Known problems note for check-passthrough-vol in Hdf5 1 12 1 (#674)

* Hdf5 1 12 doxygen version correction (#658)

* OESS-98 fix tools test for plugins

* sync fork

* Merge of changes from dev

* Move problem option to bottom of the list until fixed

* HDFFV-11106 - fix parsing optional args

* HDFFV-11106 add note

* grammer fix

* Whitespace after clang formatting

* Undo format version 11 changes

* Update check to working version

* Merge workflow and minor changes from develop

* Update supported platforms

* PR#3 merge from develop

* Merge gcc 10 diagnostics option from develop

* Merge #318 OSX changes from develop

* Merge serval small changes from dev

* fix typo

* Minor non-space formatting changes

* GH #386 copyright corrections for java folder

* revert because logic requires false return

* Merges from develop

* Remove case statement for H5I_EVENTSET

* Correct call with versioning

* Remove tabs

* Double underscore change

* Merges from develop

Remove more underscores from header guards

* Merge #380 from develop

* Correct date entry

* Split format source and commit changes on repo push

* remove pre-split setting

* Change windows TS to use older VS.

* HDFFV-11212 JNI export util and Javadoc

* Suggested review changes

* Another change found

* Committing clang-format changes

* Some Javadoc warning fixes

* Committing clang-format changes

* Updated javadoc fixes

* HDFFV-11228/9 merges from develop

* remove obsolete debug comment

* Fix conflict

* HDFFV-11229 merge changes from develop

* HDFFV-11229 merge second compare from develop

* HDFFV-11229 fix reference file

* HDFFV-11229 update autotools test script for two ref files

* HDFFV-11229 merge dev changes for long double display in tools

* Committing clang-format changes

* Update with changes from develop

* Add "option" command for clang options

* Rework CMake add_custom to use the BYPRODUCTS argument

Update pkgconfig scripts for parallel builds.
Fix install COPYING file reference.
Remove unused round defines.
Change CMake default setting of BUILD_CPP to off.

* Whitespace changes

* Rework CMake add_custom to use the BYPRODUCTS argument

* Revert CMake configure checks for round defines

* With VS 2015 minimum strdup is supported

* Doxygen comments merged from develop

* doxygen build updates

* Correct version string for map functions

* TRILAB-227 and tools debug merge from develop

* TRILAB-227 Enable test

* Quote subset args

* Use MATCHES in compiler id compare, merge from dev

* Revert test enable

* Add file to list

* doxygen version errors

* if blocks needed for build modes

* Update list of test platforms

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Attempt format uniformity in RELEASE.txt.

* BUG: DataSet assignment operator is missing (#503)

* BUG: DataSet assignment operator is missing

* Some compilers complain if the copy constructor is given explicitly
  but the assignment operator is implicitly set to default.

* Explicitly defining the assignment operator allows us to properly
  handle reference counters for shared resources.

* BUG: DataSet assignment operator is missing.

* Mimicking code of H5DataType::operator() as suggested by @bmribler.

* Added test

Description:
    Added test for DataSet::operator= that Leengit added
Platform tested:
    Linux/64 (jelly)

* Removed Author field.

* Commit clang format changes.

* Entry for Leengit's github PR #503

* Removed lines left by mistake

Co-authored-by: Binh-Minh Ribler <[email protected]>
Co-authored-by: Larry Knox <[email protected]>

* Add H5Dchunk_iter method for iterating over chunks (#6)

* Add H5Dchunk_iter method for iterating over chunks

This method iterates over all chunks in dataset, calling a user-supplied
callback with the chunk information and optional user supplied data.

The iterator is stopped when ITER_STOP is returned by the user-supplied
callback or the iterator is exhausted.

Existing methods to get chunk_info performs an iteration each time, so
to get many or all chunks causes SUM(i) for i = 0 -> N operations for N
chunks, as opposed to N operations when using this iterator for this use case.

* H5Dchunk_iter: test iterating all chunks, some chunks and failing iteration.

* H5D: move H5Dchunk_iter private methods to specific

* trace: add H5D_chunk_iter_op_t and trace H5D.c

* chunks-iter: document chunk_iter

* chunk-iter: chunk add FUNC_ENTER/FUNC_LEAVE macros

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Set initial doxygen version for H5Dchunk_iter().

* Revert "Set initial doxygen version for H5Dchunk_iter()."

This reverts commit d739e46.

* Revert "Add H5Dchunk_iter method for iterating over chunks (#6)"

This reverts commit 53e1139.

* Add flushrefresh errors with check-passthrough-vol to known problems in
RELEASE.txt.

* Minor RELEASE.txt updates.

* Hdf5 1 12 Remove version from pkgcfg file names (#672)

* OESS-98 fix tools test for plugins

* sync fork

* Merge of changes from dev

* Move problem option to bottom of the list until fixed

* HDFFV-11106 - fix parsing optional args

* HDFFV-11106 add note

* grammer fix

* Whitespace after clang formatting

* Undo format version 11 changes

* Update check to working version

* Merge workflow and minor changes from develop

* Update supported platforms

* PR#3 merge from develop

* Merge gcc 10 diagnostics option from develop

* Merge #318 OSX changes from develop

* Merge serval small changes from dev

* fix typo

* Minor non-space formatting changes

* GH #386 copyright corrections for java folder

* revert because logic requires false return

* Merges from develop

#358 patches from vtk
#361 fix header guard spelling

* Remove case statement for H5I_EVENTSET

* Correct call with versioning

* Remove tabs

* Double underscore change

* Merges from develop

#340 clang -Wformat-security warnings
#360 Fixed uninitialized warnings
Remove more underscores from header guards

* Merge #380 from develop

* Correct date entry

* Split format source and commit changes on repo push

* remove pre-split setting

* Change windows TS to use older VS.

* HDFFV-11212 JNI export util and Javadoc

* Suggested review changes

* Another change found

* Committing clang-format changes

* Some Javadoc warning fixes

* Committing clang-format changes

* Updated javadoc fixes

* HDFFV-11228/9 merges from develop

* remove obsolete debug comment

* Fix conflict

* HDFFV-11229 merge changes from develop

* HDFFV-11229 merge second compare from develop

* HDFFV-11229 fix reference file

* HDFFV-11229 update autotools test script for two ref files

* HDFFV-11229 merge dev changes for long double display in tools

* Committing clang-format changes

* Update with changes from develop

* Add "option" command for clang options

* Rework CMake add_custom to use the BYPRODUCTS argument

Update pkgconfig scripts for parallel builds.
Fix install COPYING file reference.
Remove unused round defines.
Change CMake default setting of BUILD_CPP to off.

* Whitespace changes

* Rework CMake add_custom to use the BYPRODUCTS argument

* Revert CMake configure checks for round defines

* With VS 2015 minimum strdup is supported

* Doxygen comments merged from develop

* doxygen build updates

* Correct version string for map functions

* TRILAB-227 and tools debug merge from develop

* TRILAB-227 Enable test

* Quote subset args

* Use MATCHES in compiler id compare, merge from dev

* Revert test enable

* Add file to list

* doxygen version errors

* if blocks needed for build modes

* Update list of test platforms

* Issue #669 remove version from pkgcfg filename

* remove version from h5cc script

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* More minor updates.

Co-authored-by: Allen Byrne <[email protected]>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Lee Newberg <[email protected]>
Co-authored-by: Binh-Minh Ribler <[email protected]>
Co-authored-by: Gaute Hope <[email protected]>

c++/src/CMakeLists.txt

@@ -199,11 +199,11 @@ set (_PKG_CONFIG_REQUIRES_PRIVATE "${HDF5_LIB_CORENAME}-${HDF5_PACKAGE_VERSION}"
 
 configure_file (
     ${HDF_CONFIG_DIR}/libhdf5.pc.in
-    ${HDF5_BINARY_DIR}/CMakeFiles/${HDF5_CPP_LIB_CORENAME}-${HDF5_PACKAGE_VERSION}.pc
+    ${HDF5_BINARY_DIR}/CMakeFiles/${HDF5_CPP_LIB_CORENAME}.pc
     @ONLY
 )
 install (
-    FILES ${HDF5_BINARY_DIR}/CMakeFiles/${HDF5_CPP_LIB_CORENAME}-${HDF5_PACKAGE_VERSION}.pc
+    FILES ${HDF5_BINARY_DIR}/CMakeFiles/${HDF5_CPP_LIB_CORENAME}.pc
     DESTINATION ${HDF5_INSTALL_LIB_DIR}/pkgconfig
     COMPONENT cpplibraries
 )

config/cmake/libh5cc.in

@@ -29,4 +29,4 @@ printf 'dir is %s\n' "$dir"
 
 export PKG_CONFIG_PATH=$dir/lib/pkgconfig
 
-@_PKG_CONFIG_COMPILER@ `pkg-config --define-variable=prefix=$dir --cflags --libs @_PKG_CONFIG_LIBNAME@-@_PKG_CONFIG_VERSION@` $@
+@_PKG_CONFIG_COMPILER@ `pkg-config --define-variable=prefix=$dir --cflags --libs @_PKG_CONFIG_LIBNAME@` $@

fortran/src/CMakeLists.txt

@@ -556,11 +556,11 @@ set (_PKG_CONFIG_REQUIRES_PRIVATE "${HDF5_LIB_CORENAME}-${HDF5_PACKAGE_VERSION}"
 
 configure_file (
     ${HDF_CONFIG_DIR}/libhdf5.pc.in
-    ${HDF5_BINARY_DIR}/CMakeFiles/${HDF5_F90_LIB_CORENAME}-${HDF5_PACKAGE_VERSION}.pc
+    ${HDF5_BINARY_DIR}/CMakeFiles/${HDF5_F90_LIB_CORENAME}.pc
     @ONLY
 )
 install (
-    FILES ${HDF5_BINARY_DIR}/CMakeFiles/${HDF5_F90_LIB_CORENAME}-${HDF5_PACKAGE_VERSION}.pc
+    FILES ${HDF5_BINARY_DIR}/CMakeFiles/${HDF5_F90_LIB_CORENAME}.pc
     DESTINATION ${HDF5_INSTALL_LIB_DIR}/pkgconfig
     COMPONENT fortlibraries
 )

hl/c++/src/CMakeLists.txt

@@ -110,11 +110,11 @@ set (_PKG_CONFIG_REQUIRES_PRIVATE "${HDF5_HL_LIB_CORENAME}-${HDF5_PACKAGE_VERSIO
 
 configure_file (
     ${HDF_CONFIG_DIR}/libhdf5.pc.in
-    ${HDF5_BINARY_DIR}/CMakeFiles/${HDF5_HL_CPP_LIB_CORENAME}-${HDF5_PACKAGE_VERSION}.pc
+    ${HDF5_BINARY_DIR}/CMakeFiles/${HDF5_HL_CPP_LIB_CORENAME}.pc
     @ONLY
 )
 install (
-    FILES ${HDF5_BINARY_DIR}/CMakeFiles/${HDF5_HL_CPP_LIB_CORENAME}-${HDF5_PACKAGE_VERSION}.pc
+    FILES ${HDF5_BINARY_DIR}/CMakeFiles/${HDF5_HL_CPP_LIB_CORENAME}.pc
     DESTINATION ${HDF5_INSTALL_LIB_DIR}/pkgconfig
     COMPONENT hlcpplibraries
 )

hl/fortran/src/CMakeLists.txt

@@ -343,11 +343,11 @@ set (_PKG_CONFIG_REQUIRES_PRIVATE "${HDF5_F90_LIB_CORENAME}-${HDF5_PACKAGE_VERSI
 
 configure_file (
     ${HDF_CONFIG_DIR}/libhdf5.pc.in
-    ${HDF5_BINARY_DIR}/CMakeFiles/${HDF5_HL_F90_LIB_CORENAME}-${HDF5_PACKAGE_VERSION}.pc
+    ${HDF5_BINARY_DIR}/CMakeFiles/${HDF5_HL_F90_LIB_CORENAME}.pc
     @ONLY
 )
 install (
-    FILES ${HDF5_BINARY_DIR}/CMakeFiles/${HDF5_HL_F90_LIB_CORENAME}-${HDF5_PACKAGE_VERSION}.pc
+    FILES ${HDF5_BINARY_DIR}/CMakeFiles/${HDF5_HL_F90_LIB_CORENAME}.pc
     DESTINATION ${HDF5_INSTALL_LIB_DIR}/pkgconfig
     COMPONENT hlfortlibraries
 )

hl/src/CMakeLists.txt

@@ -142,11 +142,11 @@ set (_PKG_CONFIG_REQUIRES_PRIVATE "${HDF5_LIB_CORENAME}-${HDF5_PACKAGE_VERSION}"
 
 configure_file (
     ${HDF_CONFIG_DIR}/libhdf5.pc.in
-    ${HDF5_BINARY_DIR}/CMakeFiles/${HDF5_HL_LIB_CORENAME}-${HDF5_PACKAGE_VERSION}.pc
+    ${HDF5_BINARY_DIR}/CMakeFiles/${HDF5_HL_LIB_CORENAME}.pc
     @ONLY
 )
 install (
-    FILES ${HDF5_BINARY_DIR}/CMakeFiles/${HDF5_HL_LIB_CORENAME}-${HDF5_PACKAGE_VERSION}.pc
+    FILES ${HDF5_BINARY_DIR}/CMakeFiles/${HDF5_HL_LIB_CORENAME}.pc
     DESTINATION ${HDF5_INSTALL_LIB_DIR}/pkgconfig
     COMPONENT hllibraries
 )

release_docs/RELEASE.txt

@@ -93,7 +93,7 @@ New Features
 
       (2021/03/22)
 
-    - Add CMake variable HDF5_LIB_INFIX
+    - Added CMake variable HDF5_LIB_INFIX
 
       This infix is added to all library names after 'hdf5'.
       e.g. the infix '_openmpi' results in the library name 'libhdf5_openmpi.so'
@@ -206,8 +206,8 @@ New Features
 
     - CMake option to use MSVC naming conventions with MinGW
 
-      HDF5_MSVC_NAMING_CONVENTION option enable to use MSVC naming conventions
-      when using a MinGW toolchain
+      HDF5_MSVC_NAMING_CONVENTION option enables the use of MSVC naming
+      conventions when using a MinGW toolchain
 
       (2020/10/30)
 
@@ -309,21 +309,6 @@ New Features
 
     Library:
     --------
-    - H5Dchunk_iter() added for iterating over chunks
-
-      This method iterates over all chunks in a dataset, calling a user-supplied
-      callback with the chunk information and optional user supplied data.
-
-      The iterator is stopped when ITER_STOP is returned by the user-supplied
-      callback or the iterator is exhausted.
-
-      Existing methods to get chunk_info perform an iteration each time, so
-      whereas getting many or all chunks with existing methods caused SUM(i) 
-      for i = 0 -> N operations for N chunks, using this iterator for this 
-      use case will get N chunks with N operations.
-
-      (2021/05/19)
-
     - H5Gcreate1() now rejects size_hint parameters larger than UINT32_MAX
 
       The size_hint value is ultimately stored in a uint32_t struct field,
@@ -920,6 +905,11 @@ The following platforms are not supported but have been tested for this release.
 Known Problems
 ==============
 
+    testflushrefresh.sh will fail when run with "make check-passthough-vol"
+    on centos7, with 3 Errors/Segmentation faults.  These will not occur when
+    run with "make check".  See https://github.com/HDFGroup/hdf5/issues/673
+    for details.
+
     The t_bigio test fails on several HPC platforms, generally by timeout with 
     OpenMPI 4.0.0 or with this error from spectrum-mpi: 
         *** on communicator MPI_COMM_WORLD

src/CMakeLists.txt

@@ -1332,11 +1332,11 @@ set (_PKG_CONFIG_REQUIRES_PRIVATE)
 
 configure_file (
     ${HDF_CONFIG_DIR}/libhdf5.pc.in
-    ${HDF5_BINARY_DIR}/CMakeFiles/${HDF5_LIB_CORENAME}-${HDF5_PACKAGE_VERSION}.pc
+    ${HDF5_BINARY_DIR}/CMakeFiles/${HDF5_LIB_CORENAME}.pc
     @ONLY
 )
 install (
-    FILES ${HDF5_BINARY_DIR}/CMakeFiles/${HDF5_LIB_CORENAME}-${HDF5_PACKAGE_VERSION}.pc
+    FILES ${HDF5_BINARY_DIR}/CMakeFiles/${HDF5_LIB_CORENAME}.pc
     DESTINATION ${HDF5_INSTALL_LIB_DIR}/pkgconfig
     COMPONENT libraries
 )