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author | Mohamad Chaarawi <chaarawi@hdfgroup.org> | 2013-03-28 15:44:24 (GMT) |
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committer | Mohamad Chaarawi <chaarawi@hdfgroup.org> | 2013-03-28 15:44:24 (GMT) |
commit | 98353176a6dd3b8709d95e6643210e79ed5b19c8 (patch) | |
tree | 1d65b411863a622f2ca80b50f52b1c6d45cb501b | |
parent | fd88a0006ead7571a652586c9f2eb376123b2f3b (diff) | |
parent | be4198eb4146dbcd7a380b7fb48980c73b518c74 (diff) | |
download | hdf5-98353176a6dd3b8709d95e6643210e79ed5b19c8.zip hdf5-98353176a6dd3b8709d95e6643210e79ed5b19c8.tar.gz hdf5-98353176a6dd3b8709d95e6643210e79ed5b19c8.tar.bz2 |
[svn-r23474] Bring recent trunk changes into the VOL branch including the fix to Ph5diff
-rwxr-xr-x | bin/cmakehdf5 | 19 | ||||
-rw-r--r-- | c++/src/H5Location.cpp | 2 | ||||
-rw-r--r-- | fortran/src/hdf5_fortrandll.def.in | 1 | ||||
-rw-r--r-- | fortran/test/tf.f90 | 2 | ||||
-rw-r--r-- | release_docs/INSTALL_parallel | 67 | ||||
-rw-r--r-- | release_docs/RELEASE.txt | 4 | ||||
-rw-r--r-- | src/H5AC.c | 6 | ||||
-rw-r--r-- | src/H5Dchunk.c | 2 | ||||
-rw-r--r-- | src/H5HFsection.c | 2 | ||||
-rw-r--r-- | src/H5Pfapl.c | 6 | ||||
-rw-r--r-- | tools/h5diff/ph5diff_main.c | 5 | ||||
-rw-r--r-- | tools/h5repack/h5repack.sh.in | 22 | ||||
-rw-r--r-- | tools/lib/h5tools_dump.c | 16 | ||||
-rw-r--r-- | tools/testfiles/tfletcher32.ddl | 2 | ||||
-rw-r--r-- | tools/testfiles/tshuffle.ddl | 2 | ||||
-rw-r--r-- | tools/testfiles/tuserfilter.ddl | 4 |
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)" @@ -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 } |