Merge remote-tracking branch 'origin/locking_protocol' into ts_h5fl_reg

.github/workflows/cmake-par-source.yml

@@ -140,7 +140,7 @@ jobs:
       - name: Run ctest script (OpenMPI)
         run: |
           cd "${{ runner.workspace }}/hdf5"
-          ctest -S HDF5config.cmake,CTEST_SITE_EXT=GH-${{ github.event.repository.full_name }}-OpenMPI-s,LOCAL_SUBMIT=ON,NINJA=TRUE,BUILD_GENERATOR=Unix,CTEST_SOURCE_NAME=${{ steps.set-file-base.outputs.SOURCE_BASE }} -C ${{ inputs.build_mode }} -VV -O hdf5.log
+          ctest -S HDF5config.cmake,CTEST_SITE_EXT=GH-${{ github.event.repository.full_name }}-OpenMPI-source,LOCAL_SUBMIT=ON,NINJA=TRUE,BUILD_GENERATOR=Unix,CTEST_SOURCE_NAME=${{ steps.set-file-base.outputs.SOURCE_BASE }} -C ${{ inputs.build_mode }} -VV -O hdf5.log
         shell: bash
         continue-on-error: true
 
@@ -255,7 +255,7 @@ jobs:
       - name: Run ctest script (MPICH)
         run: |
           cd "${{ runner.workspace }}/hdf5"
-          ctest -S HDF5config.cmake,CTEST_SITE_EXT=GH-${{ github.event.repository.full_name }}-MPICH-s,LOCAL_SUBMIT=ON,NINJA=TRUE,BUILD_GENERATOR=Unix,CTEST_SOURCE_NAME=${{ steps.set-file-base.outputs.SOURCE_BASE }} -C ${{ inputs.build_mode }} -VV -O hdf5.log
+          ctest -S HDF5config.cmake,CTEST_SITE_EXT=GH-${{ github.event.repository.full_name }}-MPICH-source,LOCAL_SUBMIT=ON,NINJA=TRUE,BUILD_GENERATOR=Unix,CTEST_SOURCE_NAME=${{ steps.set-file-base.outputs.SOURCE_BASE }} -C ${{ inputs.build_mode }} -VV -O hdf5.log
         shell: bash
         continue-on-error: true
 

CMakePresets.json

@@ -68,7 +68,7 @@
         "LZF_PACKAGE_NAME": {"type": "STRING", "value": "lzf"},
         "SZ_TGZ_NAME": {"type": "STRING", "value": "SZ-2.1.12.5.tar.gz"},
         "SZ_PACKAGE_NAME": {"type": "STRING", "value": "SZ"},
-        "ZFP_TGZ_NAME": {"type": "STRING", "value": "zfp-1.0.0.tar.gz"},
+        "ZFP_TGZ_NAME": {"type": "STRING", "value": "zfp-1.0.1.tar.gz"},
         "ZFP_PACKAGE_NAME": {"type": "STRING", "value": "zfp"},
         "ZSTD_TGZ_NAME": {"type": "STRING", "value": "zstd-1.5.6.tar.gz"},
         "ZSTD_PACKAGE_NAME": {"type": "STRING", "value": "zstd"}

HDF5Examples/C/H5FLT/tfiles/h5ex_d_zfp.ddl

@@ -10,7 +10,7 @@ GROUP "/" {
       FILTERS {
          USER_DEFINED_FILTER {
             FILTER_ID 32013
-            COMMENT H5Z-ZFP-1.1.1 (ZFP-1.0.0) github.com/LLNL/H5Z-ZFP
+            COMMENT H5Z-ZFP-1.1.1 (ZFP-1.0.1) github.com/LLNL/H5Z-ZFP
             PARAMS { XXXX }
          }
       }

HDF5Examples/C/H5FLT/tfiles/h5ex_d_zfp.tst

@@ -4,8 +4,8 @@ zfp filter is available for encoding and decoding.
 ....Close the file and reopen for reading ........
 Filter info is available from the dataset creation property
    Filter identifier is 32013
-   Number of parameters is 6 with the value 268456209
-   To find more about the filter check H5Z-ZFP-1.1.1 (ZFP-1.0.0) github.com/LLNL/H5Z-ZFP
+   Number of parameters is 6 with the value 269504785
+   To find more about the filter check H5Z-ZFP-1.1.1 (ZFP-1.0.1) github.com/LLNL/H5Z-ZFP
 ....Reading zfp compressed data ................
 Maximum value in DS1 is 1890.0000
 zfp filter is available now since H5Dread triggered loading of the filter.

bin/process_source.sh

@@ -0,0 +1,61 @@
+#!/bin/sh
+#
+# Copyright by The HDF Group.
+# All rights reserved.
+#
+# This file is part of HDF5.  The full HDF5 copyright notice, including
+# terms governing use, modification, and redistribution, is contained in
+# the LICENSE file, which can be found at the root of the source code
+# distribution tree, or in https://www.hdfgroup.org/licenses.
+# If you do not have access to either file, you may request a copy from
+# [email protected].
+#
+
+# A convenience script to process HDF5 source. This recreates some header files
+# from their input files and runs the trace script to update the H5ARG_TRACE
+# macros.
+#
+# This does NOT regenerate the parser code in the high-level library, since
+# that would probably generate a lot of churn due to different flex, etc.
+# versions. If you want to regenerate that code, use the genparser script
+# from the bin directory.
+
+echo
+echo "******************************"
+echo "* HDF5 process source script *"
+echo "******************************"
+echo
+echo "*** NOTE: Must be run from the source root! ***"
+echo
+
+# Run trace script
+# The trace script updates H5ARG_TRACE macros in library source files.
+echo "Running arg trace script:"
+bin/trace src/H5*.c || exit 1
+echo
+
+# Run make_err
+# make_err automatically generates the H5E headers that create error message
+# types for HDF5.
+echo "Running error generation script:"
+bin/make_err src/H5err.txt || exit 1
+echo
+
+# Run make_vers
+# make_vers automatically generates the public headers that define the API version
+# macros for HDF5.
+echo "Running API version generation script:"
+bin/make_vers src/H5vers.txt || exit 1
+echo
+
+# Run make_overflow
+# make_overflow automatically generates macros for detecting overflows for type
+# conversion.
+echo "Running overflow macro generation script:"
+bin/make_overflow src/H5overflow.txt || exit 1
+echo
+
+echo "*** SUCCESS ***"
+
+echo
+exit 0

config/cmake/cacheinit.cmake

@@ -229,7 +229,7 @@ set (ZFP_GIT_URL "https://github.com/LLNL/zfp.git" CACHE STRING "Use ZFP from  G
 set (ZFP_GIT_BRANCH "develop" CACHE STRING "" FORCE)
 
 set (ZFP_TGZ_ORIGPATH "https://github.com/LLNL/zfp/releases/download/1.0.0" CACHE STRING "Use PLUGINS from original location" FORCE)
-set (ZFP_TGZ_NAME "zfp-1.0.0.tar.gz" CACHE STRING "Use ZFP from compressed file" FORCE)
+set (ZFP_TGZ_NAME "zfp-1.0.1.tar.gz" CACHE STRING "Use ZFP from compressed file" FORCE)
 
 set (ZFP_PACKAGE_NAME "zfp" CACHE STRING "Name of ZFP package" FORCE)
 

doxygen/aliases

@@ -7,10 +7,12 @@ ALIASES += THG="The HDF Group"
 ALIASES += HDFURL="support.hdfgroup.org"
 # URL for archived files
 ALIASES += ARCURL="\HDFURL/archive/support/HDF5/doc"
+# URL for release files
+ALIASES += RELURL="\HDFURL/releases/hdf5"
 # URL for documentation
-ALIASES += DOCURL="\HDFURL/releases/hdf5/documentation"
+ALIASES += DOCURL="\RELURL/documentation"
 # URL for downloads
-ALIASES += DWNURL="\HDFURL/releases/hdf5/downloads"
+ALIASES += DWNURL="\RELURL/downloads/latest"
 # URL for RFCs
 ALIASES += RFCURL="\DOCURL/rfc"
 ALIASES += AEXURL="\HDFURL/archive/support/ftp/HDF5/examples"
@@ -260,7 +262,6 @@ ALIASES += sa_metadata_ops="\sa \li H5Pget_all_coll_metadata_ops() \li H5Pget_co
 ################################################################################
 
 ALIASES += ref_cons_semantics="<a href=\"https://\RFCURL/RFC%20PHDF5%20Consistency%20Semantics%20MC%20120328.docx.pdf\">Enabling a Strict Consistency Semantics Model in Parallel HDF5</a>"
-ALIASES += ref_file_image_ops="<a href=\"https://\RFCURL/HDF5FileImageOperations.pdf\">HDF5 File Image Operations</a>"
 ALIASES += ref_filter_pipe="<a href=\"https://\DOCURL/advanced_topics/data_flow_pline_H5Dread.md\">Data Flow Pipeline for H5Dread()</a>"
 ALIASES += ref_group_impls="<a href=\"https://\DOXURL/group___h5_g.html\">Group implementations in HDF5</a>"
 ALIASES += ref_h5lib_relver="<a href=\"https://\ARCURL/TechNotes/Version.html\">HDF5 Library Release Version Numbers</a>"
@@ -327,7 +328,6 @@ ALIASES += ref_rfc20121114="<a href=\"https://\RFCURL/DECTRIS%20Integration%20RF
 ALIASES += ref_rfc20121024="<a href=\"https://\RFCURL/FileSpaceManagement.pdf\">HDF5 File Space Management</a>"
 ALIASES += ref_rfc20120828="<a href=\"https://\RFCURL/H5HPC_MultiDset_RW_IO_RFC.pdf\">New HDF5 API Routines for HPC Applications - Read/Write Multiple Datasets in an HDF5 file</a>"
 ALIASES += ref_rfc20120523="<a href=\"https://\RFCURL/paged_aggregation.pdf\">HDF5 File Space Management: Paged Aggregation</a>"
-ALIASES += ref_rfc20120501="<a href=\"https://\RFCURL/HDF5FileImageOperations.pdf\">HDF5 File Image Operations</a>"
 ALIASES += ref_rfc20120305="<a href=\"https://\RFCURL/RFC%20PHDF5%20Consistency%20Semantics%20MC%20120328.docx.pdf\">Enabling a Strict Consistency Semantics Model in Parallel HDF5</a>"
 ALIASES += ref_rfc20120220="<a href=\"https://\RFCURL/h5repack_improve_hyperslab_over_chunked_dataset_v1.pdf\"><tt>h5repack</tt>: Improved Hyperslab selections for Large Chunked Datasets</a>"
 ALIASES += ref_rfc20120120="<a href=\"https://\RFCURL/2012-1-25-Maintainers-guide-for-datatype.docx.pdf\">A Maintainer's Guide for the Datatype Module in HDF5 Library</a>"

doxygen/dox/ExamplesAPI.dox

@@ -150,8 +150,8 @@ Languages are C, Fortran, Java (JHI5), Java Object Package, Python (High Level),
 <a href="https://\HVURL/test/org.hdfgroup.object.example.test/datasets/H5ObjectEx_D_ReadWrite.java">JavaObj</a>
   MATLAB  PyHigh  PyLow
 </td>
-<td>h5ex_d_rdwrc.h5</td>
-<td><a href="https://\SRCURL/HDF5Examples/C/H5D/tfiles/16/h5ex_d_rdwrc.tst">h5ex_d_rdwrc.tst</a></td>
+<td>h5ex_d_rdwr.h5</td>
+<td><a href="https://\SRCURL/HDF5Examples/C/H5D/tfiles/16/h5ex_d_rdwr.tst">h5ex_d_rdwr.tst</a></td>
 <td><a href="https://\SRCURL/HDF5Examples/C/H5D/tfiles/16/h5ex_d_rdwr.ddl">h5ex_d_rdwr.ddl</a></td>
 </tr>
 <tr>
@@ -483,7 +483,7 @@ FORTRAN
 </td>
 <td>h5ex_t_convert.h5</td>
 <td><a href="https://\SRCURL/HDF5Examples/C/H5T/tfiles/16/h5ex_t_convert.tst">h5ex_t_convert.tst</a></td>
-<td><a href="https://\SRCURL/HDF5Examples/C/H5T/tfiles/18/h5ex_t_convert.ddl">h5ex_t_convert.ddl</a></td>
+<td>h5ex_t_convert.ddl not applicable</td>
 </tr>
 <tr>
 <td>Read / Write Complex Compound  (Attribute)</td>

doxygen/dox/IntroHDF5.dox

@@ -625,7 +625,7 @@ For information on compiling in C, C++ and Fortran, see: \ref LBCompiling
 <a href="http://hdfeos.org/zoo/index.php">IDL, MATLAB, and NCL Examples for HDF-EOS</a>
 Examples of how to access and visualize NASA HDF-EOS files using IDL, MATLAB, and NCL.
 
-<a href="https://\AEXURL/misc-examples/">Miscellaneous Examples</a>
+<a href="https://\AEXURL/misc-examples/index.html">Miscellaneous Examples</a>
 These (very old) examples resulted from working with users, and are not fully tested. Most of them are in C, with a few in Fortran and Java.
 
 <a href="https://\AEXURL/special_values_HDF5_example.tar">Using Special Values</a>

doxygen/dox/LearnBasics.dox

@@ -75,15 +75,15 @@ These examples (C, C++, Fortran, Java, Python) are provided in the HDF5 source c
 <tr>
 <td>Read and write to a dataset
 </td>
-<td><a href="https://\SRCURL/HDF5Examples/C/TUTR/h5_rdwt.c">C</a>  <a href="https://\SRCURL/HDF5Examples/FORTRAN/TUTR/h5_rdwt.f90">Fortran</a>  <a href="https://\SRCURL/HDF5Examples/CXX/TUTR/h5tutr_rdwt.cpp">C++</a>  <a href="https://\SRCURL/HDF5Examples/JAVA/TUTR/HDF5DatasetRead.java">Java</a>  <a href="https://\SRCURL/HDF5Examples/PYTHON/h5_rdwt.py">Python</a>
+<td><a href="https://\SRCURL/HDF5Examples/C/TUTR/h5_rdwt.c">C</a>  <a href="https://\SRCURL/HDF5Examples/FORTRAN/TUTR/h5_rdwt.f90">Fortran</a>  <a href="https://\SRCURL/HDF5Examples/CXX/TUTR/h5tutr_rdwt.cpp">C++</a>  <a href="https://\SRCURL/HDF5Examples/JAVA/TUTR/HDF5DatasetRead.java">Java</a>  Python
 </td>
 <td>
 </td>
 </tr>
 <tr>
 <td>Create an attribute
 </td>
-<td><a href="https://\SRCURL/HDF5Examples/C/TUTR/h5_crtatt.c">C</a>  <a href="https://\SRCURL/HDF5Examples/FORTRAN/TUTR/h5_crtatt.f90">Fortran</a>  <a href="https://\SRCURL/HDF5Examples/CXX/TUTR/h5tutr_crtatt.cpp">C++</a>  <a href="https://\SRCURL/HDF5Examples/JAVA/TUTR/HDF5AttributeCreate.java">Java</a>  <a href="https://\SRCURL/HDF5Examples/PYTHON/h5_crtatt.py">Python</a>
+<td><a href="https://\SRCURL/HDF5Examples/C/TUTR/h5_crtatt.c">C</a>  <a href="https://\SRCURL/HDF5Examples/FORTRAN/TUTR/h5_crtatt.f90">Fortran</a>  <a href="https://\SRCURL/HDF5Examples/CXX/TUTR/h5tutr_crtatt.cpp">C++</a>  <a href="https://\SRCURL/HDF5Examples/JAVA/TUTR/HDF5AttributeCreate.java">Java</a>  Python
 </td>
 <td>
 </td>
@@ -99,7 +99,7 @@ These examples (C, C++, Fortran, Java, Python) are provided in the HDF5 source c
 <tr>
 <td>Create groups in a file using absolute and relative paths
 </td>
-<td><a href="https://\SRCURL/HDF5Examples/C/TUTR/h5_crtgrpar.c">C</a>  <a href="https://\SRCURL/HDF5Examples/FORTRAN/TUTR/h5_crtgrpar.f90">Fortran</a>  <a href="https://\SRCURL/HDF5Examples/CXX/TUTR/h5tutr_crtgrpar.cpp">C++</a>  <a href="https://\SRCURL/HDF5Examples/JAVA/TUTR/HDF5GroupAbsoluteRelativeCreate.java">Java</a>  <a href="https://\SRCURL/HDF5Examples/PYTHON/h5_crtgrpar.py">Python</a>
+<td><a href="https://\SRCURL/HDF5Examples/C/TUTR/h5_crtgrpar.c">C</a>  <a href="https://\SRCURL/HDF5Examples/FORTRAN/TUTR/h5_crtgrpar.f90">Fortran</a>  <a href="https://\SRCURL/HDF5Examples/CXX/TUTR/h5tutr_crtgrpar.cpp">C++</a>  <a href="https://\SRCURL/HDF5Examples/JAVA/TUTR/HDF5GroupAbsoluteRelativeCreate.java">Java</a>  Python
 </td>
 <td>
 </td>

doxygen/dox/LearnBasics3.dox

@@ -968,15 +968,15 @@ or on WINDOWS you may need to add the path to the bin folder to PATH.
 \section secLBCompilingCMake Compiling an Application with CMake
 
 \subsection subsecLBCompilingCMakeScripts CMake Scripts for Building Applications
-See <a href="https://\SRCURL/release_docs/USING_CMake_examples.txt">Using CMake to Build Applications</a> to build applications with different languages and options.
+See <a href="https://\SRCURL/release_docs/USING_CMake_Examples.txt">Using CMake to Build Applications</a> to build applications with different languages and options.
 
 For a more complete script (and to help resolve issues) see the script provided with the HDF5 Examples project.
 
 \subsection subsecLBCompilingCMakeExamples HDF5 Examples
 The installed HDF5 can be verified by compiling the HDF5 Examples project, included with the CMake built HDF5 binaries
 in the share folder or you can go to the <a href="https://\SRCURL/HDF5Examples">HDF5 Examples</a> in the HDF5 github repository.
 
-Go into the share directory and follow the instructions in <a href="https://\SRCURL/release_docs/USING_CMake_examples.txt">Using CMake to Build Examples</a> to build the examples.
+Go into the share directory and follow the instructions in <a href="https://\SRCURL/release_docs/USING_CMake_Examples.txt">Using CMake to Build Examples</a> to build the examples.
 
 In general, users must first set the HDF5_ROOT environment variable to the installed location of the CMake
 configuration files for HDF5. For example, on Windows the following path might be set:

doxygen/dox/Overview.dox

@@ -21,7 +21,7 @@ documents cover a mix of tasks, concepts, and reference, to help a specific
 <em>audience</em> succeed.
 
 \par Offline reading
-     You can <a href="https://\DWNURL/hdf5-1.14.5.doxygen.zip">download</a> it as an archive for offline reading.
+     You can <a href="https://\RELURL/v1_14/v1_14_5/hdf5-1.14.5.doxygen.zip">download</a> it as an archive for offline reading.
 
 \par ToDo List
      There is plenty of <a href="./todo.html">unfinished business</a>.

doxygen/dox/RFC.dox

@@ -53,7 +53,6 @@
 <tr> <td>2012-10-24</td> <td>\ref_rfc20121024</td></tr>
 <tr> <td>2012-08-28</td> <td>\ref_rfc20120828</td></tr>
 <tr> <td>2012-05-23</td> <td>\ref_rfc20120523</td></tr>
-<tr> <td>2012-05-01</td> <td>\ref_rfc20120501</td></tr>
 <tr> <td>2012-03-05</td> <td>\ref_rfc20120305</td></tr>
 <tr> <td>2012-02-20</td> <td>\ref_rfc20120220</td></tr>
 <tr> <td>2012-01-20</td> <td>\ref_rfc20120120</td></tr>

doxygen/dox/Specifications.dox

@@ -54,7 +54,101 @@
 */
 
 /** \page TBL HDF5 Table Specification Version 1.0
+The HDF5 specification defines the standard objects and storage for the standard HDF5
+objects. (For information about the HDF5 library, model and specification, see the HDF
+documentation.) This document is an additional specification do define a standard profile
+for how to store tables in HDF5. Table data in HDF5 is stored as HDF5 datasets with standard
+attributes to define the properties of the tables.
+
+\section sec_tab_spec_intro Introduction
+A generic table is a sequence of records, each record has a name and a type. Table data
+is stored as an HDF5 one dimensional compound dataset. A table is defined as a collection
+of records whose values are stored in fixed-length fields. All records have the same structure
+and all values in each field have the same data type.
+
+The dataset for a table is distinguished from other datasets by giving it an attribute
+"CLASS=TABLE". Optional attributes allow the storage of a title for the Table and for
+each column, and a fill value for each column.
+
+\section sec_tab_spec_attr Table Attributes
+The attributes for the Table are strings. They are written with the #H5LTset_attribute_string
+Lite API function. "Required" attributes must always be used. "Optional" attributes must be
+used when required.
+<table>
+<caption><b>Table 1. Attributes of an Image Dataset</b></caption>
+<tr>
+<th><b>Attribute Name</b></th>
+<th><b>Required</b><br /><b>Optional</b></th>
+<th><b>Type</b></th>
+<th><b>String Size</b></th>
+<th><b>Value</b></th>
+<th><b>Description</b></th>
+</tr>
+<tr>
+<td>CLASS</td>
+<td>Required</td>
+<td>String</td>
+<td>5</td>
+<td>&quot;TABLE&quot;</td>
+<td>This attribute is type #H5T_C_S1, with size 5. For all Tables, the value of this attribute is
+<b>TABLE</b>. This attribute identifies this data set as intended to be interpreted as Table that
+conforms to the specifications on this page.</td>
+</tr>
+<tr>
+<td>VERSION</td>
+<td>Required</td>
+<td>String</td>
+<td>3</td>
+<td>&quot;0.2&quot;</td>
+<td>This attribute is of type #H5T_C_S1, with size corresponding to the length of the version string.
+This attribute identifies the version number of this specification to which it conforms. The current
+version number is "0.2".</td>
+</tr>
+<tr>
+<td>TITLE</td>
+<td>Optional</td>
+<td>String</td>
+<td>&nbsp;</td>
+<td>&nbsp;</td>
+<td>The <b>TITLE</b> is an optional String that is to be used as the informative title of the whole table.
+The <b>TITLE</b> is set with the parameter table_title of the function #H5TBmake_table.</td>
+</tr>
+<tr>
+<td>FIELD_(n)_NAME</td>
+<td>Required</td>
+<td>String</td>
+<td>&nbsp;</td>
+<td>&nbsp;</td>
+<td>The <b>FIELD_(n)_NAME</b> is an optional String that is to be used as the informative title of column n
+of the table. For each of the fields the word <b>FIELD_</b> is concatenated with the zero based field (n)
+index together with the name of the field.</td>
+</tr>
+<tr>
+<td>FIELD_(n)_FILL</td>
+<td>Optional</td>
+<td>String</td>
+<td>&nbsp;</td>
+<td>&nbsp;</td>
+<td>The <b>FIELD_(n)_FILL</b> is an optional String that is the fill value for column n of the table.
+For each of the fields the word <b>FIELD_</b> is concatenated with the zero based field (n) index
+together with the fill value, if present. This value is written only when a fill value is defined
+for the table.</td>
+</tr>
+</table>
+
+The following section of code shows the calls necessary to the creation of a table.
+\code
+// Create a new HDF5 file using default properties.
+file_id = H5Fcreate("my_table.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+
+// Call the make table function
+H5TBmake_table("Table Title", file_id, "Table1", NFIELDS, NRECORDS, dst_size, field_names, dst_offset, field_type, chunk_size, fill_data, compress, p_data);
+
+// Close the file.
+status = H5Fclose(file_id);
+\endcode
+
+For more information see the @ref H5TB reference manual page and the @ref H5TB_UG, which includes examples.
 
-\htmlinclude TableSpec.html
 
 */