Merges from 1.14 Aug 4-9

config/cmake/ConfigureChecks.cmake

@@ -858,21 +858,23 @@ if (HDF5_BUILD_FORTRAN)
 
  list (GET PROG_OUTPUT4 0 H5_LDBL_DIG)
  list (GET PROG_OUTPUT4 1 H5_FLT128_DIG)
- endif ()
 
- if (${HDF_PREFIX}_SIZEOF___FLOAT128 EQUAL "0" OR FLT128_DIG EQUAL "0")
- set (${HDF_PREFIX}_HAVE_FLOAT128 0)
- set (${HDF_PREFIX}_SIZEOF___FLOAT128 0)
- set (_PAC_C_MAX_REAL_PRECISION ${H5_LDBL_DIG})
+ if (${HDF_PREFIX}_SIZEOF___FLOAT128 EQUAL "0" OR FLT128_DIG EQUAL "0")
+ set (${HDF_PREFIX}_HAVE_FLOAT128 0)
+ set (${HDF_PREFIX}_SIZEOF___FLOAT128 0)
+ set (_PAC_C_MAX_REAL_PRECISION ${H5_LDBL_DIG})
+ else ()
+ set (_PAC_C_MAX_REAL_PRECISION ${H5_FLT128_DIG})
+ endif ()
+ if (NOT ${_PAC_C_MAX_REAL_PRECISION})
+ set (${HDF_PREFIX}_PAC_C_MAX_REAL_PRECISION 0)
+ else ()
+ set (${HDF_PREFIX}_PAC_C_MAX_REAL_PRECISION ${_PAC_C_MAX_REAL_PRECISION})
+ endif ()
+ message (STATUS "maximum decimal precision for C var - ${${HDF_PREFIX}_PAC_C_MAX_REAL_PRECISION}")
  else ()
- set (_PAC_C_MAX_REAL_PRECISION ${H5_FLT128_DIG})
- endif ()
- if (NOT ${_PAC_C_MAX_REAL_PRECISION})
  set (${HDF_PREFIX}_PAC_C_MAX_REAL_PRECISION 0)
- else ()
- set (${HDF_PREFIX}_PAC_C_MAX_REAL_PRECISION ${_PAC_C_MAX_REAL_PRECISION})
  endif ()
- message (STATUS "maximum decimal precision for C var - ${${HDF_PREFIX}_PAC_C_MAX_REAL_PRECISION}")
 
 endif()
 

fortran/src/CMakeLists.txt

@@ -427,29 +427,34 @@ else ()
  )
 endif ()
 
+set (mod_export_files
+ h5fortran_types.mod
+ hdf5.mod
+ h5fortkit.mod
+ h5global.mod
+ h5a.mod
+ h5d.mod
+ h5e.mod
+ h5es.mod
+ h5f.mod
+ h5g.mod
+ h5i.mod
+ h5l.mod
+ h5lib.mod
+ h5o.mod
+ h5p.mod
+ h5r.mod
+ h5s.mod
+ h5t.mod
+ h5vl.mod
+ h5z.mod
+ h5_gen.mod
+)
+
 if (BUILD_STATIC_LIBS)
- set (mod_files
- ${MOD_BUILD_DIR}/h5fortran_types.mod
- ${MOD_BUILD_DIR}/hdf5.mod
- ${MOD_BUILD_DIR}/h5fortkit.mod
- ${MOD_BUILD_DIR}/h5global.mod
- ${MOD_BUILD_DIR}/h5a.mod
- ${MOD_BUILD_DIR}/h5d.mod
- ${MOD_BUILD_DIR}/h5e.mod
- ${MOD_BUILD_DIR}/h5f.mod
- ${MOD_BUILD_DIR}/h5g.mod
- ${MOD_BUILD_DIR}/h5i.mod
- ${MOD_BUILD_DIR}/h5l.mod
- ${MOD_BUILD_DIR}/h5lib.mod
- ${MOD_BUILD_DIR}/h5o.mod
- ${MOD_BUILD_DIR}/h5p.mod
- ${MOD_BUILD_DIR}/h5r.mod
- ${MOD_BUILD_DIR}/h5s.mod
- ${MOD_BUILD_DIR}/h5t.mod
- ${MOD_BUILD_DIR}/h5vl.mod
- ${MOD_BUILD_DIR}/h5z.mod
- ${MOD_BUILD_DIR}/h5_gen.mod
- )
+ foreach (mod_file ${mod_export_files})
+ set (mod_files ${mod_files} ${MOD_BUILD_DIR}/${mod_file})
+ endforeach ()
  install (
  FILES
  ${mod_files}
@@ -471,28 +476,9 @@ if (BUILD_STATIC_LIBS)
 endif ()
 
 if (BUILD_SHARED_LIBS)
- set (modsh_files
- ${MODSH_BUILD_DIR}/h5fortran_types.mod
- ${MODSH_BUILD_DIR}/hdf5.mod
- ${MODSH_BUILD_DIR}/h5fortkit.mod
- ${MODSH_BUILD_DIR}/h5global.mod
- ${MODSH_BUILD_DIR}/h5a.mod
- ${MODSH_BUILD_DIR}/h5d.mod
- ${MODSH_BUILD_DIR}/h5e.mod
- ${MODSH_BUILD_DIR}/h5f.mod
- ${MODSH_BUILD_DIR}/h5g.mod
- ${MODSH_BUILD_DIR}/h5i.mod
- ${MODSH_BUILD_DIR}/h5l.mod
- ${MODSH_BUILD_DIR}/h5lib.mod
- ${MODSH_BUILD_DIR}/h5o.mod
- ${MODSH_BUILD_DIR}/h5p.mod
- ${MODSH_BUILD_DIR}/h5r.mod
- ${MODSH_BUILD_DIR}/h5s.mod
- ${MODSH_BUILD_DIR}/h5t.mod
- ${MODSH_BUILD_DIR}/h5vl.mod
- ${MODSH_BUILD_DIR}/h5z.mod
- ${MODSH_BUILD_DIR}/h5_gen.mod
- )
+ foreach (mod_file ${mod_export_files})
+ set (modsh_files ${modsh_files} ${MODSH_BUILD_DIR}/${mod_file})
+ endforeach ()
  install (
  FILES
  ${modsh_files}

hl/fortran/src/CMakeLists.txt

@@ -235,16 +235,19 @@ endif ()
 # Add file(s) to CMake Install
 #-----------------------------------------------------------------------------
 
+set (mod_export_files
+ h5ds.mod
+ h5tb.mod
+ h5tb_const.mod
+ h5lt.mod
+ h5lt_const.mod
+ h5im.mod
+)
 
 if (BUILD_STATIC_LIBS)
- set (mod_files
- ${MOD_BUILD_DIR}/h5ds.mod
- ${MOD_BUILD_DIR}/h5tb.mod
- ${MOD_BUILD_DIR}/h5tb_const.mod
- ${MOD_BUILD_DIR}/h5lt.mod
- ${MOD_BUILD_DIR}/h5lt_const.mod
- ${MOD_BUILD_DIR}/h5im.mod
- )
+ foreach (mod_file ${mod_export_files})
+ set (mod_files ${mod_files} ${MOD_BUILD_DIR}/${mod_file})
+ endforeach ()
  install (
  FILES
  ${mod_files}
@@ -265,14 +268,9 @@ if (BUILD_STATIC_LIBS)
  endif ()
 endif ()
 if (BUILD_SHARED_LIBS)
- set (modsh_files
- ${MODSH_BUILD_DIR}/h5ds.mod
- ${MODSH_BUILD_DIR}/h5tb.mod
- ${MODSH_BUILD_DIR}/h5tb_const.mod
- ${MODSH_BUILD_DIR}/h5lt.mod
- ${MODSH_BUILD_DIR}/h5lt_const.mod
- ${MODSH_BUILD_DIR}/h5im.mod
- )
+ foreach (mod_file ${mod_export_files})
+ set (modsh_files ${modsh_files} ${MODSH_BUILD_DIR}/${mod_file})
+ endforeach ()
  install (
  FILES
  ${modsh_files}

release_docs/RELEASE.txt

@@ -260,6 +260,17 @@ Bug Fixes since HDF5-1.14.1 release
 
  Testing
  -------
+ - Fixed a testing failure in testphdf5 on Cray machines
+
+ On some Cray machines, what appears to be a bug in Cray MPICH was causing
+ calls to H5Fis_accessible to create a 0-byte file with strange Unix
+ permissions. This was causing an H5Fdelete file deletion test in the
+ testphdf5 program to fail due to a just-deleted HDF5 file appearing to
+ still be accessible on the file system. The issue in Cray MPICH has been
+ worked around for the time being by resetting the MPI_Info object on the
+ File Access Property List used to MPI_INFO_NULL before passing it to the
+ H5Fis_accessible call.
+
  - A bug was fixed in the HDF5 API test random datatype generation code
 
  A bug in the random datatype generation code could cause test failures

release_docs/USING_HDF5_VS.txt

@@ -38,7 +38,10 @@ Using Visual Studio 2010 and above with HDF5 Libraries built with Visual Studio
  library, and then optionally the HDF5 High Level, Fortran or C++
  libraries. For example, to compile a C++ application, enter:
 
- szip.lib zlib.lib hdf5.lib hdf5_cpp.lib
+ hdf5.lib hdf5_cpp.lib
+
+ For static linking:
+ libszaec.lib libaec.lib libzlib.lib libhdf5.lib libhdf5_cpp.lib
 
 
 ==========================================================================

src/H5Dchunk.c

@@ -2731,11 +2731,20 @@ H5D__chunk_read(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info)
  }
  } /* end if */
  else if (!skip_missing_chunks) {
+ /* Set up nonexistent dataset info for (fill value) read from nonexistent chunk */
+ nonexistent_dset_info.layout_io_info.contig_piece_info = chunk_info;
+ nonexistent_dset_info.file_space = chunk_info->fspace;
+ nonexistent_dset_info.mem_space = chunk_info->mspace;
+ nonexistent_dset_info.nelmts = chunk_info->piece_points;
+
+ /* Set request_nelmts. This is not normally set by the upper layers because selection I/O
+ * usually does not use strip mining (H5D__scatgath_write), and instead allocates buffers
+ * large enough for the entire I/O. Set request_nelmts to be large enough for all selected
+ * elements in this chunk because it must be at least that large */
+ nonexistent_dset_info.type_info.request_nelmts = nonexistent_dset_info.nelmts;
+
  /* Perform the actual read operation from the nonexistent chunk
  */
- nonexistent_dset_info.file_space = chunk_info->fspace;
- nonexistent_dset_info.mem_space = chunk_info->mspace;
- nonexistent_dset_info.nelmts = chunk_info->piece_points;
  if ((dset_info->io_ops.single_read)(&nonexistent_io_info, &nonexistent_dset_info) < 0)
  HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "chunked read failed");
  } /* end if */
@@ -2866,9 +2875,10 @@ H5D__chunk_read(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info)
 
  /* Perform the actual read operation */
  assert(chk_io_info->count == 1);
- chk_io_info->dsets_info[0].file_space = chunk_info->fspace;
- chk_io_info->dsets_info[0].mem_space = chunk_info->mspace;
- chk_io_info->dsets_info[0].nelmts = chunk_info->piece_points;
+ chk_io_info->dsets_info[0].layout_io_info.contig_piece_info = chunk_info;
+ chk_io_info->dsets_info[0].file_space = chunk_info->fspace;
+ chk_io_info->dsets_info[0].mem_space = chunk_info->mspace;
+ chk_io_info->dsets_info[0].nelmts = chunk_info->piece_points;
  if ((dset_info->io_ops.single_read)(chk_io_info, &chk_io_info->dsets_info[0]) < 0)
  HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "chunked read failed");
 
@@ -3055,10 +3065,19 @@ H5D__chunk_write(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info)
  /* Set up the storage buffer information for this chunk */
  cpt_store.compact.buf = chunk;
 
+ /* Set up compact dataset info for write to cached chunk */
+ cpt_dset_info.layout_io_info.contig_piece_info = chunk_info;
+ cpt_dset_info.file_space = chunk_info->fspace;
+ cpt_dset_info.mem_space = chunk_info->mspace;
+ cpt_dset_info.nelmts = chunk_info->piece_points;
+
+ /* Set request_nelmts. This is not normally set by the upper layers because selection I/O
+ * usually does not use strip mining (H5D__scatgath_write), and instead allocates buffers
+ * large enough for the entire I/O. Set request_nelmts to be large enough for all selected
+ * elements in this chunk because it must be at least that large */
+ cpt_dset_info.type_info.request_nelmts = cpt_dset_info.nelmts;
+
  /* Perform the actual write operation */
- cpt_dset_info.file_space = chunk_info->fspace;
- cpt_dset_info.mem_space = chunk_info->mspace;
- cpt_dset_info.nelmts = chunk_info->piece_points;
  if ((dset_info->io_ops.single_write)(&cpt_io_info, &cpt_dset_info) < 0)
  HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "chunked write failed");
 
@@ -3253,9 +3272,10 @@ H5D__chunk_write(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info)
 
  /* Perform the actual write operation */
  assert(chk_io_info->count == 1);
- chk_io_info->dsets_info[0].file_space = chunk_info->fspace;
- chk_io_info->dsets_info[0].mem_space = chunk_info->mspace;
- chk_io_info->dsets_info[0].nelmts = chunk_info->piece_points;
+ chk_io_info->dsets_info[0].layout_io_info.contig_piece_info = chunk_info;
+ chk_io_info->dsets_info[0].file_space = chunk_info->fspace;
+ chk_io_info->dsets_info[0].mem_space = chunk_info->mspace;
+ chk_io_info->dsets_info[0].nelmts = chunk_info->piece_points;
  if ((dset_info->io_ops.single_write)(chk_io_info, &chk_io_info->dsets_info[0]) < 0)
  HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "chunked write failed");
 

src/H5Dcompact.c

@@ -233,8 +233,9 @@ H5D__compact_io_init(H5D_io_info_t *io_info, H5D_dset_io_info_t *dinfo)
 {
  FUNC_ENTER_PACKAGE_NOERR
 
- dinfo->store->compact.buf = dinfo->dset->shared->layout.storage.u.compact.buf;
- dinfo->store->compact.dirty = &dinfo->dset->shared->layout.storage.u.compact.dirty;
+ dinfo->store->compact.buf = dinfo->dset->shared->layout.storage.u.compact.buf;
+ dinfo->store->compact.dirty = &dinfo->dset->shared->layout.storage.u.compact.dirty;
+ dinfo->layout_io_info.contig_piece_info = NULL;
 
  /* Disable selection I/O */
  io_info->use_select_io = H5D_SELECTION_IO_MODE_OFF;

src/H5Defl.c

@@ -198,6 +198,9 @@ H5D__efl_io_init(H5D_io_info_t *io_info, H5D_dset_io_info_t *dinfo)
 
  H5MM_memcpy(&dinfo->store->efl, &(dinfo->dset->shared->dcpl_cache.efl), sizeof(H5O_efl_t));
 
+ /* No "pieces" selected */
+ dinfo->layout_io_info.contig_piece_info = NULL;
+
  /* Disable selection I/O */
  io_info->use_select_io = H5D_SELECTION_IO_MODE_OFF;
  io_info->no_selection_io_cause |= H5D_SEL_IO_NOT_CONTIGUOUS_OR_CHUNKED_DATASET;

src/H5Dio.c

@@ -415,8 +415,14 @@ H5D__read(size_t count, H5D_dset_io_info_t *dset_info)
  HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get MPI-I/O transfer mode");
 
  /* Only report the collective I/O mode if we're actually performing collective I/O */
- if (xfer_mode == H5FD_MPIO_COLLECTIVE)
+ if (xfer_mode == H5FD_MPIO_COLLECTIVE) {
  H5CX_set_mpio_actual_io_mode(io_info.actual_io_mode);
+
+ /* If we did selection I/O, report that we used "link chunk" mode, since that's the most
+ * analogous to what selection I/O does */
+ if (io_info.use_select_io == H5D_SELECTION_IO_MODE_ON)
+ H5CX_set_mpio_actual_chunk_opt(H5D_MPIO_LINK_CHUNK);
+ }
  }
 #endif /* H5_HAVE_PARALLEL */
  }
@@ -1131,20 +1137,16 @@ H5D__typeinfo_init_phase2(H5D_io_info_t *io_info)
  assert(io_info);
 
  /* If selection I/O mode is default (auto), enable it here if the VFD supports it (it will be turned off
- * later if something else conflicts), otherwise disable it. If we're using the MPIO VFD, the automatic
- * selection will happen in H5D__mpio_opt_possible() inside H5D__ioinfo_adjust(). */
-#ifdef H5_HAVE_PARALLEL
- if (!io_info->using_mpi_vfd)
-#endif /* H5_HAVE_PARALLEL */
- if (io_info->use_select_io == H5D_SELECTION_IO_MODE_DEFAULT) {
- if (H5F_has_vector_select_io(io_info->dsets_info[0].dset->oloc.file,
- io_info->op_type == H5D_IO_OP_WRITE))
- io_info->use_select_io = H5D_SELECTION_IO_MODE_ON;
- else {
- io_info->use_select_io = H5D_SELECTION_IO_MODE_OFF;
- io_info->no_selection_io_cause |= H5D_SEL_IO_DEFAULT_OFF;
- }
+ * later if something else conflicts), otherwise disable it */
+ if (io_info->use_select_io == H5D_SELECTION_IO_MODE_DEFAULT) {
+ if (H5F_has_vector_select_io(io_info->dsets_info[0].dset->oloc.file,
+ io_info->op_type == H5D_IO_OP_WRITE))
+ io_info->use_select_io = H5D_SELECTION_IO_MODE_ON;
+ else {
+ io_info->use_select_io = H5D_SELECTION_IO_MODE_OFF;
+ io_info->no_selection_io_cause |= H5D_SEL_IO_DEFAULT_OFF;
  }
+ }
 
  /* If we're doing type conversion and we might be doing selection I/O, check if the buffers are large
  * enough to handle the whole I/O */

src/H5Dmpio.c

@@ -622,6 +622,9 @@ H5D__mpio_opt_possible(H5D_io_info_t *io_info)
  if (!H5FD_mpi_opt_types_g)
  local_cause[0] |= H5D_MPIO_MPI_OPT_TYPES_ENV_VAR_DISABLED;
 
+ /* Decision on whether to use selection I/O should have been made by now */
+ assert(io_info->use_select_io != H5D_SELECTION_IO_MODE_DEFAULT);
+
  /* Datatype conversions and transformations are allowed with selection I/O. If the selection I/O mode
  * is auto (default), disable collective for now and re-enable later if we can */
  if (io_info->use_select_io != H5D_SELECTION_IO_MODE_ON) {
@@ -731,25 +734,6 @@ H5D__mpio_opt_possible(H5D_io_info_t *io_info)
  HMPI_GOTO_ERROR(FAIL, "MPI_Allreduce failed", mpi_code)
  } /* end else */
 
- /* If the selection I/O mode is default (auto), decide here whether it should be on or off */
- if (io_info->use_select_io == H5D_SELECTION_IO_MODE_DEFAULT) {
- /* If the only reason(s) we've disabled collective are type conversions and/or transforms, enable
- * selection I/O and re-enable collective I/O since it's supported by selection I/O */
- if (global_cause[0] && !(global_cause[0] & ~((unsigned)H5D_MPIO_DATATYPE_CONVERSION |
- (unsigned)H5D_MPIO_DATA_TRANSFORMS))) {
- assert(!(local_cause[0] &
- ~((unsigned)H5D_MPIO_DATATYPE_CONVERSION | (unsigned)H5D_MPIO_DATA_TRANSFORMS)));
- local_cause[0] = 0;
- global_cause[0] = 0;
- io_info->use_select_io = H5D_SELECTION_IO_MODE_ON;
- }
- else {
- /* Otherwise, there's currently no benefit to selection I/O, so leave it off */
- io_info->use_select_io = H5D_SELECTION_IO_MODE_OFF;
- io_info->no_selection_io_cause |= H5D_SEL_IO_DEFAULT_OFF;
- }
- }
-
  /* Set the local & global values of no-collective-cause in the API context */
  H5CX_set_mpio_local_no_coll_cause(local_cause[0]);
  H5CX_set_mpio_global_no_coll_cause(global_cause[0]);