VFD SWMR: Merges from develop (#1670)

* Cleans up SWMR test scripts (both legacy and VFD)

* Brings over format source changes for Java

* Normalization of HL, Fortran, C++, Java w/ develop

* Removes the STATIC flavor of FUNC_ENTER macros (#1622)

* Removes the STATIC flavor of FUNC_ENTER macros

* Remove H5_NO_ALIGNMENT_RESTRICTIONS (#1426)

* Do not conditionally compile code that uses a pointer dereference
and assignment to copy a potentially unaligned variable to aligned
automatic storage, or vice versa.  Instead, always use naked `memcpy(3)`s.
Disassembling the generated code reveals that the `memcpy(3)`s optimize
(`-O3`) to a single `mov` instruction for x86_64, which is not strict
about alignment.

This change reduces the size of code and scripts by 143 lines, eases
our way to cross-compilation, and avoids invoking undefined behavior.

* Committing clang-format changes

* Per discussion, use HD and add comments.

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

* Removes unused definitions from module headers (#1624)

* Misc stuff from develop (includes some parallel things)

* Brings over SWMR test quiet mode changes from develop

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

.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/workflows/clang-format-check.yml

@@ -8,11 +8,11 @@ jobs:
     if: "!contains(github.event.head_commit.message, 'skip-ci')"
     steps:
     - uses: actions/checkout@v2
-    - name: Run clang-format style check for C programs.
+    - name: Run clang-format style check for C and java programs.
       uses: DoozyX/[email protected]
       with:
         source: '.'
-        extensions: 'c,h,cpp,hpp'
+        extensions: 'c,h,cpp,hpp,java'
         clangFormatVersion: 10
         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

@@ -9,11 +9,11 @@ jobs:
     if: "!contains(github.event.head_commit.message, 'skip-ci')"
     steps:
     - uses: actions/checkout@v2
-    - name: Run clang-format style check for C programs.
+    - name: Run clang-format style check for C and Java programs.
       uses: DoozyX/[email protected]
       with:
         source: '.'
-        extensions: 'c,h,cpp,hpp'
+        extensions: 'c,h,cpp,hpp,java'
         clangFormatVersion: 10
         inplace: True
         style: file

.github/workflows/codespell.yml

@@ -12,4 +12,4 @@ jobs:
       - 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
+          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

.github/workflows/main.yml

@@ -9,6 +9,9 @@ on:
     - '.github/**'
     - 'doc/**'
     - 'release_docs/**'
+    - 'ACKNOWLEDGEMENTS'
+    - 'COPYING**'
+    - '**.md'
 
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:

.github/workflows/pr-check.yml

@@ -1,10 +1,17 @@
-name: hdf5 dev CI
+name: PR 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, feature/vfd_swmr ]
-
+    paths-ignore:
+    - '.github/**'
+    - 'doc/**'
+    - 'release_docs/**'
+    - 'ACKNOWLEDGEMENTS'
+    - 'COPYING**'
+    - '**.md'
+
 # 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"

autogen.sh

@@ -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
 
@@ -86,22 +73,13 @@ while getopts "$optspec" optchar; do
         echo
         echo "      -h      Print this help message."
         echo
-        echo "      -p      Used by THG to use hard-codes autotools"
-        echo "              paths on THG machines. Not for non-HDF-Group"
-        echo "              users!"
-        echo
         echo "      -v      Show more verbose output."
         echo
         echo "  NOTE: Each tool can be set via an environment variable."
         echo "        These are documented inside this autogen.sh script."
         echo
         exit 0
         ;;
-    p)
-        echo "Setting THG production mode..."
-        echo
-        production=true
-        ;;
     v)
         echo "Setting verbosity: high"
         echo
@@ -117,84 +95,52 @@ while getopts "$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
@@ -291,7 +237,7 @@ echo
 
 # AUTOCONF
 autoconf_cmd="${HDF5_AUTOCONF} --force"
-echo ${autoconf_cmd}
+echo "${autoconf_cmd}"
 if [ "$verbose" = true ] ; then
     ${HDF5_AUTOCONF} --version
 fi

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

@@ -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
 
 git diff > clang_format.patch

bin/h5cc.in

@@ -40,7 +40,7 @@ HL="@HL@"
 ##    $CLINKER $H5BLD_CPPFLAGS $CPPFLAGS $H5BLD_CFLAGS $CFLAGS $LDFLAGS   ##
 ##    $LIBS $clibpath $link_objs $link_args $shared_link                  ##
 ##                                                                        ##
-## These settings can be overridden by setting HDF5_CFLAGS,                ##
+## These settings can be overridden by setting HDF5_CFLAGS,               ##
 ## HDF5_CPPFLAGS, HDF5_LDFLAGS, or HDF5_LIBS in the environment.          ##
 ##                                                                        ##
 ############################################################################

bin/make_vers

@@ -6,7 +6,7 @@ use warnings;
 # (The max_idx parameter is the only thing that needs to be changed when adding
 #       support for a new major release.  If support for a prior major release
 #       is added (like support for 1.4, etc), the min_sup_idx parameter will
-#       need to be decremented. - QAK)
+#       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;

bin/restore.sh

@@ -48,6 +48,9 @@ rm -f bin/missing
 rm -f bin/test-driver
 rm -f bin/depcomp
 
+echo "Remove files generated by autoheader"
+rm -f src/H5config.h.in
+
 echo "Remove files generated by bin/make_err"
 rm -f src/H5Epubgen.h
 rm -f src/H5Einit.h

c++/src/H5Attribute.cpp

@@ -11,6 +11,7 @@
  * [email protected].                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
+#include <cstdlib>
 #include <iostream>
 #include <string>