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[svn-r23162] synchronized DECTRIS branch (r23161) with the trunk

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This commit is contained in:
Raymond Lu 2013-01-14 15:40:19 -05:00
commit ec704e0077
20 changed files with 2321 additions and 55 deletions
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5
MANIFEST
View File

@ -2157,6 +2157,9 @@
./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
@ -2195,8 +2198,10 @@
./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

2
hl/src/CMakeLists.txt
View File

@ -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

137
hl/src/H5DO.c Normal file
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@ -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;
}

37
hl/src/H5DOprivate.h Normal file
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@ -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

42
hl/src/H5DOpublic.h Normal file
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@ -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

4
hl/src/Makefile.am
View File

@ -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

9
hl/src/Makefile.in
View File

@ -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@

1
hl/src/hdf5_hl.h
View File

@ -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 */

2
hl/test/CMakeLists.txt
View File

@ -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 "")

5
hl/test/Makefile.am
View File

@ -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

24
hl/test/Makefile.in
View File

@ -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@

643
hl/test/dectris_hl_perf.c Normal file
View File

@ -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;
}

1138
hl/test/test_dset_opt.c Normal file
View File

File diff suppressed because it is too large Load Diff

4
hl/test/test_lite.c
View File

@ -51,7 +51,6 @@
static herr_t make_attributes( hid_t loc_id, const char* obj_name );
/*-------------------------------------------------------------------------
* test dataset functions
*-------------------------------------------------------------------------
@ -2137,7 +2136,6 @@ static int test_valid_path(void)
return -1;
}
/*-------------------------------------------------------------------------
* the main program
*-------------------------------------------------------------------------
@ -2166,6 +2164,4 @@ int main( void )
error:
return 1;
}

102
src/H5Dchunk.c
View File

@ -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_TAG(dxpl_id, dset->oloc.addr, FAIL)
/* 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_TAG(ret_value, FAIL)
}
/*-------------------------------------------------------------------------

169
src/H5Dio.c
View File

@ -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")
/* 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(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")
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() */
/*-------------------------------------------------------------------------

3
src/H5Dprivate.h
View File

@ -174,5 +174,8 @@ 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 */

6
src/H5Dpublic.h
View File

@ -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 */
/*******************/

38
src/H5Pdxpl.c
View File

@ -158,6 +158,15 @@
#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 */
@ -255,7 +264,10 @@ static const H5Z_EDC_t H5D_def_enable_edc_g = H5D_XFER_EDC_DEF; /* De
static const H5Z_cb_t H5D_def_filter_cb_g = H5D_XFER_FILTER_CB_DEF; /* Default value for filter callback */
static const H5T_conv_cb_t H5D_def_conv_cb_g = H5D_XFER_CONV_CB_DEF; /* Default value for datatype conversion callback */
static const void *H5D_def_xfer_xform_g = H5D_XFER_XFORM_DEF; /* Default value for data transform */
static const hbool_t H5D_def_direct_chunk_flag_g = H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_DEF; /* Default value for the flag of direct chunk write */
static const uint32_t H5D_def_direct_chunk_filters_g = H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_DEF; /* Default value for the filters of direct chunk write */
static const hsize_t *H5D_def_direct_chunk_offset_g = H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_DEF; /* Default value for the offset of direct chunk write */
static const size_t H5D_def_direct_chunk_datasize_g = H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_DEF; /* Default value for the datasize of direct chunk write */
/*-------------------------------------------------------------------------
@ -426,6 +438,30 @@ H5P__dxfr_reg_prop(H5P_genclass_t *pclass)
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, &H5D_def_direct_chunk_flag_g,
NULL, NULL, 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, &H5D_def_direct_chunk_filters_g,
NULL, NULL, 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, &H5D_def_direct_chunk_offset_g,
NULL, NULL, 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, &H5D_def_direct_chunk_datasize_g,
NULL, NULL, 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() */

5
test/testfiles/err_compat_1
View File

@ -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