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-rw-r--r--config/linux-gnulibc110
-rwxr-xr-xconfigure67
-rw-r--r--configure.in19
-rw-r--r--src/H5Dio.c24
-rw-r--r--src/H5Dmpio.c98
-rw-r--r--testpar/t_dset.c212
-rw-r--r--testpar/testphdf5.c3
-rw-r--r--testpar/testphdf5.h1
8 files changed, 392 insertions, 42 deletions
diff --git a/config/linux-gnulibc1 b/config/linux-gnulibc1
index 5ece750..015d079 100644
--- a/config/linux-gnulibc1
+++ b/config/linux-gnulibc1
@@ -116,6 +116,16 @@ fi
# Check MPICH settings
. $srcdir/config/mpich
+
+# The ChaMPIon on NCSA tungsten doesn't work correctly for either of the following
+# cases:
+# 1. collective I/O when some processes don't have any contributions;
+# 2. complex derived MPI data type.
+if test $CC_BASENAME = cmpicc; then
+ hdf5_mpi_special_collective_io_works=${hdf5_mpi_special_collective_io_works='no'}
+ hdf5_mpi_complex_derived_datatype_works=${hdf5_mpi_complex_derived_datatype_works='no'}
+fi
+
#Comment out the following line if your system supports collective IO when some processes
#don't have any contributions to IOs.
#hdf5_mpi_special_collective_io_works=${hdf5_mpi_special_collective_io_works='no'}
diff --git a/configure b/configure
index edd71b6..adc1755 100755
--- a/configure
+++ b/configure
@@ -1,5 +1,5 @@
#! /bin/sh
-# From configure.in Id: configure.in 14047 2007-08-07 21:01:15Z mcgreevy .
+# From configure.in Id: configure.in 14061 2007-08-09 19:46:44Z mcgreevy .
# Guess values for system-dependent variables and create Makefiles.
# Generated by GNU Autoconf 2.61 for HDF5 1.8.0-beta3post1.
#
@@ -7028,6 +7028,25 @@ echo "${ECHO_T}none" >&6; }
PARALLEL="$CC_BASENAME"
;;
+ cmpicc)
+ PARALLEL=cmpicc
+ { echo "$as_me:$LINENO: checking for cmpirun" >&5
+echo $ECHO_N "checking for cmpirun... $ECHO_C" >&6; }
+
+ if test -x cmpirun; then
+ { echo "$as_me:$LINENO: result: cmpirun" >&5
+echo "${ECHO_T}cmpirun" >&6; }
+ RUNSERIAL="${RUNSERIAL:-none}"
+
+ if test -z "$RUNPARALLEL"; then
+ RUNPARALLEL="cmpirun -np \$\${NPROCS:=3}"
+ fi
+ else
+ { echo "$as_me:$LINENO: result: none" >&5
+echo "${ECHO_T}none" >&6; }
+ fi
+ ;;
+
*)
;;
esac
@@ -7907,7 +7926,7 @@ ia64-*-hpux*)
;;
*-*-irix6*)
# Find out which ABI we are using.
- echo '#line 7910 "configure"' > conftest.$ac_ext
+ echo '#line 7929 "configure"' > conftest.$ac_ext
if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
(eval $ac_compile) 2>&5
ac_status=$?
@@ -10181,11 +10200,11 @@ else
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
- (eval echo "\"\$as_me:10184: $lt_compile\"" >&5)
+ (eval echo "\"\$as_me:10203: $lt_compile\"" >&5)
(eval "$lt_compile" 2>conftest.err)
ac_status=$?
cat conftest.err >&5
- echo "$as_me:10188: \$? = $ac_status" >&5
+ echo "$as_me:10207: \$? = $ac_status" >&5
if (exit $ac_status) && test -s "$ac_outfile"; then
# The compiler can only warn and ignore the option if not recognized
# So say no if there are warnings other than the usual output.
@@ -10449,11 +10468,11 @@ else
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
- (eval echo "\"\$as_me:10452: $lt_compile\"" >&5)
+ (eval echo "\"\$as_me:10471: $lt_compile\"" >&5)
(eval "$lt_compile" 2>conftest.err)
ac_status=$?
cat conftest.err >&5
- echo "$as_me:10456: \$? = $ac_status" >&5
+ echo "$as_me:10475: \$? = $ac_status" >&5
if (exit $ac_status) && test -s "$ac_outfile"; then
# The compiler can only warn and ignore the option if not recognized
# So say no if there are warnings other than the usual output.
@@ -10553,11 +10572,11 @@ else
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
- (eval echo "\"\$as_me:10556: $lt_compile\"" >&5)
+ (eval echo "\"\$as_me:10575: $lt_compile\"" >&5)
(eval "$lt_compile" 2>out/conftest.err)
ac_status=$?
cat out/conftest.err >&5
- echo "$as_me:10560: \$? = $ac_status" >&5
+ echo "$as_me:10579: \$? = $ac_status" >&5
if (exit $ac_status) && test -s out/conftest2.$ac_objext
then
# The compiler can only warn and ignore the option if not recognized
@@ -12933,7 +12952,7 @@ else
lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
lt_status=$lt_dlunknown
cat > conftest.$ac_ext <<EOF
-#line 12936 "configure"
+#line 12955 "configure"
#include "confdefs.h"
#if HAVE_DLFCN_H
@@ -13033,7 +13052,7 @@ else
lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
lt_status=$lt_dlunknown
cat > conftest.$ac_ext <<EOF
-#line 13036 "configure"
+#line 13055 "configure"
#include "confdefs.h"
#if HAVE_DLFCN_H
@@ -15385,11 +15404,11 @@ else
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
- (eval echo "\"\$as_me:15388: $lt_compile\"" >&5)
+ (eval echo "\"\$as_me:15407: $lt_compile\"" >&5)
(eval "$lt_compile" 2>conftest.err)
ac_status=$?
cat conftest.err >&5
- echo "$as_me:15392: \$? = $ac_status" >&5
+ echo "$as_me:15411: \$? = $ac_status" >&5
if (exit $ac_status) && test -s "$ac_outfile"; then
# The compiler can only warn and ignore the option if not recognized
# So say no if there are warnings other than the usual output.
@@ -15489,11 +15508,11 @@ else
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
- (eval echo "\"\$as_me:15492: $lt_compile\"" >&5)
+ (eval echo "\"\$as_me:15511: $lt_compile\"" >&5)
(eval "$lt_compile" 2>out/conftest.err)
ac_status=$?
cat out/conftest.err >&5
- echo "$as_me:15496: \$? = $ac_status" >&5
+ echo "$as_me:15515: \$? = $ac_status" >&5
if (exit $ac_status) && test -s out/conftest2.$ac_objext
then
# The compiler can only warn and ignore the option if not recognized
@@ -17059,11 +17078,11 @@ else
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
- (eval echo "\"\$as_me:17062: $lt_compile\"" >&5)
+ (eval echo "\"\$as_me:17081: $lt_compile\"" >&5)
(eval "$lt_compile" 2>conftest.err)
ac_status=$?
cat conftest.err >&5
- echo "$as_me:17066: \$? = $ac_status" >&5
+ echo "$as_me:17085: \$? = $ac_status" >&5
if (exit $ac_status) && test -s "$ac_outfile"; then
# The compiler can only warn and ignore the option if not recognized
# So say no if there are warnings other than the usual output.
@@ -17163,11 +17182,11 @@ else
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
- (eval echo "\"\$as_me:17166: $lt_compile\"" >&5)
+ (eval echo "\"\$as_me:17185: $lt_compile\"" >&5)
(eval "$lt_compile" 2>out/conftest.err)
ac_status=$?
cat out/conftest.err >&5
- echo "$as_me:17170: \$? = $ac_status" >&5
+ echo "$as_me:17189: \$? = $ac_status" >&5
if (exit $ac_status) && test -s out/conftest2.$ac_objext
then
# The compiler can only warn and ignore the option if not recognized
@@ -19361,11 +19380,11 @@ else
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
- (eval echo "\"\$as_me:19364: $lt_compile\"" >&5)
+ (eval echo "\"\$as_me:19383: $lt_compile\"" >&5)
(eval "$lt_compile" 2>conftest.err)
ac_status=$?
cat conftest.err >&5
- echo "$as_me:19368: \$? = $ac_status" >&5
+ echo "$as_me:19387: \$? = $ac_status" >&5
if (exit $ac_status) && test -s "$ac_outfile"; then
# The compiler can only warn and ignore the option if not recognized
# So say no if there are warnings other than the usual output.
@@ -19629,11 +19648,11 @@ else
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
- (eval echo "\"\$as_me:19632: $lt_compile\"" >&5)
+ (eval echo "\"\$as_me:19651: $lt_compile\"" >&5)
(eval "$lt_compile" 2>conftest.err)
ac_status=$?
cat conftest.err >&5
- echo "$as_me:19636: \$? = $ac_status" >&5
+ echo "$as_me:19655: \$? = $ac_status" >&5
if (exit $ac_status) && test -s "$ac_outfile"; then
# The compiler can only warn and ignore the option if not recognized
# So say no if there are warnings other than the usual output.
@@ -19733,11 +19752,11 @@ else
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
- (eval echo "\"\$as_me:19736: $lt_compile\"" >&5)
+ (eval echo "\"\$as_me:19755: $lt_compile\"" >&5)
(eval "$lt_compile" 2>out/conftest.err)
ac_status=$?
cat out/conftest.err >&5
- echo "$as_me:19740: \$? = $ac_status" >&5
+ echo "$as_me:19759: \$? = $ac_status" >&5
if (exit $ac_status) && test -s out/conftest2.$ac_objext
then
# The compiler can only warn and ignore the option if not recognized
diff --git a/configure.in b/configure.in
index 221415d..901f3fb 100644
--- a/configure.in
+++ b/configure.in
@@ -662,6 +662,25 @@ case "$CC_BASENAME" in
PARALLEL="$CC_BASENAME"
;;
+ cmpicc)
+ dnl The ChaMPIon compiler on NCSA tungsten. The cmpirun command on tungsten
+ dnl isn't in the same path as cmpicc.
+ PARALLEL=cmpicc
+ AC_MSG_CHECKING([for cmpirun])
+
+ dnl Is there an cmpirun?
+ if test -x cmpirun; then
+ AC_MSG_RESULT([cmpirun])
+ RUNSERIAL="${RUNSERIAL:-none}"
+
+ if test -z "$RUNPARALLEL"; then
+ RUNPARALLEL="cmpirun -np \$\${NPROCS:=3}"
+ fi
+ else
+ AC_MSG_RESULT([none])
+ fi
+ ;;
+
*)
dnl Probably not a parallel compiler, but if `--enable-parallel'
dnl is defined below then we're still building a parallel hdf5.
diff --git a/src/H5Dio.c b/src/H5Dio.c
index 6e75a93..259eb06 100644
--- a/src/H5Dio.c
+++ b/src/H5Dio.c
@@ -289,6 +289,7 @@ H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
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(H5Dread, FAIL)
@@ -326,6 +327,13 @@ H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
if (!buf && 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;
+
/* read raw data */
if (H5D_read(dset, mem_type_id, mem_space, file_space, plist_id, buf/*out*/) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data")
@@ -373,6 +381,7 @@ H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
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(H5Dwrite, FAIL)
@@ -409,6 +418,13 @@ H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms")
if(!buf && 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, plist_id, buf) < 0)
@@ -788,6 +804,8 @@ H5D_contig_read(H5D_io_info_t *io_info, hsize_t nelmts,
FUNC_ENTER_NOAPI_NOINIT(H5D_contig_read)
+ assert (buf);
+
/* Initialize storage info for this dataset */
if (dataset->shared->dcpl_cache.efl.nused > 0)
HDmemcpy(&store.efl, &(dataset->shared->dcpl_cache.efl), sizeof(H5O_efl_t));
@@ -1066,6 +1084,8 @@ H5D_contig_write(H5D_io_info_t *io_info, hsize_t nelmts,
FUNC_ENTER_NOAPI_NOINIT(H5D_contig_write)
+ assert (buf);
+
/* Initialize storage info for this dataset */
if(dataset->shared->dcpl_cache.efl.nused > 0)
HDmemcpy(&store.efl, &(dataset->shared->dcpl_cache.efl), sizeof(H5O_efl_t));
@@ -1344,6 +1364,8 @@ H5D_chunk_read(H5D_io_info_t *io_info, hsize_t nelmts,
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_read)
+ assert (buf);
+
/* Map elements between file and memory for each chunk*/
if(H5D_create_chunk_map(dataset, mem_type, file_space, mem_space, &fm) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't build chunk mapping")
@@ -1734,6 +1756,8 @@ H5D_chunk_write(H5D_io_info_t *io_info, hsize_t nelmts,
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_write)
+ assert (buf);
+
/* Map elements between file and memory for each chunk*/
if(H5D_create_chunk_map(dataset, mem_type, file_space, mem_space, &fm) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't build chunk mapping")
diff --git a/src/H5Dmpio.c b/src/H5Dmpio.c
index 90f8974..a6981ee 100644
--- a/src/H5Dmpio.c
+++ b/src/H5Dmpio.c
@@ -988,6 +988,7 @@ H5D_link_chunk_collective_io(H5D_io_info_t *io_info,fm_map *fm,const void *buf,
for ( i = 0; i< num_chunk;i++){
if (MPI_SUCCESS != (mpi_code= MPI_Type_free( chunk_mtype+i )))
HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code);
+
if (MPI_SUCCESS != (mpi_code= MPI_Type_free( chunk_ftype+i )))
HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code);
}
@@ -1014,7 +1015,7 @@ H5D_link_chunk_collective_io(H5D_io_info_t *io_info,fm_map *fm,const void *buf,
if(H5DEBUG(D))
HDfprintf(H5DEBUG(D),"before coming to final collective IO\n");
#endif
-
+
if(H5D_final_collective_io(io_info,&chunk_final_ftype,&chunk_final_mtype,&coll_info,buf,do_write)<0)
HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL,"couldn't finish MPI-IO");
@@ -1059,7 +1060,6 @@ done:
static herr_t
H5D_multi_chunk_collective_io(H5D_io_info_t *io_info,fm_map *fm,const void *buf, hbool_t do_write)
{
-
unsigned i, total_chunk;
hsize_t ori_total_chunk;
uint8_t *chunk_io_option;
@@ -1070,6 +1070,16 @@ H5D_multi_chunk_collective_io(H5D_io_info_t *io_info,fm_map *fm,const void *buf,
H5D_storage_t store; /* union of EFL and chunk pointer in file space */
hbool_t select_chunk;
hbool_t last_io_mode_coll = TRUE;
+
+ void *chunk = NULL; /* Pointer to the data chunk in cache */
+ H5D_t *dataset=io_info->dset;/* Local pointer to dataset info */
+ H5D_istore_ud1_t udata; /*B-tree pass-through */
+ haddr_t caddr; /* Address of the cached chunk */
+ size_t accessed_bytes; /*total accessed size in a chunk */
+ unsigned idx_hint=0; /* Cache index hint */
+ hbool_t dirty = TRUE; /* Flag for cache flushing */
+ hbool_t relax=TRUE; /* Whether whole chunk is selected */
+
herr_t ret_value = SUCCEED;
#ifdef H5Dmpio_DEBUG
int mpi_rank;
@@ -1167,18 +1177,41 @@ H5D_multi_chunk_collective_io(H5D_io_info_t *io_info,fm_map *fm,const void *buf,
if(H5D_ioinfo_make_ind(io_info) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't switch to independent I/O")
+ /* Load the chunk into cache. But if the whole chunk is written,
+ * simply allocate space instead of load the chunk. */
+ if(HADDR_UNDEF==(caddr = H5D_istore_get_addr(io_info, &udata)))
+ HGOTO_ERROR(H5E_STORAGE, H5E_CANTGET, FAIL,"couldn't get chunk info from skipped list");
+
+ if (H5D_istore_if_load(dataset, caddr)) {
+ accessed_bytes = chunk_info->chunk_points * H5T_get_size(dataset->shared->type);
+ if((do_write && (accessed_bytes != dataset->shared->layout.u.chunk.size)) || !do_write)
+ relax=FALSE;
+
+ if(NULL == (chunk = H5D_istore_lock(io_info, &udata, relax, &idx_hint)))
+ HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk")
+ } else
+ chunk = NULL;
+
if(do_write) {
if((io_info->ops.write)(io_info,
chunk_info->chunk_points,H5T_get_size(io_info->dset->shared->type),
- chunk_info->fspace,chunk_info->mspace,0, NULL, buf) < 0)
+ chunk_info->fspace,chunk_info->mspace,caddr,chunk, buf) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "optimized write failed")
}
else {
if((io_info->ops.read)(io_info,
chunk_info->chunk_points,H5T_get_size(io_info->dset->shared->type),
- chunk_info->fspace,chunk_info->mspace,0, NULL, buf) < 0)
+ chunk_info->fspace,chunk_info->mspace,caddr,chunk, buf) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "optimized read failed")
- }
+ }
+
+ /* Release the cache lock on the chunk. */
+ if (H5D_istore_if_load(dataset, caddr)) {
+ if(!do_write) dirty = FALSE;
+
+ if(H5D_istore_unlock(io_info, dirty, idx_hint, chunk, accessed_bytes) < 0)
+ HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to unlock raw data chunk")
+ }
#else
if(!last_io_mode_coll)
/* using independent I/O with file setview.*/
@@ -1250,6 +1283,16 @@ H5D_multi_chunk_collective_io_no_opt(H5D_io_info_t *io_info,fm_map *fm,const voi
haddr_t chunk_addr;
H5SL_node_t *chunk_node; /* Current node in chunk skip list */
H5D_storage_t store; /* union of EFL and chunk pointer in file space */
+ H5D_chunk_info_t *chunk_info; /* chunk information */
+ hbool_t make_ind, make_coll; /* Flags to indicate that the MPI mode should change */
+
+ void *chunk = NULL; /* Pointer to the data chunk in cache */
+ H5D_t *dataset=io_info->dset;/* Local pointer to dataset info */
+ H5D_istore_ud1_t udata; /*B-tree pass-through */
+ size_t accessed_bytes; /*total accessed size in a chunk */
+ unsigned idx_hint=0; /* Cache index hint */
+ hbool_t dirty = TRUE; /* Flag for cache flushing */
+ hbool_t relax=TRUE; /* Whether whole chunk is selected */
herr_t ret_value = SUCCEED;
#ifdef H5Dmpio_DEBUG
@@ -1317,24 +1360,43 @@ H5D_multi_chunk_collective_io_no_opt(H5D_io_info_t *io_info,fm_map *fm,const voi
if(H5D_ioinfo_make_ind(io_info) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't switch to independent I/O")
+ if(HADDR_UNDEF==(chunk_addr = H5D_istore_get_addr(io_info, &udata)))
+ HGOTO_ERROR(H5E_STORAGE, H5E_CANTGET, FAIL,"couldn't get chunk info from skipped list");
+
if(make_ind) {/*independent I/O */
-
- if(do_write) {
- if((io_info->ops.write)(io_info,
+ /* Load the chunk into cache. But if the whole chunk is written,
+ * simply allocate space instead of load the chunk. */
+ if (H5D_istore_if_load(dataset, chunk_addr)) {
+ accessed_bytes = chunk_info->chunk_points * H5T_get_size(dataset->shared->type);
+ if((do_write && (accessed_bytes != dataset->shared->layout.u.chunk.size)) || !do_write)
+ relax=FALSE;
+
+ if(NULL == (chunk = H5D_istore_lock(io_info, &udata, relax, &idx_hint)))
+ HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk")
+ } else
+ chunk = NULL;
+
+ if(do_write) {
+ if((io_info->ops.write)(io_info,
chunk_info->chunk_points,H5T_get_size(io_info->dset->shared->type),
- chunk_info->fspace,chunk_info->mspace, (hsize_t)0, NULL, buf) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "optimized write failed")
- }
- else {
- if((io_info->ops.read)(io_info,
+ chunk_info->fspace,chunk_info->mspace, chunk_addr, chunk, buf) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "optimized write failed")
+ } else {
+ if((io_info->ops.read)(io_info,
chunk_info->chunk_points,H5T_get_size(io_info->dset->shared->type),
- chunk_info->fspace,chunk_info->mspace, (hsize_t)0, NULL, buf) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "optimized read failed")
- }
+ chunk_info->fspace,chunk_info->mspace, chunk_addr, chunk, buf) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "optimized read failed")
+ }
+
+ /* Release the cache lock on the chunk. */
+ if (H5D_istore_if_load(dataset, chunk_addr)) {
+ if(!do_write) dirty = FALSE;
+
+ if(H5D_istore_unlock(io_info, dirty, idx_hint, chunk, accessed_bytes) < 0)
+ HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to unlock raw data chunk")
+ }
}
else { /*collective I/O */
- if(HADDR_UNDEF==(chunk_addr = H5D_istore_get_addr(io_info,NULL)))
- HGOTO_ERROR(H5E_STORAGE, H5E_CANTGET, FAIL,"couldn't get chunk info from skipped list");
if(H5D_inter_collective_io(io_info,chunk_info->fspace,chunk_info->mspace,
chunk_addr,buf,do_write ) < 0)
HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL,"couldn't finish shared collective MPI-IO");
diff --git a/testpar/t_dset.c b/testpar/t_dset.c
index 3c18d82..91349fc 100644
--- a/testpar/t_dset.c
+++ b/testpar/t_dset.c
@@ -2286,3 +2286,215 @@ compress_readAll(void)
}
#endif /* H5_HAVE_FILTER_DEFLATE */
+/*
+ * Part 4--Non-selection for chunked dataset
+ */
+
+/*
+ * Example of using the parallel HDF5 library to create chunked
+ * dataset in one HDF5 file with collective and independent parallel
+ * MPIO access support. The Datasets are of sizes dim0 x dim1.
+ * Each process controls only a slab of size dim0 x dim1 within the
+ * dataset with the exception that one processor selects no element.
+ */
+
+void
+none_selection_chunk(void)
+{
+ hid_t fid; /* HDF5 file ID */
+ hid_t acc_tpl; /* File access templates */
+ hid_t xfer_plist; /* Dataset transfer properties list */
+ hid_t sid; /* Dataspace ID */
+ hid_t file_dataspace; /* File dataspace ID */
+ hid_t mem_dataspace; /* memory dataspace ID */
+ hid_t dataset1, dataset2; /* Dataset ID */
+ hbool_t use_gpfs = FALSE; /* Use GPFS hints */
+ const char *filename;
+ hsize_t dims[RANK]; /* dataset dim sizes */
+ DATATYPE *data_origin = NULL; /* data buffer */
+ DATATYPE *data_array = NULL; /* data buffer */
+ hsize_t chunk_dims[RANK]; /* chunk sizes */
+ hid_t dataset_pl; /* dataset create prop. list */
+
+ hsize_t start[RANK]; /* for hyperslab setting */
+ hsize_t count[RANK]; /* for hyperslab setting */
+ hsize_t stride[RANK]; /* for hyperslab setting */
+ hsize_t block[RANK]; /* for hyperslab setting */
+ hsize_t mstart[RANK]; /* for data buffer in memory */
+
+ herr_t ret; /* Generic return value */
+ int mpi_size, mpi_rank;
+
+ MPI_Comm comm = MPI_COMM_WORLD;
+ MPI_Info info = MPI_INFO_NULL;
+
+ filename = GetTestParameters();
+ if (VERBOSE_MED)
+ printf("Extend independent write test on file %s\n", filename);
+
+ /* set up MPI parameters */
+ MPI_Comm_size(MPI_COMM_WORLD,&mpi_size);
+ MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
+
+ /* setup chunk-size. Make sure sizes are > 0 */
+ chunk_dims[0] = chunkdim0;
+ chunk_dims[1] = chunkdim1;
+
+ /* -------------------
+ * START AN HDF5 FILE
+ * -------------------*/
+ /* setup file access template */
+ acc_tpl = create_faccess_plist(comm, info, facc_type, use_gpfs);
+ VRFY((acc_tpl >= 0), "");
+
+ /* create the file collectively */
+ fid=H5Fcreate(filename,H5F_ACC_TRUNC,H5P_DEFAULT,acc_tpl);
+ VRFY((fid >= 0), "H5Fcreate succeeded");
+
+ /* Release file-access template */
+ ret=H5Pclose(acc_tpl);
+ VRFY((ret >= 0), "");
+
+ /* --------------------------------------------------------------
+ * Define the dimensions of the overall datasets and create them.
+ * ------------------------------------------------------------- */
+
+ /* set up dataset storage chunk sizes and creation property list */
+ if (VERBOSE_MED)
+ printf("chunks[]=%lu,%lu\n", (unsigned long)chunk_dims[0], (unsigned long)chunk_dims[1]);
+ dataset_pl = H5Pcreate(H5P_DATASET_CREATE);
+ VRFY((dataset_pl >= 0), "H5Pcreate succeeded");
+ ret = H5Pset_chunk(dataset_pl, RANK, chunk_dims);
+ VRFY((ret >= 0), "H5Pset_chunk succeeded");
+
+ /* setup dimensionality object */
+ dims[0] = dim0;
+ dims[1] = dim1;
+ sid = H5Screate_simple (RANK, dims, NULL);
+ VRFY((sid >= 0), "H5Screate_simple succeeded");
+
+ /* create an extendible dataset collectively */
+ dataset1 = H5Dcreate(fid, DATASETNAME1, H5T_NATIVE_INT, sid, dataset_pl);
+ VRFY((dataset1 >= 0), "H5Dcreate succeeded");
+
+ /* create another extendible dataset collectively */
+ dataset2 = H5Dcreate(fid, DATASETNAME2, H5T_NATIVE_INT, sid, dataset_pl);
+ VRFY((dataset2 >= 0), "H5Dcreate succeeded");
+
+ /* release resource */
+ H5Sclose(sid);
+ H5Pclose(dataset_pl);
+
+ /* -------------------------
+ * Test collective writing to dataset1
+ * -------------------------*/
+ /* set up dimensions of the slab this process accesses */
+ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW);
+
+ /* allocate memory for data buffer. Only allocate enough buffer for
+ * each processor's data. */
+ if (mpi_rank) {
+ data_origin = (DATATYPE *)malloc(block[0]*block[1]*sizeof(DATATYPE));
+ VRFY((data_origin != NULL), "data_origin malloc succeeded");
+
+ data_array = (DATATYPE *)malloc(block[0]*block[1]*sizeof(DATATYPE));
+ VRFY((data_array != NULL), "data_array malloc succeeded");
+
+ /* put some trivial data in the data_array */
+ mstart[0] = mstart[1] = 0;
+ dataset_fill(mstart, block, data_origin);
+ MESG("data_array initialized");
+ if (VERBOSE_MED){
+ MESG("data_array created");
+ dataset_print(mstart, block, data_origin);
+ }
+ }
+
+ /* create a memory dataspace independently */
+ mem_dataspace = H5Screate_simple (RANK, block, NULL);
+ VRFY((mem_dataspace >= 0), "");
+
+ /* Process 0 has no selection */
+ if (!mpi_rank) {
+ ret = H5Sselect_none(mem_dataspace);
+ VRFY((ret >= 0), "H5Sselect_none succeeded");
+ }
+
+ /* create a file dataspace independently */
+ file_dataspace = H5Dget_space (dataset1);
+ VRFY((file_dataspace >= 0), "H5Dget_space succeeded");
+ ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
+ VRFY((ret >= 0), "H5Sset_hyperslab succeeded");
+
+ /* Process 0 has no selection */
+ if (!mpi_rank) {
+ ret = H5Sselect_none(file_dataspace);
+ VRFY((ret >= 0), "H5Sselect_none succeeded");
+ }
+
+ /* set up the collective transfer properties list */
+ xfer_plist = H5Pcreate (H5P_DATASET_XFER);
+ VRFY((xfer_plist >= 0), "H5Pcreate xfer succeeded");
+ ret=H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
+ VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
+
+ /* write data collectively */
+ ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
+ xfer_plist, data_origin);
+ VRFY((ret >= 0), "H5Dwrite succeeded");
+
+ /* read data independently */
+ ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
+ H5P_DEFAULT, data_array);
+ VRFY((ret >= 0), "");
+
+ /* verify the read data with original expected data */
+ if (mpi_rank) {
+ ret = dataset_vrfy(mstart, count, stride, block, data_array, data_origin);
+ if (ret) nerrors++;
+ }
+
+ /* -------------------------
+ * Test independent writing to dataset2
+ * -------------------------*/
+ ret=H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_INDEPENDENT);
+ VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
+
+ /* write data collectively */
+ ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
+ xfer_plist, data_origin);
+ VRFY((ret >= 0), "H5Dwrite succeeded");
+
+ /* read data independently */
+ ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
+ H5P_DEFAULT, data_array);
+ VRFY((ret >= 0), "");
+
+ /* verify the read data with original expected data */
+ if (mpi_rank) {
+ ret = dataset_vrfy(mstart, count, stride, block, data_array, data_origin);
+ if (ret) nerrors++;
+ }
+
+ /* release resource */
+ ret=H5Sclose(file_dataspace);
+ VRFY((ret >= 0), "H5Sclose succeeded");
+ ret=H5Sclose(mem_dataspace);
+ VRFY((ret >= 0), "H5Sclose succeeded");
+ ret=H5Pclose(xfer_plist);
+ VRFY((ret >= 0), "H5Pclose succeeded");
+
+
+ /* close dataset collectively */
+ ret=H5Dclose(dataset1);
+ VRFY((ret >= 0), "H5Dclose1 succeeded");
+ ret=H5Dclose(dataset2);
+ VRFY((ret >= 0), "H5Dclose2 succeeded");
+
+ /* close the file collectively */
+ H5Fclose(fid);
+
+ /* release data buffers */
+ if (data_origin) free(data_origin);
+ if (data_array) free(data_array);
+}
diff --git a/testpar/testphdf5.c b/testpar/testphdf5.c
index a45bafa..11ffcb0 100644
--- a/testpar/testphdf5.c
+++ b/testpar/testphdf5.c
@@ -365,6 +365,9 @@ int main(int argc, char **argv)
"extendible dataset collective read", PARATESTFILE);
AddTest("eidsetw2", extend_writeInd2, NULL,
"extendible dataset independent write #2", PARATESTFILE);
+ AddTest("selnone", none_selection_chunk, NULL,
+ "chunked dataset with none-selection", PARATESTFILE);
+
AddTest("calloc", test_chunk_alloc, NULL,
"parallel extend Chunked allocation on serial file", PARATESTFILE);
AddTest("fltread", test_filter_read, NULL,
diff --git a/testpar/testphdf5.h b/testpar/testphdf5.h
index 06878a5..8a6d897 100644
--- a/testpar/testphdf5.h
+++ b/testpar/testphdf5.h
@@ -211,6 +211,7 @@ void dataset_readInd(void);
void dataset_readAll(void);
void extend_readInd(void);
void extend_readAll(void);
+void none_selection_chunk(void);
void test_chunk_alloc(void);
void test_filter_read(void);
void compact_dataset(void);
generated by cgit v0.12 at 2024-07-16 14:10:15 (GMT)