CVS commit: pkgsrc/devel/hdf5

To: pkgsrc-changes%NetBSD.org@localhost
Subject: CVS commit: pkgsrc/devel/hdf5
From: "Adam Ciarcinski" <adam%netbsd.org@localhost>
Date: Sun, 6 Nov 2022 17:00:57 +0000

Module Name:    pkgsrc
Committed By:   adam
Date:           Sun Nov  6 17:00:57 UTC 2022

Modified Files:
        pkgsrc/devel/hdf5: Makefile.common PLIST distinfo
        pkgsrc/devel/hdf5/patches: patch-tools_test_h5repack_h5repack.sh.in
Added Files:
        pkgsrc/devel/hdf5/patches: patch-tools_test_h5dump_testh5dump.sh.in

Log Message:
hdf5 hdf5-c++: updated to 1.10.9

HDF5 version 1.10.9

New Features
============

    Configuration:
    -------------
    - Added new option to the h5cc scripts produced by CMake.

      Add -showconfig option to h5cc scripts to cat the
      libhdf5-settings to the standard output.

      (ADB - 2022/03/11)

    - HDF5 memory allocation sanity checking is now off by default for
      Autotools debug builds

      HDF5 can be configured to perform sanity checking on internal memory
      allocations by adding heap canaries to these allocations. However,
      enabling this option can cause issues with external filter plugins
      when working with (reallocating/freeing/allocating and passing back)
      buffers.

      Previously, this option was off by default for all CMake build types,
      but only off by default for non-debug Autotools builds. Since debug
      is the default build mode for HDF5 when built from source with
      Autotools, this can result in surprising segfaults that don't occur
      when an application is built against a release version of HDF5.
      Therefore, this option is now off by default for all build types
      across both CMake and Autotools.

      (JTH - 2022/03/01)

    - Refactored the utils folder.

      Added subfolder test and moved the 'swmr_check_compat_vfd.c file'
      from test into utils/test. Deleted the duplicate swmr_check_compat_vfd.c
      file in hl/tools/h5watch folder. Also fixed vfd check options.

      (ADB - 2021/10/18)

    - Changed autotools and CMake configurations to derive both
      compilation warnings-as-errors and warnings-only-warn configurations
      from the same files, 'config/*/*error*'.  Removed redundant files
      'config/*/*noerror*'.

      (DCY - 2021/09/29)

    Library:
    --------
    - Several improvements to parallel compression feature, including:

      * Improved support for collective I/O (for both writes and reads)

      * Significant reduction of memory usage for the feature as a whole

      * Reduction of copying of application data buffers passed to H5Dwrite

      * Addition of support for incremental file space allocation for filtered
        datasets created in parallel. Incremental file space allocation is the
        default for these types of datasets (early file space allocation is
        also still supported), while early file space allocation is still the
        default (and only supported allocation time) for unfiltered datasets
        created in parallel. Incremental file space allocation should help with
        parallel HDF5 applications that wish to use fill values on filtered
        datasets, but would typically avoid doing so since dataset creation in
        parallel would often take an excessive amount of time. Since these
        datasets previously used early file space allocation, HDF5 would
        allocate space for and write fill values to every chunk in the dataset
        at creation time, leading to noticeable overhead. Instead, with
        incremental file space allocation, allocation of file space for chunks
        and writing of fill values to those chunks will be delayed until each
        individual chunk is initially written to.

      * Addition of support for HDF5's "don't filter partial edge chunks" flag
        (https://portal.hdfgroup.org/display/HDF5/H5P_SET_CHUNK_OPTS)

      * Addition of proper support for HDF5 fill values with the feature

      * Addition of 'H5_HAVE_PARALLEL_FILTERED_WRITES' macro to H5pubconf.h
        so HDF5 applications can determine at compile-time whether the feature
        is available

      * Addition of simple examples (ph5_filtered_writes.c and
        ph5_filtered_writes_no_sel.c) under examples directory to demonstrate
        usage of the feature

      * Improved coverage of regression testing for the feature

      (JTH - 2022/2/23)

    Fortran Library:
    ----------------
    - None

    C++ Library:
    ------------
    - None

    Java Library:
    -------------
    - None

    Tools:
    ------
    - h5repack added an optional verbose value for reporting R/W timing.

      In addition to adding timing capture around the read/write calls in
      h5repack, added help text to indicate how to show timing for read/write;
           -v N, --verbose=N       Verbose mode, print object information.
              N - is an integer greater than 1, 2 displays read/write timing
      (ADB - 2022/04/01)

    High-Level APIs:
    ----------------
    - None

    C Packet Table API:
    -------------------
    - None

    Internal header file:
    ---------------------
    - None

    Documentation:
    --------------
    - None

New platforms, languages and compilers tested
==================================================
    - macOS Apple M1 11.6 Darwin 20.6.0 arm64 with Apple clang version 12.0.5

    - Fedora35 Linux 5.16.14-200.fc35 with GCC 11.2.1 and clang version 13.0.0

Bug Fixes since HDF5-1.10.8 release
===================================
    Library
    -------
    - Fixed a metadata cache bug when resizing a pinned/protected cache entry

      When resizing a pinned/protected cache entry, the metadata
      cache code previously would wait until after resizing the
      entry to attempt to log the newly-dirtied entry. This would
      cause H5C_resize_entry to mark the entry as dirty and make
      H5AC_resize_entry think that it doesn't need to add the
      newly-dirtied entry to the dirty entries skiplist.

      Thus, a subsequent H5AC__log_moved_entry would think it
      needs to allocate a new entry for insertion into the dirty
      entry skip list, since the entry doesn't exist on that list.
      This causes an assertion failure, as the code to allocate a
      new entry assumes that the entry is not dirty.

      (JRM - 2022/02/28)

    - Issue 1436 identified a problem with the H5_VERS_RELEASE check in the
      H5check_version function.

      Investigating the original fix, 812, we discovered some inconsistencies
      with a new block added to check H5_VERS_RELEASE for incompatibilities.
      This new block was not using the new warning text dealing with the
      H5_VERS_RELEASE check and would cause the warning to be duplicated.

      By removing the H5_VERS_RELEASE argument in the first check for
      H5_VERS_MAJOR and H5_VERS_MINOR, the second check would only check
      the H5_VERS_RELEASE for incompatible release versions. This adheres
      to the statement that except for the develop branch, all release versions
      in a major.minor maintenance branch should be compatible. The prerequisite
      is that an application will not use any APIs not present in all release versions.

    - Unified handling of collective metadata reads to correctly fix old bugs

      Due to MPI-related issues occurring in HDF5 from mismanagement of the
      status of collective metadata reads, they were forced to be disabled
      during chunked dataset raw data I/O in the HDF5 1.10.5 release. This
      wouldn't generally have affected application performance because HDF5
      already disables collective metadata reads during chunk lookup, since
      it is generally unlikely that the same chunks will be read by all MPI
      ranks in the I/O operation. However, this was only a partial solution
      that wasn't granular enough.

      This change now unifies the handling of the file-global flag and the
      API context-level flag for collective metadata reads in order to
      simplify querying of the true status of collective metadata reads. Thus,
      collective metadata reads are once again enabled for chunked dataset
      raw data I/O, but manually controlled at places where some processing
      occurs on MPI rank 0 only and would cause issues when collective
      metadata reads are enabled.

      (JTH - 2021/11/16, HDFFV-10501/HDFFV-10562)

    - Fixed several potential MPI deadlocks in library failure conditions

      In the parallel library, there were several places where MPI rank 0
      could end up skipping past collective MPI operations when some failure
      occurs in rank 0-specific processing. This would lead to deadlocks
      where rank 0 completes an operation while other ranks wait in the
      collective operation. These places have been rewritten to have rank 0
      push an error and try to cleanup after the failure, then continue to
      participate in the collective operation to the best of its ability.

      (JTH - 2021/11/09)

    - Fixed an issue with collective metadata reads being permanently disabled
      after a dataset chunk lookup operation. This would usually cause a
      mismatched MPI_Bcast and MPI_ERR_TRUNCATE issue in the library for
      simple cases of H5Dcreate() -> H5Dwrite() -> H5Dcreate().

      (JTH - 2021/11/08, HDFFV-11090)

    Java Library
    ------------
    - None

    Configuration
    -------------
    - Reworked corrected path searched by CMake find_package command

      The install path for cmake find_package files had been changed to use
        "share/cmake"
      for all platforms. However setting the HDF5_ROOT variable failed to locate
      the configuration files. The build variable HDF5_INSTALL_CMAKE_DIR is now
      set to the <INSTALL_DIR>/cmake folder. The location of the configuration
      files can still be specified by the "HDF5_DIR" variable.


To generate a diff of this commit:
cvs rdiff -u -r1.23 -r1.24 pkgsrc/devel/hdf5/Makefile.common
cvs rdiff -u -r1.30 -r1.31 pkgsrc/devel/hdf5/PLIST
cvs rdiff -u -r1.47 -r1.48 pkgsrc/devel/hdf5/distinfo
cvs rdiff -u -r0 -r1.1 \
    pkgsrc/devel/hdf5/patches/patch-tools_test_h5dump_testh5dump.sh.in
cvs rdiff -u -r1.2 -r1.3 \
    pkgsrc/devel/hdf5/patches/patch-tools_test_h5repack_h5repack.sh.in

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/devel/hdf5/Makefile.common
diff -u pkgsrc/devel/hdf5/Makefile.common:1.23 pkgsrc/devel/hdf5/Makefile.common:1.24
--- pkgsrc/devel/hdf5/Makefile.common:1.23      Sat Mar 26 21:52:36 2022
+++ pkgsrc/devel/hdf5/Makefile.common   Sun Nov  6 17:00:56 2022
@@ -1,8 +1,8 @@
-# $NetBSD: Makefile.common,v 1.23 2022/03/26 21:52:36 tnn Exp $
+# $NetBSD: Makefile.common,v 1.24 2022/11/06 17:00:56 adam Exp $
 # used by devel/hdf5/Makefile
 # used by devel/hdf5-c++/Makefile
 
-DISTNAME=      hdf5-1.10.7
+DISTNAME=      hdf5-1.10.9
 CATEGORIES=    devel
 MASTER_SITES=  https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${PKGVERSION_NOREV:R}/hdf5-${PKGVERSION_NOREV}/src/
 EXTRACT_SUFX=  .tar.bz2

Index: pkgsrc/devel/hdf5/PLIST
diff -u pkgsrc/devel/hdf5/PLIST:1.30 pkgsrc/devel/hdf5/PLIST:1.31
--- pkgsrc/devel/hdf5/PLIST:1.30        Fri Jul 22 14:50:32 2022
+++ pkgsrc/devel/hdf5/PLIST     Sun Nov  6 17:00:56 2022
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.30 2022/07/22 14:50:32 thor Exp $
+@comment $NetBSD: PLIST,v 1.31 2022/11/06 17:00:56 adam Exp $
 ${PLIST.hl}bin/gif2h5
 ${PLIST.hl}bin/h52gif
 bin/h5cc
@@ -19,8 +19,6 @@ bin/h5repart
 bin/h5stat
 bin/h5unjam
 ${PLIST.hl}bin/h5watch
-bin/mirror_server
-bin/mirror_server_stop
 include/H5ACpublic.h
 include/H5Apublic.h
 include/H5Cpublic.h
@@ -112,6 +110,8 @@ share/examples/hdf5/c/h5_vds-percival.c
 share/examples/hdf5/c/h5_vds-simpleIO.c
 share/examples/hdf5/c/h5_vds.c
 share/examples/hdf5/c/h5_write.c
+share/examples/hdf5/c/ph5_filtered_writes.c
+share/examples/hdf5/c/ph5_filtered_writes_no_sel.c
 share/examples/hdf5/c/ph5example.c
 share/examples/hdf5/c/run-c-ex.sh
 ${PLIST.hl}share/examples/hdf5/hl/c/ex_ds1.c

Index: pkgsrc/devel/hdf5/distinfo
diff -u pkgsrc/devel/hdf5/distinfo:1.47 pkgsrc/devel/hdf5/distinfo:1.48
--- pkgsrc/devel/hdf5/distinfo:1.47     Tue Oct 26 10:14:50 2021
+++ pkgsrc/devel/hdf5/distinfo  Sun Nov  6 17:00:56 2022
@@ -1,7 +1,8 @@
-$NetBSD: distinfo,v 1.47 2021/10/26 10:14:50 nia Exp $
+$NetBSD: distinfo,v 1.48 2022/11/06 17:00:56 adam Exp $
 
-BLAKE2s (hdf5-1.10.7.tar.bz2) = c7b34d0400c7ed6a26c4c75f800f272a868ce7fa0e7649d02dd84cc566942b96
-SHA512 (hdf5-1.10.7.tar.bz2) = bfbd045ea5d7940ac1d0f9aef964dad2e9f22d78b49c90668021106259c9612352fbcb4e89085a7fa189f58142ef83a363c6220ea89aa0d57bdfed245df0ab57
-Size (hdf5-1.10.7.tar.bz2) = 8957844 bytes
+BLAKE2s (hdf5-1.10.9.tar.bz2) = 0a4a93806ba46079b32036228e0a8d8c247abe8ec617140c76a49876c1e55352
+SHA512 (hdf5-1.10.9.tar.bz2) = 2f96373748ac873f7c9459649123a6c20ecd1cef74c0481eb9319b25b5cd41aa90e480167c2c6a8024906dc3b6f202973bf0a5de9ae51a30b1aa945a14f94b51
+Size (hdf5-1.10.9.tar.bz2) = 10703325 bytes
 SHA1 (patch-configure) = e7f141d54c39cbee2f7d703ab7d6ff582158904e
-SHA1 (patch-tools_test_h5repack_h5repack.sh.in) = b31bef7a47e15647fa6090cf1590c9dbb606d8e6
+SHA1 (patch-tools_test_h5dump_testh5dump.sh.in) = 97c70174d10e6e3671975cf3b09c74add27ce9c5
+SHA1 (patch-tools_test_h5repack_h5repack.sh.in) = 7e6f3ce52d4d282f341a93ff4c8231ec8c04a37c

Index: pkgsrc/devel/hdf5/patches/patch-tools_test_h5repack_h5repack.sh.in
diff -u pkgsrc/devel/hdf5/patches/patch-tools_test_h5repack_h5repack.sh.in:1.2 pkgsrc/devel/hdf5/patches/patch-tools_test_h5repack_h5repack.sh.in:1.3
--- pkgsrc/devel/hdf5/patches/patch-tools_test_h5repack_h5repack.sh.in:1.2      Mon Jun  7 11:52:48 2021
+++ pkgsrc/devel/hdf5/patches/patch-tools_test_h5repack_h5repack.sh.in  Sun Nov  6 17:00:56 2022
@@ -1,10 +1,19 @@
-$NetBSD: patch-tools_test_h5repack_h5repack.sh.in,v 1.2 2021/06/07 11:52:48 adam Exp $
+$NetBSD: patch-tools_test_h5repack_h5repack.sh.in,v 1.3 2022/11/06 17:00:56 adam Exp $
 
-test portability fix
+Portability fix.
 
---- tools/test/h5repack/h5repack.sh.in.orig    2020-09-04 21:50:59.000000000 +0000
+--- tools/test/h5repack/h5repack.sh.in.orig    2022-05-25 21:09:13.000000000 +0000
 +++ tools/test/h5repack/h5repack.sh.in
-@@ -928,7 +928,7 @@ TOOLFAILSV()
+@@ -891,7 +891,7 @@ TOOLTEST_FAIL()
+         echo " FAILED"
+         echo "    $failure"
+     else
+-        if [ $RET == 0 ] ; then
++        if [ $RET = 0 ] ; then
+             nerrors="`expr $nerrors + 1`"
+             echo " FAILED"
+         else
+@@ -990,7 +990,7 @@ TOOLFAILSV()
          $RUNSERIAL $H5DIFF_BIN -v $infile $outfile
      ) >$actual 2>$actual_err
      RET=$?

Added files:

Index: pkgsrc/devel/hdf5/patches/patch-tools_test_h5dump_testh5dump.sh.in
diff -u /dev/null pkgsrc/devel/hdf5/patches/patch-tools_test_h5dump_testh5dump.sh.in:1.1
--- /dev/null   Sun Nov  6 17:00:57 2022
+++ pkgsrc/devel/hdf5/patches/patch-tools_test_h5dump_testh5dump.sh.in  Sun Nov  6 17:00:56 2022
@@ -0,0 +1,20 @@
+$NetBSD: patch-tools_test_h5dump_testh5dump.sh.in,v 1.1 2022/11/06 17:00:56 adam Exp $
+
+Portability fix.
+
+--- tools/test/h5dump/testh5dump.sh.in.orig    2022-11-05 18:51:12.000000000 +0000
++++ tools/test/h5dump/testh5dump.sh.in
+@@ -883,11 +883,11 @@ TOOLTEST_FAIL() {
+     ) >&$actual
+     RET=$?
+     # Segfault occurred
+-    if [ $RET == 139 ] ; then
++    if [ $RET = 139 ] ; then
+         nerrors="`expr $nerrors + 1`"
+         echo "*FAILED - test on $infile failed with segmentation fault"
+     # Should fail but didn't
+-    elif [ $RET == 0 ] ; then
++    elif [ $RET = 0 ] ; then
+         nerrors="`expr $nerrors + 1`"
+         echo "*FAILED - test on $infile did not fail as expected"
+     else

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