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-rwxr-xr-xbin/cmakehdf519
-rw-r--r--c++/src/H5Location.cpp2
-rw-r--r--fortran/src/hdf5_fortrandll.def.in1
-rw-r--r--fortran/test/tf.f902
-rw-r--r--release_docs/INSTALL_parallel67
-rw-r--r--release_docs/RELEASE.txt4
-rw-r--r--src/H5AC.c6
-rw-r--r--src/H5Dchunk.c2
-rw-r--r--src/H5HFsection.c2
-rw-r--r--src/H5Pfapl.c6
-rw-r--r--tools/h5diff/ph5diff_main.c5
-rw-r--r--tools/h5repack/h5repack.sh.in22
-rw-r--r--tools/lib/h5tools_dump.c16
-rw-r--r--tools/testfiles/tfletcher32.ddl2
-rw-r--r--tools/testfiles/tshuffle.ddl2
-rw-r--r--tools/testfiles/tuserfilter.ddl4
16 files changed, 138 insertions, 24 deletions
diff --git a/bin/cmakehdf5 b/bin/cmakehdf5
index c024ad1..2480497 100755
--- a/bin/cmakehdf5
+++ b/bin/cmakehdf5
@@ -70,6 +70,7 @@ set (CTEST_SOURCE_DIRECTORY "../hdf5")
set (CTEST_BINARY_DIRECTORY ".")
set (CTEST_CMAKE_GENERATOR "Unix Makefiles")
set (CTEST_BUILD_CONFIGURATION "Release")
+set (CTEST_MAX_N 8)
# -- CDash variables
set (LOCAL_NO_SUBMIT TRUE) # No CDash submit.
@@ -87,6 +88,9 @@ set (ADD_BUILD_OPTIONS "-DCMAKE_INSTALL_PREFIX:PATH=/usr/local/hdf5.1.8 -DHDF5_A
include(ProcessorCount)
ProcessorCount(N)
if(NOT N EQUAL 0)
+ if(N GREATER ${CTEST_MAX_N})
+ set(N ${CTEST_MAX_N})
+ endif(N GREATER ${CTEST_MAX_N})
set(CTEST_BUILD_FLAGS -j${N})
set(ctest_test_args ${ctest_test_args} PARALLEL_LEVEL ${N})
endif()
@@ -188,22 +192,31 @@ CTEST_START (${MODEL} TRACK ${MODEL})
if (NOT LOCAL_SKIP_UPDATE)
CTEST_UPDATE (SOURCE "${CTEST_SOURCE_DIRECTORY}")
endif (NOT LOCAL_SKIP_UPDATE)
-CTEST_CONFIGURE (BUILD "${CTEST_BINARY_DIRECTORY}")
+CTEST_CONFIGURE (BUILD "${CTEST_BINARY_DIRECTORY}" RETURN_VALUE res)
+if(NOT res STREQUAL "0")
+ message (FATAL_ERROR "Configure FAILED")
+endif()
message ("Configure DONE")
CTEST_READ_CUSTOM_FILES ("${CTEST_BINARY_DIRECTORY}")
if (NOT LOCAL_NO_SUBMIT)
CTEST_SUBMIT (PARTS Update Configure Notes)
endif (NOT LOCAL_NO_SUBMIT)
-CTEST_BUILD (BUILD "${CTEST_BINARY_DIRECTORY}" APPEND)
+CTEST_BUILD (BUILD "${CTEST_BINARY_DIRECTORY}" APPEND RETURN_VALUE res)
if (NOT LOCAL_NO_SUBMIT)
CTEST_SUBMIT (PARTS Build)
endif (NOT LOCAL_NO_SUBMIT)
+if(NOT res STREQUAL "0")
+ message (FATAL_ERROR "Build FAILED")
+endif()
message ("build DONE")
if (NOT LOCAL_SKIP_TEST)
- CTEST_TEST (BUILD "${CTEST_BINARY_DIRECTORY}" APPEND)
+ CTEST_TEST (BUILD "${CTEST_BINARY_DIRECTORY}" APPEND ${ctest_test_args} RETURN_VALUE res)
if (NOT LOCAL_NO_SUBMIT)
CTEST_SUBMIT (PARTS Test)
endif (NOT LOCAL_NO_SUBMIT)
+ if(NOT res STREQUAL "0")
+ message (FATAL_ERROR "Test FAILED")
+ endif()
message ("test DONE")
endif (NOT LOCAL_SKIP_TEST)
diff --git a/c++/src/H5Location.cpp b/c++/src/H5Location.cpp
index be59f51..98878d7 100644
--- a/c++/src/H5Location.cpp
+++ b/c++/src/H5Location.cpp
@@ -279,7 +279,7 @@ bool H5Location::attrExists(const char* name) const
//--------------------------------------------------------------------------
bool H5Location::attrExists(const H5std_string& name) const
{
- attrExists(name.c_str());
+ return(attrExists(name.c_str()));
}
//--------------------------------------------------------------------------
diff --git a/fortran/src/hdf5_fortrandll.def.in b/fortran/src/hdf5_fortrandll.def.in
index 4ce185b..62030f0 100644
--- a/fortran/src/hdf5_fortrandll.def.in
+++ b/fortran/src/hdf5_fortrandll.def.in
@@ -6,6 +6,7 @@ H5LIB_mp_H5GET_LIBVERSION_F
H5LIB_mp_H5CHECK_VERSION_F
H5LIB_mp_H5GARBAGE_COLLECT_F
H5LIB_mp_H5DONT_ATEXIT_F
+H5LIB_mp_H5KIND_TO_TYPE
@H5_NOF03EXP@H5LIB_PROVISIONAL_mp_H5OFFSETOF
; H5_DBLE_INTERFACE
H5_DBLE_INTERFACE_mp_H5AREAD_DOUBLE_SCALAR
diff --git a/fortran/test/tf.f90 b/fortran/test/tf.f90
index d5c32c8..1060747 100644
--- a/fortran/test/tf.f90
+++ b/fortran/test/tf.f90
@@ -30,7 +30,7 @@
!This definition is needed for Windows DLLs
!DEC$if defined(BUILD_HDF5_DLL)
-!DEC$attributes dllexport :: verify_real
+!DEC$attributes dllexport :: verify_real_kind_7
!DEC$endif
SUBROUTINE verify_real_kind_7(string,value,correct_value,total_error)
USE HDF5
diff --git a/release_docs/INSTALL_parallel b/release_docs/INSTALL_parallel
index eacaf68..03b3ecf 100644
--- a/release_docs/INSTALL_parallel
+++ b/release_docs/INSTALL_parallel
@@ -186,6 +186,73 @@ TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
======== end of bypass ========
+2.5. Hopper (Cray XE6) (for v1.8 and later)
+-------------------------
+
+2.5.1 Building HDF5 for Hopper
+------------------------------------------
+The following steps are for building HDF5 for the Hopper compute
+nodes. They would probably work for other Cray XE6 systems but have
+not been verified.
+
+Obtain a copy from the HDF ftp server:
+http://www.hdfgroup.org/ftp/HDF5/current/src/
+(link might change, so always double check the HDF group website).
+
+$ wget http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-x.x.x.tar.gz
+
+unpack the tarball
+
+$ cd hdf5-x.x.x/
+$ CC=cc FC=ftn ./configure \
+--prefix=/project/hdf5/hdf5 --enable-parallel --enable-fortran \
+--disable-shared --disable-production
+$ make
+
+Run make check. make check should be run on the compute nodes, not the
+front end nodes. So using a PBS batch script, allocate 4 or more
+cores. Always consult with the machine's website on how to create PBS
+scripts and allocate nodes for your job. For Hopper, all the
+information can be found on:
+http://www.nersc.gov/systems/hopper-cray-xe6/
+
+save the PBS script into your HDF5 build directory. The PBS script
+should contain (besides the PBS node allocation requests)the
+following:
+
+--------------------------------------------------------------
+cd $PBS_O_WORKDIR
+
+##set RUNSERIAL and RUNPARALLEL like this in the PBS script:
+export RUNPARALLEL="aprun -n 6"
+export RUNSERIAL="aprun -n 1"
+
+##execute make check:
+make check
+--------------------------------------------------------------
+
+Once the job runs and all is well, install the binary:
+$ make install
+
+2.5.2 Hopper known issues
+------------------------------
+Sometimes when building the library with make, you might get this problem:
+
+LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo | \
+sed -e 's/-L/:/g' -e 's/
+//g'`" \
+./H5make_libsettings > H5lib_settings.c
+|| \
+(test $HDF5_Make_Ignore && echo "*** Error ignored")
+|| \
+(rm -f H5lib_settings.c ; exit 1)
+/bin/sh: line 4: 9644 Segmentation fault
+LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo | sed -e 's/-L/:/g' -e 's/
+//g'`" ./H5make_libsettings > H5lib_settings.c
+
+If that happens, you are probable running with make -j <x>. In that
+case, you need to cleanup everything and start again as detailed above
+but use serial make (do not use -j <x>).
3. Detail explanation
---------------------
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index 8a54b21..dbd3b75 100644
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -276,6 +276,10 @@ New Features
Tools:
------
+ - h5dump: Fixed displaying comporession ratio for unknown or user-defined
+ filters. HDFFV-8344 (XCAO 2013/03/19)
+ - h5dump: Changed UNKNOWN_FILTER to USER_DEFINED_FILTER for user defined filter.
+ HDFFV-8346 (XCAO 2013/03/19)
- h5dump: Added capability for "-a" option to show attributes containing "/"
by using an escape character. For example, for a dataset "/dset"
containing attribute "speed(m/h)", use "h5dump -a "/dset/speed(\/h)"
diff --git a/src/H5AC.c b/src/H5AC.c
index ed79813..db8446a 100644
--- a/src/H5AC.c
+++ b/src/H5AC.c
@@ -2998,7 +2998,7 @@ done:
*-------------------------------------------------------------------------
*/
#ifdef H5_HAVE_PARALLEL
-herr_t
+static herr_t
H5AC_construct_candidate_list(H5AC_t * cache_ptr,
H5AC_aux_t * aux_ptr,
int sync_point_op)
@@ -3212,7 +3212,7 @@ done:
*
*-------------------------------------------------------------------------
*/
-herr_t
+static herr_t
H5AC_ext_config_2_int_config(H5AC_cache_config_t * ext_conf_ptr,
H5C_auto_size_ctl_t * int_conf_ptr)
{
@@ -4157,7 +4157,7 @@ done:
*-------------------------------------------------------------------------
*/
#ifdef H5_HAVE_PARALLEL
-herr_t
+static herr_t
H5AC_propagate_flushed_and_still_clean_entries_list(H5F_t * f,
hid_t dxpl_id,
H5AC_t * cache_ptr)
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c
index e3f060a..497846b 100644
--- a/src/H5Dchunk.c
+++ b/src/H5Dchunk.c
@@ -2174,7 +2174,7 @@ done:
*
*-------------------------------------------------------------------------
*/
-herr_t
+static herr_t
H5D__chunk_cinfo_cache_reset(H5D_chunk_cached_t *last)
{
FUNC_ENTER_PACKAGE_NOERR
diff --git a/src/H5HFsection.c b/src/H5HFsection.c
index 72ea100..bf779a6 100644
--- a/src/H5HFsection.c
+++ b/src/H5HFsection.c
@@ -449,7 +449,7 @@ done:
*
*-------------------------------------------------------------------------
*/
-herr_t
+static herr_t
H5HF_sect_node_free(H5HF_free_section_t *sect, H5HF_indirect_t *iblock)
{
herr_t ret_value = SUCCEED; /* Return value */
diff --git a/src/H5Pfapl.c b/src/H5Pfapl.c
index 0636095..50fe271 100644
--- a/src/H5Pfapl.c
+++ b/src/H5Pfapl.c
@@ -2500,7 +2500,7 @@ done:
*
*-------------------------------------------------------------------------
*/
-herr_t
+static herr_t
H5P_file_image_info_del(hid_t UNUSED prop_id, const char UNUSED *name, size_t UNUSED size, void *value)
{
H5FD_file_image_info_t info; /* Image info struct */
@@ -2554,7 +2554,7 @@ done:
*
*-------------------------------------------------------------------------
*/
-herr_t
+static herr_t
H5P_file_image_info_copy(const char UNUSED *name, size_t UNUSED size, void *value)
{
herr_t ret_value = SUCCEED; /* Return value */
@@ -2629,7 +2629,7 @@ done:
*
*-------------------------------------------------------------------------
*/
-herr_t
+static herr_t
H5P_file_image_info_close(const char UNUSED *name, size_t UNUSED size, void *value)
{
herr_t ret_value = SUCCEED; /* Return value */
diff --git a/tools/h5diff/ph5diff_main.c b/tools/h5diff/ph5diff_main.c
index 1fc563b..b9bd404 100644
--- a/tools/h5diff/ph5diff_main.c
+++ b/tools/h5diff/ph5diff_main.c
@@ -275,6 +275,9 @@ void h5diff_exit(int status)
if(g_Parallel)
MPI_Finalize();
- exit(status);
+ /* Always exit(0), since MPI implementations do weird stuff when they
+ * receive a non-zero exit value. - QAK
+ */
+ exit(0);
}
diff --git a/tools/h5repack/h5repack.sh.in b/tools/h5repack/h5repack.sh.in
index 14e1d04..ca25183 100644
--- a/tools/h5repack/h5repack.sh.in
+++ b/tools/h5repack/h5repack.sh.in
@@ -244,8 +244,11 @@ VERIFY_LAYOUT_DSET()
shift
shift
shift
-
- $RUNSERIAL $H5REPACK_BIN "$@" $infile $outfile
+
+ TESTING $H5REPACK $@
+ (
+ $RUNSERIAL $H5REPACK_BIN "$@" $infile $outfile
+ )
RET=$?
if [ $RET != 0 ] ; then
echo "*FAILED*"
@@ -266,6 +269,7 @@ VERIFY_LAYOUT_DSET()
echo " PASSED"
else
echo " FAILED"
+ nerrors="`expr $nerrors + 1`"
fi
# clean up tmp files
@@ -277,6 +281,7 @@ VERIFY_LAYOUT_DSET()
# Verifying layouts from entire file
VERIFY_LAYOUT_ALL()
{
+ infile=$2
outfile=$TESTDIR/out-$1.$2
layoutfile=$TESTDIR/layout-$1.$2
expectlayout=$3
@@ -284,7 +289,10 @@ VERIFY_LAYOUT_ALL()
shift
shift
- $RUNSERIAL $H5REPACK_BIN "$@" $infile $outfile
+ TESTING $H5REPACK $@
+ (
+ $RUNSERIAL $H5REPACK_BIN "$@" $infile $outfile
+ )
RET=$?
if [ $RET != 0 ] ; then
echo "*FAILED*"
@@ -300,6 +308,7 @@ VERIFY_LAYOUT_ALL()
# check if the other layouts still exsit
VERIFY "layouts"
(
+ echo
# if CONTIGUOUS
if [ $expectlayout = "CONTIGUOUS" ]; then
TESTING $H5DUMP_BIN -pH $outfile
@@ -309,10 +318,12 @@ VERIFY_LAYOUT_ALL()
$GREP "COMPACT" $layoutfile > /dev/null
if [ $? -eq 0 ]; then
echo " FAILED"
+ nerrors="`expr $nerrors + 1`"
else
$GREP "CHUNKED" $layoutfile > /dev/null
if [ $? -eq 0 ]; then
echo " FAILED"
+ nerrors="`expr $nerrors + 1`"
else
echo " PASSED"
fi
@@ -327,10 +338,12 @@ VERIFY_LAYOUT_ALL()
$GREP "CHUNKED" $layoutfile > /dev/null
if [ $? -eq 0 ]; then
echo " FAILED"
+ nerrors="`expr $nerrors + 1`"
else
$GREP "CONTIGUOUS" $layoutfile > /dev/null
if [ $? -eq 0 ]; then
echo " FAILED"
+ nerrors="`expr $nerrors + 1`"
else
echo " PASSED"
fi
@@ -345,10 +358,12 @@ VERIFY_LAYOUT_ALL()
$GREP "CONTIGUOUS" $layoutfile > /dev/null
if [ $? -eq 0 ]; then
echo " FAILED"
+ nerrors="`expr $nerrors + 1`"
else
$GREP "COMPACT" $layoutfile > /dev/null
if [ $? -eq 0 ]; then
echo " FAILED"
+ nerrors="`expr $nerrors + 1`"
else
echo " PASSED"
fi
@@ -523,6 +538,7 @@ TOOLTEST_META()
else
#fail
echo "*FAILED*"
+ nerrors="`expr $nerrors + 1`"
fi
rm -f $outfile
diff --git a/tools/lib/h5tools_dump.c b/tools/lib/h5tools_dump.c
index dbb5f98..d6cd0a0 100644
--- a/tools/lib/h5tools_dump.c
+++ b/tools/lib/h5tools_dump.c
@@ -2958,11 +2958,14 @@ h5tools_dump_dcpl(FILE *stream, const h5tool_format_t *info,
int ndims = H5Sget_simple_extent_dims(sid, dims, NULL);
/* only print the compression ratio for these filters */
- for(i = 0; i < nfilters; i++) {
+ for(i = 0; i < nfilters && !ok; i++) {
cd_nelmts = NELMTS(cd_values);
filtn = H5Pget_filter2(dcpl_id, (unsigned)i, &filt_flags, &cd_nelmts,
cd_values, sizeof(f_name), f_name, NULL);
-
+ ok = (filtn>=0);
+
+ /* this following code will not show compression ratio for
+ user defined filter. For example, see HDFFV-8344 --xcao@hdfgroup.org
switch(filtn) {
case H5Z_FILTER_DEFLATE:
case H5Z_FILTER_SZIP:
@@ -2971,6 +2974,7 @@ h5tools_dump_dcpl(FILE *stream, const h5tool_format_t *info,
ok = 1;
break;
}
+ */
}
if(ndims && ok) {
@@ -3148,6 +3152,9 @@ h5tools_dump_dcpl(FILE *stream, const h5tool_format_t *info,
cd_nelmts = NELMTS(cd_values);
filtn = H5Pget_filter2(dcpl_id, (unsigned)i, &filt_flags, &cd_nelmts,
cd_values, sizeof(f_name), f_name, NULL);
+
+ if (filtn<0)
+ continue; /* nothing to print for invalid filter */
ctx->need_prefix = TRUE;
h5tools_simple_prefix(stream, info, ctx, curr_pos, 0);
@@ -3241,10 +3248,13 @@ h5tools_dump_dcpl(FILE *stream, const h5tool_format_t *info,
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, ncols, 0, 0);
break;
default:
+ /* filter do not have to be avaiable for showing registered filter info.
+ see HDFFV-8346 for details. --xcao@hdfgroup.org
if(H5Zfilter_avail(filtn))
h5tools_str_append(&buffer, "%s %s", "USER_REGISTERED_FILTER", BEGIN);
else
- h5tools_str_append(&buffer, "%s %s", "UNKNOWN_FILTER", BEGIN);
+ */
+ h5tools_str_append(&buffer, "%s %s", "USER_DEFINED_FILTER", BEGIN);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, ncols, 0, 0);
ctx->indent_level++;
diff --git a/tools/testfiles/tfletcher32.ddl b/tools/testfiles/tfletcher32.ddl
index 072ef23..c341ded 100644
--- a/tools/testfiles/tfletcher32.ddl
+++ b/tools/testfiles/tfletcher32.ddl
@@ -4,7 +4,7 @@ DATASET "fletcher32" {
DATASPACE SIMPLE { ( 20, 10 ) / ( 20, 10 ) }
STORAGE_LAYOUT {
CHUNKED ( 10, 5 )
- SIZE 816
+ SIZE 816 (0.980:1 COMPRESSION)
}
FILTERS {
CHECKSUM FLETCHER32
diff --git a/tools/testfiles/tshuffle.ddl b/tools/testfiles/tshuffle.ddl
index cd1b5f8..5c183fe 100644
--- a/tools/testfiles/tshuffle.ddl
+++ b/tools/testfiles/tshuffle.ddl
@@ -4,7 +4,7 @@ DATASET "shuffle" {
DATASPACE SIMPLE { ( 20, 10 ) / ( 20, 10 ) }
STORAGE_LAYOUT {
CHUNKED ( 10, 5 )
- SIZE 800
+ SIZE 800 (1.000:1 COMPRESSION)
}
FILTERS {
PREPROCESSING SHUFFLE
diff --git a/tools/testfiles/tuserfilter.ddl b/tools/testfiles/tuserfilter.ddl
index 07b478f..24745b9 100644
--- a/tools/testfiles/tuserfilter.ddl
+++ b/tools/testfiles/tuserfilter.ddl
@@ -4,10 +4,10 @@ DATASET "myfilter" {
DATASPACE SIMPLE { ( 20, 10 ) / ( 20, 10 ) }
STORAGE_LAYOUT {
CHUNKED ( 10, 5 )
- SIZE 800
+ SIZE 800 (1.000:1 COMPRESSION)
}
FILTERS {
- UNKNOWN_FILTER {
+ USER_DEFINED_FILTER {
FILTER_ID 405
COMMENT myfilter
PARAMS { 5 6 }
generated by cgit v0.12 at 2024-07-24 12:33:47 (GMT)