programs generate test files for the tests. They don't need to be
@@ -46,6 +46,7 @@ endif
# Temporary files. These files are the ones created by running `make test'.
CHECK_CLEANFILES+=combine_tables[1-2].h5 test_ds[1-9].h5 test_ds10.h5 \
test_image[1-3].h5 file_img[1-2].h5 test_lite[1-4].h5 test_table.h5 \
- test_packet_table.h5 test_packet_compress.h5 test_detach.h5
+ test_packet_table.h5 test_packet_compress.h5 test_detach.h5 \
+ test_dectris.h5
include $(top_srcdir)/config/conclude.am
diff --git a/hl/test/Makefile.in b/hl/test/Makefile.in
index f98b2bc..ad3f370 100644
--- a/hl/test/Makefile.in
+++ b/hl/test/Makefile.in
@@ -88,7 +88,7 @@ CONFIG_CLEAN_FILES = H5srcdir_str.h
CONFIG_CLEAN_VPATH_FILES =
am__EXEEXT_1 = test_lite$(EXEEXT) test_image$(EXEEXT) \
test_file_image$(EXEEXT) test_table$(EXEEXT) test_ds$(EXEEXT) \
- test_packet$(EXEEXT)
+ test_packet$(EXEEXT) test_dset_opt$(EXEEXT)
am__EXEEXT_2 = gen_test_ds$(EXEEXT)
PROGRAMS = $(noinst_PROGRAMS)
gen_test_ds_SOURCES = gen_test_ds.c
@@ -103,6 +103,10 @@ test_ds_SOURCES = test_ds.c
test_ds_OBJECTS = test_ds.$(OBJEXT)
test_ds_LDADD = $(LDADD)
test_ds_DEPENDENCIES = $(LIBH5_HL) $(LIBH5TEST) $(LIBHDF5)
+test_dset_opt_SOURCES = test_dset_opt.c
+test_dset_opt_OBJECTS = test_dset_opt.$(OBJEXT)
+test_dset_opt_LDADD = $(LDADD)
+test_dset_opt_DEPENDENCIES = $(LIBH5_HL) $(LIBH5TEST) $(LIBHDF5)
test_file_image_SOURCES = test_file_image.c
test_file_image_OBJECTS = test_file_image.$(OBJEXT)
test_file_image_LDADD = $(LDADD)
@@ -157,10 +161,11 @@ AM_V_CCLD = $(am__v_CCLD_@AM_V@)
am__v_CCLD_ = $(am__v_CCLD_@AM_DEFAULT_V@)
am__v_CCLD_0 = @echo " CCLD " $@;
am__v_CCLD_1 =
-SOURCES = gen_test_ds.c test_ds.c test_file_image.c test_image.c \
- test_lite.c test_packet.c test_table.c
-DIST_SOURCES = gen_test_ds.c test_ds.c test_file_image.c test_image.c \
- test_lite.c test_packet.c test_table.c
+SOURCES = gen_test_ds.c test_ds.c test_dset_opt.c test_file_image.c \
+ test_image.c test_lite.c test_packet.c test_table.c
+DIST_SOURCES = gen_test_ds.c test_ds.c test_dset_opt.c \
+ test_file_image.c test_image.c test_lite.c test_packet.c \
+ test_table.c
am__can_run_installinfo = \
case $$AM_UPDATE_INFO_DIR in \
n|no|NO) false;; \
@@ -460,14 +465,15 @@ TRACE = perl $(top_srcdir)/bin/trace
CHECK_CLEANFILES = *.chkexe *.chklog *.clog combine_tables[1-2].h5 \
test_ds[1-9].h5 test_ds10.h5 test_image[1-3].h5 \
file_img[1-2].h5 test_lite[1-4].h5 test_table.h5 \
- test_packet_table.h5 test_packet_compress.h5 test_detach.h5
+ test_packet_table.h5 test_packet_compress.h5 test_detach.h5 \
+ test_dectris.h5
# The tests depend on the hdf5, hdf5 test, and hdf5_hl libraries
LDADD = $(LIBH5_HL) $(LIBH5TEST) $(LIBHDF5)
# Test programs. These are our main targets. They should be listed in the
# order to be executed, generally most specific tests to least specific tests.
-TEST_PROG = test_lite test_image test_file_image test_table test_ds test_packet
+TEST_PROG = test_lite test_image test_file_image test_table test_ds test_packet test_dset_opt
# These programs generate test files for the tests. They don't need to be
# compiled every time we want to test the library. However, putting
@@ -556,6 +562,9 @@ gen_test_ds$(EXEEXT): $(gen_test_ds_OBJECTS) $(gen_test_ds_DEPENDENCIES) $(EXTRA
test_ds$(EXEEXT): $(test_ds_OBJECTS) $(test_ds_DEPENDENCIES) $(EXTRA_test_ds_DEPENDENCIES)
@rm -f test_ds$(EXEEXT)
$(AM_V_CCLD)$(LINK) $(test_ds_OBJECTS) $(test_ds_LDADD) $(LIBS)
+test_dset_opt$(EXEEXT): $(test_dset_opt_OBJECTS) $(test_dset_opt_DEPENDENCIES) $(EXTRA_test_dset_opt_DEPENDENCIES)
+ @rm -f test_dset_opt$(EXEEXT)
+ $(AM_V_CCLD)$(LINK) $(test_dset_opt_OBJECTS) $(test_dset_opt_LDADD) $(LIBS)
test_file_image$(EXEEXT): $(test_file_image_OBJECTS) $(test_file_image_DEPENDENCIES) $(EXTRA_test_file_image_DEPENDENCIES)
@rm -f test_file_image$(EXEEXT)
$(AM_V_CCLD)$(LINK) $(test_file_image_OBJECTS) $(test_file_image_LDADD) $(LIBS)
@@ -580,6 +589,7 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/gen_test_ds.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/test_ds.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/test_dset_opt.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/test_file_image.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/test_image.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/test_lite.Po@am__quote@
diff --git a/hl/test/dectris_hl_perf.c b/hl/test/dectris_hl_perf.c
new file mode 100644
index 0000000..a3e382a
--- /dev/null
+++ b/hl/test/dectris_hl_perf.c
@@ -0,0 +1,643 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * 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 test is for the DECTRIS project to the H5DOwrite_chunk function
+ *
+ */
+
+#include "hdf5.h"
+#include "hdf5_hl.h"
+#include <zlib.h>
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <sys/time.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <fcntl.h>
+#include <unistd.h>
+#include <errno.h>
+
+const char *FILENAME[] = {
+ "dectris_perf",
+ "unix.raw",
+ NULL
+};
+
+/*
+ * Print the current location on the standard output stream.
+ */
+#define FUNC __func__
+#define AT() printf (" at %s:%d in %s()...\n", \
+ __FILE__, __LINE__, FUNC);
+#define H5_FAILED() {puts("*FAILED*");fflush(stdout);}
+#define TEST_ERROR {H5_FAILED(); AT(); goto error;}
+#define TESTING(WHAT) {printf("Testing %-62s",WHAT); fflush(stdout);}
+#define PASSED() {puts(" PASSED");fflush(stdout);}
+
+#define DIRECT_UNCOMPRESSED_DSET "direct_uncompressed_dset"
+#define DIRECT_COMPRESSED_DSET "direct_compressed_dset"
+#define REG_COMPRESSED_DSET "reg_compressed_dset"
+#define REG_NO_COMPRESS_DSET "reg_no_compress_dset"
+#define RANK 3
+#define NX 100
+#define NY 1000
+#define NZ 250
+#define CHUNK_NX 1
+#define CHUNK_NY 1000
+#define CHUNK_NZ 250
+
+#define DEFLATE_SIZE_ADJUST(s) (ceil(((double)(s))*1.001)+12)
+char filename[1024];
+unsigned int *outbuf[NX];
+size_t data_size[NX];
+double total_size = 0.0;
+unsigned int *direct_buf[NX];
+double MB = 1048576.0;
+
+/*--------------------------------------------------
+ * Function to report IO rate
+ *--------------------------------------------------
+ */
+void reportTime(struct timeval start, double mbytes)
+{
+ struct timeval timeval_stop,timeval_diff;
+
+ /*end timing*/
+ gettimeofday(&timeval_stop,NULL);
+
+ /* Calculate the elapsed gettimeofday time */
+ timeval_diff.tv_usec=timeval_stop.tv_usec-start.tv_usec;
+ timeval_diff.tv_sec=timeval_stop.tv_sec-start.tv_sec;
+
+ if(timeval_diff.tv_usec<0) {
+ timeval_diff.tv_usec+=1000000;
+ timeval_diff.tv_sec--;
+ } /* end if */
+
+/*printf("mbytes=%lf, sec=%lf, usec=%lf\n", mbytes, (double)timeval_diff.tv_sec, (double)timeval_diff.tv_usec);*/
+ printf("MBytes/second: %lf\n", (double)mbytes/((double)timeval_diff.tv_sec+((double)timeval_diff.tv_usec/(double)1000000.0)));
+}
+
+/*--------------------------------------------------
+ * Create file, datasets, and initialize data
+ *--------------------------------------------------
+ */
+int create_file(hid_t fapl_id)
+{
+ hid_t file; /* handles */
+ hid_t fapl;
+ hid_t cparms;
+ hid_t dataspace, dataset;
+ hsize_t dims[RANK] = {NX, NY, NZ};
+ hsize_t chunk_dims[RANK] ={CHUNK_NX, CHUNK_NY, CHUNK_NZ};
+ unsigned int aggression = 9; /* Compression aggression setting */
+ int ret;
+ int i, j, n;
+
+ int flag;
+ int unix_file;
+
+ unsigned int *p;
+ size_t buf_size = CHUNK_NY*CHUNK_NZ*sizeof(unsigned int);
+
+ const Bytef *z_src;
+ Bytef *z_dst; /*destination buffer */
+ uLongf z_dst_nbytes = (uLongf)DEFLATE_SIZE_ADJUST(buf_size);
+ uLong z_src_nbytes = (uLong)buf_size;
+
+ TESTING("Create a file and dataset");
+
+ /*
+ * Create the data space with unlimited dimensions.
+ */
+ if((dataspace = H5Screate_simple(RANK, dims, NULL)) < 0)
+ TEST_ERROR;
+
+ /*
+ * Create a new file. If file exists its contents will be overwritten.
+ */
+ if((file = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id)) < 0)
+ TEST_ERROR;
+
+ /*
+ * Modify dataset creation properties, i.e. enable chunking and compression
+ */
+ if((cparms = H5Pcreate(H5P_DATASET_CREATE)) < 0)
+ TEST_ERROR;
+
+ if(H5Pset_chunk( cparms, RANK, chunk_dims) < 0)
+ TEST_ERROR;
+
+ /*
+ * Create a new dataset within the file using cparms
+ * creation properties.
+ */
+ if((dataset = H5Dcreate2(file, DIRECT_UNCOMPRESSED_DSET, H5T_NATIVE_INT, dataspace, H5P_DEFAULT,
+ cparms, H5P_DEFAULT)) < 0)
+ TEST_ERROR;
+
+ if(H5Dclose(dataset) < 0)
+ TEST_ERROR;
+
+ if((dataset = H5Dcreate2(file, REG_NO_COMPRESS_DSET, H5T_NATIVE_INT, dataspace, H5P_DEFAULT,
+ cparms, H5P_DEFAULT)) < 0)
+ TEST_ERROR;
+
+ if(H5Dclose(dataset) < 0)
+ TEST_ERROR;
+
+ /* Set compression */
+ if(H5Pset_deflate( cparms, aggression) < 0)
+ TEST_ERROR;
+
+ if((dataset = H5Dcreate2(file, DIRECT_COMPRESSED_DSET, H5T_NATIVE_INT, dataspace, H5P_DEFAULT,
+ cparms, H5P_DEFAULT)) < 0)
+ TEST_ERROR;
+
+ if(H5Dclose(dataset) < 0)
+ TEST_ERROR;
+
+
+ if((dataset = H5Dcreate2(file, REG_COMPRESSED_DSET, H5T_NATIVE_INT, dataspace, H5P_DEFAULT,
+ cparms, H5P_DEFAULT)) < 0)
+ TEST_ERROR;
+
+ if(H5Dclose(dataset) < 0)
+ TEST_ERROR;
+
+ if(H5Fclose(file) < 0)
+ TEST_ERROR;
+
+ if(H5Sclose(dataspace) < 0)
+ TEST_ERROR;
+
+ if(H5Pclose(cparms) < 0)
+ TEST_ERROR;
+
+ /* create a unix file*/
+ flag = O_CREAT|O_TRUNC|O_WRONLY;
+
+ if ((unix_file=open(FILENAME[1],flag,S_IRWXU))== -1)
+ TEST_ERROR;
+
+ if (close(unix_file) < 0)
+ {
+ printf(" unable to close the file\n");
+ TEST_ERROR;
+ }
+
+
+ /* Initialize data for chunks */
+ for(i = 0; i < NX; i++) {
+ p = direct_buf[i] = (unsigned int*)malloc(CHUNK_NY*CHUNK_NZ*sizeof(unsigned int));
+
+ for(j=0; j < CHUNK_NY*CHUNK_NZ; j++, p++)
+ *p = rand() % 65000;
+
+ z_src = (const Bytef*)direct_buf[i];
+
+ z_dst_nbytes = (uLongf)DEFLATE_SIZE_ADJUST(buf_size);
+ /* Allocate output (compressed) buffer */
+ outbuf[i] = (unsigned int*)malloc((size_t)z_dst_nbytes);
+ z_dst = (Bytef *)outbuf[i];
+
+ /* Perform compression from the source to the destination buffer */
+ ret = compress2(z_dst, &z_dst_nbytes, z_src, z_src_nbytes, aggression);
+
+ data_size[i] = (size_t)z_dst_nbytes;
+ total_size += data_size[i];
+
+ /* Check for various zlib errors */
+ if(Z_BUF_ERROR == ret) {
+ fprintf(stderr, "overflow");
+ TEST_ERROR;
+ } else if(Z_MEM_ERROR == ret) {
+ fprintf(stderr, "deflate memory error");
+ TEST_ERROR;
+ } else if(Z_OK != ret) {
+ fprintf(stderr, "other deflate error");
+ TEST_ERROR;
+ }
+ }
+
+
+ PASSED();
+
+error:
+ H5E_BEGIN_TRY {
+ H5Dclose(dataset);
+ H5Sclose(dataspace);
+ H5Pclose(cparms);
+ H5Fclose(file);
+ } H5E_END_TRY;
+ return 1;
+}
+
+/*--------------------------------------------------
+ * Benchmark the performance of the new function
+ * with precompressed data.
+ *--------------------------------------------------
+ */
+int
+test_direct_write_uncompressed_data(hid_t fapl_id)
+{
+ hid_t file; /* handles */
+ hid_t dataspace, dataset;
+ hid_t dxpl;
+ herr_t status;
+ int i;
+
+ unsigned filter_mask = 0;
+ hsize_t offset[RANK] = {0, 0, 0};
+
+ struct timeval timeval_start;
+
+ TESTING("H5DOwrite_chunk for uncompressed data");
+
+ if((dxpl = H5Pcreate(H5P_DATASET_XFER)) < 0)
+ TEST_ERROR;
+
+ /* Start the timer */
+ gettimeofday(&timeval_start,NULL);
+
+ /* Reopen the file and dataset */
+ if((file = H5Fopen(filename, H5F_ACC_RDWR, fapl_id)) < 0)
+ TEST_ERROR;
+
+ if((dataset = H5Dopen2(file, DIRECT_UNCOMPRESSED_DSET, H5P_DEFAULT)) < 0)
+ TEST_ERROR;
+
+
+ /* Write the compressed chunk data repeatedly to cover all the chunks in the
+ * dataset, using the direct writing function. */
+ for(i=0; i<NX; i++) {
+ status = H5DOwrite_chunk(dataset, dxpl, filter_mask, offset, CHUNK_NY*CHUNK_NZ*sizeof(unsigned int), direct_buf[i]);
+ (offset[0])++;
+ }
+
+ /*
+ * Close/release resources.
+ */
+ H5Dclose(dataset);
+ H5Pclose(dxpl);
+ H5Fclose(file);
+
+ /* Report the performance */
+ reportTime(timeval_start, (double)(NX*NY*NZ*sizeof(unsigned int)/MB));
+
+ PASSED();
+ return 0;
+
+error:
+ H5E_BEGIN_TRY {
+ H5Dclose(dataset);
+ H5Pclose(dxpl);
+ H5Fclose(file);
+ } H5E_END_TRY;
+ return 1;
+}
+
+
+/*--------------------------------------------------
+ * Benchmark the performance of the new function
+ * with precompressed data.
+ *--------------------------------------------------
+ */
+int
+test_direct_write_compressed_data(hid_t fapl_id)
+{
+ hid_t file; /* handles */
+ hid_t dataspace, dataset;
+ hid_t dxpl;
+ herr_t status;
+ int i;
+
+ unsigned filter_mask = 0;
+ hsize_t offset[RANK] = {0, 0, 0};
+
+ struct timeval timeval_start;
+
+ TESTING("H5DOwrite_chunk for pre-compressed data");
+
+ if((dxpl = H5Pcreate(H5P_DATASET_XFER)) < 0)
+ TEST_ERROR;
+
+ /* Start the timer */
+ gettimeofday(&timeval_start,NULL);
+
+ /* Reopen the file and dataset */
+ if((file = H5Fopen(filename, H5F_ACC_RDWR, fapl_id)) < 0)
+ TEST_ERROR;
+
+ if((dataset = H5Dopen2(file, DIRECT_COMPRESSED_DSET, H5P_DEFAULT)) < 0)
+ TEST_ERROR;
+
+
+ /* Write the compressed chunk data repeatedly to cover all the chunks in the
+ * dataset, using the direct writing function. */
+ for(i=0; i<NX; i++) {
+ status = H5DOwrite_chunk(dataset, dxpl, filter_mask, offset, data_size[i], outbuf[i]);
+ (offset[0])++;
+ }
+
+ /*
+ * Close/release resources.
+ */
+ H5Dclose(dataset);
+ H5Pclose(dxpl);
+ H5Fclose(file);
+
+ /* Report the performance */
+ reportTime(timeval_start, (double)(total_size/MB));
+
+ PASSED();
+ return 0;
+
+error:
+ H5E_BEGIN_TRY {
+ H5Dclose(dataset);
+ H5Pclose(dxpl);
+ H5Fclose(file);
+ } H5E_END_TRY;
+ return 1;
+}
+
+/*--------------------------------------------------
+ * Benchmark the performance of the regular H5Dwrite
+ * with compression filter enabled.
+ *--------------------------------------------------
+ */
+int
+test_compressed_write(hid_t fapl_id)
+{
+ hid_t file; /* handles */
+ hid_t dataspace, dataset;
+ hid_t mem_space;
+ hsize_t chunk_dims[RANK] ={CHUNK_NX, CHUNK_NY, CHUNK_NZ};
+ hid_t dxpl;
+ herr_t status;
+ int i;
+
+ hsize_t start[RANK]; /* Start of hyperslab */
+ hsize_t stride[RANK]; /* Stride of hyperslab */
+ hsize_t count[RANK]; /* Block count */
+ hsize_t block[RANK]; /* Block sizes */
+
+ struct timeval timeval_start;
+
+ TESTING("H5Dwrite with compression enabled");
+
+ if((dxpl = H5Pcreate(H5P_DATASET_XFER)) < 0)
+ TEST_ERROR;
+
+ if((mem_space = H5Screate_simple(RANK, chunk_dims, NULL)) < 0)
+ TEST_ERROR;
+
+ /* Start the timer */
+ gettimeofday(&timeval_start,NULL);
+
+ /* Reopen the file and dataset */
+ if((file = H5Fopen(filename, H5F_ACC_RDWR, fapl_id)) < 0)
+ TEST_ERROR;
+
+ if((dataset = H5Dopen2(file, REG_COMPRESSED_DSET, H5P_DEFAULT)) < 0)
+ TEST_ERROR;
+
+ if((dataspace = H5Dget_space(dataset)) < 0)
+ TEST_ERROR;
+
+ start[0] = start[1] = start[2] = 0;
+ stride[0] = stride[1] = stride[2] = 1;
+ count[0] = count[1] = count[2] = 1;
+ block[0] = CHUNK_NX; block[1] = CHUNK_NY; block[2] = CHUNK_NZ;
+
+ for(i=0; i<NX; i++) {
+ /*
+ * Select hyperslab for one chunk in the file
+ */
+ if((status = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, start, stride, count, block)) < 0)
+ TEST_ERROR;
+ (start[0])++;
+
+ if((status = H5Dwrite(dataset, H5T_NATIVE_INT, mem_space, dataspace,
+ H5P_DEFAULT, direct_buf[i])) < 0)
+ TEST_ERROR;
+ }
+
+ /*
+ * Close/release resources.
+ */
+ H5Dclose(dataset);
+ H5Sclose(dataspace);
+ H5Sclose(mem_space);
+ H5Pclose(dxpl);
+ H5Fclose(file);
+
+ /* Report the performance */
+ reportTime(timeval_start, (double)(NX*NY*NZ*sizeof(unsigned int)/MB));
+
+ PASSED();
+ return 0;
+
+error:
+ H5E_BEGIN_TRY {
+ H5Dclose(dataset);
+ H5Sclose(dataspace);
+ H5Sclose(mem_space);
+ H5Pclose(dxpl);
+ H5Fclose(file);
+ } H5E_END_TRY;
+ return 1;
+}
+
+/*--------------------------------------------------
+ * Benchmark the performance of the regular H5Dwrite
+ * with compression
+ *--------------------------------------------------
+ */
+int
+test_no_compress_write(hid_t fapl_id)
+{
+ hid_t file; /* handles */
+ hid_t dataspace, dataset;
+ hid_t mem_space;
+ hsize_t chunk_dims[RANK] ={CHUNK_NX, CHUNK_NY, CHUNK_NZ};
+ hid_t dxpl;
+ herr_t status;
+ int i;
+
+ hsize_t start[RANK]; /* Start of hyperslab */
+ hsize_t stride[RANK]; /* Stride of hyperslab */
+ hsize_t count[RANK]; /* Block count */
+ hsize_t block[RANK]; /* Block sizes */
+
+ struct timeval timeval_start;
+
+ TESTING("H5Dwrite without compression");
+
+ if((dxpl = H5Pcreate(H5P_DATASET_XFER)) < 0)
+ TEST_ERROR;
+
+ if((mem_space = H5Screate_simple(RANK, chunk_dims, NULL)) < 0)
+ TEST_ERROR;
+
+ /* Start the timer */
+ gettimeofday(&timeval_start,NULL);
+
+ /* Reopen the file and dataset */
+ if((file = H5Fopen(filename, H5F_ACC_RDWR, fapl_id)) < 0)
+ TEST_ERROR;
+
+ if((dataset = H5Dopen2(file, REG_NO_COMPRESS_DSET, H5P_DEFAULT)) < 0)
+ TEST_ERROR;
+
+ if((dataspace = H5Dget_space(dataset)) < 0)
+ TEST_ERROR;
+
+ start[0] = start[1] = start[2] = 0;
+ stride[0] = stride[1] = stride[2] = 1;
+ count[0] = count[1] = count[2] = 1;
+ block[0] = CHUNK_NX; block[1] = CHUNK_NY; block[2] = CHUNK_NZ;
+
+ for(i=0; i<NX; i++) {
+ /*
+ * Select hyperslab for one chunk in the file
+ */
+ if((status = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, start, stride, count, block)) < 0)
+ TEST_ERROR;
+ (start[0])++;
+
+ if((status = H5Dwrite(dataset, H5T_NATIVE_INT, mem_space, dataspace,
+ H5P_DEFAULT, direct_buf[i])) < 0)
+ TEST_ERROR;
+ }
+
+ /*
+ * Close/release resources.
+ */
+ H5Dclose(dataset);
+ H5Sclose(dataspace);
+ H5Sclose(mem_space);
+ H5Pclose(dxpl);
+ H5Fclose(file);
+
+ /* Report the performance */
+ reportTime(timeval_start, (double)(NX*NY*NZ*sizeof(unsigned int)/MB));
+
+ PASSED();
+ return 0;
+
+error:
+ H5E_BEGIN_TRY {
+ H5Dclose(dataset);
+ H5Sclose(dataspace);
+ H5Sclose(mem_space);
+ H5Pclose(dxpl);
+ H5Fclose(file);
+ } H5E_END_TRY;
+ return 1;
+}
+
+/*--------------------------------------------------
+ * Benchmark the performance for writing compressed
+ * data to a Unix file
+ *--------------------------------------------------
+ */
+int
+test_unix_write(void)
+{
+ int file, flag;
+ ssize_t op_size;
+ int i;
+ struct timeval timeval_start;
+
+ TESTING("Write compressed data to a Unix file");
+
+ /* create file*/
+ flag = O_WRONLY;
+
+ /* Start the timer */
+ gettimeofday(&timeval_start,NULL);
+
+ if ((file=open(FILENAME[1],flag))== -1)
+ TEST_ERROR;
+
+ /* Write the compressed chunk data repeatedly to cover all the chunks in the
+ * dataset, using the direct writing function. */
+ for(i=0; i<NX; i++) {
+ op_size = write(file, outbuf[i],data_size[i]);
+ if (op_size < 0)
+ {
+ printf(" Error in writing data to file because %s \n", strerror(errno));
+ TEST_ERROR;
+ }
+ else if (op_size == 0)
+ {
+ printf(" unable to write sufficent data to file because %s \n", strerror(errno));
+ TEST_ERROR;
+ }
+ }
+
+ if (close(file) < 0)
+ {
+ printf(" unable to close the file\n");
+ TEST_ERROR;
+ }
+
+ /* Report the performance */
+ reportTime(timeval_start, (double)(total_size/MB));
+
+ PASSED();
+ return 0;
+
+error:
+ return 1;
+}
+
+/*--------------------------------------------------
+ * Main function
+ *--------------------------------------------------
+ */
+int
+main (void)
+{
+ hid_t fapl = H5P_DEFAULT;
+ int i;
+
+ /* Testing setup */
+/* h5_reset();
+ fapl = h5_fileaccess();
+
+ h5_fixname(FILENAME[0], fapl, filename, sizeof filename);*/
+
+ sprintf(filename, "%s.h5", FILENAME[0]);
+
+ create_file(fapl);
+ test_direct_write_uncompressed_data(fapl);
+ test_direct_write_compressed_data(fapl);
+ test_no_compress_write(fapl);
+ test_compressed_write(fapl);
+ test_unix_write();
+
+ for(i=0; i<NX; i++) {
+ free(outbuf[i]);
+ free(direct_buf[i]);
+ }
+
+/* h5_cleanup(FILENAME, fapl);*/
+ return 0;
+}
diff --git a/hl/test/test_dset_opt.c b/hl/test/test_dset_opt.c
new file mode 100644
index 0000000..9a0ffb0
--- /dev/null
+++ b/hl/test/test_dset_opt.c
@@ -0,0 +1,1138 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+* 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. *
+* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+#include <stdlib.h>
+#include <string.h>
+#include "h5hltest.h"
+#include "H5srcdir.h"
+#include "H5DOpublic.h"
+#include <math.h>
+
+#if defined(H5_HAVE_ZLIB_H) && !defined(H5_ZLIB_HEADER)
+# define H5_ZLIB_HEADER "zlib.h"
+#endif
+#if defined(H5_ZLIB_HEADER)
+# include H5_ZLIB_HEADER /* "zlib.h" */
+#endif
+
+#define FILE_NAME "test_dectris.h5"
+
+#define DATASETNAME1 "direct_write"
+#define DATASETNAME2 "skip_one_filter"
+#define DATASETNAME3 "skip_two_filters"
+#define DATASETNAME4 "data_conv"
+#define DATASETNAME5 "contiguous_dset"
+#define DATASETNAME6 "invalid_argue"
+#define RANK 2
+#define NX 16
+#define NY 16
+#define CHUNK_NX 4
+#define CHUNK_NY 4
+
+#define DEFLATE_SIZE_ADJUST(s) (ceil(((double)(s))*1.001)+12)
+
+/* Temporary filter IDs used for testing */
+#define H5Z_FILTER_BOGUS1 305
+#define H5Z_FILTER_BOGUS2 306
+#define ADD_ON 7
+#define FACTOR 3
+
+/* Local prototypes for filter functions */
+static size_t filter_bogus1(unsigned int flags, size_t cd_nelmts,
+ const unsigned int *cd_values, size_t nbytes, size_t *buf_size, void **buf);
+static size_t filter_bogus2(unsigned int flags, size_t cd_nelmts,
+ const unsigned int *cd_values, size_t nbytes, size_t *buf_size, void **buf);
+
+/* This message derives from H5Z */
+const H5Z_class2_t H5Z_BOGUS1[1] = {{
+ H5Z_CLASS_T_VERS, /* H5Z_class_t version */
+ H5Z_FILTER_BOGUS1, /* Filter id number */
+ 1, 1, /* Encoding and decoding enabled */
+ "bogus1", /* Filter name for debugging */
+ NULL, /* The "can apply" callback */
+ NULL, /* The "set local" callback */
+ filter_bogus1, /* The actual filter function */
+}};
+
+const H5Z_class2_t H5Z_BOGUS2[1] = {{
+ H5Z_CLASS_T_VERS, /* H5Z_class_t version */
+ H5Z_FILTER_BOGUS2, /* Filter id number */
+ 1, 1, /* Encoding and decoding enabled */
+ "bogus2", /* Filter name for debugging */
+ NULL, /* The "can apply" callback */
+ NULL, /* The "set local" callback */
+ filter_bogus2, /* The actual filter function */
+}};
+
+/*-------------------------------------------------------------------------
+ * Function: test_direct_chunk_write
+ *
+ * Purpose: Test the basic functionality of H5DOwrite_chunk
+ *
+ * Return: Success: 0
+ *
+ * Failure: 1
+ *
+ * Programmer: Raymond Lu
+ * 30 November 2012
+ *
+ *-------------------------------------------------------------------------
+ */
+#ifdef H5_HAVE_FILTER_DEFLATE
+static int
+test_direct_chunk_write (hid_t file)
+{
+ hid_t dataspace = -1, dataset = -1;
+ hid_t mem_space = -1;
+ hid_t cparms = -1, dxpl = -1;
+ hsize_t dims[2] = {NX, NY};
+ hsize_t maxdims[2] = {H5S_UNLIMITED, H5S_UNLIMITED};
+ hsize_t chunk_dims[2] ={CHUNK_NX, CHUNK_NY};
+ herr_t status;
+ int ret;
+ int data[NX][NY];
+ int i, j, n;
+
+ unsigned filter_mask = 0;
+ int direct_buf[CHUNK_NX][CHUNK_NY];
+ int check_chunk[CHUNK_NX][CHUNK_NY];
+ hsize_t offset[2] = {0, 0};
+ size_t buf_size = CHUNK_NX*CHUNK_NY*sizeof(int);
+
+ const Bytef *z_src = (const Bytef*)(direct_buf);
+ Bytef *z_dst; /*destination buffer */
+ uLongf z_dst_nbytes = (uLongf)DEFLATE_SIZE_ADJUST(buf_size);
+ uLong z_src_nbytes = (uLong)buf_size;
+ int aggression = 9; /* Compression aggression setting */
+ void *outbuf = NULL; /* Pointer to new buffer */
+
+ hsize_t start[2]; /* Start of hyperslab */
+ hsize_t stride[2]; /* Stride of hyperslab */
+ hsize_t count[2]; /* Block count */
+ hsize_t block[2]; /* Block sizes */
+
+ TESTING("basic functionality of H5DOwrite_chunk");
+
+ /*
+ * Create the data space with unlimited dimensions.
+ */
+ if((dataspace = H5Screate_simple(RANK, dims, maxdims)) < 0)
+ goto error;
+
+ if((mem_space = H5Screate_simple(RANK, chunk_dims, NULL)) < 0)
+ goto error;
+
+ /*
+ * Modify dataset creation properties, i.e. enable chunking and compression
+ */
+ if((cparms = H5Pcreate(H5P_DATASET_CREATE)) < 0)
+ goto error;
+
+ if((status = H5Pset_chunk( cparms, RANK, chunk_dims)) < 0)
+ goto error;
+
+ if((status = H5Pset_deflate( cparms, (unsigned) aggression)) < 0)
+ goto error;
+
+ /*
+ * Create a new dataset within the file using cparms
+ * creation properties.
+ */
+ if((dataset = H5Dcreate2(file, DATASETNAME1, H5T_NATIVE_INT, dataspace, H5P_DEFAULT,
+ cparms, H5P_DEFAULT)) < 0)
+ goto error;
+
+ /* Initialize the dataset */
+ for(i = n = 0; i < NX; i++)
+ for(j = 0; j < NY; j++)
+ data[i][j] = n++;
+
+ if((dxpl = H5Pcreate(H5P_DATASET_XFER)) < 0)
+ goto error;
+
+ /*
+ * Write the data for the dataset. It should stay in the chunk cache.
+ * It will be evicted from the cache by the H5DOwrite_chunk calls.
+ */
+ if((status = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
+ dxpl, data)) < 0)
+ goto error;
+
+ /* Initialize data for one chunk */
+ for(i = n = 0; i < CHUNK_NX; i++)
+ for(j = 0; j < CHUNK_NY; j++)
+ direct_buf[i][j] = n++;
+
+ /* Allocate output (compressed) buffer */
+ outbuf = malloc(z_dst_nbytes);
+ z_dst = (Bytef *)outbuf;
+
+ /* Perform compression from the source to the destination buffer */
+ ret = compress2(z_dst, &z_dst_nbytes, z_src, z_src_nbytes, aggression);
+
+ /* Check for various zlib errors */
+ if(Z_BUF_ERROR == ret) {
+ fprintf(stderr, "overflow");
+ goto error;
+ } else if(Z_MEM_ERROR == ret) {
+ fprintf(stderr, "deflate memory error");
+ goto error;
+ } else if(Z_OK != ret) {
+ fprintf(stderr, "other deflate error");
+ goto error;
+ }
+
+ /* Write the compressed chunk data repeatedly to cover all the chunks in the
+ * dataset, using the direct writing function. */
+ for(i=0; i<NX/CHUNK_NX; i++) {
+ for(j=0; j<NY/CHUNK_NY; j++) {
+ status = H5DOwrite_chunk(dataset, dxpl, filter_mask, offset, z_dst_nbytes, outbuf);
+ offset[1] += CHUNK_NY;
+ }
+ offset[0] += CHUNK_NX;
+ offset[1] = 0;
+ }
+
+ if(outbuf)
+ free(outbuf);
+
+ if(H5Fflush(dataset, H5F_SCOPE_LOCAL) < 0)
+ goto error;
+
+ if(H5Dclose(dataset) < 0)
+ goto error;
+
+ if((dataset = H5Dopen2(file, DATASETNAME1, H5P_DEFAULT)) < 0)
+ goto error;
+
+ /*
+ * Select hyperslab for one chunk in the file
+ */
+ start[0] = CHUNK_NX; start[1] = CHUNK_NY;
+ stride[0] = 1; stride[1] = 1;
+ count[0] = 1; count[1] = 1;
+ block[0] = CHUNK_NX; block[1] = CHUNK_NY;
+ if((status = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, start, stride, count, block)) < 0)
+ goto error;
+
+ /* Read the chunk back */
+ if((status = H5Dread(dataset, H5T_NATIVE_INT, mem_space, dataspace, H5P_DEFAULT, check_chunk)) < 0)
+ goto error;
+
+ /* Check that the values read are the same as the values written */
+ for(i = 0; i < CHUNK_NX; i++) {
+ for(j = 0; j < CHUNK_NY; j++) {
+ if(direct_buf[i][j] != check_chunk[i][j]) {
+ printf(" 1. Read different values than written.");
+ printf(" At index %d,%d\n", i, j);
+ printf(" direct_buf=%d, check_chunk=%d\n", direct_buf[i][j], check_chunk[i][j]);
+ goto error;
+ }
+ }
+ }
+
+ /* Reinitialize different data for one chunk */
+ for(i = 0; i < CHUNK_NX; i++)
+ for(j = 0; j < CHUNK_NY; j++)
+ direct_buf[i][j] = i + j;
+
+ /* Allocate output (compressed) buffer */
+ outbuf = malloc(z_dst_nbytes);
+ z_dst = (Bytef *)outbuf;
+
+ /* Perform compression from the source to the destination buffer */
+ ret = compress2(z_dst, &z_dst_nbytes, z_src, z_src_nbytes, aggression);
+
+ /* Check for various zlib errors */
+ if(Z_BUF_ERROR == ret) {
+ fprintf(stderr, "overflow");
+ goto error;
+ } else if(Z_MEM_ERROR == ret) {
+ fprintf(stderr, "deflate memory error");
+ goto error;
+ } else if(Z_OK != ret) {
+ fprintf(stderr, "other deflate error");
+ goto error;
+ }
+
+ /* Rewrite the compressed chunk data repeatedly to cover all the chunks in the
+ * dataset, using the direct writing function. */
+ offset[0] = offset[1] = 0;
+ for(i=0; i<NX/CHUNK_NX; i++) {
+ for(j=0; j<NY/CHUNK_NY; j++) {
+ status = H5DOwrite_chunk(dataset, dxpl, filter_mask, offset, z_dst_nbytes, outbuf);
+ offset[1] += CHUNK_NY;
+ }
+ offset[0] += CHUNK_NX;
+ offset[1] = 0;
+ }
+
+ if(outbuf)
+ free(outbuf);
+
+ if(H5Fflush(dataset, H5F_SCOPE_LOCAL) < 0)
+ goto error;
+
+ if(H5Dclose(dataset) < 0)
+ goto error;
+
+ if((dataset = H5Dopen2(file, DATASETNAME1, H5P_DEFAULT)) < 0)
+ goto error;
+
+ /* Read the chunk back */
+ if((status = H5Dread(dataset, H5T_NATIVE_INT, mem_space, dataspace, H5P_DEFAULT, check_chunk)) < 0)
+ goto error;
+
+ /* Check that the values read are the same as the values written */
+ for(i = 0; i < CHUNK_NX; i++) {
+ for(j = 0; j < CHUNK_NY; j++) {
+ if(direct_buf[i][j] != check_chunk[i][j]) {
+ printf(" 2. Read different values than written.");
+ printf(" At index %d,%d\n", i, j);
+ printf(" direct_buf=%d, check_chunk=%d\n", direct_buf[i][j], check_chunk[i][j]);
+ goto error;
+ }
+ }
+ }
+
+ /*
+ * Close/release resources.
+ */
+ H5Dclose(dataset);
+ H5Sclose(mem_space);
+ H5Sclose(dataspace);
+ H5Pclose(cparms);
+ H5Pclose(dxpl);
+
+ PASSED();
+ return 0;
+
+error:
+ H5E_BEGIN_TRY {
+ H5Dclose(dataset);
+ H5Sclose(mem_space);
+ H5Sclose(dataspace);
+ H5Pclose(cparms);
+ H5Pclose(dxpl);
+ } H5E_END_TRY;
+
+ if(outbuf)
+ free(outbuf);
+
+ return 1;
+}
+#endif /* H5_HAVE_FILTER_DEFLATE */
+
+/*-------------------------------------------------------------------------
+ * Function: test_skip_compress_write1
+ *
+ * Purpose: Test skipping compression filter when it is the only filter
+ * for the dataset
+ *
+ * Return: Success: 0
+ *
+ * Failure: 1
+ *
+ * Programmer: Raymond Lu
+ * 30 November 2012
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+test_skip_compress_write1(hid_t file)
+{
+ hid_t dataspace = -1, dataset = -1;
+ hid_t mem_space = -1;
+ hid_t cparms = -1, dxpl = -1;
+ hsize_t dims[2] = {NX, NY};
+ hsize_t maxdims[2] = {H5S_UNLIMITED, H5S_UNLIMITED};
+ hsize_t chunk_dims[2] ={CHUNK_NX, CHUNK_NY};
+ herr_t status;
+ int i, j, n;
+
+ unsigned filter_mask = 0;
+ int direct_buf[CHUNK_NX][CHUNK_NY];
+ int check_chunk[CHUNK_NX][CHUNK_NY];
+ hsize_t offset[2] = {0, 0};
+ size_t buf_size = CHUNK_NX*CHUNK_NY*sizeof(int);
+ int aggression = 9; /* Compression aggression setting */
+
+ hsize_t start[2]; /* Start of hyperslab */
+ hsize_t stride[2]; /* Stride of hyperslab */
+ hsize_t count[2]; /* Block count */
+ hsize_t block[2]; /* Block sizes */
+
+ TESTING("skipping compression filter for H5DOwrite_chunk");
+
+ /*
+ * Create the data space with unlimited dimensions.
+ */
+ if((dataspace = H5Screate_simple(RANK, dims, maxdims)) < 0)
+ goto error;
+
+ if((mem_space = H5Screate_simple(RANK, chunk_dims, NULL)) < 0)
+ goto error;
+
+ /*
+ * Modify dataset creation properties, i.e. enable chunking and compression
+ */
+ if((cparms = H5Pcreate(H5P_DATASET_CREATE)) < 0)
+ goto error;
+
+ if((status = H5Pset_chunk( cparms, RANK, chunk_dims)) < 0)
+ goto error;
+
+ if((status = H5Pset_deflate( cparms, (unsigned ) aggression)) < 0)
+ goto error;
+
+ /*
+ * Create a new dataset within the file using cparms
+ * creation properties.
+ */
+ if((dataset = H5Dcreate2(file, DATASETNAME2, H5T_NATIVE_INT, dataspace, H5P_DEFAULT,
+ cparms, H5P_DEFAULT)) < 0)
+ goto error;
+
+ if((dxpl = H5Pcreate(H5P_DATASET_XFER)) < 0)
+ goto error;
+
+ /* Initialize data for one chunk */
+ for(i = n = 0; i < CHUNK_NX; i++)
+ for(j = 0; j < CHUNK_NY; j++) {
+ direct_buf[i][j] = n++;
+ }
+
+ /* write the uncompressed chunk data repeatedly to dataset, using the direct writing function.
+ * Indicate skipping the compression filter. */
+ offset[0] = CHUNK_NX;
+ offset[1] = CHUNK_NY;
+
+ filter_mask = 0x00000001;
+
+ if((status = H5DOwrite_chunk(dataset, dxpl, filter_mask, offset, buf_size, direct_buf)) < 0)
+ goto error;
+
+ if(H5Fflush(dataset, H5F_SCOPE_LOCAL) < 0)
+ goto error;
+
+ if(H5Dclose(dataset) < 0)
+ goto error;
+
+ if((dataset = H5Dopen2(file, DATASETNAME2, H5P_DEFAULT)) < 0)
+ goto error;
+
+ /*
+ * Select hyperslab for the chunk just written in the file
+ */
+ start[0] = CHUNK_NX; start[1] = CHUNK_NY;
+ stride[0] = 1; stride[1] = 1;
+ count[0] = 1; count[1] = 1;
+ block[0] = CHUNK_NX; block[1] = CHUNK_NY;
+ if((status = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, start, stride, count, block)) < 0)
+ goto error;
+
+ /* Read the chunk back */
+ if((status = H5Dread(dataset, H5T_NATIVE_INT, mem_space, dataspace, H5P_DEFAULT, check_chunk)) < 0)
+ goto error;
+
+ /* Check that the values read are the same as the values written */
+ for(i = 0; i < CHUNK_NX; i++) {
+ for(j = 0; j < CHUNK_NY; j++) {
+ if(direct_buf[i][j] != check_chunk[i][j]) {
+ printf(" 1. Read different values than written.");
+ printf(" At index %d,%d\n", i, j);
+ printf(" direct_buf=%d, check_chunk=%d\n", direct_buf[i][j], check_chunk[i][j]);
+ goto error;
+ }
+ }
+ }
+
+ /*
+ * Close/release resources.
+ */
+ H5Dclose(dataset);
+ H5Sclose(mem_space);
+ H5Sclose(dataspace);
+ H5Pclose(cparms);
+ H5Pclose(dxpl);
+
+ PASSED();
+ return 0;
+
+error:
+ H5E_BEGIN_TRY {
+ H5Dclose(dataset);
+ H5Sclose(mem_space);
+ H5Sclose(dataspace);
+ H5Pclose(cparms);
+ H5Pclose(dxpl);
+ } H5E_END_TRY;
+
+ return 1;
+}
+
+/*-------------------------------------------------------------------------
+ * Function: filter_bogus1
+ *
+ * Purpose: A bogus filte that adds ADD_ON to the original value
+ *
+ * Return: Success: Data chunk size
+ *
+ * Programmer: Raymond Lu
+ * 30 November 2012
+ *
+ *-------------------------------------------------------------------------
+ */
+static size_t
+filter_bogus1(unsigned int flags, size_t UNUSED cd_nelmts,
+ const unsigned int UNUSED *cd_values, size_t nbytes,
+ size_t *buf_size, void **buf)
+{
+ int *int_ptr=(int *)*buf; /* Pointer to the data values */
+ ssize_t buf_left=*buf_size; /* Amount of data buffer left to process */
+
+ if(flags & H5Z_FLAG_REVERSE) { /* read */
+ /* Substract the "add on" value to all the data values */
+ while(buf_left>0) {
+ *int_ptr++ -= (int)ADD_ON;
+ buf_left -= sizeof(int);
+ } /* end while */
+ } /* end if */
+ else { /* write */
+ /* Add the "add on" value to all the data values */
+ while(buf_left>0) {
+ *int_ptr++ += (int)ADD_ON;
+ buf_left -= sizeof(int);
+ } /* end while */
+ } /* end else */
+
+ return nbytes;
+}
+
+/*-------------------------------------------------------------------------
+ * Function: filter_bogus2
+ *
+ * Purpose: A bogus filter that multiplies the original value by FACTOR.
+ *
+ * Return: Success: Data chunk size
+ *
+ * Programmer: Raymond Lu
+ * 30 November 2012
+ *-------------------------------------------------------------------------
+ */
+static size_t
+filter_bogus2(unsigned int flags, size_t UNUSED cd_nelmts,
+ const unsigned int UNUSED *cd_values, size_t nbytes,
+ size_t *buf_size, void **buf)
+{
+ int *int_ptr=(int *)*buf; /* Pointer to the data values */
+ ssize_t buf_left=*buf_size; /* Amount of data buffer left to process */
+
+ if(flags & H5Z_FLAG_REVERSE) { /* read */
+ /* Substract the "add on" value to all the data values */
+ while(buf_left>0) {
+ *int_ptr++ /= (int)FACTOR;
+ buf_left -= sizeof(int);
+ } /* end while */
+ } /* end if */
+ else { /* write */
+ /* Add the "add on" value to all the data values */
+ while(buf_left>0) {
+ *int_ptr++ *= (int)FACTOR;
+ buf_left -= sizeof(int);
+ } /* end while */
+ } /* end else */
+
+ return nbytes;
+}
+
+/*-------------------------------------------------------------------------
+ * Function: test_skip_compress_write2
+ *
+ * Purpose: Test skipping compression filter when there are three filters
+ * for the dataset
+ *
+ * Return: Success: 0
+ *
+ * Failure: 1
+ *
+ * Programmer: Raymond Lu
+ * 30 November 2012
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+test_skip_compress_write2(hid_t file)
+{
+ hid_t dataspace = -1, dataset = -1;
+ hid_t mem_space = -1;
+ hid_t cparms = -1, dxpl = -1;
+ hsize_t dims[2] = {NX, NY};
+ hsize_t maxdims[2] = {H5S_UNLIMITED, H5S_UNLIMITED};
+ hsize_t chunk_dims[2] ={CHUNK_NX, CHUNK_NY};
+ herr_t status;
+ int i, j, n;
+
+ unsigned filter_mask = 0;
+ int origin_direct_buf[CHUNK_NX][CHUNK_NY];
+ int direct_buf[CHUNK_NX][CHUNK_NY];
+ int check_chunk[CHUNK_NX][CHUNK_NY];
+ hsize_t offset[2] = {0, 0};
+ size_t buf_size = CHUNK_NX*CHUNK_NY*sizeof(int);
+ int aggression = 9; /* Compression aggression setting */
+
+ hsize_t start[2]; /* Start of hyperslab */
+ hsize_t stride[2]; /* Stride of hyperslab */
+ hsize_t count[2]; /* Block count */
+ hsize_t block[2]; /* Block sizes */
+
+ TESTING("skipping compression filters but keep two other filters");
+
+ /*
+ * Create the data space with unlimited dimensions.
+ */
+ if((dataspace = H5Screate_simple(RANK, dims, maxdims)) < 0)
+ goto error;
+
+ if((mem_space = H5Screate_simple(RANK, chunk_dims, NULL)) < 0)
+ goto error;
+
+ /*
+ * Modify dataset creation properties, i.e. enable chunking and compression.
+ * The order of filters is bogus 1 + deflate + bogus 2.
+ */
+ if((cparms = H5Pcreate(H5P_DATASET_CREATE)) < 0)
+ goto error;
+
+ if((status = H5Pset_chunk( cparms, RANK, chunk_dims)) < 0)
+ goto error;
+
+ /* Register and enable first bogus filter */
+ if(H5Zregister (H5Z_BOGUS1) < 0)
+ goto error;
+
+ if(H5Pset_filter(cparms, H5Z_FILTER_BOGUS1, 0, (size_t)0, NULL) < 0)
+ goto error;
+
+ /* Enable compression filter */
+ if((status = H5Pset_deflate( cparms, (unsigned) aggression)) < 0)
+ goto error;
+
+ /* Register and enable second bogus filter */
+ if(H5Zregister (H5Z_BOGUS2) < 0)
+ goto error;
+
+ if(H5Pset_filter(cparms, H5Z_FILTER_BOGUS2, 0, (size_t)0, NULL) < 0)
+ goto error;
+
+ /*
+ * Create a new dataset within the file using cparms
+ * creation properties.
+ */
+ if((dataset = H5Dcreate2(file, DATASETNAME3, H5T_NATIVE_INT, dataspace, H5P_DEFAULT,
+ cparms, H5P_DEFAULT)) < 0)
+ goto error;
+
+ if((dxpl = H5Pcreate(H5P_DATASET_XFER)) < 0)
+ goto error;
+
+ /* Initialize data for one chunk. Apply operations of two bogus filters to the chunk */
+ for(i = n = 0; i < CHUNK_NX; i++)
+ for(j = 0; j < CHUNK_NY; j++) {
+ origin_direct_buf[i][j] = n++;
+ direct_buf[i][j] = (origin_direct_buf[i][j] + ADD_ON) * FACTOR;
+ }
+
+ /* write the uncompressed chunk data repeatedly to dataset, using the direct writing function.
+ * Indicate skipping the compression filter but keep the other two bogus filters */
+ offset[0] = CHUNK_NX;
+ offset[1] = CHUNK_NY;
+
+ /* compression filter is the middle one to be skipped */
+ filter_mask = 0x00000002;
+
+ if((status = H5DOwrite_chunk(dataset, dxpl, filter_mask, offset, buf_size, direct_buf)) < 0)
+ goto error;
+
+ if(H5Fflush(dataset, H5F_SCOPE_LOCAL) < 0)
+ goto error;
+
+ if(H5Dclose(dataset) < 0)
+ goto error;
+
+ if((dataset = H5Dopen2(file, DATASETNAME3, H5P_DEFAULT)) < 0)
+ goto error;
+
+ /*
+ * Select hyperslab for one chunk in the file
+ */
+ start[0] = CHUNK_NX; start[1] = CHUNK_NY;
+ stride[0] = 1; stride[1] = 1;
+ count[0] = 1; count[1] = 1;
+ block[0] = CHUNK_NX; block[1] = CHUNK_NY;
+ if((status = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, start, stride, count, block)) < 0)
+ goto error;
+
+ /* Read the chunk back */
+ if((status = H5Dread(dataset, H5T_NATIVE_INT, mem_space, dataspace, H5P_DEFAULT, check_chunk)) < 0)
+ goto error;
+
+ /* Check that the values read are the same as the values written */
+ for(i = 0; i < CHUNK_NX; i++) {
+ for(j = 0; j < CHUNK_NY; j++) {
+ if(origin_direct_buf[i][j] != check_chunk[i][j]) {
+ printf(" 1. Read different values than written.");
+ printf(" At index %d,%d\n", i, j);
+ printf(" origin_direct_buf=%d, check_chunk=%d\n", origin_direct_buf[i][j], check_chunk[i][j]);
+ goto error;
+ }
+ }
+ }
+
+ /*
+ * Close/release resources.
+ */
+ H5Dclose(dataset);
+ H5Sclose(mem_space);
+ H5Sclose(dataspace);
+ H5Pclose(cparms);
+ H5Pclose(dxpl);
+
+ PASSED();
+ return 0;
+
+error:
+ H5E_BEGIN_TRY {
+ H5Dclose(dataset);
+ H5Sclose(mem_space);
+ H5Sclose(dataspace);
+ H5Pclose(cparms);
+ H5Pclose(dxpl);
+ } H5E_END_TRY;
+
+ return 1;
+}
+
+/*-------------------------------------------------------------------------
+ * Function: test_data_conv
+ *
+ * Purpose: Test data conversion
+ *
+ * Return: Success: 0
+ *
+ * Failure: 1
+ *
+ * Programmer: Raymond Lu
+ * 30 November 2012
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+test_data_conv(hid_t file)
+{
+ typedef struct {
+ int a, b, c[4], d, e;
+ } src_type_t;
+ typedef struct {
+ int a, c[4], e;
+ } dst_type_t;
+
+ hid_t dataspace = -1, dataset = -1;
+ hid_t mem_space = -1;
+ hid_t cparms = -1, dxpl = -1;
+ hsize_t dims[2] = {NX, NY};
+ hsize_t maxdims[2] = {H5S_UNLIMITED, H5S_UNLIMITED};
+ hsize_t chunk_dims[2] ={CHUNK_NX, CHUNK_NY};
+ herr_t status;
+ int i, j, n;
+ const hsize_t four = 4;
+ hid_t st=-1, dt=-1;
+ hid_t array_dt;
+
+ unsigned filter_mask = 0;
+ src_type_t direct_buf[CHUNK_NX][CHUNK_NY];
+ dst_type_t check_chunk[CHUNK_NX][CHUNK_NY];
+ hsize_t offset[2] = {0, 0};
+ size_t buf_size = CHUNK_NX*CHUNK_NY*sizeof(src_type_t);
+
+ hsize_t start[2]; /* Start of hyperslab */
+ hsize_t stride[2]; /* Stride of hyperslab */
+ hsize_t count[2]; /* Block count */
+ hsize_t block[2]; /* Block sizes */
+
+ TESTING("data conversion for H5DOwrite_chunk");
+
+ /*
+ * Create the data space with unlimited dimensions.
+ */
+ if((dataspace = H5Screate_simple(RANK, dims, maxdims)) < 0)
+ goto error;
+
+ if((mem_space = H5Screate_simple(RANK, chunk_dims, NULL)) < 0)
+ goto error;
+
+ /*
+ * Modify dataset creation properties, i.e. enable chunking
+ */
+ if((cparms = H5Pcreate(H5P_DATASET_CREATE)) < 0)
+ goto error;
+
+ if((status = H5Pset_chunk( cparms, RANK, chunk_dims)) < 0)
+ goto error;
+
+ /* Build hdf5 datatypes */
+ array_dt = H5Tarray_create2(H5T_NATIVE_INT, 1, &four);
+ if((st = H5Tcreate(H5T_COMPOUND, sizeof(src_type_t))) < 0 ||
+ H5Tinsert(st, "a", HOFFSET(src_type_t, a), H5T_NATIVE_INT) < 0 ||
+ H5Tinsert(st, "b", HOFFSET(src_type_t, b), H5T_NATIVE_INT) < 0 ||
+ H5Tinsert(st, "c", HOFFSET(src_type_t, c), array_dt) < 0 ||
+ H5Tinsert(st, "d", HOFFSET(src_type_t, d), H5T_NATIVE_INT) < 0 ||
+ H5Tinsert(st, "e", HOFFSET(src_type_t, e), H5T_NATIVE_INT) < 0)
+ goto error;
+
+ if(H5Tclose(array_dt) < 0)
+ goto error;
+
+ array_dt = H5Tarray_create2(H5T_NATIVE_INT, 1, &four);
+ if((dt = H5Tcreate(H5T_COMPOUND, sizeof(dst_type_t))) < 0 ||
+ H5Tinsert(dt, "a", HOFFSET(dst_type_t, a), H5T_NATIVE_INT) < 0 ||
+ H5Tinsert(dt, "c", HOFFSET(dst_type_t, c), array_dt) < 0 ||
+ H5Tinsert(dt, "e", HOFFSET(dst_type_t, e), H5T_NATIVE_INT) < 0)
+ goto error;
+
+ if(H5Tclose(array_dt) < 0)
+ goto error;
+
+ /*
+ * Create a new dataset within the file using cparms
+ * creation properties.
+ */
+ if((dataset = H5Dcreate2(file, DATASETNAME4, st, dataspace, H5P_DEFAULT,
+ cparms, H5P_DEFAULT)) < 0)
+ goto error;
+
+ if((dxpl = H5Pcreate(H5P_DATASET_XFER)) < 0)
+ goto error;
+
+ /* Initialize data for one chunk */
+ for(i = n = 0; i < CHUNK_NX; i++) {
+ for(j = 0; j < CHUNK_NY; j++) {
+ (direct_buf[i][j]).a = i*j+0;
+ (direct_buf[i][j]).b = i*j+1;
+ (direct_buf[i][j]).c[0] = i*j+2;
+ (direct_buf[i][j]).c[1] = i*j+3;
+ (direct_buf[i][j]).c[2] = i*j+4;
+ (direct_buf[i][j]).c[3] = i*j+5;
+ (direct_buf[i][j]).d = i*j+6;
+ (direct_buf[i][j]).e = i*j+7;
+ }
+ }
+
+ /* write the chunk data to dataset, using the direct writing function.
+ * There should be no data conversion involved. */
+ offset[0] = CHUNK_NX;
+ offset[1] = CHUNK_NY;
+
+ if((status = H5DOwrite_chunk(dataset, dxpl, filter_mask, offset, buf_size, direct_buf)) < 0)
+ goto error;
+
+ if(H5Fflush(dataset, H5F_SCOPE_LOCAL) < 0)
+ goto error;
+
+ if(H5Dclose(dataset) < 0)
+ goto error;
+
+ if((dataset = H5Dopen2(file, DATASETNAME4, H5P_DEFAULT)) < 0)
+ goto error;
+
+ /*
+ * Select hyperslab for the chunk just written in the file
+ */
+ start[0] = CHUNK_NX; start[1] = CHUNK_NY;
+ stride[0] = 1; stride[1] = 1;
+ count[0] = 1; count[1] = 1;
+ block[0] = CHUNK_NX; block[1] = CHUNK_NY;
+ if((status = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, start, stride, count, block)) < 0)
+ goto error;
+
+ /* Read the chunk back. Data should be converted */
+ if((status = H5Dread(dataset, dt, mem_space, dataspace, H5P_DEFAULT, check_chunk)) < 0)
+ goto error;
+
+ /* Check that the values read are the same as the values written */
+ for(i = 0; i < CHUNK_NX; i++) {
+ for(j = 0; j < CHUNK_NY; j++) {
+ if ((direct_buf[i][j]).a != (check_chunk[i][j]).a ||
+ (direct_buf[i][j]).c[0] != (check_chunk[i][j]).c[0] ||
+ (direct_buf[i][j]).c[1] != (check_chunk[i][j]).c[1] ||
+ (direct_buf[i][j]).c[2] != (check_chunk[i][j]).c[2] ||
+ (direct_buf[i][j]).c[3] != (check_chunk[i][j]).c[3] ||
+ (direct_buf[i][j]).e != (check_chunk[i][j]).e) {
+ printf(" 1. Read different values than written.");
+ printf(" At index %d,%d\n", i, j);
+ printf(" src={a=%d, b=%d, c=[%d,%d,%d,%d], d=%d, e=%d\n",
+ (direct_buf[i][j]).a, (direct_buf[i][j]).b, (direct_buf[i][j]).c[0], (direct_buf[i][j]).c[1],
+ (direct_buf[i][j]).c[2], (direct_buf[i][j]).c[3], (direct_buf[i][j]).d, (direct_buf[i][j]).e);
+ printf(" dst={a=%d, c=[%d,%d,%d,%d], e=%d\n",
+ (check_chunk[i][j]).a, (check_chunk[i][j]).c[0], (check_chunk[i][j]).c[1], (check_chunk[i][j]).c[2],
+ (check_chunk[i][j]).c[3], (check_chunk[i][j]).e);
+
+ goto error;
+ }
+ }
+ }
+
+ /*
+ * Close/release resources.
+ */
+ H5Dclose(dataset);
+ H5Sclose(mem_space);
+ H5Sclose(dataspace);
+ H5Pclose(cparms);
+ H5Pclose(dxpl);
+ H5Tclose(st);
+ H5Tclose(dt);
+
+
+ PASSED();
+ return 0;
+
+error:
+ H5E_BEGIN_TRY {
+ H5Dclose(dataset);
+ H5Sclose(mem_space);
+ H5Sclose(dataspace);
+ H5Pclose(cparms);
+ H5Pclose(dxpl);
+ H5Tclose(st);
+ H5Tclose(dt);
+ } H5E_END_TRY;
+
+ return 1;
+}
+
+/*-------------------------------------------------------------------------
+ * Function: test_invalid_parameters
+ *
+ * Purpose: Test invalid parameters for H5DOwrite_chunk
+ *
+ * Return: Success: 0
+ *
+ * Failure: 1
+ *
+ * Programmer: Raymond Lu
+ * 30 November 2012
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+test_invalid_parameters(hid_t file)
+{
+ hid_t dataspace = -1, dataset = -1;
+ hid_t mem_space = -1;
+ hid_t cparms = -1, dxpl = -1;
+ hsize_t dims[2] = {NX, NY};
+ hsize_t chunk_dims[2] ={CHUNK_NX, CHUNK_NY};
+ herr_t status;
+ int i, j, n;
+
+ unsigned filter_mask = 0;
+ int direct_buf[CHUNK_NX][CHUNK_NY];
+ hsize_t offset[2] = {0, 0};
+ size_t buf_size = CHUNK_NX*CHUNK_NY*sizeof(int);
+ int aggression = 9; /* Compression aggression setting */
+
+ TESTING("invalid parameters for H5DOwrite_chunk");
+
+ /*
+ * Create the data space with unlimited dimensions.
+ */
+ if((dataspace = H5Screate_simple(RANK, dims, NULL)) < 0)
+ goto error;
+
+ if((mem_space = H5Screate_simple(RANK, chunk_dims, NULL)) < 0)
+ goto error;
+
+ /*
+ * Modify dataset creation properties
+ */
+ if((cparms = H5Pcreate(H5P_DATASET_CREATE)) < 0)
+ goto error;
+
+ /*
+ * Create a new contiguous dataset to verify H5DOwrite_chunk doesn't work
+ */
+ if((dataset = H5Dcreate2(file, DATASETNAME5, H5T_NATIVE_INT, dataspace, H5P_DEFAULT,
+ cparms, H5P_DEFAULT)) < 0)
+ goto error;
+
+ if((dxpl = H5Pcreate(H5P_DATASET_XFER)) < 0)
+ goto error;
+
+ /* Initialize data for one chunk */
+ for(i = n = 0; i < CHUNK_NX; i++)
+ for(j = 0; j < CHUNK_NY; j++) {
+ direct_buf[i][j] = n++;
+ }
+
+ /* Try to write the chunk data to contiguous dataset. It should fail */
+ offset[0] = CHUNK_NX;
+ offset[1] = CHUNK_NY;
+
+ H5E_BEGIN_TRY {
+ if((status = H5DOwrite_chunk(dataset, dxpl, filter_mask, offset, buf_size, direct_buf)) != FAIL)
+ goto error;
+ } H5E_END_TRY;
+
+ if(H5Dclose(dataset) < 0)
+ goto error;
+
+ /* Create a chunked dataset with compression filter */
+ if((status = H5Pset_chunk( cparms, RANK, chunk_dims)) < 0)
+ goto error;
+
+ if((status = H5Pset_deflate( cparms, (unsigned ) aggression)) < 0)
+ goto error;
+
+ /*
+ * Create a new dataset within the file using cparms
+ * creation properties.
+ */
+ if((dataset = H5Dcreate2(file, DATASETNAME6, H5T_NATIVE_INT, dataspace, H5P_DEFAULT,
+ cparms, H5P_DEFAULT)) < 0)
+ goto error;
+
+ /* Check invalid dataset ID */
+ H5E_BEGIN_TRY {
+ if((status = H5DOwrite_chunk(-1, dxpl, filter_mask, offset, buf_size, direct_buf)) != FAIL)
+ goto error;
+ } H5E_END_TRY;
+
+ /* Check invalid DXPL ID */
+ H5E_BEGIN_TRY {
+ if((status = H5DOwrite_chunk(dataset, -1, filter_mask, offset, buf_size, direct_buf)) != FAIL)
+ goto error;
+ } H5E_END_TRY;
+
+ /* Check invalid OFFSET */
+ H5E_BEGIN_TRY {
+ if((status = H5DOwrite_chunk(dataset, dxpl, filter_mask, NULL, buf_size, direct_buf)) != FAIL)
+ goto error;
+ } H5E_END_TRY;
+
+ /* Check when OFFSET is out of dataset range */
+ offset[0] = NX + 1;
+ offset[1] = NY;
+ H5E_BEGIN_TRY {
+ if((status = H5DOwrite_chunk(dataset, dxpl, filter_mask, offset, buf_size, direct_buf)) != FAIL)
+ goto error;
+ } H5E_END_TRY;
+
+ /* Check when OFFSET is not on chunk boundary */
+ offset[0] = CHUNK_NX;
+ offset[1] = CHUNK_NY + 1;
+ H5E_BEGIN_TRY {
+ if((status = H5DOwrite_chunk(dataset, dxpl, filter_mask, offset, buf_size, direct_buf)) != FAIL)
+ goto error;
+ } H5E_END_TRY;
+
+ /* Check invalid buffer size */
+ offset[0] = CHUNK_NX;
+ offset[1] = CHUNK_NY;
+ buf_size = 0;
+ H5E_BEGIN_TRY {
+ if((status = H5DOwrite_chunk(dataset, dxpl, filter_mask, offset, buf_size, direct_buf)) != FAIL)
+ goto error;
+ } H5E_END_TRY;
+
+ /* Check invalid data buffer */
+ buf_size = CHUNK_NX*CHUNK_NY*sizeof(int);
+ H5E_BEGIN_TRY {
+ if((status = H5DOwrite_chunk(dataset, dxpl, filter_mask, offset, buf_size, NULL)) != FAIL)
+ goto error;
+ } H5E_END_TRY;
+
+ if(H5Dclose(dataset) < 0)
+ goto error;
+
+ /*
+ * Close/release resources.
+ */
+ H5Sclose(mem_space);
+ H5Sclose(dataspace);
+ H5Pclose(cparms);
+ H5Pclose(dxpl);
+
+ PASSED();
+ return 0;
+
+error:
+ H5E_BEGIN_TRY {
+ H5Dclose(dataset);
+ H5Sclose(mem_space);
+ H5Sclose(dataspace);
+ H5Pclose(cparms);
+ H5Pclose(dxpl);
+ } H5E_END_TRY;
+
+ return 1;
+}
+
+/*-------------------------------------------------------------------------
+ * Function: Main function
+ *
+ * Purpose: Test direct chunk write function H5DOwrite_chunk
+ *
+ * Return: Success: 0
+ *
+ * Failure: 1
+ *
+ * Programmer: Raymond Lu
+ * 30 November 2012
+ *
+ *-------------------------------------------------------------------------
+ */
+int main( void )
+{
+ hid_t file_id;
+ int nerrors=0;
+
+ /*
+ * Create a new file. If file exists its contents will be overwritten.
+ */
+ if((file_id = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+ goto error;
+
+ /* Test direct chunk write */
+#ifdef H5_HAVE_FILTER_DEFLATE
+ nerrors += test_direct_chunk_write(file_id);
+#endif /* H5_HAVE_FILTER_DEFLATE */
+ nerrors += test_skip_compress_write1(file_id);
+ nerrors += test_skip_compress_write2(file_id);
+ nerrors += test_data_conv(file_id);
+ nerrors += test_invalid_parameters(file_id);
+
+ if(H5Fclose(file_id) < 0)
+ goto error;
+
+ /* check for errors */
+ if (nerrors)
+ goto error;
+
+ return 0;
+
+error:
+ return 1;
+}
diff --git a/hl/test/test_lite.c b/hl/test/test_lite.c
index 2c7594c..5375cde 100644
--- a/hl/test/test_lite.c
+++ b/hl/test/test_lite.c
@@ -51,7 +51,6 @@
static herr_t make_attributes( hid_t loc_id, const char* obj_name );
-
/*-------------------------------------------------------------------------
* test dataset functions
*-------------------------------------------------------------------------
@@ -2145,7 +2144,6 @@ static int test_valid_path(void)
return -1;
}
-
/*-------------------------------------------------------------------------
* the main program
*-------------------------------------------------------------------------
@@ -2174,6 +2172,4 @@ int main( void )
error:
return 1;
-
-
}
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c
index 2d08f67..390857d 100644
--- a/src/H5Dchunk.c
+++ b/src/H5Dchunk.c
@@ -281,6 +281,108 @@ H5FL_DEFINE(H5D_chunk_info_t);
/* Declare a free list to manage the chunk sequence information */
H5FL_BLK_DEFINE_STATIC(chunk);
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__chunk_direct_write
+ *
+ * Purpose: Internal routine to write a chunk
+ * directly into the file.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Raymond Lu
+ * 30 July 2012
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D__chunk_direct_write(const H5D_t *dset, hid_t dxpl_id, uint32_t filters, hsize_t *offset,
+ size_t data_size, const void *buf)
+{
+ const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset layout */
+ H5D_chunk_ud_t udata; /* User data for querying chunk info */
+ hsize_t chunk_idx;
+ H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */
+ H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */
+ const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /*raw data chunk cache */
+ int space_ndims; /* Dataset's space rank */
+ hsize_t space_dim[H5O_LAYOUT_NDIMS]; /* Dataset's dataspace dimensions */
+ H5FD_t *lf;
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_STATIC
+
+ /* Allocate data space and initialize it if it hasn't been. */
+ if(!(*dset->shared->layout.ops->is_space_alloc)(&dset->shared->layout.storage)) {
+ /* Allocate storage */
+ if(H5D__alloc_storage(dset, dxpl_id, H5D_ALLOC_WRITE, FALSE, NULL) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize storage")
+ } /* end if */
+
+
+ /* Retrieve the dataset dimensions */
+ if((space_ndims = H5S_get_simple_extent_dims(dset->shared->space, space_dim, NULL)) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to get simple dataspace info")
+
+ /* Calculate the index of this chunk */
+ if(H5V_chunk_index((unsigned)space_ndims, offset,
+ layout->u.chunk.dim, layout->u.chunk.down_chunks, &chunk_idx) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't get chunk index")
+
+ /* Find out the file address of the chunk */
+ if(H5D__chunk_lookup(dset, dxpl_id, offset, chunk_idx,
+ &udata) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address")
+
+ udata.filter_mask = filters;
+
+ /* Check if the chunk needs to be 'inserted' (could exist already and
+ * the 'insert' operation could resize it)
+ */
+ {
+ H5D_chk_idx_info_t idx_info; /* Chunked index info */
+
+ /* Compose chunked index info struct */
+ idx_info.f = dset->oloc.file;
+ idx_info.dxpl_id = dxpl_id;
+ idx_info.pline = &(dset->shared->dcpl_cache.pline);
+ idx_info.layout = &(dset->shared->layout.u.chunk);
+ idx_info.storage = &(dset->shared->layout.storage.u.chunk);
+
+ /* Set up the size of chunk for user data */
+ udata.nbytes = data_size;
+
+ /* Create the chunk it if it doesn't exist, or reallocate the chunk
+ * if its size changed.
+ */
+ if((dset->shared->layout.storage.u.chunk.ops->insert)(&idx_info, &udata) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert/resize chunk")
+
+ /* Make sure the address of the chunk is returned. */
+ if(!H5F_addr_defined(udata.addr))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "chunk address isn't defined")
+ } /* end if */
+
+ /* Fill the DXPL cache values for later use */
+ if(H5D__get_dxpl_cache(dxpl_id, &dxpl_cache) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
+
+ /* Evict the entry from the cache if present, but do not flush
+ * it to disk */
+ if(UINT_MAX != udata.idx_hint) {
+ if(H5D__chunk_cache_evict(dset, dxpl_id, dxpl_cache,
+ rdcc->slot[udata.idx_hint], FALSE) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTREMOVE, FAIL, "unable to evict chunk")
+ } /* end if */
+
+ /* Write the data to the file */
+ if(H5F_block_write(dset->oloc.file, H5FD_MEM_DRAW, udata.addr, data_size, dxpl_id, buf) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to write raw data to file")
+
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+}
/*-------------------------------------------------------------------------
diff --git a/src/H5Dio.c b/src/H5Dio.c
index 0493a9e..6407ea8 100644
--- a/src/H5Dio.c
+++ b/src/H5Dio.c
@@ -28,6 +28,8 @@
#include "H5Eprivate.h" /* Error handling */
#include "H5FLprivate.h" /* Free Lists */
#include "H5Iprivate.h" /* IDs */
+#include "H5MMprivate.h" /* Memory management */
+#include "H5Sprivate.h" /* Dataspace */
#ifdef H5_HAVE_PARALLEL
/* Remove this if H5R_DATASET_REGION is no longer used in this file */
@@ -56,6 +58,8 @@ static herr_t H5D__read(H5D_t *dataset, hid_t mem_type_id,
static herr_t H5D__write(H5D_t *dataset, hid_t mem_type_id,
const H5S_t *mem_space, const H5S_t *file_space, hid_t dset_xfer_plist,
const void *buf);
+static herr_t H5D__pre_write(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
+ hid_t file_space_id, hid_t dxpl_id, const void *buf);
/* Setup/teardown routines */
static herr_t H5D__ioinfo_init(H5D_t *dset, const H5D_dxpl_cache_t *dxpl_cache,
@@ -136,6 +140,10 @@ H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
if(NULL == dset->oloc.file)
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
+
+ if(mem_space_id < 0 || file_space_id < 0)
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
+
if(H5S_ALL != mem_space_id) {
if(NULL == (mem_space = (const H5S_t *)H5I_object_verify(mem_space_id, H5I_DATASPACE)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
@@ -213,37 +221,51 @@ herr_t
H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
hid_t file_space_id, hid_t dxpl_id, const void *buf)
{
- H5D_t *dset = NULL;
- const H5S_t *mem_space = NULL;
- const H5S_t *file_space = NULL;
- char fake_char;
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_API(FAIL)
H5TRACE6("e", "iiiii*x", dset_id, mem_type_id, mem_space_id, file_space_id,
dxpl_id, buf);
+ if(!dset_id)
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
+
+ if(H5D__pre_write(dset_id, mem_type_id, mem_space_id, file_space_id, dxpl_id, buf) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't prepare for writing data")
+
+done:
+ FUNC_LEAVE_API(ret_value)
+} /* end H5Dwrite() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__pre_write
+ *
+ * Purpose: Preparation for writing data.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Raymond Lu
+ * 2 November 2012
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__pre_write(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
+ hid_t file_space_id, hid_t dxpl_id, const void *buf)
+{
+ H5D_t *dset = NULL;
+ H5P_genplist_t *plist; /* Property list pointer */
+ hbool_t direct_write = FALSE;
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_STATIC
+
/* check arguments */
if(NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
if(NULL == dset->oloc.file)
- HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
- if(H5S_ALL != mem_space_id) {
- if(NULL == (mem_space = (const H5S_t *)H5I_object_verify(mem_space_id, H5I_DATASPACE)))
- HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
-
- /* Check for valid selection */
- if(H5S_SELECT_VALID(mem_space) != TRUE)
- HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "memory selection+offset not within extent")
- } /* end if */
- if(H5S_ALL != file_space_id) {
- if(NULL == (file_space = (const H5S_t *)H5I_object_verify(file_space_id, H5I_DATASPACE)))
- HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
-
- /* Check for valid selection */
- if(H5S_SELECT_VALID(file_space) != TRUE)
- HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "file selection+offset not within extent")
- } /* end if */
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a file")
/* Get the default dataset transfer property list if the user didn't provide one */
if(H5P_DEFAULT == dxpl_id)
@@ -251,23 +273,102 @@ H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
else
if(TRUE != H5P_isa_class(dxpl_id, H5P_DATASET_XFER))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms")
- if(!buf && (NULL == file_space || H5S_GET_SELECT_NPOINTS(file_space) != 0))
- HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer")
- /* If the buffer is nil, and 0 element is selected, make a fake buffer.
- * This is for some MPI package like ChaMPIon on NCSA's tungsten which
- * doesn't support this feature.
- */
- if(!buf)
- buf = &fake_char;
+ /* Get the plist structure */
+ if(NULL == (plist = H5P_object_verify(dxpl_id, H5P_DATASET_XFER)))
+ HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "can't find object for ID")
+
+ if(H5P_get(plist, H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_NAME, &direct_write) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "error getting flag for direct chunk write")
+
+ /* Direct chunk write */
+ if(direct_write) {
+ uint32_t direct_filters = 0;
+ hsize_t *direct_offset;
+ size_t direct_datasize = 0;
+ int ndims = 0;
+ hsize_t dims[H5O_LAYOUT_NDIMS];
+ hsize_t internal_offset[H5O_LAYOUT_NDIMS];
+ int i;
+
+ if(H5D_CHUNKED != dset->shared->layout.type)
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a chunked dataset")
+
+ if(H5P_get(plist, H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_NAME, &direct_filters) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "error getting filter info for direct chunk write")
+
+ if(H5P_get(plist, H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_NAME, &direct_offset) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "error getting offset info for direct chunk write")
+
+ if(H5P_get(plist, H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_NAME, &direct_datasize) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "error getting data size for direct chunk write")
+
+ /* The library's chunking code requires the offset terminates with a zero. So transfer the
+ * offset array to an internal offset array */
+ if((ndims = H5S_get_simple_extent_dims(dset->shared->space, dims, NULL)) < 0)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't retrieve dataspace extent dims")
+
+ for(i=0; i<ndims; i++) {
+ /* Make sure the offset doesn't exceed the dataset's dimensions */
+ if(direct_offset[i] > dims[i])
+ HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "offset exceeds dimensions of dataset")
+
+ /* Make sure the offset fall right on a chunk's boundary */
+ if(direct_offset[i] % dset->shared->layout.u.chunk.dim[i])
+ HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "offset doesn't fall on chunks's boundary")
+
+ internal_offset[i] = direct_offset[i];
+ }
+
+ /* Terminate the offset with a zero */
+ internal_offset[ndims] = 0;
+
+ /* write raw data */
+ if(H5D__chunk_direct_write(dset, dxpl_id, direct_filters, internal_offset, direct_datasize, buf) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write chunk directly")
+ } else { /* Normal write */
+ const H5S_t *mem_space = NULL;
+ const H5S_t *file_space = NULL;
+ char fake_char;
+
+ if(mem_space_id < 0 || file_space_id < 0)
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
- /* write raw data */
- if(H5D__write(dset, mem_type_id, mem_space, file_space, dxpl_id, buf) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data")
+ if(H5S_ALL != mem_space_id) {
+ if(NULL == (mem_space = (const H5S_t *)H5I_object_verify(mem_space_id, H5I_DATASPACE)))
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
+
+ /* Check for valid selection */
+ if(H5S_SELECT_VALID(mem_space) != TRUE)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "memory selection+offset not within extent")
+ } /* end if */
+ if(H5S_ALL != file_space_id) {
+ if(NULL == (file_space = (const H5S_t *)H5I_object_verify(file_space_id, H5I_DATASPACE)))
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
+
+ /* Check for valid selection */
+ if(H5S_SELECT_VALID(file_space) != TRUE)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "file selection+offset not within extent")
+ } /* end if */
+
+ if(!buf && (NULL == file_space || H5S_GET_SELECT_NPOINTS(file_space) != 0))
+ HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer")
+
+ /* If the buffer is nil, and 0 element is selected, make a fake buffer.
+ * This is for some MPI package like ChaMPIon on NCSA's tungsten which
+ * doesn't support this feature.
+ */
+ if(!buf)
+ buf = &fake_char;
+
+ /* write raw data */
+ if(H5D__write(dset, mem_type_id, mem_space, file_space, dxpl_id, buf) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data")
+ }
done:
- FUNC_LEAVE_API(ret_value)
-} /* end H5Dwrite() */
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D__pre_write() */
/*-------------------------------------------------------------------------
diff --git a/src/H5Dprivate.h b/src/H5Dprivate.h
index 16c374e..61bcf47 100644
--- a/src/H5Dprivate.h
+++ b/src/H5Dprivate.h
@@ -176,5 +176,8 @@ H5_DLL herr_t H5D_chunk_idx_reset(H5O_storage_chunk_t *storage, hbool_t reset_ad
H5_DLL herr_t H5D_btree_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE * stream,
int indent, int fwidth, unsigned ndims);
+H5_DLL herr_t H5D__chunk_direct_write(const H5D_t *dset, hid_t dxpl_id, uint32_t filters,
+ hsize_t *offset, size_t data_size, const void *buf);
+
#endif /* _H5Dprivate_H */
diff --git a/src/H5Dpublic.h b/src/H5Dpublic.h
index c878d4a..523f2b2 100644
--- a/src/H5Dpublic.h
+++ b/src/H5Dpublic.h
@@ -34,6 +34,12 @@
#define H5D_CHUNK_CACHE_NBYTES_DEFAULT ((size_t) -1)
#define H5D_CHUNK_CACHE_W0_DEFAULT -1.
+/* Property names for H5LTDdirect_chunk_write */
+#define H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_NAME "direct_chunk_flag"
+#define H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_NAME "direct_chunk_filters"
+#define H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_NAME "direct_chunk_offset"
+#define H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_NAME "direct_chunk_datasize"
+
/*******************/
/* Public Typedefs */
/*******************/
diff --git a/src/H5Pdxpl.c b/src/H5Pdxpl.c
index 4c98dd6..30d13bb 100644
--- a/src/H5Pdxpl.c
+++ b/src/H5Pdxpl.c
@@ -128,6 +128,15 @@
#define H5D_XFER_XFORM_COPY H5P__dxfr_xform_copy
#define H5D_XFER_XFORM_CMP H5P__dxfr_xform_cmp
#define H5D_XFER_XFORM_CLOSE H5P__dxfr_xform_close
+/* Definitions for properties of direct chunk write */
+#define H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_SIZE sizeof(hbool_t)
+#define H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_DEF FALSE
+#define H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_SIZE sizeof(uint32_t)
+#define H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_DEF 0
+#define H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_SIZE sizeof(hsize_t *)
+#define H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_DEF NULL
+#define H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_SIZE sizeof(size_t)
+#define H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_DEF 0
/******************/
/* Local Typedefs */
@@ -220,6 +229,10 @@ H5P__dxfr_reg_prop(H5P_genclass_t *pclass)
H5Z_cb_t filter_cb = H5D_XFER_FILTER_CB_DEF; /* Default value for filter callback */
H5T_conv_cb_t conv_cb = H5D_XFER_CONV_CB_DEF; /* Default value for datatype conversion callback */
void *def_xfer_xform = H5D_XFER_XFORM_DEF; /* Default value for data transform */
+ hbool_t direct_chunk_flag = H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_DEF; /* Default value for the flag of direct chunk write */
+ uint32_t direct_chunk_filters = H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_DEF; /* Default value for the filters of direct chunk write */
+ hsize_t *direct_chunk_offset = H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_DEF; /* Default value for the offset of direct chunk write */
+ size_t direct_chunk_datasize = H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_DEF; /* Default value for the datasize of direct chunk write */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_STATIC
@@ -320,6 +333,30 @@ H5P__dxfr_reg_prop(H5P_genclass_t *pclass)
if(H5P_register_real(pclass, H5D_XFER_XFORM_NAME, H5D_XFER_XFORM_SIZE, &def_xfer_xform, NULL, NULL, NULL, H5D_XFER_XFORM_DEL, H5D_XFER_XFORM_COPY, H5D_XFER_XFORM_CMP, H5D_XFER_XFORM_CLOSE) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class")
+ /* Register the property of flag for direct chunk write */
+ /* (Note: this property should not have an encode/decode callback -QAK) */
+ if(H5P_register_real(pclass, H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_NAME, H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_SIZE, &direct_chunk_flag,
+ NULL, NULL, NULL, NULL, NULL, NULL, NULL) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class")
+
+ /* Register the property of filter for direct chunk write */
+ /* (Note: this property should not have an encode/decode callback -QAK) */
+ if(H5P_register_real(pclass, H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_NAME, H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_SIZE, &direct_chunk_filters,
+ NULL, NULL, NULL, NULL, NULL, NULL, NULL) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class")
+
+ /* Register the property of offset for direct chunk write */
+ /* (Note: this property should not have an encode/decode callback -QAK) */
+ if(H5P_register_real(pclass, H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_NAME, H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_SIZE, &direct_chunk_offset,
+ NULL, NULL, NULL, NULL, NULL, NULL, NULL) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class")
+
+ /* Register the property of datasize for direct chunk write */
+ /* (Note: this property should not have an encode/decode callback -QAK) */
+ if(H5P_register_real(pclass, H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_NAME, H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_SIZE, &direct_chunk_datasize,
+ NULL, NULL, NULL, NULL, NULL, NULL, NULL) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class")
+
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5P__dxfr_reg_prop() */
diff --git a/test/testfiles/err_compat_1 b/test/testfiles/err_compat_1
index e2b37ab..5f4fd47 100644
--- a/test/testfiles/err_compat_1
+++ b/test/testfiles/err_compat_1
@@ -57,6 +57,9 @@ HDF5-DIAG: Error detected in HDF5 (version (number)) thread (IDs):
#001: (file name) line (number) in test_error2(): H5Dwrite shouldn't succeed
major: Error API
minor: Write failed
- #002: (file name) line (number) in H5Dwrite(): not a dataset
+ #002: (file name) line (number) in H5Dwrite(): can't prepare for writing data
+ major: Dataset
+ minor: Write failed
+ #003: (file name) line (number) in H5D__pre_write(): not a dataset
major: Invalid arguments to routine
minor: Inappropriate type
generated by cgit v0.12 at 2024-07-18 06:02:42 (GMT)