Merge remote-tracking branch 'origin/develop' into h5e_refactor

qkoziol · May 3, 2024 · 4eaadb7 · 4eaadb7
2 parents a5dcea4 + e4f079e
commit 4eaadb7
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Showing 39 changed files with 407 additions and 1,152 deletions.
diff --git a/.github/workflows/abi-report.yml b/.github/workflows/abi-report.yml
@@ -46,7 +46,7 @@ jobs:
       - uses: actions/[email protected]
 
       - name: Get published binary (Linux)
-        uses: actions/download-artifact@c850b930e6ba138125429b7e5c93fc707a7f8427 # v4.1.4
+        uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
         with:
             name: tgz-ubuntu-2204_gcc-binary
             path: ${{ github.workspace }}

diff --git a/.github/workflows/cmake-bintest.yml b/.github/workflows/cmake-bintest.yml
@@ -35,7 +35,7 @@ jobs:
 
       # Get files created by cmake-ctest script
       - name: Get published binary (Windows)
-        uses: actions/download-artifact@c850b930e6ba138125429b7e5c93fc707a7f8427 # v4.1.4
+        uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
         with:
               name: zip-vs2022_cl-${{ inputs.build_mode }}-binary
               path: ${{ github.workspace }}/hdf5
@@ -109,7 +109,7 @@ jobs:
           distribution: 'temurin'
 
       - name: Get published binary (Linux)
-        uses: actions/download-artifact@c850b930e6ba138125429b7e5c93fc707a7f8427 # v4.1.4
+        uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
         with:
               name: tgz-ubuntu-2204_gcc-${{ inputs.build_mode }}-binary
               path: ${{ github.workspace }}
@@ -161,7 +161,7 @@ jobs:
           distribution: 'temurin'
 
       - name: Get published binary (MacOS)
-        uses: actions/download-artifact@c850b930e6ba138125429b7e5c93fc707a7f8427 # v4.1.4
+        uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
         with:
               name: tgz-osx12-${{ inputs.build_mode }}-binary
               path: ${{ github.workspace }}

diff --git a/.github/workflows/cmake-ctest.yml b/.github/workflows/cmake-ctest.yml
@@ -62,7 +62,7 @@ jobs:
 
       # Get files created by release script
       - name: Get zip-tarball (Windows)
-        uses: actions/download-artifact@c850b930e6ba138125429b7e5c93fc707a7f8427 # v4.1.4
+        uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
         with:
               name: zip-tarball
               path: ${{ github.workspace }}
@@ -146,7 +146,7 @@ jobs:
 
       # Get files created by release script
       - name: Get tgz-tarball (Linux)
-        uses: actions/download-artifact@c850b930e6ba138125429b7e5c93fc707a7f8427 # v4.1.4
+        uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
         with:
               name: tgz-tarball
               path: ${{ github.workspace }}
@@ -270,7 +270,7 @@ jobs:
 
       # Get files created by release script
       - name: Get tgz-tarball (MacOS)
-        uses: actions/download-artifact@c850b930e6ba138125429b7e5c93fc707a7f8427 # v4.1.4
+        uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
         with:
               name: tgz-tarball
               path: ${{ github.workspace }}
@@ -351,7 +351,7 @@ jobs:
 
       # Get files created by release script
       - name: Get tgz-tarball (Linux S3)
-        uses: actions/download-artifact@c850b930e6ba138125429b7e5c93fc707a7f8427 # v4.1.4
+        uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
         with:
               name: tgz-tarball
               path: ${{ github.workspace }}
@@ -432,7 +432,7 @@ jobs:
 
       # Get files created by release script
       - name: Get zip-tarball (Windows_intel)
-        uses: actions/download-artifact@c850b930e6ba138125429b7e5c93fc707a7f8427 # v4.1.4
+        uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
         with:
               name: zip-tarball
               path: ${{ github.workspace }}
@@ -522,7 +522,7 @@ jobs:
 
       # Get files created by release script
       - name: Get tgz-tarball (Linux_intel)
-        uses: actions/download-artifact@c850b930e6ba138125429b7e5c93fc707a7f8427 # v4.1.4
+        uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
         with:
               name: tgz-tarball
               path: ${{ github.workspace }}

diff --git a/.github/workflows/nvhpc-cmake.yml b/.github/workflows/nvhpc-cmake.yml
@@ -59,6 +59,7 @@ jobs:
           -DHDF5_BUILD_FORTRAN:BOOL=ON \
           -DHDF5_BUILD_JAVA:BOOL=OFF \
           -DMPIEXEC_MAX_NUMPROCS:STRING="2" \
+          -DMPIEXEC_PREFLAGS:STRING="--mca;opal_warn_on_missing_libcuda;0" \
           $GITHUB_WORKSPACE
 
       - name: CMake Build

diff --git a/.github/workflows/release-files.yml b/.github/workflows/release-files.yml
@@ -73,7 +73,7 @@ jobs:
 
       # Get files created by tarball script
       - name: Get doxygen (Linux)
-        uses: actions/download-artifact@c850b930e6ba138125429b7e5c93fc707a7f8427 # v4.1.4
+        uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
         with:
               name: docs-doxygen
               path: ${{ github.workspace }}/${{ steps.get-file-base.outputs.FILE_BASE }}.doxygen
@@ -82,68 +82,68 @@ jobs:
         run: zip -r ${{ steps.get-file-base.outputs.FILE_BASE }}.doxygen.zip ./${{ steps.get-file-base.outputs.FILE_BASE }}.doxygen
 
       - name: Get tgz-tarball (Linux)
-        uses: actions/download-artifact@c850b930e6ba138125429b7e5c93fc707a7f8427 # v4.1.4
+        uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
         with:
               name: tgz-tarball
               path: ${{ github.workspace }}
 
       - name: Get zip-tarball (Windows)
-        uses: actions/download-artifact@c850b930e6ba138125429b7e5c93fc707a7f8427 # v4.1.4
+        uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
         with:
               name: zip-tarball
               path: ${{ github.workspace }}
 
       # Get files created by cmake-ctest script
       - name: Get published binary (Windows)
-        uses: actions/download-artifact@c850b930e6ba138125429b7e5c93fc707a7f8427 # v4.1.4
+        uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
         with:
               name: zip-vs2022_cl-binary
               path: ${{ github.workspace }}
 
       - name: Get published binary (MacOS)
-        uses: actions/download-artifact@c850b930e6ba138125429b7e5c93fc707a7f8427 # v4.1.4
+        uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
         with:
               name: tgz-osx12-binary
               path: ${{ github.workspace }}
 
       - name: Get published binary (Linux)
-        uses: actions/download-artifact@c850b930e6ba138125429b7e5c93fc707a7f8427 # v4.1.4
+        uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
         with:
               name: tgz-ubuntu-2204_gcc-binary
               path: ${{ github.workspace }}
 
       - name: Get published deb binary (Linux)
-        uses: actions/download-artifact@c850b930e6ba138125429b7e5c93fc707a7f8427 # v4.1.4
+        uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
         with:
               name: deb-ubuntu-2204_gcc-binary
               path: ${{ github.workspace }}
 
       - name: Get published rpm binary (Linux)
-        uses: actions/download-artifact@c850b930e6ba138125429b7e5c93fc707a7f8427 # v4.1.4
+        uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
         with:
               name: rpm-ubuntu-2204_gcc-binary
               path: ${{ github.workspace }}
 
       - name: Get published binary (Linux S3)
-        uses: actions/download-artifact@c850b930e6ba138125429b7e5c93fc707a7f8427 # v4.1.4
+        uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
         with:
               name: tgz-ubuntu-2204_gcc_s3-binary
               path: ${{ github.workspace }}
 
       - name: Get published binary (Windows_intel)
-        uses: actions/download-artifact@c850b930e6ba138125429b7e5c93fc707a7f8427 # v4.1.4
+        uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
         with:
               name: zip-vs2022_intel-binary
               path: ${{ github.workspace }}
 
       - name: Get published binary (Linux_intel)
-        uses: actions/download-artifact@c850b930e6ba138125429b7e5c93fc707a7f8427 # v4.1.4
+        uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
         with:
               name: tgz-ubuntu-2204_intel-binary
               path: ${{ github.workspace }}
 
       - name: Get published abi reports (Linux)
-        uses: actions/download-artifact@c850b930e6ba138125429b7e5c93fc707a7f8427 # v4.1.4
+        uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
         with:
               name: abi-reports
               path: ${{ github.workspace }}
@@ -168,7 +168,7 @@ jobs:
           echo "${{ steps.get-file-base.outputs.FILE_BASE }}" > ./last-file.txt
 
       - name: Get NEWSLETTER
-        uses: actions/download-artifact@c850b930e6ba138125429b7e5c93fc707a7f8427 # v4.1.4
+        uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
         with:
               name: NEWSLETTER
               path: ${{ github.workspace }}
@@ -232,7 +232,7 @@ jobs:
               ls ${{ runner.workspace }}
 
       - name: dev-only-docs
-        uses: peaceiris/actions-gh-pages@373f7f263a76c20808c831209c920827a82a2847 # v3.9.3
+        uses: peaceiris/actions-gh-pages@4f9cc6602d3f66b9c108549d475ec49e8ef4d45e # v4.0.0
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: ${{ github.workspace }}/${{ steps.get-file-base.outputs.FILE_BASE }}.doxygen

diff --git a/.github/workflows/scorecard.yml b/.github/workflows/scorecard.yml
@@ -67,6 +67,6 @@ jobs:
 
       # Upload the results to GitHub's code scanning dashboard.
       - name: "Upload to code-scanning"
-        uses: github/codeql-action/upload-sarif@1b1aada464948af03b950897e5eb522f92603cc2 # v3.24.9
+        uses: github/codeql-action/upload-sarif@d39d31e687223d841ef683f52467bd88e9b21c14 # v3.25.3
         with:
           sarif_file: results.sarif
diff --git a/bin/trace b/bin/trace
@@ -307,14 +307,12 @@ sub rewrite_func ($$$$$) {
         # First remove:
         #   * /*in*/, /*out*/, /*in_out*/, and /*in,out*/ comments
         #   * preprocessor lines that start with #
-        #   * H5FL_TRACKING_PARAMS macros (free list code only)
         #
         # then split the function arguments on commas
         $args =~ s/\/\*\s*in\s*\*\///g;  # Get rid of /*in*/
         $args =~ s/\/\*\s*out\s*\*\///g; # Get rid of /*out*/
         $args =~ s/\/\*\s*in,\s*out\s*\*\///g; # Get rid of /*in,out*/
         $args =~ s/\/\*\s*in_out\s*\*\///g; # Get rid of /*in_out*/
-        $args =~ s/H5FL_TRACK_PARAMS//g; # Remove free list macro
         $args =~ s/\n#.*?\n/\n/g;        # Remove lines beginning with '#'
         my @args = split /,[\s\n]*/, $args;
         my $argno = 0;

diff --git a/config/cmake/ConfigureChecks.cmake b/config/cmake/ConfigureChecks.cmake
@@ -495,16 +495,6 @@ if (HDF5_WANT_DCONV_EXCEPTION)
 endif ()
 MARK_AS_ADVANCED (HDF5_WANT_DCONV_EXCEPTION)
 
-# ----------------------------------------------------------------------
-# Check if they would like the function stack support compiled in
-#-----------------------------------------------------------------------------
-option (HDF5_ENABLE_CODESTACK "Enable the function stack tracing (for developer debugging)." OFF)
-mark_as_advanced (HDF5_ENABLE_CODESTACK)
-if (HDF5_ENABLE_CODESTACK)
-  set (${HDF_PREFIX}_HAVE_CODESTACK 1)
-endif ()
-MARK_AS_ADVANCED (HDF5_ENABLE_CODESTACK)
-
 # ----------------------------------------------------------------------
 # Check if they would like to show all warnings (not suppressed internally)
 #-----------------------------------------------------------------------------

diff --git a/config/cmake/H5pubconf.h.in b/config/cmake/H5pubconf.h.in
@@ -110,9 +110,6 @@
 /* Define to 1 if CLOCK_MONOTONIC_COARSE is available */
 #cmakedefine H5_HAVE_CLOCK_MONOTONIC_COARSE @H5_HAVE_CLOCK_MONOTONIC_COARSE@
 
-/* Define if the function stack tracing code is to be compiled in */
-#cmakedefine H5_HAVE_CODESTACK @H5_HAVE_CODESTACK@
-
 /* Define to 1 if you have the <curl/curl.h> header file. */
 #cmakedefine H5_HAVE_CURL_CURL_H @H5_HAVE_CURL_H@
 

diff --git a/config/cmake/HDF5DeveloperBuild.cmake b/config/cmake/HDF5DeveloperBuild.cmake
@@ -157,17 +157,6 @@ if (HDF5_ENABLE_DEBUG_H5C_SANITY_CHECKS)
   # list (APPEND HDF5_DEBUG_APIS H5C_DO_MEMORY_SANITY_CHECKS=1)
 endif ()
 
-option (HDF5_ENABLE_DEBUG_H5FL_TRACK "Enable tracking of free list allocations" OFF)
-mark_as_advanced (HDF5_ENABLE_DEBUG_H5FL_TRACK)
-if (HDF5_ENABLE_DEBUG_H5FL_TRACK)
-  list (APPEND HDF5_DEBUG_APIS H5FL_TRACK)
-
-  # Free list tracking requires the codestack functionality
-  set (HDF5_ENABLE_CODESTACK ON CACHE BOOL "Enable the function stack tracing (for developer debugging)." FORCE)
-else ()
-  unset (HDF5_ENABLE_CODESTACK CACHE)
-endif ()
-
 option (HDF5_ENABLE_DEBUG_H5FS_ASSERT "Enable extra debugging of H5FS module" OFF)
 mark_as_advanced (HDF5_ENABLE_DEBUG_H5FS_ASSERT)
 if (HDF5_ENABLE_DEBUG_H5FS_ASSERT)
@@ -178,7 +167,7 @@ endif ()
 # free lists entirely for developer build modes, as they can
 # make certain types of issues (like references to stale pointers)
 # much more difficult to debug
-if (NOT HDF5_ENABLE_DEBUG_H5FL AND NOT HDF5_ENABLE_DEBUG_H5FL_TRACK)
+if (NOT HDF5_ENABLE_DEBUG_H5FL)
   list (APPEND HDF5_DEVELOPER_DEFS H5_NO_FREE_LISTS)
 endif ()
 

diff --git a/config/cmake/grepTest.cmake b/config/cmake/grepTest.cmake
@@ -11,6 +11,7 @@
 #
 # grepTest.cmake executes a command and captures the output in a file. File is then compared
 # against a reference file. Exit status of command can also be compared.
+cmake_policy(SET CMP0007 NEW)
 
 # arguments checking
 if (NOT TEST_PROGRAM)
@@ -67,6 +68,11 @@ execute_process (
 
 message (STATUS "COMMAND Result: ${TEST_RESULT}")
 
+# append the test result status with a predefined text
+if (TEST_APPEND)
+  file (APPEND ${TEST_FOLDER}/${TEST_OUTPUT} "${TEST_APPEND} ${TEST_RESULT}\n")
+endif ()
+
 message (STATUS "COMMAND Error: ${TEST_ERROR}")
 
 # remove special output
@@ -75,15 +81,22 @@ if (EXISTS "${TEST_FOLDER}/${TEST_OUTPUT}")
   string (FIND "${TEST_STREAM}" "_pmi_alps" TEST_FIND_RESULT)
   if (TEST_FIND_RESULT GREATER -1)
     string (REGEX REPLACE "^.*_pmi_alps[^\n]+\n" "" TEST_STREAM "${TEST_STREAM}")
-    file (WRITE ${TEST_FOLDER}/${TEST_OUTPUT} "${TEST_STREAM}")
+    file (WRITE ${TEST_FOLDER}/${TEST_OUTPUT} ${TEST_STREAM})
   endif ()
   string (FIND "${TEST_STREAM}" "ulimit -s" TEST_FIND_RESULT)
   if (TEST_FIND_RESULT GREATER -1)
     string (REGEX REPLACE "^.*ulimit -s[^\n]+\n" "" TEST_STREAM "${TEST_STREAM}")
-    file (WRITE ${TEST_FOLDER}/${TEST_OUTPUT} "${TEST_STREAM}")
+    file (WRITE ${TEST_FOLDER}/${TEST_OUTPUT} ${TEST_STREAM})
   endif ()
 endif ()
 
+if (TEST_REF_FILTER)
+  #message (STATUS "TEST_REF_FILTER: ${TEST_APPEND}${TEST_REF_FILTER}")
+  file (READ ${TEST_FOLDER}/${TEST_REFERENCE} TEST_STREAM)
+  string (REGEX REPLACE "${TEST_REF_APPEND}" "${TEST_REF_FILTER}" TEST_STREAM "${TEST_STREAM}")
+  file (WRITE ${TEST_FOLDER}/${TEST_REFERENCE} "${TEST_STREAM}")
+endif ()
+
 # if the TEST_ERRREF exists grep the error output with the error reference
 set (TEST_ERRREF_RESULT 0)
 if (TEST_ERRREF)
@@ -96,26 +109,25 @@ if (TEST_ERRREF)
       string (REGEX MATCH "${TEST_ERRREF}" TEST_MATCH ${TEST_ERR_STREAM})
       string (COMPARE EQUAL "${TEST_ERRREF}" "${TEST_MATCH}" TEST_ERRREF_RESULT)
       if (NOT TEST_ERRREF_RESULT)
+        # dump the output unless nodisplay option is set
+        if (NOT TEST_NO_DISPLAY)
+          execute_process (
+              COMMAND ${CMAKE_COMMAND} -E echo ${TEST_ERR_STREAM}
+              RESULT_VARIABLE TEST_ERRREF_RESULT
+          )
+        endif ()
         message (FATAL_ERROR "Failed: The error output of ${TEST_PROGRAM} did not contain ${TEST_ERRREF}")
       endif ()
     endif ()
   endif ()
 
-  #always compare output file to reference unless this must be skipped
+  # compare output files to references unless this must be skipped
   set (TEST_COMPARE_RESULT 0)
   if (NOT TEST_SKIP_COMPARE)
     if (EXISTS "${TEST_FOLDER}/${TEST_REFERENCE}")
       file (READ ${TEST_FOLDER}/${TEST_REFERENCE} TEST_STREAM)
       list (LENGTH TEST_STREAM test_len)
       if (test_len GREATER 0)
-        if (WIN32)
-          configure_file(${TEST_FOLDER}/${TEST_REFERENCE} ${TEST_FOLDER}/${TEST_REFERENCE}.tmp NEWLINE_STYLE CRLF)
-          if (EXISTS "${TEST_FOLDER}/${TEST_REFERENCE}.tmp")
-            file(RENAME ${TEST_FOLDER}/${TEST_REFERENCE}.tmp ${TEST_FOLDER}/${TEST_REFERENCE})
-          endif ()
-          #file (READ ${TEST_FOLDER}/${TEST_REFERENCE} TEST_STREAM)
-          #file (WRITE ${TEST_FOLDER}/${TEST_REFERENCE} "${TEST_STREAM}")
-        endif ()
         if (NOT TEST_SORT_COMPARE)
           # now compare the output with the reference
           execute_process (
@@ -138,7 +150,14 @@ if (TEST_ERRREF)
           list (LENGTH test_act len_act)
           file (STRINGS ${TEST_FOLDER}/${TEST_REFERENCE} test_ref)
           list (LENGTH test_ref len_ref)
+          if (NOT len_act EQUAL len_ref)
+            set (TEST_COMPARE_RESULT 1)
+          endif ()
           if (len_act GREATER 0 AND len_ref GREATER 0)
+            if (TEST_SORT_COMPARE)
+              list (SORT test_act)
+              list (SORT test_ref)
+            endif ()
             math (EXPR _FP_LEN "${len_ref} - 1")
             foreach (line RANGE 0 ${_FP_LEN})
               list (GET test_act ${line} str_act)
@@ -200,7 +219,7 @@ if (TEST_FILTER)
 endif ()
 
 if (NOT DEFINED ENV{HDF5_NOCLEANUP})
-  if (EXISTS "${TEST_FOLDER}/${TEST_OUTPUT}")
+  if (EXISTS "${TEST_FOLDER}/${TEST_OUTPUT}" AND NOT TEST_SAVE)
     file (REMOVE ${TEST_FOLDER}/${TEST_OUTPUT})
   endif ()
 

diff --git a/config/cmake/libhdf5.settings.cmake.in b/config/cmake/libhdf5.settings.cmake.in
@@ -88,7 +88,6 @@ Dimension scales w/ new references: @DIMENSION_SCALES_WITH_NEW_REF@
     Packages w/ extra debug output: @INTERNAL_DEBUG_OUTPUT@
                        API Tracing: @HDF5_ENABLE_TRACE@
               Using memory checker: @HDF5_ENABLE_USING_MEMCHECKER@
-            Function Stack Tracing: @HDF5_ENABLE_CODESTACK@
                   Use file locking: @HDF5_FILE_LOCKING_SETTING@
          Strict File Format Checks: @HDF5_STRICT_FORMAT_CHECKS@
       Optimization Instrumentation: @HDF5_Enable_Instrument@