Merge pull request #2418 from fortnern/select_io_tconv

Initial implementation of selection I/O with type conversion

.autom4te.cfg

@@ -1,5 +1,4 @@
 # Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
 # All rights reserved.
 #
 # This file is part of HDF5.  The full HDF5 copyright notice, including

.clang-format

@@ -1,7 +1,20 @@
 ---
-Language:        Cpp
 BasedOnStyle:  LLVM
 AlignConsecutiveAssignments: true
+BraceWrapping:
+  AfterFunction:   true
+  #llvm10-11: AfterControlStatement: false - Never
+  BeforeCatch:     true
+  BeforeElse:      true
+  #llvm11:   BeforeLambdaBody: false
+  #llvm11:   BeforeWhile:     false
+BreakBeforeBraces: Stroustrup
+BreakAfterJavaFieldAnnotations: true
+BreakStringLiterals: true
+ColumnLimit:     110    # Update $max_trace_macro_line_len in bin/trace also
+IndentWidth:     4
+---
+Language:        Cpp
 #llvm11: AlignConsecutiveBitFields: false
 AlignConsecutiveDeclarations: true
 AlignConsecutiveMacros: true
@@ -22,17 +35,6 @@ AlwaysBreakAfterReturnType: AllDefinitions
 #  - H5_ATTR_CONST
 #  - H5_ATTR_PURE
 #  - H5_ATTR_FALLTHROUGH
-BraceWrapping:
-  AfterFunction:   true
-  #llvm10-11: AfterControlStatement: false - Never
-  BeforeCatch:     true
-  BeforeElse:      true
-  #llvm11:   BeforeLambdaBody: false
-  #llvm11:   BeforeWhile:     false
-BreakBeforeBraces: Stroustrup
-BreakAfterJavaFieldAnnotations: true
-BreakStringLiterals: true
-ColumnLimit:     110    # Update $max_trace_macro_line_len in bin/trace also
 ForEachMacros: ['ALL_MEMBERS', 'UNIQUE_MEMBERS']
 IncludeCategories:
   - Regex:           '^"(llvm|llvm-c|clang|clang-c)/'
@@ -55,7 +57,6 @@ IndentCaseLabels: true
 #llvm11: IndentCaseBlocks: false
 IndentGotoLabels: false
 #llvm11: IndentExternBlock: AfterExternBlock
-IndentWidth:     4
 #llvm11: InsertTrailingCommas: None
 MacroBlockBegin: "^BEGIN_FUNC"
 MacroBlockEnd: "^END_FUNC"
@@ -92,5 +93,8 @@ StatementMacros:
 #llvm11: WhitespaceSensitiveMacros:
 #llvm11:   - STRINGIZE
 #llvm11:   - PP_STRINGIZE
+---
+Language:      Java
+BreakAfterJavaFieldAnnotations: true
+JavaImportGroups: ['java', 'hdf', 'hdf.hdf5lib', 'org']
 ...
-

.github/CODEOWNERS

@@ -2,41 +2,10 @@
 # Each line is a file pattern followed by one or more owners.
 
 # These owners will be the default owners for everything in the repo.
-*       @lrknox
+* @lrknox @derobins @byrnHDF @fortnern @jhendersonHDF @qkoziol @vchoi-hdfgroup @bmribler @raylu-hdf
 
 # Order is important. The last matching pattern has the most precedence.
 # So if a pull request only touches javascript files, only these owners
 # will be requested to review.
-*.cmake           @byrnHDF @ChristopherHogan @gnuoyd @derobins
-CMakeLists.txt    @byrnHDF @ChristopherHogan @gnuoyd @derobins
-CMakeTests.*      @byrnHDF @ChristopherHogan @gnuoyd @derobins
-
-/bin/             @lrknox @ChristopherHogan @gnuoyd @derobins @qkoziol
-
-/c++/             @bmribler @byrnHDF @ChristopherHogan @gnuoyd @derobins
-
-/config/          @lrknox @byrnHDF @ChristopherHogan @gnuoyd @derobins @qkoziol
-
-/doc/             @ChristopherHogan @gnuoyd @jrmainzer
-
-/examples/        @lrknox @bmribler @ChristopherHogan @gnuoyd @derobins
-
-/fortran/         @brtnfld @epourmal
-
-/hl/              @bmribler @byrnHDF @ChristopherHogan @gnuoyd @derobins
-
-/java/            @jhendersonHDF @byrnHDF
-
-/m4/              @lrknox @ChristopherHogan @gnuoyd @derobins
-
-/release_docs/    @lrknox @bmribler @byrnHDF
-
-/src/             @jhendersonHDF @fortnern @soumagne @vchoi-hdfgroup @ChristopherHogan @gnuoyd @derobins @jrmainzer @qkoziol
-
-/test/            @jhendersonHDF @fortnern @soumagne @vchoi-hdfgroup @ChristopherHogan @gnuoyd @derobins @jrmainzer @qkoziol
-
-/testpar/         @jhendersonHDF @ChristopherHogan @gnuoyd @jrmainzer @qkoziol
-
-/tools/           @byrnHDF @bmribler @ChristopherHogan @gnuoyd @derobins
-
-/utils/           @lrknox @byrnHDF @ChristopherHogan @gnuoyd @derobins
+/fortran/         @brtnfld
+/java/            @jhendersonHDF @byrnHDF @derobins

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,25 @@
+---
+name: Bug report
+about: Report a problem with HDF5
+title: "[BUG]"
+labels: bug
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Platform (please complete the following information)**
+ - HDF5 version (if building from a maintenance branch, please include the commit hash)
+ - OS and version
+ - Compiler and version
+ - Build system (e.g. CMake, Autotools) and version
+ - Any configure options you specified
+ - MPI library and version (parallel HDF5)
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature-request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an improvement to HDF5
+title: "[Feature Request]"
+labels: enhancement
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/PULL_REQUEST_TEMPLATE/pull_request_template.md

@@ -0,0 +1,8 @@
+## Describe your changes
+
+## Issue ticket number (GitHub or JIRA)
+
+## Checklist before requesting a review
+- [ ] My code conforms to the guidelines in CONTRIBUTING.md
+- [ ] I made an entry in release_docs/RELEASE.txt (bug fixes, new features)
+- [ ] I added a test (bug fixes, new features)

.github/workflows/clang-format-check.yml

@@ -7,12 +7,12 @@ jobs:
     runs-on: ubuntu-latest
     if: "!contains(github.event.head_commit.message, 'skip-ci')"
     steps:
-    - uses: actions/checkout@v2
-    - name: Run clang-format style check for C programs.
-      uses: DoozyX/clang-format-lint-action@v0.11
+    - uses: actions/checkout@v3
+    - name: Run clang-format style check for C and Java programs.
+      uses: DoozyX/clang-format-lint-action@v0.13
       with:
         source: '.'
-        extensions: 'c,h,cpp,hpp'
-        clangFormatVersion: 10
+        extensions: 'c,h,cpp,hpp,java'
+        clangFormatVersion: 13
         style: file
         exclude: './config ./hl/src/H5LTanalyze.c ./hl/src/H5LTparse.c ./hl/src/H5LTparse.h ./src/H5Epubgen.h ./src/H5Einit.h ./src/H5Eterm.h ./src/H5Edefin.h ./src/H5version.h ./src/H5overflow.h'

.github/workflows/clang-format-fix.yml

@@ -8,13 +8,13 @@ jobs:
     runs-on: ubuntu-latest
     if: "!contains(github.event.head_commit.message, 'skip-ci')"
     steps:
-    - uses: actions/checkout@v2
-    - name: Run clang-format style check for C programs.
-      uses: DoozyX/clang-format-lint-action@v0.11
+    - uses: actions/checkout@v3
+    - name: Run clang-format style check for C and Java programs.
+      uses: DoozyX/clang-format-lint-action@v0.13
       with:
         source: '.'
-        extensions: 'c,h,cpp,hpp'
-        clangFormatVersion: 10
+        extensions: 'c,h,cpp,hpp,java'
+        clangFormatVersion: 13
         inplace: True
         style: file
         exclude: './config ./hl/src/H5LTanalyze.c ./hl/src/H5LTparse.c ./hl/src/H5LTparse.h ./src/H5Epubgen.h ./src/H5Einit.h ./src/H5Eterm.h ./src/H5Edefin.h ./src/H5version.h ./src/H5overflow.h'

.github/workflows/codespell.yml

@@ -8,8 +8,8 @@ jobs:
     name: Check for spelling errors
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - uses: codespell-project/actions-codespell@master
         with:
-          skip: ./bin/trace,./hl/tools/h5watch/h5watch.c,./tools/test/h5jam/tellub.c
-          ignore_words_list: isnt,inout,nd,parms,parm,ba,offsetP,ser,ois,had,fiter,fo,clude,refere,minnum,offsetp,creat,ans:,eiter,lastr,ans,isn't,ifset,sur,trun,dne,tthe,hda,filname,te,htmp,minnum,ro,oce
+          skip: ./bin/trace,./hl/tools/h5watch/h5watch.c,./tools/test/h5jam/tellub.c,./config/sanitizer/LICENSE,./tools/test/h5repack/testfiles/*.dat
+          ignore_words_list: isnt,inout,nd,parms,parm,ba,offsetP,ser,ois,had,fiter,fo,clude,refere,minnum,offsetp,creat,ans:,eiter,lastr,ans,isn't,ifset,sur,trun,dne,tthe,hda,filname,te,htmp,minnum,ake,gord,numer,ro,oce

.github/workflows/main.yml

@@ -4,218 +4,481 @@ name: hdf5 dev CI
 on:
   workflow_dispatch:
   push:
-    branches: [ develop, hdf5_1_12, hdf5_1_10, hdf5_1_8 ]
+  pull_request:
+    branches: [ develop, hdf5_1_14, hdf5_1_12, hdf5_1_10, hdf5_1_8 ]
     paths-ignore:
-    - '.github/**'
-    - 'doc/**'
-    - 'release_docs/**'
-    - 'ACKNOWLEDGEMENTS'
-    - 'COPYING**'
-    - '**.md'
+      - '.github/CODEOWNERS'
+      - '.github/FUNDING.yml'
+      - 'doc/**'
+      - 'release_docs/**'
+      - 'ACKNOWLEDGEMENTS'
+      - 'COPYING**'
+      - '**.md'
     
-# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+# A workflow run is made up of one or more jobs that can run sequentially or
+# in parallel. We just have one job, but the matrix items defined below will
+# run in parallel.
 jobs:
-  # This workflow contains a single job called "build"
-  build:
+
+  # A workflow that builds the library and runs all the tests
+  build_and_test:
+
     strategy:
-#      fail-fast: false
+
+      # The current matrix has three dimensions:
+      #
+      # * config name
+      # * thread-safety on/off
+      # * release vs. debug build
+      #
+      # Most configuration information is added via the 'include' mechanism,
+      # which will append the key-value pairs in the configuration where the
+      # names match.
+
       matrix:
-        name: ["Windows Latest MSVC", "Ubuntu Latest GCC", "Ubuntu Debug GCC", "macOS Latest Clang", "Ubuntu Autotools GCC", "Windows TS MSVC", "Ubuntu TS GCC", "TS Debug GCC", "macOS TS Clang", "TS Autotools GCC"]
+
+        name:
+          - "Windows MSVC CMake"
+          - "Ubuntu gcc CMake"
+          - "Ubuntu gcc Autotools"
+          - "Ubuntu gcc Autotools parallel (build only)"
+          - "MacOS Clang CMake"
+
+        thread_safety:
+          - enabled: true
+            text: " TS"
+          - enabled: false
+            text: ""
+
+        build_mode:
+          - text: " REL"
+            cmake: "Release"
+            autotools: "production"
+          - text: " DBG"
+            cmake: "Debug"
+            autotools: "debug"
+
+        # This is where we list the bulk of the options for each configuration.
+        # The key-value pair values are usually appropriate for being CMake or
+        # Autotools configure values, so be aware of that.
+
         include:
-          - name: "Windows Latest MSVC"
-            artifact: "Windows-MSVC.tar.xz"
+
+          # Windows w/ MSVC + CMake
+          #
+          # No Fortran, parallel, or VFDs that rely on POSIX things
+          - name: "Windows MSVC CMake"
             os: windows-2022
-            build_type: "Release"
             toolchain: ""
             cpp: ON
             fortran: OFF
             java: ON
-            ts: OFF
-            hl: ON
             parallel: OFF
+            mirror_vfd: OFF
+            direct_vfd: OFF
             generator: "-G \"Visual Studio 17 2022\" -A x64"
-          - name: "Ubuntu Latest GCC"
-            artifact: "Linux.tar.xz"
+            run_tests: true
+
+          # Linux (Ubuntu) w/ gcc + CMake
+          #
+          # We might think about adding Clang, but MacOS already tests that
+          # so it's not critical
+          - name: "Ubuntu gcc CMake"
             os: ubuntu-latest
-            build_type: "Release"
             cpp: ON
             fortran: ON
             java: ON
-            ts: OFF
-            hl: ON
             parallel: OFF
+            mirror_vfd: ON
+            direct_vfd: ON
             toolchain: "config/toolchain/GCC.cmake"
             generator: "-G Ninja"
-          - name: "macOS Latest Clang"
-            artifact: "macOS.tar.xz"
-            os: macos-latest
-            build_type: "Release"
-            cpp: ON
-            fortran: OFF
-            java: ON
-            ts: OFF
-            hl: ON
-            parallel: OFF
-            toolchain: "config/toolchain/clang.cmake"
-            generator: "-G Ninja"
-          - name: "Ubuntu Debug GCC"
-            artifact: "LinuxDBG.tar.xz"
+            run_tests: true
+
+          # Linux (Ubuntu) w/ gcc + Autotools
+          #
+          # Keep this identical to the CMake configs. Note the difference in
+          # the values.
+          - name: "Ubuntu gcc Autotools"
             os: ubuntu-latest
-            build_type: "Debug"
-            cpp: ON
-            fortran: OFF
-            java: OFF
-            ts: OFF
-            hl: ON
-            parallel: OFF
-            toolchain: "config/toolchain/GCC.cmake"
-            generator: "-G Ninja"
-          - name: "Ubuntu Autotools GCC"
-            artifact: "LinuxA.tar.xz"
-            os: ubuntu-latest
-            build_type: "Release"
             cpp: enable
             fortran: enable
             java: enable
-            ts: disable
-            hl: enable
             parallel: disable
+            mirror_vfd: enable
+            direct_vfd: enable
+            deprec_sym: enable
+            default_api: v114
             toolchain: ""
             generator: "autogen"
-#  Threadsafe runs
-          - name: "Windows TS MSVC"
-            artifact: "Windows-MSVCTS.tar.xz"
-            os: windows-2019
-            build_type: "Release"
-            toolchain: ""
-            cpp: OFF
-            fortran: OFF
-            java: OFF
-            ts: ON
-            hl: OFF
-            parallel: OFF
-            generator: "-G \"Visual Studio 16 2019\" -A x64"
-          - name: "Ubuntu TS GCC"
-            artifact: "LinuxTS.tar.xz"
+            flags: ""
+            run_tests: true
+
+          # Parallel Linux (Ubuntu) w/ gcc + Autotools
+          #
+          # The GitHub runners are inadequate for running parallel HDF5 tests,
+          # so we catch most issues in daily testing. What we have here is just
+          # a compile check to make sure nothing obvious is broken.
+          - name: "Ubuntu gcc Autotools parallel (build only)"
             os: ubuntu-latest
-            build_type: "Release"
-            cpp: OFF
+            cpp: disable
+            fortran: enable
+            java: disable
+            parallel: enable
+            mirror_vfd: disable
+            direct_vfd: disable
+            deprec_sym: enable
+            default_api: v114
+            toolchain: ""
+            generator: "autogen"
+            flags: "CC=mpicc"
+            run_tests: false
+
+          # MacOS w/ Clang + CMake
+          #
+          # We could also build with the Autotools via brew installing them,
+          # but that seems unnecessary
+          - name: "MacOS Clang CMake"
+            os: macos-11
+            cpp: ON
             fortran: OFF
-            java: OFF
-            ts: ON
-            hl: OFF
-            parallel: OFF
-            toolchain: "config/toolchain/GCC.cmake"
-            generator: "-G Ninja"
-          - name: "macOS TS Clang"
-            artifact: "macOSTS.tar.xz"
-            os: macos-latest
-            build_type: "Release"
-            cpp: OFF
-            fortran: OFF
-            java: OFF
-            ts: ON
-            hl: OFF
+            java: ON
             parallel: OFF
+            mirror_vfd: ON
+            direct_vfd: OFF
             toolchain: "config/toolchain/clang.cmake"
             generator: "-G Ninja"
-          - name: "TS Debug GCC"
-            artifact: "LinuxTSDBG.tar.xz"
+            run_tests: true
+
+
+          #
+          # SPECIAL AUTOTOOLS BUILDS
+          #
+          # These do not run tests and are not built into the matrix and instead
+          # become NEW configs as their name would clobber one of the matrix
+          # names (so make sure the names are UNIQUE).
+          #
+
+          - name: "Ubuntu gcc Autotools v1.6 default API (build only)"
             os: ubuntu-latest
-            build_type: "Debug"
-            cpp: OFF
-            fortran: OFF
-            java: OFF
-            ts: ON
-            hl: OFF
-            parallel: OFF
-            toolchain: "config/toolchain/GCC.cmake"
-            generator: "-G Ninja"
-          - name: "TS Autotools GCC"
-            artifact: "LinuxATS.tar.xz"
-            os: ubuntu-latest
-            build_type: "Release"
-            cpp: disable
-            fortran: disable
-            java: disable
-            ts: enable
-            hl: disable
+            cpp: enable
+            fortran: enable
+            java: enable
             parallel: disable
+            mirror_vfd: enable
+            direct_vfd: enable
+            deprec_sym: enable
+            default_api: v16
             toolchain: ""
             generator: "autogen"
-#          - name: "Ubuntu Parallel GCC"
-#            artifact: "LinuxPar.tar.xz"
-#            os: ubuntu-latest
-#            build_type: "Release"
-#            cpp: OFF
-#            fortran: OFF
-#            parallel: ON
-#            toolchain: "config/toolchain/GCC.cmake"
-#            generator: "-G Ninja"
+            flags: ""
+            run_tests: false
+            thread_safety:
+              enabled: false
+              text: ""
+            build_mode:
+              text: " DBG"
+              cmake: "Debug"
+              autotools: "debug"
+
+          - name: "Ubuntu gcc Autotools v1.8 default API (build only)"
+            os: ubuntu-latest
+            cpp: enable
+            fortran: enable
+            java: enable
+            parallel: disable
+            mirror_vfd: enable
+            direct_vfd: enable
+            deprec_sym: enable
+            default_api: v18
+            toolchain: ""
+            generator: "autogen"
+            flags: ""
+            run_tests: false
+            thread_safety:
+              enabled: false
+              text: ""
+            build_mode:
+              text: " DBG"
+              cmake: "Debug"
+              autotools: "debug"
+
+          - name: "Ubuntu gcc Autotools v1.10 default API (build only)"
+            os: ubuntu-latest
+            cpp: enable
+            fortran: enable
+            java: enable
+            parallel: disable
+            mirror_vfd: enable
+            direct_vfd: enable
+            deprec_sym: enable
+            default_api: v110
+            toolchain: ""
+            generator: "autogen"
+            flags: ""
+            run_tests: false
+            thread_safety:
+              enabled: false
+              text: ""
+            build_mode:
+              text: " DBG"
+              cmake: "Debug"
+              autotools: "debug"
+
+          - name: "Ubuntu gcc Autotools v1.12 default API (build only)"
+            os: ubuntu-latest
+            cpp: enable
+            fortran: enable
+            java: enable
+            parallel: disable
+            mirror_vfd: enable
+            direct_vfd: enable
+            deprec_sym: enable
+            default_api: v112
+            toolchain: ""
+            generator: "autogen"
+            flags: ""
+            run_tests: false
+            thread_safety:
+              enabled: false
+              text: ""
+            build_mode:
+              text: " DBG"
+              cmake: "Debug"
+              autotools: "debug"
+
+          - name: "Ubuntu gcc Autotools v1.14 default API (build only)"
+            os: ubuntu-latest
+            cpp: enable
+            fortran: enable
+            java: enable
+            parallel: disable
+            mirror_vfd: enable
+            direct_vfd: enable
+            deprec_sym: enable
+            default_api: v114
+            toolchain: ""
+            generator: "autogen"
+            flags: ""
+            run_tests: false
+            thread_safety:
+              enabled: false
+              text: ""
+            build_mode:
+              text: " DBG"
+              cmake: "Debug"
+              autotools: "debug"
+
+          - name: "Ubuntu gcc Autotools no deprecated symbols (build only)"
+            os: ubuntu-latest
+            cpp: enable
+            fortran: enable
+            java: enable
+            parallel: disable
+            mirror_vfd: enable
+            direct_vfd: enable
+            deprec_sym: disable
+            default_api: default
+            toolchain: ""
+            generator: "autogen"
+            flags: ""
+            run_tests: false
+            thread_safety:
+              enabled: false
+              text: ""
+            build_mode:
+              text: " DBG"
+              cmake: "Debug"
+              autotools: "debug"
+
+          - name: "Ubuntu gcc Autotools -Werror (build only)"
+            os: ubuntu-latest
+            cpp: enable
+            fortran: disable
+            java: disable
+            parallel: disable
+            mirror_vfd: disable
+            direct_vfd: enable
+            deprec_sym: enable
+            default_api: v114
+            toolchain: ""
+            generator: "autogen"
+            flags: "CFLAGS=-Werror"
+            run_tests: false
+            thread_safety:
+              enabled: false
+              text: ""
+            build_mode:
+              text: " DBG"
+              cmake: "Debug"
+              autotools: "debug"
+
+          - name: "Ubuntu gcc Autotools -Werror (build only)"
+            os: ubuntu-latest
+            cpp: enable
+            fortran: disable
+            java: disable
+            parallel: disable
+            mirror_vfd: disable
+            direct_vfd: enable
+            deprec_sym: enable
+            default_api: v114
+            toolchain: ""
+            generator: "autogen"
+            flags: "CFLAGS=-Werror"
+            run_tests: false
+            thread_safety:
+              enabled: false
+              text: ""
+            build_mode:
+              text: " REL"
+              cmake: "Release"
+              autotools: "production"
+
+    # Sets the job's name from the properties
+    name: "${{ matrix.name }}${{ matrix.build_mode.text }}${{ matrix.thread_safety.text }}"
+
+    # Don't run the action if the commit message says to skip CI
+    if: "!contains(github.event.head_commit.message, 'skip-ci')"
 
-    name: ${{ matrix.name }}
     # The type of runner that the job will run on
     runs-on: ${{ matrix.os }}
-    if: "!contains(github.event.head_commit.message, 'skip-ci')"
-          
+
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
-    - name: Install Dependencies (Linux)
-      run: sudo apt-get install ninja-build
-      if: matrix.os == 'ubuntu-latest'
-    - name: Install Autotools Dependencies (Linux)
-      run: sudo apt-get install automake autoconf libtool libtool-bin
-      if: matrix.generator == 'autogen'
-    - name: Install Dependencies (Windows)
-      run: choco install ninja
-      if: matrix.os == 'windows-latest'
-    - name: Install Dependencies (macOS)
-      run: brew install ninja
-      if: matrix.os == 'macos-latest'
-    - name: Set environment for MSVC (Windows)
-      if:  matrix.os == 'windows-latest'
-      run: |
-        # Set these env vars so cmake picks the correct compiler
-        echo "CXX=cl.exe" >> $GITHUB_ENV
-        echo "CC=cl.exe" >> $GITHUB_ENV
+
+      #
+      # SETUP
+      #
+
+      #Useful for debugging
+      - name: Dump matrix context
+        run: echo '${{ toJSON(matrix) }}'
+
+      - name: Install CMake Dependencies (Linux)
+        run: sudo apt-get install ninja-build
+        if: matrix.os == 'ubuntu-latest'
+
+      - name: Install Autotools Dependencies (Linux, serial)
+        run: |
+           sudo apt update
+           sudo apt install automake autoconf libtool libtool-bin
+           sudo apt install gcc-11 g++-11 gfortran-11
+           echo "CC=gcc-11" >> $GITHUB_ENV
+           echo "CXX=g++-11" >> $GITHUB_ENV
+           echo "FC=gfortran-11" >> $GITHUB_ENV
+        if: (matrix.generator == 'autogen') && (matrix.parallel != 'enable')
+
+      - name: Install Autotools Dependencies (Linux, parallel)
+        run: |
+           sudo apt update
+           sudo apt install automake autoconf libtool libtool-bin
+           sudo apt install openmpi-bin openmpi-common mpi-default-dev
+           echo "CC=mpicc" >> $GITHUB_ENV
+           echo "FC=mpif90" >> $GITHUB_ENV
+        if: (matrix.generator == 'autogen') && (matrix.parallel == 'enable')
+
+      - name: Install Dependencies (Windows)
+        run: choco install ninja
+        if: matrix.os == 'windows-latest'
+
+      - name: Install Dependencies (macOS)
+        run: brew install ninja
+        if: matrix.os == 'macos-11'
+
+      - name: Set environment for MSVC (Windows)
+        run: |
+          # Set these environment variables so CMake picks the correct compiler
+          echo "CXX=cl.exe" >> $GITHUB_ENV
+          echo "CC=cl.exe" >> $GITHUB_ENV
+        if:  matrix.os == 'windows-latest'
     
-    # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-    - name: Get Sources
-      uses: actions/checkout@v2
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - name: Get Sources
+        uses: actions/checkout@v3
 
-    - name: Autotools Configure 
-      if: matrix.generator == 'autogen'
-      run: |
-        sh ./autogen.sh
-        mkdir "${{ runner.workspace }}/build"
-        cd "${{ runner.workspace }}/build"
-        $GITHUB_WORKSPACE/configure --enable-shared --${{ matrix.ts }}-threadsafe --${{ matrix.hl }}-hl --${{ matrix.parallel }}-parallel --${{ matrix.cpp }}-cxx --${{ matrix.fortran }}-fortran --${{ matrix.java }}-java
-      shell: bash
+      #
+      # AUTOTOOLS CONFIGURE
+      #
 
-    - name: Configure
-      if: matrix.generator != 'autogen'
-      run: |
-        mkdir "${{ runner.workspace }}/build"
-        cd "${{ runner.workspace }}/build"
-        cmake ${{ matrix.generator }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -DCMAKE_TOOLCHAIN_FILE=${{ matrix.toolchain }} -DBUILD_SHARED_LIBS=ON -DHDF5_ENABLE_ALL_WARNINGS=ON -DHDF5_ENABLE_THREADSAFE:BOOL=${{ matrix.ts }} -DHDF5_BUILD_HL_LIB:BOOL=${{ matrix.hl }} -DHDF5_ENABLE_PARALLEL:BOOL=${{ matrix.parallel }} -DHDF5_BUILD_CPP_LIB:BOOL=${{ matrix.cpp }} -DHDF5_BUILD_FORTRAN=${{ matrix.fortran }} -DHDF5_BUILD_JAVA=${{ matrix.java }} $GITHUB_WORKSPACE
-      shell: bash
+      - name: Autotools Configure
+        run: |
+          sh ./autogen.sh
+          mkdir "${{ runner.workspace }}/build"
+          cd "${{ runner.workspace }}/build"
+          ${{ matrix.flags }} $GITHUB_WORKSPACE/configure --enable-build-mode=${{ matrix.build_mode.autotools }} --${{ matrix.deprec_sym }}-deprecated-symbols --with-default-api-version=${{ matrix.default_api }} --enable-shared --${{ matrix.parallel }}-parallel --${{ matrix.cpp }}-cxx --${{ matrix.fortran }}-fortran --${{ matrix.java }}-java --${{ matrix.mirror_vfd }}-mirror-vfd --${{ matrix.direct_vfd }}-direct-vfd
+        shell: bash
+        if: (matrix.generator == 'autogen') && (! matrix.thread_safe.enabled)
 
-    - name: Autotools Build
-      if: matrix.generator == 'autogen'
-      run: make
-      working-directory: ${{ runner.workspace }}/build      
+      - name: Autotools Configure (Thread-Safe)
+        run: |
+          sh ./autogen.sh
+          mkdir "${{ runner.workspace }}/build"
+          cd "${{ runner.workspace }}/build"
+          ${{ matrix.flags }} $GITHUB_WORKSPACE/configure --enable-build-mode=${{ matrix.build_mode.autotools }} --enable-shared --enable-threadsafe --disable-hl --${{ matrix.parallel }}-parallel --${{ matrix.mirror_vfd }}-mirror-vfd --${{ matrix.direct_vfd }}-direct-vfd
+        shell: bash
+        if: (matrix.generator == 'autogen') && (matrix.thread_safe.enabled)
 
-    - name: Build
-      if: matrix.generator != 'autogen'
-      run: cmake --build . --config ${{ matrix.build_type }}
-      working-directory: ${{ runner.workspace }}/build      
+      #
+      # CMAKE CONFIGURE
+      #
 
-    - name: Autotools Test
-      if: matrix.generator == 'autogen'
-      run: make check
-      working-directory: ${{ runner.workspace }}/build
+      - name: CMake Configure
+        run: |
+          mkdir "${{ runner.workspace }}/build"
+          cd "${{ runner.workspace }}/build"
+          cmake ${{ matrix.generator }} -DCMAKE_BUILD_TYPE=${{ matrix.build_mode.cmake }} -DCMAKE_TOOLCHAIN_FILE=${{ matrix.toolchain }} -DBUILD_SHARED_LIBS=ON -DHDF5_ENABLE_ALL_WARNINGS=ON -DHDF5_ENABLE_PARALLEL:BOOL=${{ matrix.parallel }} -DHDF5_BUILD_CPP_LIB:BOOL=${{ matrix.cpp }} -DHDF5_BUILD_FORTRAN=${{ matrix.fortran }} -DHDF5_BUILD_JAVA=${{ matrix.java }} -DHDF5_ENABLE_MIRROR_VFD:BOOL=${{ matrix.mirror_vfd }} -DHDF5_ENABLE_DIRECT_VFD:BOOL=${{ matrix.direct_vfd }} $GITHUB_WORKSPACE
+        shell: bash
+        if: (matrix.generator != 'autogen') && (! matrix.thread_safe.enabled)
 
-    - name: Test
-      if: matrix.generator != 'autogen'
-      run: ctest --build . -C ${{ matrix.build_type }} -V
-      working-directory: ${{ runner.workspace }}/build
+
+      - name: CMake Configure (Thread-Safe)
+        run: |
+          mkdir "${{ runner.workspace }}/build"
+          cd "${{ runner.workspace }}/build"
+          cmake ${{ matrix.generator }} -DCMAKE_BUILD_TYPE=${{ matrix.build_mode.cmake }} -DCMAKE_TOOLCHAIN_FILE=${{ matrix.toolchain }} -DBUILD_SHARED_LIBS=ON -DHDF5_ENABLE_ALL_WARNINGS=ON -DHDF5_ENABLE_THREADSAFE:BOOL=ON -DHDF5_ENABLE_PARALLEL:BOOL=${{ matrix.parallel }} -DHDF5_BUILD_HL_LIB:BOOL=OFF -DHDF5_ENABLE_MIRROR_VFD:BOOL=${{ matrix.mirror_vfd }} -DHDF5_ENABLE_DIRECT_VFD:BOOL=${{ matrix.direct_vfd }} $GITHUB_WORKSPACE
+        shell: bash
+        if: (matrix.generator != 'autogen') && (matrix.thread_safe.enabled)
+
+      #
+      # BUILD
+      #
+
+      - name: Autotools Build
+        run: make
+        working-directory: ${{ runner.workspace }}/build
+        if: matrix.generator == 'autogen'
+
+      - name: CMake Build
+        run: cmake --build . --config ${{ matrix.build_mode.cmake }}
+        working-directory: ${{ runner.workspace }}/build
+        if: matrix.generator != 'autogen'
+
+      #
+      # RUN TESTS
+      #
+
+      - name: Autotools Run Tests
+        run: make check
+        working-directory: ${{ runner.workspace }}/build
+        if: (matrix.generator == 'autogen') && (matrix.run_tests)
+
+      - name: CMake Run Tests
+        run: ctest --build . -C ${{ matrix.build_mode.cmake }} -V
+        working-directory: ${{ runner.workspace }}/build
+        # Skip Debug MSVC while we investigate H5L Java test timeouts
+        if: (matrix.generator != 'autogen') && (matrix.run_tests) && ! ((matrix.name == 'Windows MSVC CMake') && (matrix.build_mode.cmake == 'Debug'))
+
+      #
+      # INSTALL (note that this runs even when we don't run the tests)
+      #
+
+      - name: Autotools Install
+        run: make install
+        working-directory: ${{ runner.workspace }}/build
+        if: (matrix.generator == 'autogen')
+
+      - name: Autotools Verify Install
+        run: make check-install
+        working-directory: ${{ runner.workspace }}/build
+        if: (matrix.generator == 'autogen')

.github/workflows/pr-check.yml

@@ -1,213 +0,0 @@
-name: hdf5 dev CI
-
-# Controls when the action will run. Triggers the workflow on push or pull request
-on:
-  pull_request:
-    branches: [ develop, hdf5_1_12, hdf5_1_10, hdf5_1_8 ]
-
-# A workflow run is made up of one or more jobs that can run sequentially or in parallel
-jobs:
-  # This workflow contains a single job called "build"
-  build:
-    strategy:
-#      fail-fast: false
-      matrix:
-        name: ["Windows Latest MSVC", "Ubuntu Latest GCC", "Ubuntu Debug GCC", "macOS Latest Clang", "Ubuntu Autotools GCC", "Windows TS MSVC", "Ubuntu TS GCC", "TS Debug GCC", "macOS TS Clang", "TS Autotools GCC"]
-        include:
-          - name: "Windows Latest MSVC"
-            artifact: "Windows-MSVC.tar.xz"
-            os: windows-2022
-            build_type: "Release"
-            toolchain: ""
-            cpp: ON
-            fortran: OFF
-            java: ON
-            ts: OFF
-            hl: ON
-            parallel: OFF
-            generator: "-G \"Visual Studio 17 2022\" -A x64"
-          - name: "Ubuntu Latest GCC"
-            artifact: "Linux.tar.xz"
-            os: ubuntu-latest
-            build_type: "Release"
-            cpp: ON
-            fortran: ON
-            java: ON
-            ts: OFF
-            hl: ON
-            parallel: OFF
-            toolchain: "config/toolchain/GCC.cmake"
-            generator: "-G Ninja"
-          - name: "macOS Latest Clang"
-            artifact: "macOS.tar.xz"
-            os: macos-latest
-            build_type: "Release"
-            cpp: ON
-            fortran: OFF
-            java: ON
-            ts: OFF
-            hl: ON
-            parallel: OFF
-            toolchain: "config/toolchain/clang.cmake"
-            generator: "-G Ninja"
-          - name: "Ubuntu Debug GCC"
-            artifact: "LinuxDBG.tar.xz"
-            os: ubuntu-latest
-            build_type: "Debug"
-            cpp: ON
-            fortran: OFF
-            java: OFF
-            ts: OFF
-            hl: ON
-            parallel: OFF
-            toolchain: "config/toolchain/GCC.cmake"
-            generator: "-G Ninja"
-          - name: "Ubuntu Autotools GCC"
-            artifact: "LinuxA.tar.xz"
-            os: ubuntu-latest
-            build_type: "Release"
-            cpp: enable
-            fortran: enable
-            java: enable
-            ts: disable
-            hl: enable
-            parallel: disable
-            toolchain: ""
-            generator: "autogen"
-#  Threadsafe runs
-          - name: "Windows TS MSVC"
-            artifact: "Windows-MSVCTS.tar.xz"
-            os: windows-2019
-            build_type: "Release"
-            toolchain: ""
-            cpp: OFF
-            fortran: OFF
-            java: OFF
-            ts: ON
-            hl: OFF
-            parallel: OFF
-            generator: "-G \"Visual Studio 16 2019\" -A x64"
-          - name: "Ubuntu TS GCC"
-            artifact: "LinuxTS.tar.xz"
-            os: ubuntu-latest
-            build_type: "Release"
-            cpp: OFF
-            fortran: OFF
-            java: OFF
-            ts: ON
-            hl: OFF
-            parallel: OFF
-            toolchain: "config/toolchain/GCC.cmake"
-            generator: "-G Ninja"
-          - name: "macOS TS Clang"
-            artifact: "macOSTS.tar.xz"
-            os: macos-latest
-            build_type: "Release"
-            cpp: OFF
-            fortran: OFF
-            java: OFF
-            ts: ON
-            hl: OFF
-            parallel: OFF
-            toolchain: "config/toolchain/clang.cmake"
-            generator: "-G Ninja"
-          - name: "TS Debug GCC"
-            artifact: "LinuxTSDBG.tar.xz"
-            os: ubuntu-latest
-            build_type: "Debug"
-            cpp: OFF
-            fortran: OFF
-            java: OFF
-            ts: ON
-            hl: OFF
-            parallel: OFF
-            toolchain: "config/toolchain/GCC.cmake"
-            generator: "-G Ninja"
-          - name: "TS Autotools GCC"
-            artifact: "LinuxATS.tar.xz"
-            os: ubuntu-latest
-            build_type: "Release"
-            cpp: disable
-            fortran: disable
-            java: disable
-            ts: enable
-            hl: disable
-            parallel: disable
-            toolchain: ""
-            generator: "autogen"
-#          - name: "Ubuntu Parallel GCC"
-#            artifact: "LinuxPar.tar.xz"
-#            os: ubuntu-latest
-#            build_type: "Release"
-#            cpp: OFF
-#            fortran: OFF
-#            parallel: ON
-#            toolchain: "config/toolchain/GCC.cmake"
-#            generator: "-G Ninja"
-
-    name: ${{ matrix.name }}
-    # The type of runner that the job will run on
-    runs-on: ${{ matrix.os }}
-    if: "!contains(github.event.head_commit.message, 'skip-ci')"
-          
-    # Steps represent a sequence of tasks that will be executed as part of the job
-    steps:
-    - name: Install Dependencies (Linux)
-      run: sudo apt-get install ninja-build
-      if: matrix.os == 'ubuntu-latest'
-    - name: Install Autotools Dependencies (Linux)
-      run: sudo apt-get install automake autoconf libtool libtool-bin
-      if: matrix.generator == 'autogen'
-    - name: Install Dependencies (Windows)
-      run: choco install ninja
-      if: matrix.os == 'windows-latest'
-    - name: Install Dependencies (macOS)
-      run: brew install ninja
-      if: matrix.os == 'macos-latest'
-    - name: Set environment for MSVC (Windows)
-      if:  matrix.os == 'windows-latest'
-      run: |
-        # Set these env vars so cmake picks the correct compiler
-        echo "CXX=cl.exe" >> $GITHUB_ENV
-        echo "CC=cl.exe" >> $GITHUB_ENV
-    
-    # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-    - name: Get Sources
-      uses: actions/checkout@v2
-
-    - name: Autotools Configure 
-      if: matrix.generator == 'autogen'
-      run: |
-        sh ./autogen.sh
-        mkdir "${{ runner.workspace }}/build"
-        cd "${{ runner.workspace }}/build"
-        $GITHUB_WORKSPACE/configure --enable-shared --${{ matrix.ts }}-threadsafe --${{ matrix.hl }}-hl --${{ matrix.parallel }}-parallel --${{ matrix.cpp }}-cxx --${{ matrix.fortran }}-fortran --${{ matrix.java }}-java
-      shell: bash
-
-    - name: Configure
-      if: matrix.generator != 'autogen'
-      run: |
-        mkdir "${{ runner.workspace }}/build"
-        cd "${{ runner.workspace }}/build"
-        cmake ${{ matrix.generator }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -DCMAKE_TOOLCHAIN_FILE=${{ matrix.toolchain }} -DBUILD_SHARED_LIBS=ON -DHDF5_ENABLE_ALL_WARNINGS=ON -DHDF5_ENABLE_THREADSAFE:BOOL=${{ matrix.ts }} -DHDF5_BUILD_HL_LIB:BOOL=${{ matrix.hl }} -DHDF5_ENABLE_PARALLEL:BOOL=${{ matrix.parallel }} -DHDF5_BUILD_CPP_LIB:BOOL=${{ matrix.cpp }} -DHDF5_BUILD_FORTRAN=${{ matrix.fortran }} -DHDF5_BUILD_JAVA=${{ matrix.java }} $GITHUB_WORKSPACE
-      shell: bash
-
-    - name: Autotools Build
-      if: matrix.generator == 'autogen'
-      run: make
-      working-directory: ${{ runner.workspace }}/build      
-
-    - name: Build
-      if: matrix.generator != 'autogen'
-      run: cmake --build . --config ${{ matrix.build_type }}
-      working-directory: ${{ runner.workspace }}/build      
-
-    - name: Autotools Test
-      if: matrix.generator == 'autogen'
-      run: make check
-      working-directory: ${{ runner.workspace }}/build
-
-    - name: Test
-      if: matrix.generator != 'autogen'
-      run: ctest --build . -C ${{ matrix.build_type }} -V
-      working-directory: ${{ runner.workspace }}/build

.h5chkright.ini

@@ -1,5 +1,4 @@
 # Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
 # All rights reserved.
 #
 # This file is part of HDF5.  The full HDF5 copyright notice, including

CMakeFilters.cmake

@@ -33,9 +33,7 @@ if (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT" OR HDF5_ALLOW_EXTERNAL_SUPPORT MAT
     set (ZLIB_URL ${TGZPATH}/${ZLIB_TGZ_NAME})
     if (NOT EXISTS "${ZLIB_URL}")
       set (HDF5_ENABLE_Z_LIB_SUPPORT OFF CACHE BOOL "" FORCE)
-      if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
-        message (VERBOSE "Filter ZLIB file ${ZLIB_URL} not found")
-      endif ()
+      message (VERBOSE "Filter ZLIB file ${ZLIB_URL} not found")
     endif ()
     set (SZIP_URL ${TGZPATH}/${SZIP_TGZ_NAME})
     if (USE_LIBAEC)
@@ -43,9 +41,7 @@ if (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT" OR HDF5_ALLOW_EXTERNAL_SUPPORT MAT
     endif ()
     if (NOT EXISTS "${SZIP_URL}")
       set (HDF5_ENABLE_SZIP_SUPPORT OFF CACHE BOOL "" FORCE)
-      if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
-        message (VERBOSE "Filter SZIP file ${SZIP_URL} not found")
-      endif ()
+      message (VERBOSE "Filter SZIP file ${SZIP_URL} not found")
     endif ()
   else ()
     set (ZLIB_USE_EXTERNAL 0)
@@ -81,9 +77,7 @@ if (HDF5_ENABLE_Z_LIB_SUPPORT)
         set (H5_HAVE_FILTER_DEFLATE 1)
         set (H5_HAVE_ZLIB_H 1)
         set (H5_HAVE_LIBZ 1)
-        if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
-          message (VERBOSE "Filter HDF5_ZLIB is built")
-        endif ()
+        message (VERBOSE "Filter HDF5_ZLIB is built")
       else ()
         message (FATAL_ERROR " ZLib is Required for ZLib support in HDF5")
       endif ()
@@ -99,9 +93,7 @@ if (HDF5_ENABLE_Z_LIB_SUPPORT)
   endif ()
   set (LINK_COMP_LIBS ${LINK_COMP_LIBS} ${ZLIB_STATIC_LIBRARY})
   INCLUDE_DIRECTORIES (${ZLIB_INCLUDE_DIRS})
-  if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
-    message (VERBOSE "Filter HDF5_ZLIB is ON")
-  endif ()
+  message (VERBOSE "Filter HDF5_ZLIB is ON")
 endif ()
 
 #-----------------------------------------------------------------------------
@@ -142,13 +134,9 @@ if (HDF5_ENABLE_SZIP_SUPPORT)
       set (H5_HAVE_FILTER_SZIP 1)
       set (H5_HAVE_SZLIB_H 1)
       set (H5_HAVE_LIBSZ 1)
-      if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
-        message (VERBOSE "Filter SZIP is built")
-      endif ()
+      message (VERBOSE "Filter SZIP is built")
       if (USE_LIBAEC)
-        if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
-          message (VERBOSE "... with library AEC")
-        endif ()
+        message (VERBOSE "... with library AEC")
         set (SZIP_PACKAGE_NAME ${LIBAEC_PACKAGE_NAME})
       else ()
         set (SZIP_PACKAGE_NAME ${SZIP_PACKAGE_NAME})
@@ -159,9 +147,7 @@ if (HDF5_ENABLE_SZIP_SUPPORT)
   endif ()
   set (LINK_COMP_LIBS ${LINK_COMP_LIBS} ${SZIP_STATIC_LIBRARY})
   INCLUDE_DIRECTORIES (${SZIP_INCLUDE_DIRS})
-  if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
-    message (VERBOSE "Filter SZIP is ON")
-  endif ()
+  message (VERBOSE "Filter SZIP is ON")
   if (H5_HAVE_FILTER_SZIP)
     set (EXTERNAL_FILTERS "${EXTERNAL_FILTERS} DECODE")
   endif ()

CMakeInstallation.cmake

@@ -52,7 +52,7 @@ endif ()
 # Set includes needed for build
 #-----------------------------------------------------------------------------
 set (HDF5_INCLUDES_BUILD_TIME
-    ${HDF5_SRC_DIR} ${HDF5_CPP_SRC_DIR} ${HDF5_HL_SRC_DIR}
+    ${HDF5_SRC_INCLUDE_DIRS} ${HDF5_CPP_SRC_DIR} ${HDF5_HL_SRC_DIR}
     ${HDF5_TOOLS_SRC_DIR} ${HDF5_SRC_BINARY_DIR}
 )
 
@@ -242,7 +242,7 @@ if (NOT HDF5_EXTERNALLY_CONFIGURED)
     endif ()
     install (
         FILES ${release_files}
-        DESTINATION ${HDF5_INSTALL_DATA_DIR}
+        DESTINATION ${HDF5_INSTALL_DOC_DIR}
         COMPONENT hdfdocuments
     )
   endif ()
@@ -273,7 +273,7 @@ if (NOT HDF5_EXTERNALLY_CONFIGURED AND NOT HDF5_NO_PACKAGES)
   else ()
     set (CPACK_PACKAGE_INSTALL_DIRECTORY "${CPACK_PACKAGE_VENDOR}/${CPACK_PACKAGE_NAME}/${CPACK_PACKAGE_VERSION}")
   endif ()
-  set (CPACK_PACKAGE_ICON "${HDF_RESOURCES_EXT_DIR}/hdf.bmp")
+  set (CPACK_PACKAGE_ICON "${HDF_RESOURCES_DIR}/hdf.bmp")
 
   set (CPACK_GENERATOR "TGZ")
   if (WIN32)
@@ -296,10 +296,10 @@ if (NOT HDF5_EXTERNALLY_CONFIGURED AND NOT HDF5_NO_PACKAGES)
     endif ()
     # set the install/unistall icon used for the installer itself
     # There is a bug in NSI that does not handle full unix paths properly.
-    set (CPACK_NSIS_MUI_ICON "${HDF_RESOURCES_EXT_DIR}\\\\hdf.ico")
-    set (CPACK_NSIS_MUI_UNIICON "${HDF_RESOURCES_EXT_DIR}\\\\hdf.ico")
+    set (CPACK_NSIS_MUI_ICON "${HDF_RESOURCES_DIR}\\\\hdf.ico")
+    set (CPACK_NSIS_MUI_UNIICON "${HDF_RESOURCES_DIR}\\\\hdf.ico")
     # set the package header icon for MUI
-    set (CPACK_PACKAGE_ICON "${HDF_RESOURCES_EXT_DIR}\\\\hdf.bmp")
+    set (CPACK_PACKAGE_ICON "${HDF_RESOURCES_DIR}\\\\hdf.bmp")
     set (CPACK_NSIS_DISPLAY_NAME "${CPACK_NSIS_PACKAGE_NAME}")
     if (OVERRIDE_INSTALL_VERSION)
       set (CPACK_PACKAGE_INSTALL_DIRECTORY "${CPACK_PACKAGE_VENDOR}\\\\${CPACK_PACKAGE_NAME}\\\\${OVERRIDE_INSTALL_VERSION}")
@@ -329,7 +329,7 @@ if (NOT HDF5_EXTERNALLY_CONFIGURED AND NOT HDF5_NO_PACKAGES)
     set (CPACK_RESOURCE_FILE_LICENSE "${HDF5_BINARY_DIR}/COPYING.txt")
 # .. variable:: CPACK_WIX_PRODUCT_ICON
 #  The Icon shown next to the program name in Add/Remove programs.
-    set(CPACK_WIX_PRODUCT_ICON "${HDF_RESOURCES_EXT_DIR}\\\\hdf.ico")
+    set(CPACK_WIX_PRODUCT_ICON "${HDF_RESOURCES_DIR}\\\\hdf.ico")
 #
 # .. variable:: CPACK_WIX_UI_BANNER
 #
@@ -360,14 +360,14 @@ if (NOT HDF5_EXTERNALLY_CONFIGURED AND NOT HDF5_NO_PACKAGES)
     list (APPEND CPACK_GENERATOR "DragNDrop")
     set (CPACK_COMPONENTS_ALL_IN_ONE_PACKAGE ON)
     set (CPACK_PACKAGING_INSTALL_PREFIX "/${CPACK_PACKAGE_INSTALL_DIRECTORY}")
-    set (CPACK_PACKAGE_ICON "${HDF_RESOURCES_EXT_DIR}/hdf.icns")
+    set (CPACK_PACKAGE_ICON "${HDF_RESOURCES_DIR}/hdf.icns")
 
     option (HDF5_PACK_MACOSX_FRAMEWORK  "Package the HDF5 Library in a Frameworks" OFF)
     if (HDF5_PACK_MACOSX_FRAMEWORK AND HDF5_BUILD_FRAMEWORKS)
       set (CPACK_BUNDLE_NAME "${HDF5_PACKAGE_STRING}")
       set (CPACK_BUNDLE_LOCATION "/")    # make sure CMAKE_INSTALL_PREFIX ends in /
       set (CMAKE_INSTALL_PREFIX "/${CPACK_BUNDLE_NAME}.framework/Versions/${CPACK_PACKAGE_VERSION}/${CPACK_PACKAGE_NAME}/")
-      set (CPACK_BUNDLE_ICON "${HDF_RESOURCES_EXT_DIR}/hdf.icns")
+      set (CPACK_BUNDLE_ICON "${HDF_RESOURCES_DIR}/hdf.icns")
       set (CPACK_BUNDLE_PLIST "${HDF5_BINARY_DIR}/CMakeFiles/Info.plist")
       set (CPACK_SHORT_VERSION_STRING "${CPACK_PACKAGE_VERSION}")
       #-----------------------------------------------------------------------------
@@ -382,7 +382,7 @@ if (NOT HDF5_EXTERNALLY_CONFIGURED AND NOT HDF5_NO_PACKAGES)
           ${HDF5_BINARY_DIR}/CMakeFiles/PkgInfo @ONLY
       )
       configure_file (
-          ${HDF_RESOURCES_EXT_DIR}/version.plist.in
+          ${HDF_RESOURCES_DIR}/version.plist.in
           ${HDF5_BINARY_DIR}/CMakeFiles/version.plist @ONLY
       )
       install (

CMakeLists.txt

@@ -1,14 +1,22 @@
-cmake_minimum_required (VERSION 3.12)
+cmake_minimum_required (VERSION 3.18)
 project (HDF5 C)
 
 if (POLICY CMP0074)
+  # find_package() uses <PackageName>_ROOT variables.
   cmake_policy (SET CMP0074 NEW)
 endif ()
 
 if (POLICY CMP0083)
+  # To control generation of Position Independent Executable (PIE) or not,
+  # some flags are required at link time.
   cmake_policy (SET CMP0083 NEW)
 endif ()
 
+# Avoid warning about DOWNLOAD_EXTRACT_TIMESTAMP in CMake 3.24:
+if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.24.0")
+    cmake_policy(SET CMP0135 NEW)
+endif()
+
 #-----------------------------------------------------------------------------
 # Instructions for use : Normal Build
 #
@@ -36,16 +44,6 @@ if (CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_CURRENT_BINARY_DIR)
       )
 endif ()
 
-# CMake version 3.14 added option --ignore-eol to compare files
-#     cmake -E compare_files --ignore-eol file1 file2
-set (CMAKE_IGNORE_EOL "--ignore-eol")
-if (CMAKE_VERSION VERSION_LESS "3.14.0")
-  set (CMAKE_IGNORE_EOL "")
-  if (WIN32)
-    message (FATAL_ERROR "Windows builds require a minimum of CMake 3.14")
-  endif()
-endif ()
-
 #-----------------------------------------------------------------------------
 # Instructions for use : Sub-Project Build
 #
@@ -212,7 +210,6 @@ set (HDF5_HL_F90_C_LIBSH_TARGET   "${HDF5_HL_F90_C_LIB_CORENAME}-shared")
 #-----------------------------------------------------------------------------
 set (HDF_CONFIG_DIR          ${HDF5_SOURCE_DIR}/config)
 set (HDF_RESOURCES_DIR       ${HDF5_SOURCE_DIR}/config/cmake)
-set (HDF_RESOURCES_EXT_DIR   ${HDF5_SOURCE_DIR}/config/cmake_ext_mod)
 set (HDF5_SRC_DIR            ${HDF5_SOURCE_DIR}/src)
 set (HDF5_TEST_SRC_DIR       ${HDF5_SOURCE_DIR}/test)
 set (HDF5_CPP_SRC_DIR        ${HDF5_SOURCE_DIR}/c++)
@@ -234,6 +231,8 @@ set (HDF5_JAVA_LOGGING_NOP_JAR     ${HDF5_SOURCE_DIR}/java/lib/ext/slf4j-nop-1.7
 set (HDF5_JAVA_LOGGING_SIMPLE_JAR  ${HDF5_SOURCE_DIR}/java/lib/ext/slf4j-simple-1.7.33.jar)
 set (HDF5_DOXYGEN_DIR              ${HDF5_SOURCE_DIR}/doxygen)
 
+set (HDF5_SRC_INCLUDE_DIRS ${HDF5_SRC_DIR})
+
 #-----------------------------------------------------------------------------
 # parse the full version number from H5public.h and include in H5_VERS_INFO
 #-----------------------------------------------------------------------------
@@ -246,9 +245,7 @@ string (REGEX REPLACE ".*#define[ \t]+H5_VERS_RELEASE[ \t]+([0-9]*).*$"
     "\\1" H5_VERS_RELEASE ${_h5public_h_contents})
 string (REGEX REPLACE ".*#define[ \t]+H5_VERS_SUBRELEASE[ \t]+\"([0-9A-Za-z._-]*)\".*$"
     "\\1" H5_VERS_SUBRELEASE ${_h5public_h_contents})
-if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
-  message (TRACE "VERSION: ${H5_VERS_MAJOR}.${H5_VERS_MINOR}.${H5_VERS_RELEASE}-${H5_VERS_SUBRELEASE}")
-endif ()
+message (TRACE "VERSION: ${H5_VERS_MAJOR}.${H5_VERS_MINOR}.${H5_VERS_RELEASE}-${H5_VERS_SUBRELEASE}")
 
 #-----------------------------------------------------------------------------
 # parse the full soversion number from config/lt_vers.am and include in H5_SOVERS_INFO
@@ -261,9 +258,7 @@ string (REGEX REPLACE ".*LT_VERS_REVISION[ \t]+=[ \t]+([0-9]*).*$"
 string (REGEX REPLACE ".*LT_VERS_AGE[ \t]+=[ \t]+([0-9]*).*$"
     "\\1" H5_LIB_SOVERS_RELEASE ${_lt_vers_am_contents})
 math (EXPR H5_LIB_SOVERS_MAJOR ${H5_LIB_SOVERS_INTERFACE}-${H5_LIB_SOVERS_RELEASE})
-if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
-  message (VERBOSE "SOVERSION: ${H5_LIB_SOVERS_MAJOR}.${H5_LIB_SOVERS_RELEASE}.${H5_LIB_SOVERS_MINOR}")
-endif ()
+message (VERBOSE "SOVERSION: ${H5_LIB_SOVERS_MAJOR}.${H5_LIB_SOVERS_RELEASE}.${H5_LIB_SOVERS_MINOR}")
 string (REGEX MATCH ".*LT_TOOLS_VERS_INTERFACE[ \t]+=[ \t]+([0-9]*).*$" H5_TOOLS_SOVERS_EXISTS ${_lt_vers_am_contents})
 if (H5_TOOLS_SOVERS_EXISTS)
   string (REGEX REPLACE ".*LT_TOOLS_VERS_INTERFACE[ \t]+=[ \t]+([0-9]*).*$"
@@ -273,9 +268,7 @@ if (H5_TOOLS_SOVERS_EXISTS)
   string (REGEX REPLACE ".*LT_TOOLS_VERS_AGE[ \t]+=[ \t]+([0-9]*).*$"
       "\\1" H5_TOOLS_SOVERS_RELEASE ${_lt_vers_am_contents})
   math (EXPR H5_TOOLS_SOVERS_MAJOR ${H5_TOOLS_SOVERS_INTERFACE}-${H5_TOOLS_SOVERS_RELEASE})
-  if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
-    message (VERBOSE "SOVERSION_TOOLS: ${H5_TOOLS_SOVERS_MAJOR}.${H5_TOOLS_SOVERS_RELEASE}.${H5_TOOLS_SOVERS_MINOR}")
-  endif ()
+  message (VERBOSE "SOVERSION_TOOLS: ${H5_TOOLS_SOVERS_MAJOR}.${H5_TOOLS_SOVERS_RELEASE}.${H5_TOOLS_SOVERS_MINOR}")
 endif ()
 string (REGEX MATCH ".*LT_CXX_VERS_INTERFACE[ \t]+=[ \t]+([0-9]*).*$" H5_CXX_SOVERS_EXISTS ${_lt_vers_am_contents})
 if (H5_CXX_SOVERS_EXISTS)
@@ -286,9 +279,7 @@ if (H5_CXX_SOVERS_EXISTS)
   string (REGEX REPLACE ".*LT_CXX_VERS_AGE[ \t]+=[ \t]+([0-9]*).*$"
       "\\1" H5_CXX_SOVERS_RELEASE ${_lt_vers_am_contents})
   math (EXPR H5_CXX_SOVERS_MAJOR ${H5_CXX_SOVERS_INTERFACE}-${H5_CXX_SOVERS_RELEASE})
-  if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
-    message (VERBOSE "SOVERSION_CXX: ${H5_CXX_SOVERS_MAJOR}.${H5_CXX_SOVERS_RELEASE}.${H5_CXX_SOVERS_MINOR}")
-  endif ()
+  message (VERBOSE "SOVERSION_CXX: ${H5_CXX_SOVERS_MAJOR}.${H5_CXX_SOVERS_RELEASE}.${H5_CXX_SOVERS_MINOR}")
 endif ()
 string (REGEX MATCH ".*LT_F_VERS_INTERFACE[ \t]+=[ \t]+([0-9]*).*$" H5_F_SOVERS_EXISTS ${_lt_vers_am_contents})
 if (H5_F_SOVERS_EXISTS)
@@ -299,9 +290,7 @@ if (H5_F_SOVERS_EXISTS)
   string (REGEX REPLACE ".*LT_F_VERS_AGE[ \t]+=[ \t]+([0-9]*).*$"
       "\\1" H5_F_SOVERS_RELEASE ${_lt_vers_am_contents})
   math (EXPR H5_F_SOVERS_MAJOR ${H5_F_SOVERS_INTERFACE}-${H5_F_SOVERS_RELEASE})
-  if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
-    message (VERBOSE "SOVERSION_F: ${H5_F_SOVERS_MAJOR}.${H5_F_SOVERS_RELEASE}.${H5_F_SOVERS_MINOR}")
-  endif ()
+  message (VERBOSE "SOVERSION_F: ${H5_F_SOVERS_MAJOR}.${H5_F_SOVERS_RELEASE}.${H5_F_SOVERS_MINOR}")
 endif ()
 string (REGEX MATCH ".*LT_HL_VERS_INTERFACE[ \t]+=[ \t]+([0-9]*).*$" H5_HL_SOVERS_EXISTS ${_lt_vers_am_contents})
 if (H5_HL_SOVERS_EXISTS)
@@ -312,9 +301,7 @@ if (H5_HL_SOVERS_EXISTS)
   string (REGEX REPLACE ".*LT_HL_VERS_AGE[ \t]+=[ \t]+([0-9]*).*$"
       "\\1" H5_HL_SOVERS_RELEASE ${_lt_vers_am_contents})
   math (EXPR H5_HL_SOVERS_MAJOR ${H5_HL_SOVERS_INTERFACE}-${H5_HL_SOVERS_RELEASE})
-  if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
-    message (VERBOSE "SOVERSION_HL: ${H5_HL_SOVERS_MAJOR}.${H5_HL_SOVERS_RELEASE}.${H5_HL_SOVERS_MINOR}")
-  endif ()
+  message (VERBOSE "SOVERSION_HL: ${H5_HL_SOVERS_MAJOR}.${H5_HL_SOVERS_RELEASE}.${H5_HL_SOVERS_MINOR}")
 endif ()
 string (REGEX MATCH ".*LT_HL_CXX_VERS_INTERFACE[ \t]+=[ \t]+([0-9]*).*$" H5_HL_CXX_SOVERS_EXISTS ${_lt_vers_am_contents})
 if (H5_HL_CXX_SOVERS_EXISTS)
@@ -325,9 +312,7 @@ if (H5_HL_CXX_SOVERS_EXISTS)
   string (REGEX REPLACE ".*LT_HL_CXX_VERS_AGE[ \t]+=[ \t]+([0-9]*).*$"
       "\\1" H5_HL_CXX_SOVERS_RELEASE ${_lt_vers_am_contents})
   math (EXPR H5_HL_CXX_SOVERS_MAJOR ${H5_HL_CXX_SOVERS_INTERFACE}-${H5_HL_CXX_SOVERS_RELEASE})
-  if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
-    message (VERBOSE "SOVERSION_HL_CXX: ${H5_HL_CXX_SOVERS_MAJOR}.${H5_HL_CXX_SOVERS_RELEASE}.${H5_HL_CXX_SOVERS_MINOR}")
-  endif ()
+  message (VERBOSE "SOVERSION_HL_CXX: ${H5_HL_CXX_SOVERS_MAJOR}.${H5_HL_CXX_SOVERS_RELEASE}.${H5_HL_CXX_SOVERS_MINOR}")
 endif ()
 string (REGEX MATCH ".*LT_HL_F_VERS_INTERFACE[ \t]+=[ \t]+([0-9]*).*$" H5_HL_F_SOVERS_EXISTS ${_lt_vers_am_contents})
 if (H5_HL_F_SOVERS_EXISTS)
@@ -338,9 +323,7 @@ if (H5_HL_F_SOVERS_EXISTS)
   string (REGEX REPLACE ".*LT_HL_F_VERS_AGE[ \t]+=[ \t]+([0-9]*).*$"
       "\\1" H5_HL_F_SOVERS_RELEASE ${_lt_vers_am_contents})
   math (EXPR H5_HL_F_SOVERS_MAJOR ${H5_HL_F_SOVERS_INTERFACE}-${H5_HL_F_SOVERS_RELEASE})
-  if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
-    message (VERBOSE "SOVERSION_HL_F: ${H5_HL_F_SOVERS_MAJOR}.${H5_HL_F_SOVERS_RELEASE}.${H5_HL_F_SOVERS_MINOR}")
-  endif ()
+  message (VERBOSE "SOVERSION_HL_F: ${H5_HL_F_SOVERS_MAJOR}.${H5_HL_F_SOVERS_RELEASE}.${H5_HL_F_SOVERS_MINOR}")
 endif ()
 string (REGEX MATCH ".*LT_JAVA_VERS_INTERFACE[ \t]+=[ \t]+([0-9]*).*$" H5_JAVA_SOVERS_EXISTS ${_lt_vers_am_contents})
 if(H5_JAVA_SOVERS_EXISTS)
@@ -351,9 +334,7 @@ if(H5_JAVA_SOVERS_EXISTS)
   string (REGEX REPLACE ".*LT_JAVA_VERS_AGE[ \t]+=[ \t]+([0-9]*).*$"
       "\\1" H5_JAVA_SOVERS_RELEASE ${_lt_vers_am_contents})
   math (EXPR H5_JAVA_SOVERS_MAJOR ${H5_JAVA_SOVERS_INTERFACE}-${H5_JAVA_SOVERS_RELEASE})
-  if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
-    message (VERBOSE "SOVERSION_JAVA: ${H5_JAVA_SOVERS_MAJOR}.${H5_JAVA_SOVERS_RELEASE}.${H5_JAVA_SOVERS_MINOR}")
-  endif ()
+  message (VERBOSE "SOVERSION_JAVA: ${H5_JAVA_SOVERS_MAJOR}.${H5_JAVA_SOVERS_RELEASE}.${H5_JAVA_SOVERS_MINOR}")
 endif ()
 
 #-----------------------------------------------------------------------------
@@ -430,11 +411,11 @@ set (HDF5_PACKAGE_BUGREPORT "help@hdfgroup.org")
 #-----------------------------------------------------------------------------
 # Include some macros for reusable code
 #-----------------------------------------------------------------------------
-include (${HDF_RESOURCES_EXT_DIR}/HDFMacros.cmake)
+include (${HDF_RESOURCES_DIR}/HDFMacros.cmake)
 
 HDF_DIR_PATHS(${HDF5_PACKAGE_NAME})
 
-include (${HDF_RESOURCES_EXT_DIR}/HDFLibMacros.cmake)
+include (${HDF_RESOURCES_DIR}/HDFLibMacros.cmake)
 include (${HDF_RESOURCES_DIR}/HDF5PluginMacros.cmake)
 include (${HDF_RESOURCES_DIR}/HDF5Macros.cmake)
 
@@ -562,15 +543,6 @@ if (HDF5_ENABLE_COVERAGE)
   endif ()
 endif ()
 
-#-----------------------------------------------------------------------------
-# Option to indicate using dmalloc
-#-----------------------------------------------------------------------------
-# option (HDF5_ENABLE_USING_DMALLOC "Indicate that dmalloc is used" OFF)
-# if (HDF5_ENABLE_USING_DMALLOC)
-#   find_package (DMALLOC)
-#   set (H5_HAVE_DMALLOC DMALLOC_FOUND)
-# endif ()
-
 #-----------------------------------------------------------------------------
 # Option to indicate using a memory checker
 #-----------------------------------------------------------------------------
@@ -579,14 +551,6 @@ if (HDF5_ENABLE_USING_MEMCHECKER)
   set (H5_USING_MEMCHECKER 1)
 endif ()
 
-#-----------------------------------------------------------------------------
-# Option to indicate internal memory allocation sanity checks are enabled
-#-----------------------------------------------------------------------------
-option (HDF5_MEMORY_ALLOC_SANITY_CHECK "Indicate that internal memory allocation sanity checks are enabled" OFF)
-if (HDF5_MEMORY_ALLOC_SANITY_CHECK)
-  set (H5_MEMORY_ALLOC_SANITY_CHECK 1)
-endif ()
-
 #-----------------------------------------------------------------------------
 # Option to enable/disable using pread/pwrite for VFDs
 #-----------------------------------------------------------------------------
@@ -654,6 +618,13 @@ if (${HDF_CFG_NAME} MATCHES "Debug")
   mark_as_advanced (HDF5_ENABLE_INSTRUMENT)
 endif ()
 
+#-----------------------------------------------------------------------------
+# Add some definitions for Developer Builds
+#-----------------------------------------------------------------------------
+if (${HDF_CFG_NAME} MATCHES "Developer")
+  include (${HDF_RESOURCES_DIR}/HDF5DeveloperBuild.cmake)
+endif ()
+
 #-----------------------------------------------------------------------------
 # Option to embed library info into executables
 #-----------------------------------------------------------------------------
@@ -667,7 +638,7 @@ else ()
 endif ()
 
 include (${HDF_RESOURCES_DIR}/HDFCompilerFlags.cmake)
-set (CMAKE_MODULE_PATH ${HDF_RESOURCES_DIR} ${HDF_RESOURCES_EXT_DIR} ${CMAKE_MODULE_PATH})
+set (CMAKE_MODULE_PATH ${HDF_RESOURCES_DIR} ${HDF_RESOURCES_DIR} ${CMAKE_MODULE_PATH})
 
 #-----------------------------------------------------------------------------
 # Option to Enable HDFS
@@ -742,6 +713,56 @@ if (H5_HAVE_PARALLEL)
   endif ()
 endif ()
 
+# Determine whether to build the HDF5 Subfiling VFD
+set (H5FD_SUBFILING_DIR ${HDF5_SRC_DIR}/H5FDsubfiling)
+set (HDF5_SRC_INCLUDE_DIRS
+    ${HDF5_SRC_INCLUDE_DIRS}
+    ${H5FD_SUBFILING_DIR}
+)
+option (HDF5_ENABLE_SUBFILING_VFD "Build Parallel HDF5 Subfiling VFD" OFF)
+if (HDF5_ENABLE_SUBFILING_VFD)
+  if (NOT HDF5_ENABLE_PARALLEL)
+    message (FATAL_ERROR "Subfiling VFD requires a parallel HDF5 build")
+  else ()
+    # Check for MPI_Comm_split_type
+    CHECK_SYMBOL_EXISTS (MPI_Comm_split_type "mpi.h" H5_HAVE_MPI_Comm_split_type)
+    if (NOT H5_HAVE_MPI_Comm_split_type)
+      message (FATAL_ERROR "Subfiling VFD requires MPI-3 support for MPI_Comm_split_type")
+    endif ()
+  endif()
+
+  if (NOT DEFINED Threads_FOUND)
+    set (THREADS_PREFER_PTHREAD_FLAG ON)
+    find_package (Threads REQUIRED)
+  endif ()
+
+  # For now, make sure we're using pthreads. Once Subfiling can be
+  # supported on Windows, we should allow Win32 threads as well
+  if (NOT ${Threads_FOUND} OR NOT ${CMAKE_USE_PTHREADS_INIT})
+    message (FATAL_ERROR "Subfiling requires pthreads for system thread library")
+  endif ()
+
+  CHECK_INCLUDE_FILE("stdatomic.h" HAVE_STDATOMIC_H)
+  if (NOT HAVE_STDATOMIC_H)
+    message (FATAL_ERROR "Subfiling VFD requires atomic operations support. C11 stdatomic.h NOT available.")
+  else()
+    set (H5_HAVE_STDATOMIC_H 1)
+  endif()
+
+  set (H5_HAVE_SUBFILING_VFD 1)
+  # IOC VFD is currently only built when subfiling is enabled
+  set (H5_HAVE_IOC_VFD 1)
+
+  message (STATUS "Setting up to use Mercury components")
+  set (H5FD_SUBFILING_MERCURY_DIR ${H5FD_SUBFILING_DIR}/mercury/src/util)
+  set (HDF5_SRC_INCLUDE_DIRS
+      ${HDF5_SRC_INCLUDE_DIRS}
+      ${H5FD_SUBFILING_MERCURY_DIR}
+  )
+  set (H5_HAVE_MERCURY_H 1)
+  set (CMAKE_REQUIRED_INCLUDES "${H5FD_SUBFILING_MERCURY_DIR}")
+endif()
+
 #option (DEFAULT_API_VERSION "Enable v1.14 API (v16, v18, v110, v112, v114)" "v114")
 set (DEFAULT_API_VERSION "v114" CACHE STRING "Enable v1.14 API (v16, v18, v110, v112, v114)")
 set_property (CACHE DEFAULT_API_VERSION PROPERTY STRINGS v16 v18 v110 v112 v114)
@@ -791,6 +812,17 @@ if (DEFAULT_API_VERSION MATCHES "v114")
   set (H5_USE_114_API_DEFAULT 1)
 endif ()
 
+#-----------------------------------------------------------------------------
+# Option to use 1.16.x API
+#-----------------------------------------------------------------------------
+if (NOT DEFAULT_API_VERSION)
+  set (DEFAULT_API_VERSION "v116")
+endif ()
+set (H5_USE_116_API_DEFAULT 0)
+if (DEFAULT_API_VERSION MATCHES "v116")
+  set (H5_USE_116_API_DEFAULT 1)
+endif ()
+
 #-----------------------------------------------------------------------------
 # Include user macros
 #-----------------------------------------------------------------------------
@@ -825,51 +857,32 @@ option (HDF5_ENABLE_THREADSAFE "Enable thread-safety" OFF)
 if (HDF5_ENABLE_THREADSAFE)
   # check for unsupported options
   if (WIN32)
-    if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
-      message (VERBOSE " **** thread-safety option not supported with static library **** ")
-      message (VERBOSE " **** thread-safety option will not be used building static library **** ")
-    endif ()
-  endif ()
-  if (HDF5_ENABLE_PARALLEL)
-    if (NOT ALLOW_UNSUPPORTED)
-      message (FATAL_ERROR " **** parallel and thread-safety options are not supported, override with ALLOW_UNSUPPORTED option **** ")
-    else ()
-      if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
-        message (VERBOSE " **** Allowing unsupported parallel and thread-safety options **** ")
-      endif ()
-    endif ()
+    message (VERBOSE " **** thread-safety option not supported with static library **** ")
+    message (VERBOSE " **** thread-safety option will not be used building static library **** ")
   endif ()
   if (HDF5_BUILD_FORTRAN)
     if (NOT ALLOW_UNSUPPORTED)
       message (FATAL_ERROR " **** Fortran and thread-safety options are not supported, override with ALLOW_UNSUPPORTED option **** ")
     else ()
-      if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
-        message (VERBOSE " **** Allowing unsupported Fortran and thread-safety options **** ")
-      endif ()
+      message (VERBOSE " **** Allowing unsupported Fortran and thread-safety options **** ")
     endif ()
   endif ()
   if (HDF5_BUILD_CPP_LIB)
     if (NOT ALLOW_UNSUPPORTED)
       message (FATAL_ERROR " **** C++ and thread-safety options are not supported, override with ALLOW_UNSUPPORTED option **** ")
     else ()
-      if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
-        message (VERBOSE " **** Allowing unsupported C++ and thread-safety options **** ")
-      endif ()
+      message (VERBOSE " **** Allowing unsupported C++ and thread-safety options **** ")
     endif ()
   endif ()
   if (HDF5_BUILD_HL_LIB)
     if (NOT ALLOW_UNSUPPORTED)
       message (FATAL_ERROR " **** HL and thread-safety options are not supported, override with ALLOW_UNSUPPORTED option **** ")
     else ()
-      if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
-        message (VERBOSE " **** Allowing unsupported HL and thread-safety options **** ")
-      endif ()
+      message (VERBOSE " **** Allowing unsupported HL and thread-safety options **** ")
     endif ()
   endif ()
   if (H5_HAVE_IOEO)
-    if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
-      message (VERBOSE " **** Win32 threads requires WINVER>=0x600 (Windows Vista/7/8) **** ")
-    endif ()
+    message (VERBOSE " **** Win32 threads requires WINVER>=0x600 (Windows Vista/7/8) **** ")
     set (H5_HAVE_WIN_THREADS 1)
   else ()
     if (NOT H5_HAVE_PTHREAD_H)
@@ -962,8 +975,13 @@ if (BUILD_TESTING)
     mark_as_advanced (HDF5_TEST_FHEAP_PASSTHROUGH VOL)
   endif ()
 
-  option (HDF_TEST_EXPRESS "Control testing framework (0-3)" "0")
+  set (H5_TEST_EXPRESS_LEVEL_DEFAULT "3")
+  set (HDF_TEST_EXPRESS "${H5_TEST_EXPRESS_LEVEL_DEFAULT}"
+      CACHE STRING "Control testing framework (0-3) (0 = exhaustive testing; 3 = quicker testing)")
   mark_as_advanced (HDF_TEST_EXPRESS)
+  if (NOT "${HDF_TEST_EXPRESS}" STREQUAL "")
+    set (H5_TEST_EXPRESS_LEVEL_DEFAULT "${HDF_TEST_EXPRESS}")
+  endif ()
 
   enable_testing ()
   include (CTest)
@@ -1096,11 +1114,9 @@ set (H5_FC_FUNC_ "H5_FC_FUNC_(name,NAME) name ## _")
 if (EXISTS "${HDF5_SOURCE_DIR}/fortran" AND IS_DIRECTORY "${HDF5_SOURCE_DIR}/fortran")
   option (HDF5_BUILD_FORTRAN "Build FORTRAN support" OFF)
   if (HDF5_BUILD_FORTRAN)
-    include (${HDF_RESOURCES_EXT_DIR}/HDFUseFortran.cmake)
+    include (${HDF_RESOURCES_DIR}/HDFUseFortran.cmake)
 
-    if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
-      message (VERBOSE "Fortran compiler ID is ${CMAKE_Fortran_COMPILER_ID}")
-    endif ()
+    message (VERBOSE "Fortran compiler ID is ${CMAKE_Fortran_COMPILER_ID}")
     include (${HDF_RESOURCES_DIR}/HDFFortranCompilerFlags.cmake)
     include (${HDF_RESOURCES_DIR}/HDF5UseFortran.cmake)
     set (LINK_Fortran_LIBS ${LINK_LIBS})
@@ -1111,6 +1127,7 @@ if (EXISTS "${HDF5_SOURCE_DIR}/fortran" AND IS_DIRECTORY "${HDF5_SOURCE_DIR}/for
 
     # Parallel IO usage requires MPI to be Linked and Included
     if (H5_HAVE_PARALLEL)
+      find_package(MPI REQUIRED COMPONENTS Fortran)
       set (LINK_Fortran_LIBS ${LINK_Fortran_LIBS} ${MPI_Fortran_LIBRARIES})
       if (MPI_Fortran_LINK_FLAGS)
         set (CMAKE_Fortran_EXE_LINKER_FLAGS "${MPI_Fortran_LINK_FLAGS} ${CMAKE_EXE_LINKER_FLAGS}")
@@ -1149,9 +1166,7 @@ if (EXISTS "${HDF5_SOURCE_DIR}/c++" AND IS_DIRECTORY "${HDF5_SOURCE_DIR}/c++")
       if (NOT ALLOW_UNSUPPORTED)
         message (FATAL_ERROR " **** Parallel and C++ options are mutually exclusive, override with ALLOW_UNSUPPORTED option **** ")
       else ()
-        if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0")
-          message (VERBOSE " **** Allowing unsupported Parallel and C++ options **** ")
-        endif ()
+        message (VERBOSE " **** Allowing unsupported Parallel and C++ options **** ")
       endif ()
     endif ()
 

CODE_OF_CONDUCT.md

@@ -0,0 +1,128 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+help@hdfgroup.org.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.

CONTRIBUTING.md

@@ -0,0 +1,142 @@
+# How to contribute to HDF5
+
+The HDF Group encourages community members to contribute to the HDF5 project. We accept and are very grateful for any contributions,
+from minor typos and bug fixes to new features. The HDF Group is committed to work with the code contributors and make contribution
+process enjoyable and straightforward.
+
+This document describes guiding principles for the HDF5 code contributors and does not pretend to address any possible
+contribution. If in doubt, please do not hesitate to ask us for guidance.
+***Note that no contribution may be accepted unless the donor agrees with the HDF Group software license terms
+found in the COPYING file in every branch's top source directory.***
+
+
+> We will assume that you are familiar with `git` and `GitHub`.  If not, you may go through the GitHub tutorial found at
+[https://guides.github.com/activities/hello-world/](https://guides.github.com/activities/hello-world/).  This tutorial should only take
+around 10 minutes.
+
+## Table of Contents
+
+* [Workflow](#workflow)
+* [Acceptance criteria for a pull request](#criteria)
+* [Release Note](#releasenote)
+* [Check List](#checklist)
+
+# Workflow <A NAME="workflow"></A>
+
+The process for contributing code to HDF5 is as follows:
+
+* Open an issue on [HDF5 GitHub](https://github.com/HDFGroup/hdf5/issues).
+
+> This step is ***required*** unless the change is minor (e.g., typo fix).
+
+* Fork the [HDF5](https://github.com/HDFGroup/hdf5) repository.
+* Make the desired changes to the HDF5 software.
+    * New features should always go to _develop_ branch first and later should be merged to the appropriate maintenance branches.
+    * Bug fixes should go to all appropriate branches (_develop_ and maintenance).
+* Build and test your changes. Detailed instructions on building and testing HDF5 can be found in the `INSTALL*` files in the `release_docs` directory.
+* Push your changes to GitHub.
+* Issue a pull request and address any code formatting and testing issues reported.
+
+Once a pull request is correctly formatted and passes **ALL** CI tests, it will be reviewed and evaluated by The HDF Group developers and HDF5
+community members who can approve pull requests. The HDF Group developers will work with you to ensure that the pull request satisfies the acceptance
+criteria described in the next section.
+
+# Acceptance criteria for a pull request <A NAME="criteria"></A>
+
+We appreciate every contribution we receive, but we may not accept them all.  Those that we *do* satisfy the following criteria:
+
+* **The pull request has a clear purpose** - What does the pull request address? How does it benefit the HDF5 community?
+If the pull request does not have a clear purpose and benefits, it will not be accepted.
+
+* **The pull request is documented** - The HDF5 developers must understand not only *what* a change is doing, but *how* it is doing it.
+  Documenting the code makes it easier for us to understand your patch and maintain the code in the future.
+
+* **The pull request passes HDF5 regression testing** - Any issue fixed or functionality added should be accompanied by the corresponding
+tests and pass HDF5 regression testing run by The HDF Group. We do not expect you to perform comprehensive testing across multiple platforms
+before we accept the pull request. If the pull request does not pass regression testing after the merge, The HDF Group developers will work
+with you on the fixes.
+
+* **The pull request does not compromise the principles behind HDF5** - HDF5 has a 100% commitment to backward compatibility.
+    * Any file ever created with HDF5 must be readable by any future version of HDF5.
+   If your patch's purpose is to modify the HDF5 data model or file format,
+ **please** discuss this with us first. File format changes and features required by those changes can be introduced only in a new major release.
+    * HDF5 has a commitment to remaining *machine-independent*; data created on one platform/environment/architecture **must** remain readable by HDF5 on any other.
+    * For binary compatibility, no changes are allowed to public APIs and data structures in the maintenance releases; new APIs can be added.
+
+* **New features are documented** - Any new features should have proper documentation; talk to us if you have any questions.
+
+* **When to Write a Release Note** - Generally, a release note must be written for every change that is made to the code for which
+users might see a change in the way the software works. In other words, if a user might see a difference in the way the software works,
+a note should be written. By code we mean the text that will be compiled into one of the company's software products. The code includes
+configuration changes and changes to tools users might work with to configure and build our software.
+
+    * Notes should be added for known problems. Known problems are issues that we know about and have not yet been able to fix.
+
+    * Any change made to address a user-reported problem should be described in a release note.
+
+    * A release note does not need to be written for changes to the code that users will not see. Here are some examples. If you add a
+comment, you do not need to write a release note describing the comment you added. If you rewrite some code to make it read more
+clearly and if there is no change in functionality or performance, then you do not need to write a release note. If you change the
+process by which user software is made, you may not need to write a release note since the change was not made to the code.
+
+    * Users. We have different kinds of users. A release note may be written to be helpful to
+application developers and not system administrators. Users who may find the RELEASE.txt file helpful include the following:
+application developers, library developers, and system administrators.
+
+
+# Release Note <A NAME="releasenote"></A>
+
+* **Entry Syntax**
+The release note entry syntax is shown below.
+
+```
+    - Title/Problem
+
+      Problem/Solution
+
+      Signature
+```
+
+* **Entry Elements** - The elements of the entry - title, problem, solution, and signature - are described in more detail in the table
+below. Descriptions of the problem and the solution should be clear without any ambiguities and should be short without losing clarity or specifics.
+
+    * **Title** - The title or tag should identify one or more categories that will help readers decide if the entry is something they need to study. Can be combined with the `Problem` element
+    * **Problem** - Describe the problem and how users might see the problem in a paragraph.
+You might also consider the following as you describe the problem:
+        * Under what specific conditions does this issue arise?
+        * Under what specific conditions are we sure this issue will not arise?
+        * For a performance issue, instead of saying something is a performance issue, describe what the performance impact of issue is?
+    * **Solution** - Describe the solution in another paragraph.
+You might also consider the following as you describe the solution:
+        * What was done to resolve the issue?
+        * What is the functional impact?
+        * Is there a workaround – a way for users design their software so as not to encounter the issue? If so, what is the workaround?
+        * For a performance fix, how has the performance improved? Links to published documentation would be good.
+    * **Signature** - Each entry must be signed with the initials of the author, the date in YYYY/MM/DD format, and the JIRA ticket number. The
+following is an example entry written by developer Xavier Zolo on April 16, 2014 about JIRA ticket HDFFV-5555: (XYZ - 2014/04/16, HDFFV-5555). The
+signature is enclosed in parentheses. JIRA or Github numbers should not be used in the description of the problem or the solution. They are like
+abbreviations that customers and external users will not be able to interpret.
+
+# Checklist <A NAME="checklist"></A>
+
+Please make sure that you check the items applicable to your pull request:
+
+* Code
+  * [ ] Does the pull request have a corresponding GitHub issue and clear purpose?
+  * [ ] Does the pull request follow HDF5 best practices (naming conventions, code portability, code structure, etc.)? <<TODO: link to the document>>
+  * [ ] If changes were done to Autotools build, were they added to CMake and vice versa?
+  * [ ] Is the pull request applicable to any other branches? If yes, which ones? Please document it in the GitHub issue.
+  * [ ] Is the new code sufficiently documented for future maintenance?
+  * [ ] Does the new feature require a change to an existing API? See "API Compatibility Macros" document (https://portal.hdfgroup.org/display/HDF5/API+Compatibility+Macros)
+* Documentation
+  * [ ] Was the change described in the release_docs/RELEASE.txt file?
+  * [ ] Was MANIFEST updated if new files had been added to the source?
+  * [ ] Was the new function documented in the corresponding public header file using [Doxygen](https://docs.hdfgroup.org/hdf5/develop/_r_m_t.html)?
+  * [ ] Was new functionality documented for the HDF5 community (the level of documentation depends on the feature; ask us what would be appropriate)
+* Testing
+  * [ ] Does the pull request have tests?
+  * [ ] Does the pull request affect HDF5 library performance?
+
+We want as many contributions as we can get, and we are here to help. Feel free to reach out to us if you have any questions
+
+Thank you for your contribution!

CTestConfig.cmake

@@ -12,7 +12,7 @@
 ## This file should be placed in the root directory of your project.
 ## Then modify the CMakeLists.txt file in the root directory of your
 ## project to incorporate the testing dashboard.
-## # The following are required to uses Dart and the Cdash dashboard
+## # The following are required to use Dart and the CDash dashboard
 ##   ENABLE_TESTING()
 ##   INCLUDE(CTest)
 set (CTEST_PROJECT_NAME "HDF5")

Makefile.am

@@ -1,6 +1,5 @@
 #
 # Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
 # All rights reserved.
 #
 # This file is part of HDF5.  The full HDF5 copyright notice, including

Makefile.dist

@@ -1,7 +1,6 @@
 # Top-level distributed Makefile 			       -*- makefile -*-
 
 # Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
 # All rights reserved.
 #
 # This file is part of HDF5.  The full HDF5 copyright notice, including

README.md

@@ -1,18 +1,24 @@
-HDF5 version 1.13.2-1 currently under development
+HDF5 version 1.15.0 currently under development
 
 ![HDF5 Logo](doxygen/img/HDF5.png)
 
+[![develop build status](https://img.shields.io/github/actions/workflow/status/HDFGroup/hdf5/main.yml?branch=develop&label=develop)](https://github.com/HDFGroup/hdf5/actions?query=branch%3Adevelop)
+[![1.14 build status](https://img.shields.io/github/actions/workflow/status/HDFGroup/hdf5/main.yml?branch=hdf5_1_14&label=1.14)](https://github.com/HDFGroup/hdf5/actions?query=branch%3Ahdf5_1_14)
+[![1.12 build status](https://img.shields.io/github/actions/workflow/status/HDFGroup/hdf5/main.yml?branch=hdf5_1_12&label=1.12)](https://github.com/HDFGroup/hdf5/actions?query=branch%3Ahdf5_1_12)
+[![1.10 build status](https://img.shields.io/github/actions/workflow/status/HDFGroup/hdf5/main.yml?branch=hdf5_1_10&label=1.10)](https://github.com/HDFGroup/hdf5/actions?query=branch%3Ahdf5_1_10)
+[![1.8 build status](https://img.shields.io/github/actions/workflow/status/HDFGroup/hdf5/main.yml?branch=hdf5_1_8&label=1.8)](https://github.com/HDFGroup/hdf5/actions?query=branch%3Ahdf5_1_8)
+[![BSD](https://img.shields.io/badge/License-BSD-blue.svg)](https://github.com/HDFGroup/hdf5/blob/develop/COPYING)
+
 *Please refer to the release_docs/INSTALL file for installation instructions.*
 
-THE HDF GROUP
----------------
+This repository contains a high-performance library's source code and a file format
+specification that implement the HDF5® data model. The model has been adopted across
+many industries and this implementation has become a de facto data management standard
+in science, engineering, and research communities worldwide.
 
-The HDF Group is the developer of HDF5®, a high-performance software library and
-data format that has been adopted across multiple industries and has become a
-de facto standard in scientific and research communities.
-
-More information about The HDF Group, the HDF5 Community and the HDF5 software
-project, tools and services can be found at the Group's website.
+The HDF Group is the developer, maintainer, and steward of HDF5 software. Find more
+information about The HDF Group, the HDF5 Community, and other HDF5 software projects,
+tools, and services at The HDF Group's website.
     
    https://www.hdfgroup.org/
 
@@ -77,13 +83,19 @@ RELEASE SCHEDULE
 HDF5 does not release on a regular schedule. Instead, releases are driven by
 new features and bug fixes, though we try to have at least one release of each
 maintenance branch per year. Future HDF5 releases indicated on this schedule
-are tentative. 
+are tentative.
+
+**NOTE**: HDF5 1.12 is being retired early due to its incomplete and incompatible VOL
+layer.
 
 | Release | New Features |
 | ------- | ------------ |
-| 1.13.2 | VFD SWMR, Onion VFD, Selection I/O |
-| 1.13.3 | Multi-Dataset I/O |
-| 1.13.4 | Subfiling |
+| 1.8.23 | last HDF5 1.8 release |
+| 1.10.10 | CVE fixes, performance improvements, H5Dchunk\_iter() |
+| 1.12.3 | CVE fixes, performance improvements, H5Dchunk\_iter(), last HDF5 1.12 release |
+| 1.14.1 | selection I/O with datatype conversion |
+| 2.0.0 | TBD |
+| TBD | VFD SWMR |
 
 This list of feature release versions is also tentative, and the specific release
 in which a feature is introduced may change.

acsite.m4

@@ -2,7 +2,6 @@ dnl -------------------------------------------------------------------------
 dnl -------------------------------------------------------------------------
 dnl
 dnl Copyright by The HDF Group.
-dnl Copyright by the Board of Trustees of the University of Illinois.
 dnl All rights reserved.
 dnl
 dnl This file is part of HDF5.  The full HDF5 copyright notice, including

autogen.sh

@@ -1,10 +1,10 @@
 #!/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   
+# 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 COPYING 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
@@ -50,17 +50,7 @@
 # Note that aclocal will attempt to include libtool's share/aclocal
 # directory.
 #
-# This script takes two potential options:
-#
-# -p
-#
-# When this is selected, the autotools versions are set to the paths
-# and versions used by The HDF Group to produce the released versions
-# of the library.
-#
-# NOTE: This is probably temporary. Once we update our dev machines
-# to have recent versions of the autotools this option will probably
-# be removed.
+# Aside from -h for help, this script takes one potential option:
 #
 # -v
 #
@@ -72,9 +62,6 @@ echo "* HDF5 autogen.sh script *"
 echo "**************************"
 echo
 
-# Default is not production
-production=false
-
 # Default is not verbose output
 verbose=false
 
@@ -86,10 +73,6 @@ while getopts "$optspec" optchar; do
         echo
         echo "      -h      Print this help message."
         echo
-        echo "      -p      Used by THG to use hard-codes autotools"
-        echo "              paths on THG machines. Not for non-HDF-Group"
-        echo "              users!"
-        echo
         echo "      -v      Show more verbose output."
         echo
         echo "  NOTE: Each tool can be set via an environment variable."
@@ -97,11 +80,6 @@ while getopts "$optspec" optchar; do
         echo
         exit 0
         ;;
-    p)
-        echo "Setting THG production mode..."
-        echo
-        production=true
-        ;;
     v)
         echo "Setting verbosity: high"
         echo
@@ -117,84 +95,52 @@ while getopts "$optspec" optchar; do
     esac
 done
 
-if [ "$production" = true ] ; then
-
-    # Production mode
-    #
-    # Hard-code canonical HDF Group tool locations.
-
-    # If paths to tools are not specified, assume they are
-    # located in /usr/hdf/bin/AUTOTOOLS and set paths accordingly.
-    if test -z ${HDF5_AUTOCONF}; then
-        HDF5_AUTOCONF=/usr/hdf/bin/AUTOTOOLS/autoconf
-    fi
-    if test -z ${HDF5_AUTOMAKE}; then
-        HDF5_AUTOMAKE=/usr/hdf/bin/AUTOTOOLS/automake
-    fi
-    if test -z ${HDF5_AUTOHEADER}; then
-        HDF5_AUTOHEADER=/usr/hdf/bin/AUTOTOOLS/autoheader
-    fi
-    if test -z ${HDF5_ACLOCAL}; then
-        HDF5_ACLOCAL=/usr/hdf/bin/AUTOTOOLS/aclocal
-    fi
-    if test -z ${HDF5_LIBTOOL}; then
-        HDF5_LIBTOOL=/usr/hdf/bin/AUTOTOOLS/libtool
-    fi
-    if test -z ${HDF5_M4}; then
-        HDF5_M4=/usr/hdf/bin/AUTOTOOLS/m4
-    fi
-
-else
-
-    # Not in production mode
-    #
-    # If paths to autotools are not specified, use whatever the system
-    # has installed as the default. We use 'which <tool>' to
-    # show exactly what's being used.
-    if test -z ${HDF5_AUTOCONF}; then
-        HDF5_AUTOCONF=$(which autoconf)
-    fi
-    if test -z ${HDF5_AUTOMAKE}; then
-        HDF5_AUTOMAKE=$(which automake)
-    fi
-    if test -z ${HDF5_AUTOHEADER}; then
-        HDF5_AUTOHEADER=$(which autoheader)
-    fi
-    if test -z ${HDF5_ACLOCAL}; then
-        HDF5_ACLOCAL=$(which aclocal)
-    fi
-    if test -z ${HDF5_LIBTOOL}; then
-        case "`uname`" in
-        Darwin*)
-            # libtool on OS-X is non-gnu
-            HDF5_LIBTOOL=$(which glibtool)
-            ;;
-        *)
-            HDF5_LIBTOOL=$(which libtool)
-            ;;
-        esac
-    fi
-    if test -z ${HDF5_M4}; then
-        HDF5_M4=$(which m4)
-    fi
-
-fi # production
+# If paths to autotools are not specified, use whatever the system
+# has installed as the default. We use 'command -v <tool>' to
+# show exactly what's being used (shellcheck complains that 'which'
+# is non-standard and deprecated).
+if test -z "${HDF5_AUTOCONF}"; then
+    HDF5_AUTOCONF="$(command -v autoconf)"
+fi
+if test -z "${HDF5_AUTOMAKE}"; then
+    HDF5_AUTOMAKE="$(command -v automake)"
+fi
+if test -z "${HDF5_AUTOHEADER}"; then
+    HDF5_AUTOHEADER="$(command -v autoheader)"
+fi
+if test -z "${HDF5_ACLOCAL}"; then
+    HDF5_ACLOCAL="$(command -v aclocal)"
+fi
+if test -z "${HDF5_LIBTOOL}"; then
+    case "$(uname)" in
+    Darwin*)
+        # libtool on OS-X is non-gnu
+        HDF5_LIBTOOL="$(command -v glibtool)"
+        ;;
+    *)
+        HDF5_LIBTOOL="$(command -v libtool)"
+        ;;
+    esac
+fi
+if test -z "${HDF5_M4}"; then
+    HDF5_M4="$(command -v m4)"
+fi
 
 
 # Make sure that these versions of the autotools are in the path
-AUTOCONF_DIR=`dirname ${HDF5_AUTOCONF}`
-LIBTOOL_DIR=`dirname ${HDF5_LIBTOOL}`
-M4_DIR=`dirname ${HDF5_M4}`
+AUTOCONF_DIR=$(dirname "${HDF5_AUTOCONF}")
+LIBTOOL_DIR=$(dirname "${HDF5_LIBTOOL}")
+M4_DIR=$(dirname "${HDF5_M4}")
 PATH=${AUTOCONF_DIR}:${LIBTOOL_DIR}:${M4_DIR}:$PATH
 
 # Make libtoolize match the specified libtool
-case "`uname`" in
+case "$(uname)" in
 Darwin*)
     # On OS X, libtoolize could be named glibtoolize or
     # libtoolize. Try the former first, then fall back
     # to the latter if it's not found.
     HDF5_LIBTOOLIZE="${LIBTOOL_DIR}/glibtoolize"
-    if [ ! -f $HDF5_LIBTOOLIZE ] ; then
+    if [ ! -f "$HDF5_LIBTOOLIZE" ] ; then
         HDF5_LIBTOOLIZE="${LIBTOOL_DIR}/libtoolize"
     fi
     ;;
@@ -249,7 +195,7 @@ echo
 
 # LIBTOOLIZE
 libtoolize_cmd="${HDF5_LIBTOOLIZE} --copy --force"
-echo ${libtoolize_cmd}
+echo "${libtoolize_cmd}"
 if [ "$verbose" = true ] ; then
     ${HDF5_LIBTOOLIZE} --version
 fi
@@ -264,7 +210,7 @@ if test -e "${LIBTOOL_DIR}/../share/aclocal" ; then
     aclocal_include="-I ${LIBTOOL_DIR}/../share/aclocal"
 fi
 aclocal_cmd="${HDF5_ACLOCAL} --force -I m4 ${aclocal_include}"
-echo ${aclocal_cmd}
+echo "${aclocal_cmd}"
 if [ "$verbose" = true ] ; then
     ${HDF5_ACLOCAL} --version
 fi
@@ -273,7 +219,7 @@ echo
 
 # AUTOHEADER
 autoheader_cmd="${HDF5_AUTOHEADER} --force"
-echo ${autoheader_cmd}
+echo "${autoheader_cmd}"
 if [ "$verbose" = true ] ; then
     ${HDF5_AUTOHEADER} --version
 fi
@@ -282,7 +228,7 @@ echo
 
 # AUTOMAKE
 automake_cmd="${HDF5_AUTOMAKE} --copy --add-missing --force-missing"
-echo ${automake_cmd}
+echo "${automake_cmd}"
 if [ "$verbose" = true ] ; then
     ${HDF5_AUTOMAKE} --version
 fi
@@ -290,8 +236,11 @@ ${automake_cmd} || exit 1
 echo
 
 # AUTOCONF
-autoconf_cmd="${HDF5_AUTOCONF} --force"
-echo ${autoconf_cmd}
+# The "obsolete" warnings category flags our Java macros as obsolete.
+# Since there is no clear way to upgrade them (Java support in the Autotools
+# is not great) and they work well enough for now, we suppress those warnings.
+autoconf_cmd="${HDF5_AUTOCONF} --force --warnings=no-obsolete"
+echo "${autoconf_cmd}"
 if [ "$verbose" = true ] ; then
     ${HDF5_AUTOCONF} --version
 fi

bin/Makefile.am

@@ -1,6 +1,5 @@
 #
 # Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
 # All rights reserved.
 #
 # This file is part of HDF5.  The full HDF5 copyright notice, including

bin/README.md

@@ -0,0 +1,31 @@
+# Scripts in `bin` and their purpose
+
+Programs run via `autogen.sh` (or the equivalent in CMake) are indicated.
+
+|Program|Purpose|
+|-------|-------|
+|`buildhdf5`|Convenience script to build HDF5 using the Autotools|
+|`checkapi`|Checks if public API calls are used in internal functions|
+|`checkposix`|Checks if C/POSIX calls are prefixed with `HD`|
+|`chkcopyright`|Checks if files have appropriate copyright statements|
+|`cmakehdf5`|Convenience script to build HDF5 using CMake|
+|`debug-ohdr`|Examines debug output from `H5O_open/close` to look for open objects|
+|`format_source`|Runs `clang-format` over the source files, applying our rules|
+|`genparser`|Creates the flex/bison-based parser files in the high-level library|
+|`h5cc.in`|Input file from which h5cc is created|
+|`h5redeploy.in`|Input file from which h5redeploy is created|
+|`h5vers`|Updates the library version number|
+|`make_err`|Generates the H5E header files (called in `autogen.sh`)|
+|`make_vers`|Generates H5version.h (called in `autogen.sh`)|
+|`make_overflow`|Generates H5overflow.h (called in `autogen.sh`)|
+|`output_filter`|Used in the tools test code to strip extraneous output before we diff files|
+|`restore.sh`|Removes files generated by `autogen.sh`|
+|`runbkprog`|Used by CMake to run test programs in the background|
+|`switch_maint_mode`|Switches maintainer mode on/off in `configure.ac`|
+|`trace`|Adds `TRACE` macros to HDF5 C library source files (run by `autogen.sh`)|
+|`warnhist`|Generates compiler warning statistics for gcc/clang when fed output of make|
+
+## TODO
+
+* chkcopyright is currently semi-broken as it doesn't handle the full variety of copyright headers we need. We're leaving it in place, though, in the hopes that someone will update it in the future.
+* Extending warnhist to better understand the output of additional compilers/languages would be nice.

bin/batch/ctest.qsub.in.cmake

@@ -11,11 +11,13 @@ CTEST_CMD=`which ctest`
 
 cd @HDF5_BINARY_DIR@
 if [[ $SUMMARY_FILE == *"ctestS"* ]]; then
-  CMD="${CTEST_CMD} . -E MPI_TEST_ -C Release -j 32 -T test"
+  CMD="${CTEST_CMD} -S ctest_serial.cmake"
+  qsub -t 60 -n 1 -q debug-flat-quad -A ${ACCOUNT_ID} ${CMD} >& ${SUMMARY_FILE}
+  echo "Done running ctest serial command."
+  touch ctestS.done
 else
-  CMD="${CTEST_CMD} . -R MPI_TEST_ ${SKIP_TESTS} -C Release -T test"
+  CMD="${CTEST_CMD} -S ctest_parallel.cmake"
+  qsub -t 60 -n 1 -q debug-flat-quad -A ${ACCOUNT_ID} ${CMD} >& ${SUMMARY_FILE}
+  echo "Done running ctest parallel command."
+  touch ctestP.done
 fi
-
-qsub -t 60 -n 1 -q debug-flat-quad -A ${ACCOUNT_ID} ${CMD} >& ${SUMMARY_FILE}
-
-echo "Done running ctest parallel command."

bin/batch/ctestP.lsf.in.cmake

@@ -14,6 +14,7 @@
 
 cd @HDF5_BINARY_DIR@
 echo "Run parallel test command. Test output will be in build/ctestP.out"
-ctest . -R MPI_TEST_ -C Release -T test >& ctestP.out
+ctest -S ctest_parallel.cmake >& ctestP.out
 
 echo "Done running ctest parallel command."
+touch ctestP.done

bin/batch/ctestP.sl.in.cmake

@@ -8,7 +8,8 @@
 #SBATCH --job-name=h5_ctestP
 
 cd @HDF5_BINARY_DIR@
-ctest . -R MPI_TEST_ -C Release -T test >& ctestP.out
-
-echo "Done running ctestP.sl"
+echo "Run parallel test command. Test output will be in build/ctestP.out"
+ctest -S ctest_parallel.cmake >& ctestP.out
 
+echo "Done running ctest parallel command."
+touch ctestP.done

bin/batch/ctestS.lsf.in.cmake

@@ -11,8 +11,7 @@
 
 cd @HDF5_BINARY_DIR@
 echo "Run command. Test output will be in build/ctestS.out"
-ctest . -E MPI_TEST_ -C Release -j 32 -T test >& ctestS.out
+ctest -S ctest_serial.cmake >& ctestS.out
 
-##$CMD  >& ctestS.out
 echo "Done running command."
-
+touch ctestS.done

bin/batch/ctestS.sl.in.cmake

@@ -8,8 +8,8 @@
 #SBATCH --job-name=h5_ctestS
 
 cd @HDF5_BINARY_DIR@
-CMD="ctest . -E MPI_TEST_ -C Release -j 32 -T test"
+echo "Run command. Test output will be in build/ctestS.out"
+ctest -S ctest_serial.cmake >& ctestS.out
 
-echo "Run $CMD. Test output will be in build/ctestS.out"
-$CMD  >& ctestS.out
-echo "Done running $CMD"
+echo "Done running command."
+touch ctestS.done

bin/batch/ctest_parallel.cmake.in

@@ -0,0 +1,12 @@
+if(NOT "$ENV{CI_SITE_NAME}" STREQUAL "")
+  set(CTEST_SITE "$ENV{CI_SITE_NAME}")
+endif()
+if(NOT "$ENV{CI_BUILD_NAME}" STREQUAL "")
+  set(CTEST_BUILD_NAME "$ENV{CI_BUILD_NAME}")
+endif()
+
+ctest_start ("$ENV{CI_MODEL}" "@HDF5_SOURCE_DIR@" "@HDF5_BINARY_DIR@" APPEND)
+ctest_test (BUILD "@HDF5_BINARY_DIR@" APPEND INCLUDE MPI_TEST_ RETURN_VALUE res)
+if (${res} LESS 0 OR ${res} GREATER 0)
+      file (APPEND ${CTEST_SCRIPT_DIRECTORY}/FailedCTest.txt "Failed Tests: ${res}\n")
+      endif ()

bin/batch/ctest_serial.cmake.in

@@ -0,0 +1,12 @@
+if(NOT "$ENV{CI_SITE_NAME}" STREQUAL "")
+  set(CTEST_SITE "$ENV{CI_SITE_NAME}")
+endif()
+if(NOT "$ENV{CI_BUILD_NAME}" STREQUAL "")
+  set(CTEST_BUILD_NAME "$ENV{CI_BUILD_NAME}")
+endif()
+
+ctest_start ("$ENV{CI_MODEL}" "@HDF5_SOURCE_DIR@" "@HDF5_BINARY_DIR@" APPEND)
+ctest_test (BUILD "@HDF5_BINARY_DIR@" APPEND EXCLUDE MPI_TEST_ PARALLEL_LEVEL 32 RETURN_VALUE res)
+if (${res} LESS 0 OR ${res} GREATER 0)
+      file (APPEND ${CTEST_SCRIPT_DIRECTORY}/FailedCTest.txt "Failed Tests: ${res}\n")
+      endif ()

bin/batch/knl_ctestP.sl.in.cmake

@@ -9,8 +9,8 @@
 #SBATCH --job-name=h5_ctestP
 
 cd @HDF5_BINARY_DIR@
-#run parallel tests except t_cache_image test
-ctest . -R MPI_TEST_ -C Release -T test >& ctestP.out
-
-echo "Done running $CMD"
+echo "Run parallel test command. Test output will be in build/ctestP.out"
+ctest -S ctest_parallel.cmake >& ctestP.out
 
+echo "Done running ctest parallel command."
+touch ctestP.done

bin/batch/knl_ctestS.sl.in.cmake

@@ -9,9 +9,8 @@
 #SBATCH --job-name=h5_ctestS
 
 cd @HDF5_BINARY_DIR@
-CMD="ctest . -E MPI_TEST_ -C Release -j 32 -T test"
-
-echo "Run $CMD. Test output will be in build/ctestS.out"
-$CMD  >& ctestS.out
-echo "Done running $CMD"
+echo "Run command. Test output will be in build/ctestS.out"
+ctest -S ctest_serial.cmake >& ctestS.out
 
+echo "Done running command."
+touch ctestS.done

bin/batch/ray_ctestP.lsf.in.cmake

@@ -15,6 +15,8 @@
 
 cd @HDF5_BINARY_DIR@
 echo "Run parallel test command. Test output will be in build/ctestP.out"
-ctest . -R 'MPI_TEST_' -C Release -T test >& ctestP.out
+ctest -S ctest_parallel.cmake >& ctestP.out
 
 echo "Done running ctest parallel command."
+touch ctestP.done
+~                

bin/batch/ray_ctestS.lsf.in.cmake

@@ -11,8 +11,7 @@
 
 cd @HDF5_BINARY_DIR@
 echo "Run command. Test output will be in build/ctestS.out"
-ctest . -E 'MPI_TEST_' -C Release -j 32 -T test >& ctestS.out
+ctest -S ctest_serial.cmake >& ctestS.out
 
-##$CMD  >& ctestS.out
 echo "Done running command."
-
+touch ctestS.done

bin/bbrelease

@@ -1,7 +1,6 @@
 #!/bin/sh
 #
 # Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
 # All rights reserved.
 #
 # This file is part of HDF5.  The full HDF5 copyright notice, including
@@ -28,15 +27,17 @@
 USAGE()
 {
 cat << EOF
-Usage: $0 -d <dir> [--docver BRANCHNAME] [-h] [--private] [--revision] <methods> ...
+Usage: $0 -d <dir> [-h] [--private] [--revision [--branch BRANCHNAME]] <methods> ...
    -d DIR       The name of the directory where the release(s) should be
                 placed.
-   --docver BRANCHNAME  This is added for 1.8 and beyond to get the correct
-                        version of documentation files from the hdf5docs
+   --branch BRANCHNAME  This is to get the correct version of the branch name from the
                         repository.  BRANCHNAME for v1.8 should be hdf5_1_8.
    -h           print the help page.
    --private    Make a private release with today's date in version information.
    --revision   Make a private release with the code revision number in version information.
+                This allows --branch to be used for the file name.
+   --branch BRANCHNAME  This is to get the correct version of the branch name from the
+                        repository.  BRANCHNAME for v1.8 should be hdf5_1_8.
 
 This must be run at the top level of the source directory.
 The other command-line options are the names of the programs to use
@@ -47,7 +48,6 @@ for compressing the resulting tar archive (if none are given then
     gzip        -- use gzip with "-9" and append ".gz" to the output name.
     bzip2       -- use bzip2 with "-9" and append ".bz2" to the output name.
     zip         -- convert all text files to DOS style and form a zip file for Windows use.
-    doc         -- produce the latest doc tree in addition to the archive.
 
 An md5 checksum is produced for each archive created and stored in the md5 file.
 
@@ -154,7 +154,6 @@ today=`date +%Y%m%d`
 pmode='no'
 revmode='no'
 tmpdir="../#release_tmp.$$"     # tmp work directory
-DOC_URL=https://git@bitbucket.hdfgroup.org/scm/hdffv/hdf5doc.git
 CPPLUS_RM_NAME=cpplus_RM
 
 # Restore previous Version information
@@ -189,8 +188,8 @@ while [ -n "$1" ]; do
         --revision)
             revmode=yes
             ;;
-        --docver)
-            DOCVERSION=$1
+        --branch)
+            BRANCHNAME=$1
             shift
             ;;
         -*)
@@ -239,14 +238,17 @@ if [ X$revmode = Xyes ]; then
     # Copy old version of config/lt_vers.am, since it's hard to
     # "undo" changes to it.
     cp config/lt_vers.am $tmpdir
-    branch=`git branch | grep '*' | awk '{print $NF}'`
+    if [ "${BRANCHNAME}" = "" ]; then
+        BRANCHNAME=`git symbolic-ref -q --short HEAD`
+    fi
     revision=`git rev-parse --short HEAD`
     # Set version information to m.n.r-r$revision.
     # (h5vers does not correctly handle just m.n.r-$today.)
     VERS=`echo $VERS | sed -e s/-.*//`-$revision
     echo Private release of $VERS
+    HDF5_VERS=hdf5-$BRANCHNAME-$revision
+    echo file base of $HDF5_VERS
     bin/h5vers -s $VERS
-    HDF5_VERS=hdf5-$branch-$revision
     # use a generic directory name for revision releases
     HDF5_IN_VERS=hdfsrc
 else
@@ -280,11 +282,6 @@ for f in README.md release_docs/RELEASE.txt; do
     chmod 644 $f
 done
 
-# develop is different than branches.
-if [ "${DOCVERSION}" ]; then
-    DOC_URL=https://git@bitbucket.hdfgroup.org/scm/hdffv/hdf5doc.git -b ${DOCVERSION}
-fi
-
 # Create the tar file
 test "$verbose" && echo "   Running tar..." 1>&2
 (cd "$tmpdir" && exec tar -ch --exclude-vcs -f "$HDF5_VERS.tar" "./$HDF5_IN_VERS" || exit 1 )
@@ -313,23 +310,6 @@ for comp in $methods; do
             tar2zip $HDF5_IN_VERS $tmpdir/$HDF5_VERS.tar $DEST/$HDF5_VERS.zip 1>&2
             (cd $DEST; md5sum $HDF5_VERS.zip >> $MD5file)
             ;;
-        doc)
-            if [ "${DOCVERSION}" = "" ]; then
-                DOCVERSION=master
-            fi
-            test "$verbose" && echo "   Creating docs..." 1>&2
-            # Check out docs from git repo
-            (cd $tmpdir; git clone $DOC_URL > /dev/null) || exit 1
-            # Create doxygen C++ RM
-            (cd c++/src && doxygen cpp_doc_config > /dev/null ) || exit 1
-            # Replace version of C++ RM with just-created version
-            rm -rf $tmpdir/${DOCVERSION}/html/$CPPLUS_RM_NAME
-            mv c++/src/$CPPLUS_RM_NAME $tmpdir/${DOCVERSION}/html/$CPPLUS_RM_NAME
-            # Compress the docs and move them to the release area
-            mv $tmpdir/$DOCVERSION $tmpdir/${HDF5_VERS}_docs
-            (cd $tmpdir && tar cf ${HDF5_VERS}_docs.tar ${HDF5_VERS}_docs)
-            mv $tmpdir/${HDF5_VERS}_docs.tar $DEST
-            ;;
         *)
             echo "***Error*** Unknown method $comp"
             exit 1

bin/buildhdf5

@@ -1,7 +1,6 @@
 #!/bin/sh
 #
 # Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
 # All rights reserved.
 #
 # This file is part of HDF5.  The full HDF5 copyright notice, including

bin/checkapi

@@ -1,7 +1,6 @@
 #!/usr/bin/env perl
 #
 # Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
 # All rights reserved.
 #
 # This file is part of HDF5.  The full HDF5 copyright notice, including

bin/checkposix

@@ -4,7 +4,6 @@ use warnings;
 
 #
 # Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
 # All rights reserved.
 #
 # This file is part of HDF5.  The full HDF5 copyright notice, including
@@ -136,7 +135,7 @@ foreach $arg (@ARGV) {
 
             # These are Windows system calls. Ignore them.
             next if $name =~ /^(_get_osfhandle|GetFileInformationByHandle|SetFilePointer|GetLastError|SetEndOfFile)$/;
-            next if $name =~ /^(FindNextFile|FindClose|_tzset|Wgettimeofday|GetSystemTimeAsFileTime|Wgetlogin|GetUserName)$/;
+            next if $name =~ /^(FindNextFile|FindClose|_tzset|Wgettimeofday|GetSystemTimeAsFileTime|GetUserName)$/;
             next if $name =~ /^(DeleteCriticalSection|TlsFree|TlsGetValue|CreateThread)$/;
             next if $name =~ /^(ExpandEnvironmentStringsA|LockFileEx|UnlockFileEx)$/;
             next if $name =~ /^(DllMain|LocalAlloc|LocalFree)$/;
@@ -144,7 +143,7 @@ foreach $arg (@ARGV) {
             next if $name =~ /^(_beginthread|(Initialize|Enter|Leave)CriticalSection|TlsAlloc)$/;
 
             # These are MPI function calls. Ignore them.
-            next if $name =~ /^(MPI_|MPE_)/;
+            next if $name =~ /^(MPI_)/;
 
             # These are POSIX threads function calls. Ignore them.
             next if $name =~ /^pthread_/;

bin/chkconfigure

@@ -1,82 +0,0 @@
-#!/bin/sh
-##
-## Copyright by the Board of Trustees of the University of Illinois.
-## 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 COPYING 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
-## help@hdfgroup.org.  
-##
-# Check that all the configure files are properly generated.
-#
-# Programmer: Albert Cheng
-# Created Date: 2004/12/07
-
-#
-# Configure: should be generated by autoconf version 2.69.
-# autoconf:  should be of version 2.69.
-
-# variable initialization
-nerrors=0
-AUTOCONFVERSION=2.69
-AUTOCONFVERSIONLEAD='Generated by GNU Autoconf'
-CONFIGUREFILES="configure"
-
-
-# Function definitions
-#
-# PRINTMSG
-# Print a one line message left justified in a field of 70 characters
-# without newline.  More output for this line later.
-#
-PRINTMSG() {
-    SPACES="                                                               "
-    echo "$* $SPACES" | cut -c1-70 | tr -d '\012'
-}
-
-# print result passed.
-PASSED() {
-    echo " PASSED"
-}
-
-# print result failed.
-FAILED() {
-    echo "*FAILED*"
-}
-
-
-# Main body
-
-# Check configure files
-# The autoconf version should be among the first 5 lines.
-echo "Check autoconf version. Should be version $AUTOCONFVERSION"
-for xf in $CONFIGUREFILES; do
-    PRINTMSG $xf
-    if [ ! -f $xf ]; then
-	FAILED
-	echo File not found
-	nerrors=`expr $nerrors + 1`
-	continue
-    fi
-    autoconf_version=`head -5 $xf | grep "$AUTOCONFVERSIONLEAD"`
-    echo $autoconf_version | grep "$AUTOCONFVERSIONLEAD $AUTOCONFVERSION" > /dev/null 2>&1
-    if [ $? -eq 0 ]; then
-	PASSED
-    else
-	FAILED
-	echo "Expected: $AUTOCONFVERSIONLEAD $AUTOCONFVERSION"
-	echo "Got:      $autoconf_version"
-	nerrors=`expr $nerrors + 1`
-    fi
-done
-
-
-# Summary
-echo $0 found $nerrors errors
-if [ $nerrors != 0 ]; then
-    exit 1
-fi
-exit 0

bin/chkcopyright

@@ -1,7 +1,6 @@
 #! /bin/sh
 #
 # Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
 # All rights reserved.
 #
 # This file is part of HDF5.  The full HDF5 copyright notice, including
@@ -10,7 +9,6 @@
 # distribution tree, or in https://www.hdfgroup.org/licenses.
 # If you do not have access to either file, you may request a copy from
 # help@hdfgroup.org.
-#
 
 # Check Copyright notice.
 # Check that all the files have the proper copyright notice.
@@ -39,8 +37,8 @@ NFIXEDFILES=0		# Number of files fixed.
 NFIXFAILEDFILES=0	# Number of files fix failed.
 NUMBEGINLINES=60	# Copyright notice should be located within the
 			# this number of lines at the beginning of the file.
-UICOPYRIGHTSTR="Copyright by the Board of Trustees of the University of Illinois"
 THGCOPYRIGHTSTR="Copyright by The HDF Group."
+UICOPYRIGHTSTR="Copyright by the Board of Trustees of the University of Illinois"
 
 PASSEDLOG=/tmp/h5chkright_passed.$$
 SKIPPEDLOG=/tmp/h5chkright_skipped.$$
@@ -111,113 +109,92 @@ BUILDCOPYRIGHT()
     # C and C++ source Copyright notice
     cat > ${C_COPYRIGHT} << \EOF
  * Copyright by The HDF Group.                                               *
- * Copyright by the Board of Trustees of the University of Illinois.         *
  * 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 files COPYING and Copyright.html.  COPYING can be found at the root   *
- * of the source code distribution tree; Copyright.html can be found at the  *
- * root level of an installed copy of the electronic HDF5 document set and   *
- * is linked from the top-level documents page.  It can also be found at     *
- * http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
- * access to either file, you may request a copy from help@hdfgroup.org.     *
+ * the COPYING 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     *
+ * help@hdfgroup.org.                                                        *
 EOF
 
     # Fortran9X source Copyright notice
     cat > ${FTN_COPYRIGHT} << \EOF
 !   Copyright by The HDF Group.                                               *
-!   Copyright by the Board of Trustees of the University of Illinois.         *
 !   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 files COPYING and Copyright.html.  COPYING can be found at the root   *
-!   of the source code distribution tree; Copyright.html can be found at the  *
-!   root level of an installed copy of the electronic HDF5 document set and   *
-!   is linked from the top-level documents page.  It can also be found at     *
-!   http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
-!   access to either file, you may request a copy from help@hdfgroup.org.     *
+!   the COPYING 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     *
+!   help@hdfgroup.org.                                                        *
 EOF
 
     # HTML file Copyright notice
     cat > ${HTM_COPYRIGHT} << \EOF
   * Copyright by The HDF Group.                                               *
-  * Copyright by the Board of Trustees of the University of Illinois.         *
   * 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 files COPYING and Copyright.html.  COPYING can be found at the root   *
-  * of the source code distribution tree; Copyright.html can be found at the  *
-  * root level of an installed copy of the electronic HDF5 document set and   *
-  * is linked from the top-level documents page.  It can also be found at     *
-  * http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
-  * access to either file, you may request a copy from help@hdfgroup.org.     *
+  * the COPYING 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     *
+  * help@hdfgroup.org.                                                        *
 EOF
 
     # Shell style Copyright notice
     cat > ${SH_COPYRIGHT} << \EOF
 # Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
 # 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 files COPYING and Copyright.html.  COPYING can be found at the root
-# of the source code distribution tree; Copyright.html can be found at the
-# root level of an installed copy of the electronic HDF5 document set and
-# is linked from the top-level documents page.  It can also be found at
-# http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have
-# access to either file, you may request a copy from help@hdfgroup.org.
+# the COPYING 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
+# help@hdfgroup.org.
 EOF
 
     # Shell style Copyright notice (2nd type)
     cat > ${SH_COPYRIGHT2} << \EOF
 ## Copyright by The HDF Group.
-## Copyright by the Board of Trustees of the University of Illinois.
 ## 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 files COPYING and Copyright.html.  COPYING can be found at the root
-## of the source code distribution tree; Copyright.html can be found at the
-## root level of an installed copy of the electronic HDF5 document set and
-## is linked from the top-level documents page.  It can also be found at
-## http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have
-## access to either file, you may request a copy from help@hdfgroup.org.
+## the COPYING 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
+## help@hdfgroup.org.
 EOF
 
     # Windows Batch file Copyright notice
     cat > ${WINBAT_COPYRIGHT} << \EOF
 @REM Copyright by The HDF Group.
-@REM Copyright by the Board of Trustees of the University of Illinois.
 @REM All rights reserved.
 @REM
 @REM This file is part of HDF5.  The full HDF5 copyright notice, including
 @REM terms governing use, modification, and redistribution, is contained in
-@REM the files COPYING and Copyright.html.  COPYING can be found at the root
-@REM of the source code distribution tree; Copyright.html can be found at the
-@REM root level of an installed copy of the electronic HDF5 document set and
-@REM is linked from the top-level documents page.  It can also be found at
-@REM http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have
-@REM access to either file, you may request a copy from help@hdfgroup.org.
+@REM the COPYING file, which can be found at the root of the source code
+@REM distribution tree, or in https://www.hdfgroup.org/licenses.
+@REM If you do not have access to either file, you may request a copy from
+@REM help@hdfgroup.org.
 EOF
 
     # configure.ac file Copyright notice
     cat > ${CONFIGURE_AC_COPYRIGHT} << \EOF
 dnl Copyright by The HDF Group.
-dnl Copyright by the Board of Trustees of the University of Illinois.
 dnl All rights reserved.
 dnl
 dnl This file is part of HDF5.  The full HDF5 copyright notice, including
 dnl terms governing use, modification, and redistribution, is contained in
-dnl the files COPYING and Copyright.html.  COPYING can be found at the root
-dnl of the source code distribution tree; Copyright.html can be found at the
-dnl root level of an installed copy of the electronic HDF5 document set and
-dnl is linked from the top-level documents page.  It can also be found at
-dnl http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have
-dnl access to either file, you may request a copy from help@hdfgroup.org.
+dnl the COPYING file, which can be found at the root of the source code
+dnl distribution tree, or in https://www.hdfgroup.org/licenses.
+dnl If you do not have access to either file, you may request a copy from
+dnl help@hdfgroup.org.
 EOF
 
 }
@@ -364,7 +341,7 @@ FindLineInFile()
 # $1 file which contains the expected copyright notice.
 # $2 file in which to look for the copyright notice.
 # Copyright notice must be found within the beginning $NUMBEGINLINES of lines.
-# Hunt for the particular string $UICOPYRIGHTSTR which signifies the beginning
+# Hunt for the particular string $THGCOPYRIGHTSTR which signifies the beginning
 # of the copyright notice.
 #
 MATCH_COPYRIGHT()
@@ -379,7 +356,7 @@ MATCH_COPYRIGHT()
     nlines=`wc -l ${COPYRIGHTFILE}  | cut -f1 -d' '`
     # Find a line that contains the copyright string and its line number in
     # the file.
-    begin=`FindLineInFile "${UICOPYRIGHTSTR}" $f`
+    begin=`FindLineInFile "${THGCOPYRIGHTSTR}" $f`
     if [ "$begin" -le 0 ] ; then
 	# Not found, generate an empty dummy file
 	cp /dev/null ${EXTRACTEDFILE}
@@ -404,7 +381,7 @@ MATCH_COPYRIGHT()
 # $1 file which contains the expected copyright notice.
 # $2 file in which to look for the copyright notice.
 # Copyright notice must be found within the beginning $NUMBEGINLINES of lines.
-# Hunt for the particular string $UICOPYRIGHTSTR which signifies the beginning
+# Hunt for the particular string $THGCOPYRIGHTSTR which signifies the beginning
 # of the copyright notice.
 #
 FIX_COPYRIGHT()
@@ -427,7 +404,12 @@ FIX_COPYRIGHT()
     # the file.
     insertbegin=`FindLineInFile "${THGCOPYRIGHTSTR}" $f`
     if [ $insertbegin -gt 0 ]; then
-	insertend=`expr $insertbegin + $nlines`		# no need to -1.  See below.
+        insertUIbegin=`FindLineInFile "${UICOPYRIGHTSTR}" $f`
+            if [ $insertUIbegin -gt 0 ]; then
+	        insertend=`expr $insertbegin + $nlines + 1`
+            else
+                insertend=`expr $insertbegin + $nlines`
+            fi
     else
 	insertbegin=`FindLineInFile "${UICOPYRIGHTSTR}" $f`
 	if [ $insertbegin -gt 0 ]; then

bin/debug-ohdr

@@ -1,7 +1,6 @@
 #!/usr/bin/env perl
 #
 # Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
 # All rights reserved.
 #
 # This file is part of HDF5.  The full HDF5 copyright notice, including

bin/dependencies

@@ -1,51 +0,0 @@
-#!/usr/bin/env perl
-#
-# Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
-# 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 COPYING 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
-# help@hdfgroup.org.
-#
-use warnings;
-
-my $depend_file;
-my $new_depend_file;
-my $srcdir;
-my $top_srcdir;
-my $top_builddir;
-
-while ($_ = shift @ARGV) {
-    if (/^--top_srcdir=([^ \t\n]*)/) {
-        $top_srcdir = $1;
-        $top_srcdir =~ s/\+/\\\+/g;
-        $top_srcdir =~ s/\./\\\./g;
-    } elsif (/^--top_builddir=([^ \t\n]*)/) {
-        $top_builddir = $1;
-        $top_builddir =~ s/\+/\\\+/g;
-        $top_builddir =~ s/\./\\\./g;
-    } else {
-        $depend_file = $_;
-        $new_depend_file = "$_.new";
-        last;
-    }
-}
-
-open(DEPEND, "<$depend_file") || die "cannot open file $depend_file: $!\n";
-open(NEW, ">$new_depend_file") || die "cannot open file $new_depend_file: $!\n";
-
-while (<DEPEND>) {
-    s/\.o(\b)/\.lo$1/g;
-    s/ $top_srcdir/ \$\(top_srcdir\)/g;
-    s/ $top_builddir/ \$\(top_builddir\)/g;
-    print NEW $_;
-}
-
-close(DEPEND);
-close(NEW);
-
-`mv $new_depend_file $depend_file`;

bin/deploy

@@ -1,58 +0,0 @@
-#!/bin/sh
-#
-# Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
-# 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 COPYING 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
-# help@hdfgroup.org.
-#
-# Deploy the HDF5 binary.
-#
-# Programmer: Albert Cheng
-# Created Date: 2004/12/15
-#
-# Modifications
-
-# Function definitions
-#
-# Print Usage page
-USAGE()
-{
-cat << EOF
-Usage: $0 <dir>
-   Install the binary to directory <dir>
-
-Examples:
-
-    $ bin/deploy /usr/local/hdf5
-    ....
-
-EOF
-
-}
-
-
-# Variables
-
-if [ $# != 1 ]; then
-    USAGE
-    exit 1
-fi
-
-installdir=$1
-# create installdir if it does not exist yet.
-if [ -d $installdir ] || mkdir $installdir ; then
-    ${MAKE:-gmake} install prefix=$installdir  && \
-	( cd $installdir/bin; ./h5redeploy -force)
-    exit $?
-else
-    echo $installdir is not a valid directory
-    USAGE
-    exit 1
-fi
-

bin/distdep

@@ -1,27 +0,0 @@
-#!/bin/sh
-#! -*-perl-*-
-eval 'exec perl -p -x -S $0 ${1+"$@"}'
-  if 0;
-#
-# Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
-# 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 COPYING 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
-# help@hdfgroup.org.
-#
-
-# Usage: $0 [<].depend
-
-# Takes dependency info and generates on stdout dependencies suitable for
-# distribution by removing all the system include files from the list and
-# removing all but the base name of other include files (since the Makefiles
-# contain the logic for searching).
-
-($h,$_)=/\s*\\/?$h.$`:("",$h.$_);
-s|( +/\S*)*( *)|$2?" \\\n   ":""|eg;
-#s|(([-\w\.]+)/)+([-\w\.]+)|\3|g;

bin/errors

@@ -1,139 +0,0 @@
-#!/usr/bin/env perl
-require 5.003;
-use warnings;
-use Text::Tabs;
-
-# NOTE: THE FORMAT OF HRETURN_ERROR AND HGOTO_ERROR MACROS HAS
-# CHANGED. THIS SCRIPT NO LONGER WORKS! --rpm
-
-# Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
-# 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 COPYING 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
-# help@hdfgroup.org.
-#
-# Robb Matzke
-# 30 Aug 1997
-#
-# Purpose: This script will read standard input which should be a
-#	   function prologue followed by a C function and will emit
-#	   on standard output the same source code with the function
-#	   prologue containing documentation for the various errors
-#	   that occur in the function.
-#
-#	   Errors are raised by calling HGOTO_ERROR() or
-#	   HRETURN_ERROR(). The reason for the error message is a
-#	   comment which appears immediately after the error macro
-#	   call and is contained entirely on one line:
-#
-#		HRETURN_ERROR (...); /*entry not found*/
-#
-#	   If such a comment doesn't exist, then the previous comment
-#	   is used, subject to the constraint that raising an error
-#	   clears the previous comment.
-#
-#	         /* Entry not found */
-#		 HGOTO_ERROR (...);
-#
-# 	   Emacs users can use this script interactively with the
-#	   c-mark-function and shell-command-on-region functions which
-#	   are normally bound to M-C-h and M-|.
-
-
-# Split STDIN into the prolog and the function body.  Preserve leading
-# white space.
-$_ = join "", <STDIN>;
-my ($head, $prolog, $body) = (/^(\s*)(\/\*(.*?)\*\/)?(.*)/s)[0,2,3];
-$prolog = "" unless $prolog;
-
-# Find each error and the comment that goes with it.
-for ($_=$body,$comment=""; /\/\*|H(RETURN|GOTO)_ERROR/s;) {
-   $_ = $&.$';
-
-   if (/^H(RETURN|GOTO)_ERROR\s*\(\s*H5E_(\w+)\s*,\s*H5E_(\w+)\s*,/s) {
-      ($major, $minor, $_) = ($2, $3, $');
-      $comment=$1 if /^.*?\)\s*;\s*\/\*\s*(.*?)\s*\*\//;
-      $comment =~ s/^\s*\*+\s*/ /mg; # leading asterisks.
-      $comment =~ s/^\s+//s;         # leading white space.
-      $comment =~ s/\s+$//s;         # trailing white space.
-      $comment =~ s/(\w)$/$1./s;     # punctuation.
-      $comment ||= "***NO COMMENT***";
-      $errors{"$major\000$minor\000\u$comment"} = 1;
-      $comment = "";
-
-   } else {
-      ($comment) = /^\/\*\s*(.*?)\s*\*\//s;
-      $_ = $';
-   }
-}
-
-
-# Format an error so it isn't too wide.
-sub fmt_error ($) {
-   local ($_) = @_;
-
-   my ($prefix,$space,$err) = /^((.*?)([A-Z_0-9]+\s+[A-Z_0-9]+\s+))/;
-   $_ = $';
-   tr/\n /  /s;
-   my $w = 70 - length expand $prefix;
-   s/(.{$w}\S+)\s+(\S)/$1."\n".$space.' 'x(length $err).$2/eg;
-   return $prefix . $_."\n";
-}
-
-
-
-# Sort the errors by major, then minor, then comment.  Duplicate
-# triplets have already been removed.
-sub by_triplet {
-   my ($a_maj, $a_min, $a_com) = split /\000/, $a;
-   my ($b_maj, $b_min, $b_com) = split /\000/, $b;
-   $a_maj cmp $b_maj || $a_min cmp $b_min || $a_com cmp $b_com;
-}
-@errors = map {sprintf "%-9s %-13s %s\n", split /\000/}
-          sort by_triplet keys %errors;
-
-
-
-# Add the list of errors to the prologue depending on the type of
-# prolog.
-if (($front, $back) = $prolog=~/^(.*?Errors:\s*?(?=\n)).*?\n\s*\*\s*\n(.*)/s) {
-   #| * Errors:							      |#
-   #| *		__list_of_error_messages__ (zero or more lines)	      |#
-   #| *								      |#
-   print $head, "/*", $front, "\n";
-   map {print fmt_error " *\t\t".$_} @errors;
-   print " *\n", $back, "*/", $body;
-
-} elsif (($front,$back) = $prolog =~
-	 /(.*?\n\s*ERRORS:?\s*?(?=\n)).*?\n\s*\n(.*)/s) {
-   #| ERRORS							      |#
-   #|		__list_of_error_messages__ (zero or more lines)	      |#
-   #|								      |#
-   print $head, "/*", $front, "\n";
-   map {print fmt_error "    ".$_} @errors;
-   print "\n", $back, "*/", $body;
-
-} elsif ($prolog eq "") {
-   # No prolog present.
-   print $head;
-   print "\n/*", "-"x73, "\n * Function:\t\n *\n * Purpose:\t\n *\n";
-   print " * Errors:\n";
-   map {print fmt_error " *\t\t".$_} @errors;
-   print " *\n * Return:\tSuccess:\t\n *\n *\t\tFailure:\t\n *\n";
-   print " * Programmer:\t\n *\n * Modifications:\n *\n *", '-'x73, "\n";
-   print " */\n", $body;
-
-} else {
-   # Prolog format not recognized.
-   print $head, "/*", $prolog, "*/\n\n";
-   print "/*\n * Errors returned by this function...\n";
-   map {print fmt_error " *\t".$_} @errors;
-   print " */\n", $body;
-}
-
-

bin/format_source

@@ -20,7 +20,7 @@ find . \( -type d -path ./config -prune -and -not -path ./config \) \
         -or -name H5version.h \
         -or -name H5overflow.h \
         \) \) \
-    -and \( -iname *.h -or -iname *.c -or -iname *.cpp -or -iname *.hpp \) \) \
+    -and \( -iname *.h -or -iname *.c -or -iname *.cpp -or -iname *.hpp -or -iname *.java \) \) \
     | xargs clang-format -style=file -i -fallback-style=none
 
 exit 0

bin/format_source_patch

@@ -1,34 +0,0 @@
-#!/bin/bash
-#
-# Recursively format all C & C++ sources and header files, except those in the
-# 'config' directory and generated files, such as H5LTanalyze.c, etc.
-#
-# Note that any files or directories that are excluded here should also be
-# added to the 'exclude' list in .github/workflows/clang-format-check.yml
-#
-# (Remember to update both bin/format_source and bin/format_source_patch)
-
-find . \( -type d -path ./config -prune -and -not -path ./config \) \
-    -or \( \( \! \( \
-        -name H5LTanalyze.c \
-        -or -name H5LTparse.c \
-        -or -name H5LTparse.h \
-        -or -name H5Epubgen.h \
-        -or -name H5Einit.h \
-        -or -name H5Eterm.h \
-        -or -name H5Edefin.h \
-        -or -name H5version.h \
-        -or -name H5overflow.h \
-        \) \) \
-    -and \( -iname *.h -or -iname *.c -or -iname *.cpp -or -iname *.hpp \) \) \
-    | xargs clang-format -style=file -i -fallback-style=none
-
-git diff > clang_format.patch
-
-# Delete if 0 size
-if [ ! -s clang_format.patch ]
-then
-    rm clang_format.patch
-fi
-
-exit 0

bin/gcov_script

@@ -1,51 +0,0 @@
-#! /bin/sh
-#
-# Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
-# 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 COPYING 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
-# help@hdfgroup.org.
-
-# A script to generate coverage files for HDF5 using gcov.
-# Configures, builds, and runs tests in-place; the output files will be placed
-# in a directory called gcov_logs.
-# Must be invoked from the root hdf5 directory.
-# This script has been tested on kagiso.
-
-CFLAGS="$CFLAGS -ftest-coverage -fprofile-arcs"
-export CFLAGS
-LDFLAGS="$LDFLAGS -lgcov"
-export LDFLAGS
-CC=gcc
-export CC
-./configure
-make
-make check
-mkdir gcov_logs
-cd src
-for j in *.h *.c
-  do
-  ln -s ../$j .libs/$j
-  done 
-cd .libs
-for j in *.gcda
-  do
-  gcov -b $j >> gcov.log 2>&1
-  done
-for j in *.gcov
-   do
-   mv $j ../../gcov_logs
-   done
-mv gcov.log ../../gcov_logs
-for j in *.c *.h
-  do
-  rm $j
-  done
-cd ../..
-
-

bin/genparser

@@ -3,7 +3,7 @@
 # Copyright by The HDF Group.
 # All rights reserved.
 #
-# This file is part of HDF5. The full HDF5 copyright notice, including
+# This file is part of HDF5.  The full HDF5 copyright notice, including
 # terms governing use, modification, and redistribution, is contained in
 # the COPYING file, which can be found at the root of the source code
 # distribution tree, or in https://www.hdfgroup.org/licenses.
@@ -21,7 +21,7 @@
 #
 # There is NO dependency in either the autotools or CMake to regenerate
 # the parser code. If you modify H5LT analyze.l or H5LTparse.y, you
-# will need to run this scrpit manually on a system with a suitable
+# will need to run this script manually on a system with a suitable
 # lexer and parser generator.
 #
 # IMPORTANT OS X NOTE
@@ -236,6 +236,7 @@ do
     echo '#pragma GCC diagnostic ignored "-Wsign-conversion"                ' >> tmp.out
     echo '#pragma GCC diagnostic ignored "-Wstrict-overflow"                ' >> tmp.out
     echo '#pragma GCC diagnostic ignored "-Wstrict-prototypes"              ' >> tmp.out
+    echo '#pragma GCC diagnostic ignored "-Wimplicit-fallthrough"           ' >> tmp.out
     echo '#if !defined (__clang__)                                          ' >> tmp.out
     echo '#pragma GCC diagnostic ignored "-Wlarger-than="                   ' >> tmp.out
     echo '#pragma GCC diagnostic ignored "-Wsuggest-attribute=const"        ' >> tmp.out

bin/h5cc.in

@@ -1,7 +1,6 @@
 #! /bin/sh
 ##
 # Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
 # All rights reserved.
 #
 # This file is part of HDF5.  The full HDF5 copyright notice, including

bin/h5redeploy.in

@@ -1,7 +1,6 @@
 #! /bin/sh
 #
 # Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
 # All rights reserved.
 #
 # This file is part of HDF5.  The full HDF5 copyright notice, including

bin/h5vers

@@ -7,7 +7,6 @@ require 5.003;
 use strict;
 
 # Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
 # All rights reserved.
 #
 # This file is part of HDF5.  The full HDF5 copyright notice, including
@@ -377,7 +376,7 @@ if ($H5_JAVA) {
   my $version_string2 = sprintf("%d, %d, %d", @newver[0,1,2]);
 
   $data =~ s/\@version HDF5 .* <BR>/\@version HDF5 $version_string1 <BR>/;
-  $data =~ s/    public final static int LIB_VERSION\[\] = \{ \d*, \d*, \d* \};/    public final static int LIB_VERSION[] = \{ $version_string2 \};/;
+  $data =~ s/    public final static int LIB_VERSION\[\] = \{\d*,.\d*,.\d*\};/    public final static int LIB_VERSION[] = \{$version_string2\};/;
 
   write_file($H5_JAVA, $data);
 }
@@ -394,7 +393,7 @@ if ($TESTH5_JAVA) {
   my $version_string1 = sprintf("%d, %d, %d", @newver[0,1,2]);
   my $version_string2 = sprintf("int majnum = %d, minnum = %d, relnum = %d", @newver[0,1,2]);
 
-  $data =~ s/        int libversion\[\] = \{ .* \};/        int libversion\[\] = \{ $version_string1 \};/;
+  $data =~ s/        int libversion\[\] = \{.*\};/        int libversion\[\] = \{$version_string1\};/;
   $data =~ s/        int majnum = \d*, minnum = \d*, relnum = \d*;/        $version_string2;/;
 
   write_file($TESTH5_JAVA, $data);

bin/iostats

@@ -1,7 +1,6 @@
 #!/usr/bin/env perl
 #
 # Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
 # All rights reserved.
 #
 # This file is part of HDF5.  The full HDF5 copyright notice, including

bin/make_err

@@ -5,7 +5,6 @@ use warnings;
 
 #
 # Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
 # All rights reserved.
 #
 # This file is part of HDF5.  The full HDF5 copyright notice, including
@@ -32,7 +31,6 @@ sub print_copyright ($) {
 
     print $fh "/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *\n";
     print $fh " * Copyright by The HDF Group.                                               *\n";
-    print $fh " * Copyright by the Board of Trustees of the University of Illinois.         *\n";
     print $fh " * All rights reserved.                                                      *\n";
     print $fh " *                                                                           *\n";
     print $fh " * This file is part of HDF5.  The full HDF5 copyright notice, including     *\n";

bin/make_overflow

@@ -10,7 +10,6 @@ my @ctypes = ( () );
 
 #
 # Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
 # All rights reserved.
 #
 # This file is part of HDF5.  The full HDF5 copyright notice, including
@@ -61,7 +60,6 @@ sub print_copyright ($) {
 
     print $fh "/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *\n";
     print $fh " * Copyright by The HDF Group.                                               *\n";
-    print $fh " * Copyright by the Board of Trustees of the University of Illinois.         *\n";
     print $fh " * All rights reserved.                                                      *\n";
     print $fh " *                                                                           *\n";
     print $fh " * This file is part of HDF5.  The full HDF5 copyright notice, including     *\n";

bin/make_vers

@@ -8,8 +8,8 @@ use warnings;
 #       is added (like support for 1.4, etc), the min_sup_idx parameter will
 #       need to be decremented.)
 
-# Max. library "index" (0 = v1.0, 1 = 1.2, 2 = 1.4, 3 = 1.6, 4 = 1.8, 5 = 1.10, 6 = 1.12, 7 = 1.14, etc)
-$max_idx = 7;
+# Max. library "index" (0 = v1.0, 1 = 1.2, 2 = 1.4, 3 = 1.6, 4 = 1.8, 5 = 1.10, 6 = 1.12, 7 = 1.14, 8 = 1.16, etc)
+$max_idx = 8;
 
 # Min. supported previous library version "index" (0 = v1.0, 1 = 1.2, etc)
 $min_sup_idx = 3;
@@ -19,7 +19,6 @@ $indent = 2;
 
 #
 # Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
 # All rights reserved.
 #
 # This file is part of HDF5.  The full HDF5 copyright notice, including
@@ -46,7 +45,6 @@ sub print_copyright ($) {
 
     print $fh "/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *\n";
     print $fh " * Copyright by The HDF Group.                                               *\n";
-    print $fh " * Copyright by the Board of Trustees of the University of Illinois.         *\n";
     print $fh " * All rights reserved.                                                      *\n";
     print $fh " *                                                                           *\n";
     print $fh " * This file is part of HDF5.  The full HDF5 copyright notice, including     *\n";

bin/mkdirs

@@ -1,33 +0,0 @@
-#! /bin/sh
-#
-# Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
-# 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 COPYING 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
-# help@hdfgroup.org.
-#
-# This is a small program which will create directories n-levels deep.
-# You just call it with something like:
-#
-#       mkdirs /tmp/foo/bar/baz
-#
-# and it will create all the directories from /tmp down to baz which
-# don't exist.
-#
-chmodprog="${CHMODPROG-chmod}"
-mkdirprog="${MKDIRPROG-mkdir}"
-
-make_dir () {
-  if test ! -d $1; then
-    make_dir `echo $1 | sed -e 's#/[^/]*$##'`
-    $mkdirprog $1
-    $chmodprog 755 $1
-  fi
-}
-
-make_dir `echo $1 | sed -e 's#/$##'`

bin/newer

@@ -1,43 +0,0 @@
-#!/bin/sh
-#
-# Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
-# 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 COPYING 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
-# help@hdfgroup.org.
-#
-# Compare the modification time of file argument 1 against other file arguments.
-# Return true (0) if argument 1 is newer than all others, otherwise return
-# false (1).  If any of the argument is not a file, return false (1).
-#
-# Programmer: Albert Cheng
-# Created Date: 2005/07/06
-# Modification:
-#    Albert Cheng 2005/8/30
-#    Changed from two arguments to multiple arguments.
-
-if test $# -lt 2; then
-    exit 1
-fi
-if test ! -f $1; then
-    exit 1
-fi
-f1=$1
-shift
-
-for f in $*; do
-    if test ! -f $f; then
-	exit 1
-    fi
-    if test X = X`find $f1 -newer $f -print`; then
-	exit 1
-    fi
-done
-
-# passed all tests.  Must be a file newer than all others.
-exit 0

bin/output_filter.sh

@@ -61,26 +61,21 @@ STDOUT_FILTER() {
 # Remove them from the stderr result file.
 # $1 is the file name of the file to be filtered.
 # Cases of filter needed:
-# 1. MPE:
-# In parallel mode and if MPE library is used, it prints the following
-# two message lines whether the MPE tracing is used or not.
-#    Writing logfile.
-#    Finished writing logfile.
-# 2. LANL MPI:
+# * LANL MPI:
 # The LANL MPI will print some messages like the following,
 #    LA-MPI: *** mpirun (1.5.10)
 #    LA-MPI: *** 3 process(es) on 2 host(s): 2*fln21 1*fln22
 #    LA-MPI: *** libmpi (1.5.10)
 #    LA-MPI: *** Copyright 2001-2004, ACL, Los Alamos National Laboratory
-# 3. h5diff debug output:
+# * h5diff debug output:
 #    Debug output all have prefix "h5diff debug: ".
-# 4. AIX system prints messages like these when it is aborting:
+# * AIX system prints messages like these when it is aborting:
 #    ERROR: 0031-300  Forcing all remote tasks to exit due to exit code 1 in task 0
 #    ERROR: 0031-250  task 4: Terminated
 #    ERROR: 0031-250  task 3: Terminated
 #    ERROR: 0031-250  task 2: Terminated
 #    ERROR: 0031-250  task 1: Terminated
-# 5. LLNL Blue-Gene mpirun prints messages like there when it exit non-zero:
+# * LLNL Blue-Gene mpirun prints messages like there when it exit non-zero:
 #    <Apr 12 15:01:49.075658> BE_MPI (ERROR): The error message in the job record is as follows:
 #    <Apr 12 15:01:49.075736> BE_MPI (ERROR):   "killed by exit(1) on node 0"
 STDERR_FILTER() {
@@ -91,12 +86,6 @@ STDERR_FILTER() {
     cp $result_file $tmp_file
     sed -e '/ BE_MPI (ERROR): /d' \
 	< $tmp_file > $result_file
-    # Filter MPE messages
-    if test -n "$pmode"; then
-	cp $result_file $tmp_file
-	sed -e '/^Writing logfile./d' -e '/^Finished writing logfile./d' \
-	    < $tmp_file > $result_file
-    fi
     # Filter LANL MPI messages
     # and LLNL srun messages
     # and AIX error messages

bin/pkgscrpts/h5rmflags

@@ -1,7 +1,6 @@
 #! /bin/sh
 #
 # Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
 # All rights reserved.
 #
 # This file is part of HDF5.  The full HDF5 copyright notice, including

bin/pkgscrpts/makeHDF5BinaryTarfiles.pl

@@ -2,7 +2,6 @@
 # makeTarFiles.pl
 
 # Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
 # All rights reserved.
 #
 # This file is part of HDF5.  The full HDF5 copyright notice, including

bin/pkgscrpts/makeInternalREADME.pl

@@ -1,215 +0,0 @@
-#!/usr/bin/perl
-# makeInternalREADME.pl
-#
-# Copyright by The HDF Group.
-# All rights reserved.
-#
-# This file is part of HDF4.  The full HDF4 copyright notice, including
-# terms governing use, modification, and redistribution, is contained in
-# the files COPYING and Copyright.html.  COPYING can be found at the root
-# of the source code distribution tree; Copyright.html can be found at the
-# root level of an installed copy of the electronic HDF4 document set and
-# is linked from the top-level documents page.  It can also be found at
-# http://hdfgroup.org/HDF4/doc/Copyright.html.  If you do not have
-# access to either file, you may request a copy from help@hdfgroup.org.
-#
-
-use warnings;
-use strict;
-
-my $section2="For information on compilers and settings used to build these HDF5 
-libraries, please refer to:
-
-    ./lib/libhdf5.settings
-
-The contents of this directory are:
-
-    COPYING     - Copyright notice
-    README      - This file
-    RELEASE.txt - Detailed information regarding this release
-    bin/        - Directory containing HDF5 pre-compiled utilities
-    include/    - Directory containing HDF5 include files
-    lib/        - Directory containing HDF5 libraries and settings
-    share/      - Directory containing example code in C, C++, and 
-                  Fortran using HDF5 and HDF5 HL library APIs. The 
-                  shell scripts provided with these examples will 
-                  compile and run them, and will also test the 
-                  h5cc, h5c++, and h5fc compile scripts found
-                  in the installed bin directory.
-
-These binaries were built with the ZLIB and SZIP (version 2.1, Encoder 
-ENABLED) external libraries which are included in the lib directory for 
-convenience.
-
-We also provide the ZLIB and SZIP source code on our ftp server at:
-
-   ftp://ftp.hdfgroup.org/lib-external/
-
-The official ZLIB and SZIP pages are at:
-
-   ZLIB: http://www.zlib.net/
-   SZIP: http://hdfgroup.org/doc_resource/SZIP/
-
-";
-
-my $section3 = "If using the shared libraries, you must add the HDF5 library path 
-to the LD_LIBRARY_PATH variable.
-";
-
-my $section4 = "We provide scripts for compiling applications with the HDF5 libraries:
-
-    bin/h5cc  - for C
-    bin/h5fc  - for F90 (if Fortran 90 library is included with the binaries)
-    bin/h5c++ - for C++ (if C++ library is included with the binaries)
-
-After you have installed the binaries to their final destination, you can use 
-these scripts (h5cc, h5fc, h5c++) to compile.  However, you must first run 
-./h5redeploy in the bin directory to change site specific paths in the scripts.
-
-You may also need to change other variables in the scripts, depending
-on how things are set up on your system.  Here are some of the variables
-to check:
-
-  prefix      - Path to the HDF5 top level installation directory
-  CCBASE      - Name of the C compiler
-  CLINKERBASE - Name of the linker
-  LIBS        - Libraries your application will link with
-
-For further details refer to the INSTALL files in  
-    ftp://ftp.hdfgroup.org/HDF5/current/src/unpacked/release_docs/
-or in the ./release_docs/ directory of the HDF5 source code, which can be found 
-on the HDF Group ftp server at ftp://ftp.hdfgroup.org/HDF5/current/src/.
-
-Please send questions, comments, and suggestions to the appropriate 
-contact address from http://www.hdfgroup.org/about/contact.html 
-
-
-";
-
-my $indirectory = ".";
-$indirectory = shift;
-my $linktype = "shared";
-if ($indirectory =~ /static/) {
-   $linktype = "static";
-}
-my $modestring="";
-if ($indirectory =~ /32/) {
-    $modestring = "in 32 bit mode ";
-}
-
-my $version;
-
-my $outfile = "$indirectory/README";
-open OUTFILE, ">$outfile" or die "$!Couldn't open $outfile - check permissions for $indirectory\n";
-my $hostname;
-my $cmd = "grep \"HDF5 Version\" $indirectory/lib/libhdf5.settings";
-$_ = `$cmd`;
-#print OUTFILE $_, "\n";
-s/HDF5 Version://;
-s/^\s+//;
-chomp;
-$version = $_;
-#print OUTFILE $_, "\n";
-
-my $versionstring=  "This directory contains the $linktype binary distribution of HDF5-".$version;
-
-$cmd = "grep \"Uname information:\" $indirectory/lib/libhdf5.settings";
-$_ = `$cmd`;
-s/Uname information://;
-s/^\s+//;
-#print OUTFILE $_;
-chomp;
-#s/(^\w+)(\s)(\S+)/$1/;
-#s/(^.*)(-)(.*)(200[7-8])(.*)(\s)(\S+)/$1 $5/;
-#my $platformstring = "\nthat was compiled on:" . $_ . " ";
-my $platformstring = "";
-my $hostnamestring = $_;
-my @hostnamestring = split / /, $hostnamestring;
-#print OUTFILE "Size of hostnamestring is ", scalar @hostnamestring, "\n";
-#print OUTFILE $hostnamestring[0] . "\t" . $hostnamestring[2]."\t".$hostnamestring[19]."\n";
-$hostname = $hostnamestring[1];
-#my $size = scalar @hostnamestring;
-if ($hostname =~ /loyalty/) {
-   $platformstring = "\nthat was compiled " . $modestring . "on: " . $hostnamestring[0]." " . $hostnamestring[2]." " . $hostnamestring[-1] . " ";
-}
-elsif ($hostname =~ /freedom/) {
-   $platformstring = "\nthat was compiled " . $modestring . "on: " . $hostnamestring[0]." " . $hostnamestring[2]." " . $hostnamestring[-1] . " ";
-} elsif ($hostname =~ /emu/) {
-   $platformstring = "\nthat was compiled " . $modestring . "on: " . $hostnamestring[0]." " . $hostnamestring[2] . " " . $hostnamestring[-2] . " ";
-} elsif ($hostname =~ /fred/) {
-   $platformstring = "\nthat was compiled " . $modestring . "on: " . $hostnamestring[0]." " . $hostnamestring[2] . " " . $hostnamestring[-1] . " ";
-} else {
-   $_ = $hostnamestring[2];
-   my $pos = index $_, '-';
-   my $os = substr $_, 0, $pos;
-   $platformstring = "\nthat was compiled " . $modestring . "on: " . $hostnamestring[0] . " " . $os . " " . $hostnamestring[-2] . " ";
-}
-
-
-my $mappingstring = ""; 
-#no mappingstring for 1.6.  Put it back for 1.8.
-#$cmd = "grep \"Default API Mapping:\" $indirectory/lib/libhdf5.settings";
-#$_ = `$cmd`;
-#s/Default API Mapping://;
-#s/^\s+//;
-#chomp;
-#if (/v\d+/) {
-#   s/v//;
-#   s/(\d)(\d)/$1\.$2/g;
-#   $mappingstring = "using the default\nAPI mapping for VERSION ".$_.".";
-#   
-#}
-print OUTFILE $versionstring;
-print OUTFILE $platformstring."\n\n";
-#print OUTFILE $mappingstring;
-
-#if ($hostname eq "loyalty.hdfgroup.uiuc.edu" || $hostname eq "freedom.hdfgroup.uiuc.edu") {
-#   print OUTFILE "  It includes the C APIs,\nbuilt using the following ";
-#   print OUTFILE "compilers:\n\n";
-#}
-#else {
-if ($linktype eq "shared" &&  !($hostname =~ /32/)) {
-    print OUTFILE "\n\nIt includes the C, C++, F90 and Java APIs, built using the following\n";
-} else {
-    print OUTFILE "\n\nIt includes the C, C++, and F90 APIs, built using the following\n";
-}
-print OUTFILE "compilers:\n\n";
-#}
-
-# Only the gcc compiler version is in libhdf5.settings, so for now I looked 
-# up the versions and hardcoded them here.  We will put them in libhdf5.settings
-# for the next release.
-if ($indirectory =~ /gnu484/) {
-   print OUTFILE "\tgcc, g++, and gfortran 4.8.4\n\n";
-} elsif ($hostname =~ /jam/ || $hostname =~ /koala/) {
-   print OUTFILE "\tgcc, g++, and gfortran 4.1.2\n\n";
-} elsif ($hostname =~ /platypus/) {
-   print OUTFILE "\tgcc, g++, and gfortran 4.4.7\n\n";
-   if ($linktype eq "shared" &&  !($hostname =~ /32/)) {
-       print OUTFILE "\tjava 1.8.0_51\n\n";
-   }
-} elsif ($hostname =~ /moohan/) {
-   print OUTFILE "\tgcc, g++, and gfortran 4.8.5\n\n";
-   if ($linktype eq "shared" &&  !($hostname =~ /32/)) {
-       print OUTFILE "\tjava 1.8.0_51\n\n";
-   }
-} elsif ($hostname =~ /emu/) {
-   print OUTFILE "\tSun C and C++ 5.12, Sun Fortran 95 8.6\n\n";
-} elsif ($hostname =~ /loyalty/ || $hostname =~ /freedom/) {
-   print OUTFILE "\tgcc, g++, and gfortran 4.6.1\n\n";    
-} elsif ($hostname =~ /duck/) {
-   print OUTFILE "\tApple clang/clang++ 3.0 from Xcode 4.6.1 and gfortran 4.8.2\n\n";
-} elsif ($hostname =~ /kite/) {
-   print OUTFILE "\tApple clang/clang++ 5.1 from Xcode 5.0.2 and gfortran 4.8.2\n\n";
-} elsif ($hostname =~ /quail/) {
-   print OUTFILE "\tgcc, g++ 5.1 from Xcode 5.1 and gfortran 4.8.2\n\n";
-} elsif ($hostname =~ /osx1010test/) {
-   print OUTFILE "\tgcc, g++ 5.1 from Xcode 5.1 and gfortran 4.8.2\n\n";
-}
-
-print OUTFILE $section2;
-
-print OUTFILE $section3;
-
-print OUTFILE $section4;
-

bin/pkgscrpts/makeOuterREADME.pl

@@ -1,182 +0,0 @@
-#!/usr/bin/perl
-# makeOuterREADME.pl
-
-# Copyright by The HDF Group.
-# All rights reserved.
-#
-# This file is part of HDF4.  The full HDF4 copyright notice, including
-# terms governing use, modification, and redistribution, is contained in
-# the files COPYING and Copyright.html.  COPYING can be found at the root
-# of the source code distribution tree; Copyright.html can be found at the
-# root level of an installed copy of the electronic HDF4 document set and
-# is linked from the top-level documents page.  It can also be found at
-# http://hdfgroup.org/HDF4/doc/Copyright.html.  If you do not have
-# access to either file, you may request a copy from help@hdfgroup.org.
-#
-
-use warnings;
-use strict;
-
-my $indirectory = ".";
-$indirectory = shift;
-
-my $outdirectory = ".";
-$outdirectory = shift;
-
-my $outsubdir = shift;
-
-my $version;
-
-my $outfile = "$outdirectory/$outsubdir/README";
-open OUTFILE, ">$outfile";
-my $hostname="";
-my $cmd = "grep \"HDF5 Version\" $indirectory-static/lib/libhdf5.settings";
-$_ = `$cmd`;
-print OUTFILE $_, "\n";
-s/HDF5 Version://;
-s/^\s+//;
-chomp;
-$version = $_;
-#print OUTFILE $_, "\n";
-my $versionstring=  "This directory contains the precompiled HDF5 $version binary distribution\n(include files, libraries, utilities) for";
-
-$cmd = "grep \"Uname information:\" $indirectory-static/lib/libhdf5.settings";
-$_ = `$cmd`;
-s/Uname information://;
-s/^\s+//;
-chomp;
-print "String to work with is $_\n";
-my $platformstring = "";
-my $hostnamestring = $_;
-my @hostnamestring = split / /, $hostnamestring;
-$platformstring = "$hostnamestring[0] ";
-if ($indirectory =~ /jam/ || $indirectory =~ /koala/) {
-   $hostnamestring = $hostnamestring[2];
-   my $pos = index $hostnamestring, "-";
-   if ($pos > 0) {
-      $platformstring .=  substr $hostnamestring, 0, $pos;
-   } else {
-      $platformstring .= $hostnamestring[2];
-   }
-   $platformstring .= " ".$hostnamestring[-3];
-} elsif ($indirectory =~ /linew/) {
-   $platformstring .= "$hostnamestring[2] $hostnamestring[-2]";
-} else {
-   $platformstring .= "$hostnamestring[2] $hostnamestring[-1]";
-}
-
-print OUTFILE $versionstring." ".$platformstring.":\n\n";
-my $line1;
-my $line3;
-my $line5;
-my $compilerstring="";
-my $compilerstring1="";
-my $compilerstring2="";
-
-
-print $indirectory, "\n";
- 
-if ($indirectory =~ /ostrich/) {
-#   $line1 = "  hdf5-$version-$outsubdir-16API.tar.gz - Includes C, C++, F90 APIs (using\n";
-   $line3 = "  hdf5-$version-$outsubdir-static.tar.gz  - Includes C, C++, F90 APIs (using";
-   $line5 = "  hdf5-$version-$outsubdir-shared.tar.gz  - Includes C, C++, F90 APIs (using";
-   $compilerstring = " gcc, g++, and gfortran 4.4.7)";
-}
-elsif ($indirectory =~ /platypus/) {
-#   $line1 = "  hdf5-$version-$outsubdir-16API.tar.gz - Includes C, C++, F90 APIs (using\n";
-   $line3 = "  hdf5-$version-$outsubdir-static.tar.gz  - Includes C, C++, F90 APIs (using";
-   $compilerstring1 = " gcc, g++, and gfortran 4.4.7)\n";
-   if ($indirectory =~ /32/) {
-      $line5 = "  hdf5-$version-$outsubdir-shared.tar.gz  - Includes C, C++, F90 and Java APIs (using";
-      $compilerstring2 = " gcc, g++, and gfortran 4.4.7)\n";
-   } else {
-      $line5 = "  hdf5-$version-$outsubdir-shared.tar.gz  - Includes C, C++, F90 and Java APIs (using";
-      $compilerstring2 = " gcc, g++, and gfortran 4.4.7 and java 1.8.0_51)\n";
-   }
-}
-elsif ($indirectory =~ /moohan/) {
-#   $line1 = "  hdf5-$version-$outsubdir-16API.tar.gz - Includes C, C++, F90 APIs (using\n";
-   $line3 = "  hdf5-$version-$outsubdir-static.tar.gz  - Includes C, C++, F90 APIs (using";
-   $compilerstring1 = " gcc, g++, and gfortran 4.8.5)\n";
-   if ($indirectory =~ /32/) {
-      $line5 = "  hdf5-$version-$outsubdir-shared.tar.gz  - Includes C, C++, F90 and Java APIs (using";
-      $compilerstring2 = " gcc, g++, and gfortran 4.4.7)\n";
-   } else {
-      $line5 = "  hdf5-$version-$outsubdir-shared.tar.gz  - Includes C, C++, F90 and Java APIs (using";
-      $compilerstring2 = " gcc, g++, and gfortran 4.8.5 and java 1.8.0_51)\n";
-   }
-}
-elsif ($indirectory =~ /emu/) {
-#   $line1 = "  hdf5-$version-$outsubdir-16API.tar.gz - Includes C, C++, F90 APIs (using\n";
-   $line3 = "  hdf5-$version-$outsubdir-static.tar.gz  - Includes C, C++, F90 APIs (using";
-   $line5 = "  hdf5-$version-$outsubdir-shared.tar.gz  - Includes C, C++, F90 APIs (using";
-   $compilerstring = " Sun C and C++ 5.12, Sun Fortran 95 8.6)\n";
-}
-elsif ($indirectory =~ /kite/) {
-   $line3 = "  hfd5-$version-$outsubdir-static.tar.gz  - Includes C, C++, F90 APIs (using";
-   $line5 = "  hfd5-$version-$outsubdir-shared.tar.gz  - Includes C, C++, F90 APIs (using";
-   $compilerstring = " Apple clang/clang++ 5.1 from Xcode 5.0.2,
-                                                              gfortran 4.8.2)\n";
-}
-elsif ($indirectory =~ /quail/) {
-   $line3 = "  hfd5-$version-$outsubdir-static.tar.gz  - Includes C, C++, F90 APIs (using";
-   $line5 = "  hfd5-$version-$outsubdir-shared.tar.gz  - Includes C, C++, F90 APIs (using";
-   $compilerstring = " Apple clang/clang++ 6.0 from Xcode 5.1,
-                                                              gfortran 4.9.2)\n";
-}
-elsif ($indirectory =~ /osx1010test/) {
-   $line3 = "  hdf5-$version-$outsubdir-static.tar.gz  - Includes C, C++, F90 APIs (using";
-   $line5 = "  hdf5-$version-$outsubdir-shared.tar.gz  - Includes C, C++, F90 APIs (using";
-   $compilerstring = " Apple clang/clang++ 6.1 from Xcode 6.1,
-                                                              gfortran 4.9.2)\n";
-}
-elsif ($indirectory =~ /osx1011test/) {
-   $line3 = "  hdf5-$version-$outsubdir-static.tar.gz  - Includes C, C++, F90 APIs (using";
-   $line5 = "  hdf5-$version-$outsubdir-shared.tar.gz  - Includes C, C++, F90 APIs (using";
-   $compilerstring = " Apple clang/clang++ 7.0.2 from Xcode 7.0,
-                                                              gfortran 5.2.0)\n";
-}
-
-    print OUTFILE $line3;
-    print OUTFILE $compilerstring1."\n";
-if ($line5 ne "") {
-    print OUTFILE $line5;
-    print OUTFILE $compilerstring2."\n";
-}
-#elsif ($indirectory =~ /-16API/) {
-#    print OUTFILE $line1;
-#    print OUTFILE $compilerstring;
-#    print OUTFILE "                               USES THE VERSION 1.6 DEFAULT API\n";
-#    print OUTFILE "                               MAPPING.\n\n";
-#}
-
-print OUTFILE "  utilities/ - Directory containing the compiled HDF5 utilities.\n";
-print OUTFILE "               These utilities are STATICALLY linked and will run as is.\n\n";
-#print OUTFILE "             The tools can be downloaded separately, or ALL in one\n";
-#print OUTFILE "             compressed file (5-$version-$outsubdir-static-util.tar.gz).\n\n";
-print OUTFILE "\n";
-print OUTFILE "To obtain the HDF5 distribution, 'unzip' and 'untar' the distribution\n";
-print OUTFILE "file:\n\n";
-print OUTFILE "  gzip -cd <gz file from above> | tar xvf -\n";
-
-
-#$cmd = "grep \"Configured by:\" $indirectory/$key-static/lib/libhdf5.settings";
-#$_ = `$cmd`;
-#s/Configured by://;
-#s/^\s+//;
-#print OUTFILE $_;
-#chomp;
-#my $hostnamestring = $_;
-#s/(^\w+)(\s)(\S+)/$1/;
-#s/(^.*)(-)(.*)(200[7-8])(.*)(\s)(\S+)/$1 $5/;
-#my $platformstring = $_ . ":\n\n";
-#my @hostnamestring = split /@/, $hostnamestring;
-#print "Size of hostnamestring is ", scalar @hostnamestring, "\n";
-#print $hostnamestring[0] . "\t" . $hostnamestring[2]."\t".$hostnamestring[19]."\n";
-#my $platformstring = $hostnamestring[1].":\n\n";
-#$hostnamestring = $hostnamestring[1];
-#my $pos = index $hostnamestring, ".";
-#if ($pos > 0) {
-#   @hostnamestring = split /\./, $hostnamestring;
-#   $platformstring = $hostnamestring[0].":\n\n";
-#}

bin/release

@@ -1,7 +1,6 @@
 #!/bin/sh
 #
 # Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
 # All rights reserved.
 #
 # This file is part of HDF5.  The full HDF5 copyright notice, including
@@ -53,23 +52,23 @@ for compressing the resulting tar archive (if none are given then
                    information is available in the README_HPC file.
     doc         -- produce the latest doc tree in addition to the archive.
 
-An md5 checksum is produced for each archive created and stored in the md5 file.
+A sha256 checksum is produced for each archive created and stored in the sha256 file.
 
 Examples:
 
     $ bin/release -d /tmp
     /tmp/hdf5-1.8.13-RELEASE.txt
-    /tmp/hdf5-1.8.13.md5
+    /tmp/hdf5-1.8.13.sha256
     /tmp/hdf5-1.8.13.tar
 
     $ bin/release -d /tmp gzip
     /tmp/hdf5-1.8.13-RELEASE.txt
-    /tmp/hdf5-1.8.13.md5
+    /tmp/hdf5-1.8.13.sha256
     /tmp/hdf5-1.8.13.tar.gz
 
     $ bin/release -d /tmp tar gzip zip
     /tmp/hdf5-1.8.13-RELEASE.txt
-    /tmp/hdf5-1.8.13.md5
+    /tmp/hdf5-1.8.13.sha256
     /tmp/hdf5-1.8.13.tar
     /tmp/hdf5-1.8.13.tar.gz
     /tmp/hdf5-1.8.13.tar.zip
@@ -206,7 +205,7 @@ tar2cmakezip()
     # step 3: add LIBAEC.tar.gz, ZLib.tar.gz and cmake files
     cp /mnt/scr1/pre-release/hdf5/CMake/LIBAEC.tar.gz $cmziptmpsubdir
     cp /mnt/scr1/pre-release/hdf5/CMake/ZLib.tar.gz $cmziptmpsubdir
-    cp /mnt/scr1/pre-release/hdf5/CMake/HDF5Examples-1.14.4-Source.zip $cmziptmpsubdir
+    cp /mnt/scr1/pre-release/hdf5/CMake/HDF5Examples-2.0.2-Source.zip $cmziptmpsubdir
     cp /mnt/scr1/pre-release/hdf5/CMake/hdf5_plugins-master.zip $cmziptmpsubdir
     cp $cmziptmpsubdir/$version/config/cmake/scripts/CTestScript.cmake $cmziptmpsubdir
     cp $cmziptmpsubdir/$version/config/cmake/scripts/HDF5config.cmake $cmziptmpsubdir
@@ -298,7 +297,7 @@ tar2cmaketgz()
     # step 3: add LIBAEC.tar.gz, ZLib.tar.gz and cmake files
     cp /mnt/scr1/pre-release/hdf5/CMake/LIBAEC.tar.gz $cmgztmpsubdir
     cp /mnt/scr1/pre-release/hdf5/CMake/ZLib.tar.gz $cmgztmpsubdir
-    cp /mnt/scr1/pre-release/hdf5/CMake/HDF5Examples-1.14.4-Source.tar.gz $cmgztmpsubdir
+    cp /mnt/scr1/pre-release/hdf5/CMake/HDF5Examples-2.0.2-Source.tar.gz $cmgztmpsubdir
     cp /mnt/scr1/pre-release/hdf5/CMake/hdf5_plugins-master.tar.gz $cmgztmpsubdir
     cp $cmgztmpsubdir/$version/config/cmake/scripts/CTestScript.cmake $cmgztmpsubdir
     cp $cmgztmpsubdir/$version/config/cmake/scripts/HDF5config.cmake $cmgztmpsubdir
@@ -377,7 +376,7 @@ tar2hpccmaketgz()
     # step 3: add LIBAEC.tar.gz, ZLib.tar.gz and cmake files
     cp /mnt/scr1/pre-release/hdf5/CMake/LIBAEC.tar.gz $cmgztmpsubdir
     cp /mnt/scr1/pre-release/hdf5/CMake/ZLib.tar.gz $cmgztmpsubdir
-    cp /mnt/scr1/pre-release/hdf5/CMake/HDF5Examples-1.14.4-Source.tar.gz $cmgztmpsubdir
+    cp /mnt/scr1/pre-release/hdf5/CMake/HDF5Examples-2.0.2-Source.tar.gz $cmgztmpsubdir
     cp /mnt/scr1/pre-release/hdf5/CMake/hdf5_plugins-master.tar.gz $cmgztmpsubdir
     cp $cmgztmpsubdir/$version/config/cmake/scripts/CTestScript.cmake $cmgztmpsubdir
     cp $cmgztmpsubdir/$version/config/cmake/scripts/HDF5config.cmake $cmgztmpsubdir
@@ -532,43 +531,43 @@ test "$verbose" && echo "   Running tar..." 1>&2
 (cd "$tmpdir" && exec tar -ch --exclude-vcs -f "$HDF5_VERS.tar" "./$HDF5_VERS" || exit 1 )
 
 # Compress
-MD5file=$HDF5_VERS.md5
-cp /dev/null $DEST/$MD5file
+SHA256=$HDF5_VERS.sha256
+cp /dev/null $DEST/$SHA256
 for comp in $methods; do
     case $comp in
         tar)
             cp -p $tmpdir/$HDF5_VERS.tar $DEST/$HDF5_VERS.tar
-            (cd $DEST; md5sum $HDF5_VERS.tar >> $MD5file)
+            (cd $DEST; sha256sum $HDF5_VERS.tar >> $SHA256)
             ;;
         gzip)
             test "$verbose" && echo "   Running gzip..." 1>&2
             gzip -9 <$tmpdir/$HDF5_VERS.tar >$DEST/$HDF5_VERS.tar.gz
-            (cd $DEST; md5sum $HDF5_VERS.tar.gz >> $MD5file)
+            (cd $DEST; sha256sum $HDF5_VERS.tar.gz >> $SHA256)
             ;;
         cmake-tgz)
             test "$verbose" && echo "   Creating CMake tar.gz file..." 1>&2
             tar2cmaketgz $HDF5_VERS $tmpdir/$HDF5_VERS.tar $DEST/CMake-$HDF5_VERS.tar.gz 1>&2
-            (cd $DEST; md5sum CMake-$HDF5_VERS.tar.gz >> $MD5file)
+            (cd $DEST; sha256sum CMake-$HDF5_VERS.tar.gz >> $SHA256)
             ;;
         hpc-cmake-tgz)
             test "$verbose" && echo "   Creating HPC-CMake tar.gz file..." 1>&2
             tar2hpccmaketgz $HDF5_VERS $tmpdir/$HDF5_VERS.tar $DEST/HPC-CMake-$HDF5_VERS.tar.gz 1>&2
-            (cd $DEST; md5sum HPC-CMake-$HDF5_VERS.tar.gz >> $MD5file)
+            (cd $DEST; sha256sum HPC-CMake-$HDF5_VERS.tar.gz >> $SHA256)
             ;;
         bzip2)
             test "$verbose" && echo "   Running bzip2..." 1>&2
             bzip2 -9 <$tmpdir/$HDF5_VERS.tar >$DEST/$HDF5_VERS.tar.bz2
-            (cd $DEST; md5sum $HDF5_VERS.tar.bz2 >> $MD5file)
+            (cd $DEST; sha256sum $HDF5_VERS.tar.bz2 >> $SHA256)
             ;;
         zip)
             test "$verbose" && echo "   Creating zip ball..." 1>&2
             tar2zip $HDF5_VERS $tmpdir/$HDF5_VERS.tar $DEST/$HDF5_VERS.zip 1>&2
-            (cd $DEST; md5sum $HDF5_VERS.zip >> $MD5file)
+            (cd $DEST; sha256sum $HDF5_VERS.zip >> $SHA256)
             ;;
         cmake-zip)
             test "$verbose" && echo "   Creating CMake-zip ball..." 1>&2
             tar2cmakezip $HDF5_VERS $tmpdir/$HDF5_VERS.tar $DEST/CMake-$HDF5_VERS.zip 1>&2
-            (cd $DEST; md5sum CMake-$HDF5_VERS.zip >> $MD5file)
+            (cd $DEST; sha256sum CMake-$HDF5_VERS.zip >> $SHA256)
             ;;
         doc)
             if [ "${DOCVERSION}" = "" ]; then

bin/restore.sh

@@ -1,10 +1,10 @@
 #!/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   
+# 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 COPYING 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

bin/runbkgprog

@@ -5,7 +5,6 @@ $indent=4;
 
 #
 # Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
 # All rights reserved.
 #
 # This file is part of HDF5.  The full HDF5 copyright notice, including

bin/switch_maint_mode

@@ -1,7 +1,6 @@
 #!/bin/sh
 #
 # Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
 # All rights reserved.
 #
 # This file is part of HDF5.  The full HDF5 copyright notice, including

bin/trace

@@ -1,7 +1,6 @@
 #!/usr/bin/env perl
 ##
 # Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
 # All rights reserved.
 #
 # This file is part of HDF5.  The full HDF5 copyright notice, including
@@ -77,7 +76,6 @@ $Source = "";
                "H5G_obj_t"                  => "Go",
                "H5G_stat_t"                 => "Gs",
                "hsize_t"                    => "h",
-               "H5_alloc_stats_t"           => "Ha",
                "H5_atclose_func_t"          => "Hc",
                "hssize_t"                   => "Hs",
                "H5E_major_t"                => "i",     # H5E_major_t is typedef'd to hid_t
@@ -88,6 +86,7 @@ $Source = "";
                "H5_index_t"                 => "Ii",
                "H5I_iterate_func_t"         => "II",
                "H5_iter_order_t"            => "Io",
+               "H5FD_subfiling_ioc_select_t" => "IO",
                "H5I_future_realize_func_t"  => "IR",
                "int"                        => "Is",
                "int32_t"                    => "Is",
@@ -188,6 +187,7 @@ $Source = "";
                "H5Z_filter_t"               => "Zf",
                "H5Z_filter_func_t"          => "ZF",
                "ssize_t"                    => "Zs",
+
 # Types below must be defined here, as they appear in function arguments,
 # but they are not yet supported in the H5_trace_args() routine yet.  If
 # they are used as an actual parameter type (and not just as a pointer to
@@ -198,6 +198,7 @@ $Source = "";
                "H5FD_t"                     => "#",
                "H5FD_hdfs_fapl_t"           => "#",
                "H5FD_mirror_fapl_t"         => "#",
+               "H5FD_onion_fapl_t"         => "#",
                "H5FD_ros3_fapl_t"           => "#",
                "H5FD_splitter_vfd_config_t" => "#",
                "H5L_class_t"                => "#",

bin/warnhist

@@ -8,12 +8,10 @@ use warnings;
 #
 # This file is part of HDF5.  The full HDF5 copyright notice, including
 # terms governing use, modification, and redistribution, is contained in
-# the files COPYING and Copyright.html.  COPYING can be found at the root
-# of the source code distribution tree; Copyright.html can be found at the
-# root level of an installed copy of the electronic HDF5 document set and
-# is linked from the top-level documents page.  It can also be found at
-# http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have
-# access to either file, you may request a copy from help@hdfgroup.org.
+# the COPYING 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
+# help@hdfgroup.org.
 #
 # Quincey Koziol
 #  9 Aug 2013
@@ -229,6 +227,9 @@ while (<>) {
     # Skip variables with the word 'warning' in them
     next if $_ =~ /_warning_/;
 
+    # Skip AMD Optimizing Compiler (aocc) lines "<#> warning(s) generated."
+    next if $_ =~ / warnings? generated\./;
+
     # "Hide" the C++ '::' symbol until we've parsed out the parts of the line
     while($_ =~ /\:\:/) {
 	$_ =~ s/\:\:/@@@@/g;
@@ -244,6 +245,18 @@ while (<>) {
     } elsif($_ =~ /^\s*[Ww]arning:.*/) {
         $name = $last_c_name;
         ($toss, $warning, $extra, $extra2) = split /\:/, $_;
+    # Check for file-scope gcc Fortran warning output
+    } elsif($_ =~ /f\d\d\d: Warning:/) {
+        # These are interspersed with the "compiling a file" output
+        # when compiling with `make -j` and thus difficult to tie to
+        # any particular file. They are due to things like inappropriate
+        # build options and don't have a line number.
+        #
+        # They start with f, as in f951
+        $name = "(generic)";
+        $line = int(rand(1000000)); # Hack to avoid counting as duplictates
+
+        ($warning) = $_ =~ /\[(.*)\]/x;
     # Check for FORTRAN warning output
     } elsif($_ =~ /^Warning:.*/) {
         $name = $last_fort_name;
@@ -382,7 +395,7 @@ while (<>) {
 	    $warning =~ s/"[A-Za-z_0-9]*"/"-"/g;
 	}
 
-	# Genericize [GCC?] C/C++ warning text about suggessted attribute
+	# Genericize [GCC?] C/C++ warning text about suggested attribute
 	if($warning =~ /attribute=[A-Za-z_0-9]*\]/) {
 	    $warning =~ s/=[A-Za-z_0-9]*\]/=-\]/g;
 	}

bin/yodconfigure

@@ -1,76 +0,0 @@
-#!/bin/sh
-#
-# Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
-# 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 COPYING 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
-# help@hdfgroup.org.
-#
-# Fix configure file so that it can launch configure testing executable
-# via the proper launching command, e.g., yod.  (Thus the name yodconfigure
-# is used.)
-#
-# Author: Albert Cheng
-
-if [ "$1" = -f ]; then
-    FORCEMODE=yes
-    echo turn FORCEMODE to $FORCEMODE
-    shift
-fi
-
-if [ $# -ne 1 ]; then
-    echo "Usage: $0 [-f] <configure file>"
-    echo "   -f   apply the change even if it has been applied already."
-    exit 1
-fi
-confile=$1
-
-if [ ! -w $confile ]; then
-    echo "$0: $confile is not writable"
-    exit 1
-fi
-
-ACTRY_NAME="ACTRY()"
-if grep ^"$ACTRY_NAME"$ $confile >/dev/null 2>&1 && [ "$FORCEMODE" != yes ]; then
-    echo "$0: $confile is already yodconfigure ready.  Use -f to force yodconfigure again."
-    exit 1
-fi
-
-# Insert the ACTRY function after the 1st line which is the #!/bin/sh.
-# Change all "eval $ac_try" commands to call ACTRY.
-# auto-configure have changed the ac_try syntax from 'eval $ac_try' to
-# 'eval "$ac_try"'.  Thus requiring two very similar global-substitute.
-# The single quotes around EOF tell shell NOT to expand or do substitution in
-# the body of ed input.
-#
-ed - $confile <<'EOF'
-1a
-# ===inserted by yodconfigure ====
-# ACTRY will figure out when it is approprirate to run the command by the
-# $RUNSERIAL launcher (e.g., yod -sz 1) and when to just run it as is.
-# So far, ./a.out and ./conftest are names of real executable that should
-# be run by $RUNSERIAL.
-#
-# (uncomment the echo line if you want to see what is going on.)
-ACTRY()
-{
-#echo ACTRY: args are: $* > /dev/tty
-if [ "$1" = ./a.out -o "$1" = ./conftest ]; then
-#    echo $RUNSERIAL $* > /dev/tty
-    $RUNSERIAL $*
-else
-    $*
-fi
-}
-# === end of ACTRY inserted by yodconfigure ====
-.
-g/eval $ac_try/s/eval/eval ACTRY/
-g/eval "$ac_try"/s/eval/eval ACTRY/
-w
-q
-EOF

c++/CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required (VERSION 3.12)
+cmake_minimum_required (VERSION 3.18)
 project (HDF5_CPP CXX)
 
 add_subdirectory (src)

c++/Makefile.am

@@ -1,6 +1,5 @@
 #
 # Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
 # All rights reserved.
 #
 # This file is part of HDF5.  The full HDF5 copyright notice, including

c++/examples/CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required (VERSION 3.12)
+cmake_minimum_required (VERSION 3.18)
 project (HDF5_CPP_EXAMPLES CXX)
 
 # --------------------------------------------------------------------
@@ -34,7 +34,7 @@ set (tutr_examples
 
 foreach (example ${examples})
   add_executable (cpp_ex_${example} ${HDF5_CPP_EXAMPLES_SOURCE_DIR}/${example}.cpp)
-  target_include_directories (cpp_ex_${example} PRIVATE "${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_include_directories (cpp_ex_${example} PRIVATE "${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   if (NOT BUILD_SHARED_LIBS)
     TARGET_C_PROPERTIES (cpp_ex_${example} STATIC)
     target_link_libraries (cpp_ex_${example} PRIVATE ${HDF5_CPP_LIB_TARGET} ${HDF5_LIB_TARGET})
@@ -59,7 +59,7 @@ endforeach ()
 
 foreach (example ${tutr_examples})
   add_executable (cpp_ex_${example} ${HDF5_CPP_EXAMPLES_SOURCE_DIR}/${example}.cpp)
-  target_include_directories (cpp_ex_${example} PRIVATE "${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_include_directories (cpp_ex_${example} PRIVATE "${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   if (NOT BUILD_SHARED_LIBS)
     TARGET_C_PROPERTIES (cpp_ex_${example} STATIC)
     target_link_libraries (cpp_ex_${example} PRIVATE ${HDF5_CPP_LIB_TARGET} ${HDF5_LIB_TARGET})

c++/examples/CMakeTests.cmake

@@ -16,17 +16,31 @@
 ##############################################################################
 ##############################################################################
   # Remove any output file left over from previous test run
+set (CPP_EX_CLEANFILES
+    Group.h5
+    SDS.h5
+    SDScompound.h5
+    SDSextendible.h5
+    Select.h5
+)
 add_test (
     NAME CPP_ex-clear-objects
     COMMAND    ${CMAKE_COMMAND}
-        -E remove
-             Group.h5
-             SDS.h5
-             SDScompound.h5
-             SDSextendible.h5
-             Select.h5
+        -E remove ${CPP_EX_CLEANFILES}
+)
+set_tests_properties (CPP_ex-clear-objects PROPERTIES
+    FIXTURES_SETUP clear_cppex
+    WORKING_DIRECTORY ${PROJECT_BINARY_DIR}
+)
+add_test (
+    NAME CPP_ex-clean-objects
+    COMMAND    ${CMAKE_COMMAND}
+        -E remove ${CPP_EX_CLEANFILES}
+)
+set_tests_properties (CPP_ex-clean-objects PROPERTIES
+    FIXTURES_CLEANUP clear_cppex
+    WORKING_DIRECTORY ${PROJECT_BINARY_DIR}
 )
-set_tests_properties (CPP_ex-clear-objects PROPERTIES FIXTURES_SETUP clear_cppex)
 
 foreach (example ${examples})
   if (HDF5_ENABLE_USING_MEMCHECKER)
@@ -41,7 +55,7 @@ foreach (example ${examples})
         -D "TEST_OUTPUT=cpp_ex_${example}.txt"
         #-D "TEST_REFERENCE=cpp_ex_${example}.out"
         -D "TEST_FOLDER=${PROJECT_BINARY_DIR}"
-        -P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake"
+        -P "${HDF_RESOURCES_DIR}/runTest.cmake"
     )
   endif ()
   set_tests_properties (CPP_ex_${example} PROPERTIES FIXTURES_REQUIRED clear_cppex)
@@ -53,19 +67,32 @@ endforeach ()
 #the following dependencies are handled by the order of the files
 #  SET_TESTS_PROPERTIES(CPP_ex_readdata PROPERTIES DEPENDS CPP_ex_create)
 #  SET_TESTS_PROPERTIES(CPP_ex_chunks PROPERTIES DEPENDS CPP_ex_extend_ds)
-
+set (CPP_EX_TUTR_CLEANFILES
+    h5tutr_cmprss.h5
+    h5tutr_dset.h5
+    h5tutr_extend.h5
+    h5tutr_group.h5
+    h5tutr_groups.h5
+    h5tutr_subset.h5
+)
 add_test (
     NAME CPP_ex_tutr-clear-objects
     COMMAND    ${CMAKE_COMMAND}
-        -E remove
-            h5tutr_cmprss.h5
-            h5tutr_dset.h5
-            h5tutr_extend.h5
-            h5tutr_group.h5
-            h5tutr_groups.h5
-            h5tutr_subset.h5
+        -E remove ${CPP_EX_TUTR_CLEANFILES}
+)
+set_tests_properties (CPP_ex_tutr-clear-objects PROPERTIES
+    FIXTURES_SETUP clear_cppex_tutr
+    WORKING_DIRECTORY ${PROJECT_BINARY_DIR}
+)
+add_test (
+    NAME CPP_ex_tutr-clean-objects
+    COMMAND    ${CMAKE_COMMAND}
+        -E remove ${CPP_EX_TUTR_CLEANFILES}
+)
+set_tests_properties (CPP_ex_tutr-clean-objects PROPERTIES
+    FIXTURES_CLEANUP clear_cppex_tutr
+    WORKING_DIRECTORY ${PROJECT_BINARY_DIR}
 )
-set_tests_properties (CPP_ex_tutr-clear-objects PROPERTIES FIXTURES_SETUP clear_cppex_tutr)
 
 foreach (example ${tutr_examples})
   if (HDF5_ENABLE_USING_MEMCHECKER)
@@ -77,10 +104,10 @@ foreach (example ${tutr_examples})
         -D "TEST_ARGS:STRING="
         -D "TEST_EXPECT=0"
         -D "TEST_SKIP_COMPARE=TRUE"
-        -D "TEST_OUTPUT=cpp_ex_${example}.txt"
-        #-D "TEST_REFERENCE=cpp_ex_${example}.out"
+        -D "TEST_OUTPUT=tutr_cpp_ex_${example}.txt"
+        #-D "TEST_REFERENCE=cpp_ex_tutr_${example}.out"
         -D "TEST_FOLDER=${PROJECT_BINARY_DIR}"
-        -P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake"
+        -P "${HDF_RESOURCES_DIR}/runTest.cmake"
     )
   endif ()
   set_tests_properties (CPP_ex_${example} PROPERTIES FIXTURES_REQUIRED clear_cppex_tutr)

c++/examples/Makefile.am

@@ -1,6 +1,5 @@
 #
 # Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
 # All rights reserved.
 #
 # This file is part of HDF5.  The full HDF5 copyright notice, including

c++/examples/chunks.cpp

@@ -1,6 +1,5 @@
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
  * Copyright by The HDF Group.                                               *
- * Copyright by the Board of Trustees of the University of Illinois.         *
  * All rights reserved.                                                      *
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *

c++/examples/compound.cpp

@@ -1,6 +1,5 @@
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
  * Copyright by The HDF Group.                                               *
- * Copyright by the Board of Trustees of the University of Illinois.         *
  * All rights reserved.                                                      *
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *

c++/examples/create.cpp

@@ -1,6 +1,5 @@
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
  * Copyright by The HDF Group.                                               *
- * Copyright by the Board of Trustees of the University of Illinois.         *
  * All rights reserved.                                                      *
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *

c++/examples/extend_ds.cpp

@@ -1,6 +1,5 @@
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
  * Copyright by The HDF Group.                                               *
- * Copyright by the Board of Trustees of the University of Illinois.         *
  * All rights reserved.                                                      *
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *

c++/examples/h5group.cpp

@@ -1,6 +1,5 @@
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
  * Copyright by The HDF Group.                                               *
- * Copyright by the Board of Trustees of the University of Illinois.         *
  * All rights reserved.                                                      *
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
@@ -70,7 +69,7 @@ main(void)
         dims[1]                     = 20;
         cdims[0]                    = 20;
         cdims[1]                    = 20;
-        DataSpace *       dataspace = new DataSpace(RANK, dims); // create new dspace
+        DataSpace        *dataspace = new DataSpace(RANK, dims); // create new dspace
         DSetCreatPropList ds_creatplist;                         // create dataset creation prop list
         ds_creatplist.setChunk(2, cdims);                        // then modify it for compression
         ds_creatplist.setDeflate(6);

c++/examples/h5tutr_cmprss.cpp

@@ -1,6 +1,5 @@
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
  * Copyright by The HDF Group.                                               *
- * Copyright by the Board of Trustees of the University of Illinois.         *
  * All rights reserved.                                                      *
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *

c++/examples/h5tutr_crtatt.cpp

@@ -1,6 +1,5 @@
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
  * Copyright by The HDF Group.                                               *
- * Copyright by the Board of Trustees of the University of Illinois.         *
  * All rights reserved.                                                      *
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *

c++/examples/h5tutr_crtdat.cpp

@@ -1,6 +1,5 @@
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
  * Copyright by The HDF Group.                                               *
- * Copyright by the Board of Trustees of the University of Illinois.         *
  * All rights reserved.                                                      *
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *

c++/examples/h5tutr_crtgrp.cpp

@@ -1,6 +1,5 @@
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
  * Copyright by The HDF Group.                                               *
- * Copyright by the Board of Trustees of the University of Illinois.         *
  * All rights reserved.                                                      *
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *

c++/examples/h5tutr_crtgrpar.cpp

@@ -1,6 +1,5 @@
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
  * Copyright by The HDF Group.                                               *
- * Copyright by the Board of Trustees of the University of Illinois.         *
  * All rights reserved.                                                      *
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *

c++/examples/h5tutr_crtgrpd.cpp

@@ -1,6 +1,5 @@
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
  * Copyright by The HDF Group.                                               *
- * Copyright by the Board of Trustees of the University of Illinois.         *
  * All rights reserved.                                                      *
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *

c++/examples/h5tutr_extend.cpp

@@ -1,6 +1,5 @@
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
  * Copyright by The HDF Group.                                               *
- * Copyright by the Board of Trustees of the University of Illinois.         *
  * All rights reserved.                                                      *
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *

c++/examples/h5tutr_rdwt.cpp

@@ -1,6 +1,5 @@
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
  * Copyright by The HDF Group.                                               *
- * Copyright by the Board of Trustees of the University of Illinois.         *
  * All rights reserved.                                                      *
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *

c++/examples/h5tutr_subset.cpp

@@ -1,6 +1,5 @@
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
  * Copyright by The HDF Group.                                               *
- * Copyright by the Board of Trustees of the University of Illinois.         *
  * All rights reserved.                                                      *
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *

c++/examples/readdata.cpp

@@ -1,6 +1,5 @@
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
  * Copyright by The HDF Group.                                               *
- * Copyright by the Board of Trustees of the University of Illinois.         *
  * All rights reserved.                                                      *
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *

c++/examples/run-c++-ex.sh.in

@@ -40,16 +40,16 @@ EXIT_FAILURE=1
 # This script uses the value of `prefix` in the user's environment, if
 # it is set, below.  The content of $() is evaluated in a sub-shell, so
 # if `prefix` is set in the user's environment, the shell statements in
-# $() won't clobbered it.
+# $() won't clobber it.
 #
 prefix_relto_examplesdir=$(
 prefix=@prefix@
 examplesdir=@examplesdir@
 if [ ${examplesdir##${prefix}/} != ${examplesdir} ]; then
-	echo $(echo ${examplesdir##${prefix}/} | \
-	    sed 's,[^/][^/]*,..,g')
+    echo $(echo ${examplesdir##${prefix}/} | \
+        sed 's,[^/][^/]*,..,g')
 else
-	echo $prefix
+    echo $prefix
 fi
 )
 

c++/examples/testh5c++.sh.in

@@ -1,7 +1,6 @@
 #! /bin/sh
 #
 # Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
 # All rights reserved.
 #
 # This file is part of HDF5.  The full HDF5 copyright notice, including

c++/examples/writedata.cpp

@@ -1,6 +1,5 @@
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
  * Copyright by The HDF Group.                                               *
- * Copyright by the Board of Trustees of the University of Illinois.         *
  * All rights reserved.                                                      *
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *

c++/src/C2Cppfunction_map.htm

@@ -10402,13 +10402,13 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
   normal'>void H5Location::moveLink(const char* src_name,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-spacerun:yes'>            </span>const Group&amp;
+  normal'><span style='mso-spacerun:yes'>            </span>const Group&amp;
   dst, const char* dst_name,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-spacerun:yes'>            </span>const
+  normal'><span style='mso-spacerun:yes'>            </span>const
   LinkCreatPropList&amp; lcpl = LinkCreatPropList::DEFAULT,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-spacerun:yes'>            </span>const
+  normal'><span style='mso-spacerun:yes'>            </span>const
   LinkAccPropList&amp; lapl = LinkAccPropList::DEFAULT)</p>
   </td>
   <td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -10441,13 +10441,13 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
   normal'>void H5Location::moveLink(const H5std_string&amp; src_name,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-spacerun:yes'>            </span>const Group&amp;
+  normal'><span style='mso-spacerun:yes'>            </span>const Group&amp;
   dst, const H5std_string&amp; dst_name,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-spacerun:yes'>            </span>const
+  normal'><span style='mso-spacerun:yes'>            </span>const
   LinkCreatPropList&amp; lcpl = LinkCreatPropList::DEFAULT,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-spacerun:yes'>            </span>const
+  normal'><span style='mso-spacerun:yes'>            </span>const
   LinkAccPropList&amp; lapl = LinkAccPropList::DEFAULT)</p>
   </td>
   <td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -10480,10 +10480,10 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
   normal'>void H5Location::moveLink(const char* src_name, const char* dst_name,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-spacerun:yes'>            </span>const
+  normal'><span style='mso-spacerun:yes'>            </span>const
   LinkCreatPropList&amp; lcpl = LinkCreatPropList::DEFAULT,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-spacerun:yes'>            </span>const
+  normal'><span style='mso-spacerun:yes'>            </span>const
   LinkAccPropList&amp; lapl = LinkAccPropList::DEFAULT)</p>
   </td>
   <td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -10516,13 +10516,13 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
   normal'>void H5Location::moveLink(const H5std_string&amp; src_name,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-spacerun:yes'>            </span>const
+  normal'><span style='mso-spacerun:yes'>            </span>const
   H5std_string&amp; dst_name,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-spacerun:yes'>            </span>const
+  normal'><span style='mso-spacerun:yes'>            </span>const
   LinkCreatPropList&amp; lcpl = LinkCreatPropList::DEFAULT,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-spacerun:yes'>            </span>const
+  normal'><span style='mso-spacerun:yes'>            </span>const
   LinkAccPropList&amp; lapl = LinkAccPropList::DEFAULT)</p>
   </td>
   <td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -10693,7 +10693,7 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
   normal'>const LinkCreatPropList&amp; lcpl = LinkCreatPropList::DEFAULT,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'>const<span style='mso-spacerun:yes'>  </span>LinkAccPropList&amp;
+  normal'>const<span style='mso-spacerun:yes'>  </span>LinkAccPropList&amp;
   lapl = LinkAccPropList::DEFAULT) </p>
   </td>
   <td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -10770,13 +10770,13 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
   normal'>void H5Location::link(const char *curr_name,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-spacerun:yes'>             </span>const Group&amp;
+  normal'><span style='mso-spacerun:yes'>             </span>const Group&amp;
   new_loc, const char *new_name,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-spacerun:yes'>             </span>const
+  normal'><span style='mso-spacerun:yes'>             </span>const
   LinkCreatPropList&amp; lcpl = LinkCreatPropList::DEFAULT,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-spacerun:yes'>             </span>const
+  normal'><span style='mso-spacerun:yes'>             </span>const
   LinkAccPropList&amp; lapl = LinkAccPropList::DEFAULT)</p>
   </td>
   <td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -10809,13 +10809,13 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
   normal'>void H5Location::link(const H5std_string&amp; curr_name,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-spacerun:yes'>             </span>const Group&amp;
+  normal'><span style='mso-spacerun:yes'>             </span>const Group&amp;
   new_loc, const H5std_string&amp; new_name,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-spacerun:yes'>             </span>const
+  normal'><span style='mso-spacerun:yes'>             </span>const
   LinkCreatPropList&amp; lcpl = LinkCreatPropList::DEFAULT,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-spacerun:yes'>             </span>const
+  normal'><span style='mso-spacerun:yes'>             </span>const
   LinkAccPropList&amp; lapl = LinkAccPropList::DEFAULT)</p>
   </td>
   <td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -10848,13 +10848,13 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
   normal'>void H5Location::link(const char *curr_name,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-spacerun:yes'>             </span>const hid_t
+  normal'><span style='mso-spacerun:yes'>             </span>const hid_t
   same_loc, const char *new_name,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-spacerun:yes'>             </span>const
+  normal'><span style='mso-spacerun:yes'>             </span>const
   LinkCreatPropList&amp; lcpl = LinkCreatPropList::DEFAULT,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-spacerun:yes'>             </span>const
+  normal'><span style='mso-spacerun:yes'>             </span>const
   LinkAccPropList&amp; lapl = LinkAccPropList::DEFAULT)</p>
   </td>
   <td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -10887,13 +10887,13 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
   normal'>void H5Location::link(const H5std_string&amp; curr_name,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-spacerun:yes'>             </span>const hid_t
+  normal'><span style='mso-spacerun:yes'>             </span>const hid_t
   same_loc, const H5std_string&amp; new_name,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-spacerun:yes'>             </span>const
+  normal'><span style='mso-spacerun:yes'>             </span>const
   LinkCreatPropList&amp; lcpl = LinkCreatPropList::DEFAULT,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-spacerun:yes'>             </span>const
+  normal'><span style='mso-spacerun:yes'>             </span>const
   LinkAccPropList&amp; lapl = LinkAccPropList::DEFAULT)</p>
   </td>
   <td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -10932,10 +10932,10 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
   normal'>void H5Location::link(const char *target_name, const char *link_name,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-spacerun:yes'>             </span>const
+  normal'><span style='mso-spacerun:yes'>             </span>const
   LinkCreatPropList&amp; lcpl = LinkCreatPropList::DEFAULT,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-spacerun:yes'>             </span>const
+  normal'><span style='mso-spacerun:yes'>             </span>const
   LinkAccPropList&amp; lapl = LinkAccPropList::DEFAULT)</p>
   </td>
   <td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -10968,13 +10968,13 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
   normal'>void H5Location::link(const H5std_string&amp; target_name,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-spacerun:yes'>             </span>const
+  normal'><span style='mso-spacerun:yes'>             </span>const
   H5std_string&amp; link_name,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-spacerun:yes'>             </span>const
+  normal'><span style='mso-spacerun:yes'>             </span>const
   LinkCreatPropList&amp; lcpl = LinkCreatPropList::DEFAULT,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-spacerun:yes'>             </span>const
+  normal'><span style='mso-spacerun:yes'>             </span>const
   LinkAccPropList&amp; lapl = LinkAccPropList::DEFAULT)</p>
   </td>
   <td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -11085,7 +11085,7 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
   normal'>void CommonFG::unlink( const char* name,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-spacerun:yes'>             </span>const
+  normal'><span style='mso-spacerun:yes'>             </span>const
   LinkAccPropList&amp; lapl = LinkAccPropList::DEFAULT)</p>
   </td>
   <td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -11119,7 +11119,7 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
   normal'>void CommonFG::unlink( const H5std_string&amp; name,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-spacerun:yes'>             </span>const
+  normal'><span style='mso-spacerun:yes'>             </span>const
   LinkAccPropList&amp; lapl = LinkAccPropList::DEFAULT)</p>
   </td>
   <td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -11153,7 +11153,7 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
   normal'>void H5Location::unlink( const char* name,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-spacerun:yes'>             </span>const
+  normal'><span style='mso-spacerun:yes'>             </span>const
   LinkAccPropList&amp; lapl = LinkAccPropList::DEFAULT)</p>
   </td>
   <td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -11187,7 +11187,7 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
   normal'>void H5Location::unlink( const H5std_string&amp; name,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-spacerun:yes'>             </span>const LinkAccPropList&amp;
+  normal'><span style='mso-spacerun:yes'>             </span>const LinkAccPropList&amp;
   lapl = LinkAccPropList::DEFAULT)</p>
   </td>
   <td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -11495,7 +11495,7 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
   normal'>H5L_info2_t getLinkInfo(const char* link_name,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-tab-count:1'>               </span>const
+  normal'><span style='mso-tab-count:1'>               </span>const
   LinkAccPropList&amp; lapl = LinkAccPropList::DEFAULT)</p>
   </td>
   <td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -11528,7 +11528,7 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
   normal'>H5L_info2_t getLinkInfo(const H5std_string&amp; link_name,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-tab-count:1'>               </span>const
+  normal'><span style='mso-tab-count:1'>               </span>const
   LinkAccPropList&amp; lapl = LinkAccPropList::DEFAULT)</p>
   </td>
   <td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -14522,7 +14522,7 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
   normal'>void DSetCreatPropList::setFilter(H5Z_filter_t filter_id, unsigned
   int flags,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-spacerun:yes'>        </span>size_t cd_nelmts, const
+  normal'><span style='mso-spacerun:yes'>        </span>size_t cd_nelmts, const
   unsigned int cd_values[])</p>
   </td>
   <td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -14597,10 +14597,10 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
   normal'>H5Z_filter_t DSetCreatPropList::getFilter(int filter_number,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-spacerun:yes'>        </span>unsigned int
+  normal'><span style='mso-spacerun:yes'>        </span>unsigned int
   &amp;flags, size_t &amp;cd_nelmts, unsigned int* cd_values,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-spacerun:yes'>        </span>size_t namelen, char
+  normal'><span style='mso-spacerun:yes'>        </span>size_t namelen, char
   name[], unsigned int&amp; filter_config)</p>
   </td>
   <td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -14639,10 +14639,10 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
   normal'>void DSetCreatPropList::getFilterById(H5Z_filter_t filter_id,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-spacerun:yes'>        </span>unsigned int
+  normal'><span style='mso-spacerun:yes'>        </span>unsigned int
   &amp;flags, size_t &amp;cd_nelmts, unsigned int* cd_values,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-spacerun:yes'>        </span>size_t namelen, char
+  normal'><span style='mso-spacerun:yes'>        </span>size_t namelen, char
   name[], unsigned int &amp;filter_config)</p>
   </td>
   <td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
@@ -19291,10 +19291,10 @@ normal'><span style='font-size:14.0pt;mso-bidi-font-size:11.0pt;line-height:
   normal'>void H5Library::setFreeListLimits(int reg_global_lim, int
   reg_list_lim,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-spacerun:yes'>        </span>int arr_global_lim, int
+  normal'><span style='mso-spacerun:yes'>        </span>int arr_global_lim, int
   arr_list_lim, int blk_global_lim,</p>
   <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
-  normal'><span style='mso-spacerun:yes'>        </span>int blk_list_lim)</p>
+  normal'><span style='mso-spacerun:yes'>        </span>int blk_list_lim)</p>
   </td>
   <td width=35 valign=top style='width:26.05pt;border-top:none;border-left:
   none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;

c++/src/CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required (VERSION 3.12)
+cmake_minimum_required (VERSION 3.18)
 project (HDF5_CPP_SRC CXX)
 
 #-----------------------------------------------------------------------------
@@ -80,7 +80,7 @@ set (CPP_HDRS
 if (NOT ONLY_SHARED_LIBS)
   add_library (${HDF5_CPP_LIB_TARGET} STATIC ${CPP_SOURCES} ${CPP_HDRS})
   target_include_directories (${HDF5_CPP_LIB_TARGET}
-      PRIVATE "${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>"
+      PRIVATE "${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>"
       INTERFACE "$<INSTALL_INTERFACE:$<INSTALL_PREFIX>/include>"
   )
   target_compile_options(${HDF5_CPP_LIB_TARGET} PRIVATE "${HDF5_CMAKE_CXX_FLAGS}")
@@ -98,7 +98,7 @@ endif ()
 if (BUILD_SHARED_LIBS)
   add_library (${HDF5_CPP_LIBSH_TARGET} SHARED ${CPP_SOURCES} ${CPP_HDRS})
   target_include_directories (${HDF5_CPP_LIBSH_TARGET}
-      PRIVATE "${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>"
+      PRIVATE "${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>"
       INTERFACE "$<INSTALL_INTERFACE:$<INSTALL_PREFIX>/include>"
   )
   target_compile_options(${HDF5_CPP_LIBSH_TARGET} PRIVATE "${HDF5_CMAKE_CXX_FLAGS}")
@@ -173,8 +173,8 @@ endif ()
 #-----------------------------------------------------------------------------
 set (_PKG_CONFIG_PREFIX ${CMAKE_INSTALL_PREFIX})
 set (_PKG_CONFIG_EXEC_PREFIX \${prefix})
-set (_PKG_CONFIG_LIBDIR \${exec_prefix}/lib)
-set (_PKG_CONFIG_INCLUDEDIR \${prefix}/include)
+set (_PKG_CONFIG_LIBDIR \${exec_prefix}/${HDF5_INSTALL_LIB_DIR})
+set (_PKG_CONFIG_INCLUDEDIR \${prefix}/${HDF5_INSTALL_INCLUDE_DIR})
 set (_PKG_CONFIG_LIBNAME "${HDF5_CPP_LIB_CORENAME}")
 set (_PKG_CONFIG_VERSION "${HDF5_PACKAGE_VERSION}")
 
@@ -187,8 +187,8 @@ if (BUILD_SHARED_LIBS)
   set (_PKG_CONFIG_SH_LIBS "${_PKG_CONFIG_SH_LIBS} -l${HDF5_CPP_LIB_CORENAME}")
 endif ()
 
-set (_PKG_CONFIG_REQUIRES "${HDF5_LIB_CORENAME}-${HDF5_PACKAGE_VERSION}")
-set (_PKG_CONFIG_REQUIRES_PRIVATE "${HDF5_LIB_CORENAME}-${HDF5_PACKAGE_VERSION}")
+set (_PKG_CONFIG_REQUIRES "${HDF5_LIB_CORENAME} = ${HDF5_PACKAGE_VERSION}")
+set (_PKG_CONFIG_REQUIRES_PRIVATE "${HDF5_LIB_CORENAME} = ${HDF5_PACKAGE_VERSION}")
 
 configure_file (
     ${HDF_CONFIG_DIR}/libhdf5.pc.in

c++/src/H5AbstractDs.cpp

@@ -1,6 +1,5 @@
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
  * Copyright by The HDF Group.                                               *
- * Copyright by the Board of Trustees of the University of Illinois.         *
  * All rights reserved.                                                      *
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *

c++/src/H5AbstractDs.h

@@ -1,7 +1,6 @@
 // C++ informative line for the emacs editor: -*- C++ -*-
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
  * Copyright by The HDF Group.                                               *
- * Copyright by the Board of Trustees of the University of Illinois.         *
  * All rights reserved.                                                      *
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *

c++/src/H5Alltypes.h

@@ -1,7 +1,6 @@
 // C++ informative line for the emacs editor: -*- C++ -*-
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
  * Copyright by The HDF Group.                                               *
- * Copyright by the Board of Trustees of the University of Illinois.         *
  * All rights reserved.                                                      *
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *