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

.github/workflows/cmake-script.yml

@@ -96,6 +96,7 @@ jobs:
               set (CTEST_DROP_SITE_INIT "my.cdash.org")
               # Change following line to submit to your CDash dashboard to a different CDash project
               #set (CTEST_DROP_LOCATION_INIT "/submit.php?project=HDF5")
+              set (SITE_BUILDNAME_SUFFIX "${{ steps.set-file-base.outputs.FILE_BASE }}")
               set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} --log-level=VERBOSE")
               set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_JAVA:BOOL=ON")
               set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_CPP_LIB:BOOL=ON")
@@ -184,6 +185,7 @@ jobs:
             set (CTEST_DROP_SITE_INIT "my.cdash.org")
             # Change following line to submit to your CDash dashboard to a different CDash project
             #set (CTEST_DROP_LOCATION_INIT "/submit.php?project=HDF5")
+            set (SITE_BUILDNAME_SUFFIX "${{ steps.set-file-base.outputs.FILE_BASE }}")
             set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} --log-level=VERBOSE")
             set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_JAVA:BOOL=ON")
             set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_CPP_LIB:BOOL=ON")
@@ -284,6 +286,7 @@ jobs:
             set (CTEST_DROP_SITE_INIT "my.cdash.org")
             # Change following line to submit to your CDash dashboard to a different CDash project
             #set (CTEST_DROP_LOCATION_INIT "/submit.php?project=HDF5")
+            set (SITE_BUILDNAME_SUFFIX "${{ steps.set-file-base.outputs.FILE_BASE }}")
             set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} --log-level=VERBOSE")
             set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_JAVA:BOOL=ON")
             set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_CPP_LIB:BOOL=ON")
@@ -369,6 +372,7 @@ jobs:
             set (CTEST_DROP_SITE_INIT "my.cdash.org")
             # Change following line to submit to your CDash dashboard to a different CDash project
             #set (CTEST_DROP_LOCATION_INIT "/submit.php?project=HDF5")
+            set (SITE_BUILDNAME_SUFFIX "${{ steps.set-file-base.outputs.FILE_BASE }}")
             set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} --log-level=VERBOSE")
             set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_JAVA:BOOL=ON")
             set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_CPP_LIB:BOOL=ON")
@@ -468,7 +472,8 @@ jobs:
             set (CTEST_DROP_SITE_INIT "my.cdash.org")
             # Change following line to submit to your CDash dashboard to a different CDash project
             #set (CTEST_DROP_LOCATION_INIT "/submit.php?project=HDF5")
-            set (CMAKE_GENERATOR_TOOLSET "Intel C++ Compiler 2024,fortran=ifx")
+            #set (CMAKE_GENERATOR_TOOLSET "Intel C++ Compiler 2024,fortran=ifx")
+            set (SITE_BUILDNAME_SUFFIX "${{ steps.set-file-base.outputs.FILE_BASE }}")
             set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} --log-level=VERBOSE")
             set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_TOOLCHAIN_FILE:STRING=config/toolchain/intel.cmake")
             set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_JAVA:BOOL=ON")
@@ -566,6 +571,7 @@ jobs:
             set (CTEST_DROP_SITE_INIT "my.cdash.org")
             # Change following line to submit to your CDash dashboard to a different CDash project
             #set (CTEST_DROP_LOCATION_INIT "/submit.php?project=HDF5")
+            set (SITE_BUILDNAME_SUFFIX "${{ steps.set-file-base.outputs.FILE_BASE }}")
             set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} --log-level=VERBOSE")
             set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_JAVA:BOOL=ON")
             set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_CPP_LIB:BOOL=ON")

.github/workflows/daily-build.yml

@@ -40,7 +40,7 @@ jobs:
     - name: Read inputs
       id: getinputs
       run: |
-        echo "INPUTS_IGNORE=${{ github.event.inputs.use_ignore }}" >> $GITHUB_OUTPUT
+        echo "INPUTS_IGNORE=${{ inputs.use_ignore }}" >> $GITHUB_OUTPUT
 
     - run: echo "use_ignore is ${{ steps.getinputs.outputs.INPUTS_IGNORE }}."
 

bin/genparser

@@ -200,14 +200,14 @@ if [ "$verbose" = true ] ; then
 fi
 ${HDF5_FLEX} --nounistd -PH5LTyy -o ${path_to_hl_src}/H5LTanalyze.c ${path_to_hl_src}/H5LTanalyze.l
 
-# fix H5LTparse.c and H5LTlparse.h to declare H5LTyyparse return type as an
-# hid_t instead of int.  Currently the generated function H5LTyyparse is
-# generated with a return value of type int, which is a mapping to the
+# Fix H5LTparse.c and H5LTparse.h to declare H5LTyyparse return type as an
+# hid_t instead of int.  Currently, the H5LTyyparse function is generated
+# with a return value of type int, which is a mapping to the
 # flex yyparse function.  The return value in the HL library should be
 # an hid_t.
-# I propose to not use flex to generate this function, but for now I am
-# adding a perl command to find and replace this function declaration in
-# H5LTparse.c.
+# Use Perl command to find and replace this function declaration
+# in H5LTparse.c. This is a temporary solution until a method that does not
+# use flex is implemented.
 perl -0777 -pi -e 's/int yyparse/hid_t yyparse/igs' ${path_to_hl_src}/H5LTparse.c
 perl -0777 -pi -e 's/int\nyyparse/hid_t\nyyparse/igs' ${path_to_hl_src}/H5LTparse.c
 perl -0777 -pi -e 's/int H5LTyyparse/hid_t H5LTyyparse/igs' ${path_to_hl_src}/H5LTparse.c

release_docs/RELEASE.txt

@@ -819,7 +819,16 @@ New Features
 
     Documentation:
     --------------
-    -
+    - Documented that leaving HDF5 threads running at termination is unsafe
+
+      Added doc/threadsafety-warning.md as a warning that threads which use
+      HDF5 resources must be closed before either process exit or library
+      close.  If HDF5 threads are alive during either of these operations,
+      their resources will not be cleaned up properly and undefined behavior
+      is possible.
+
+      This document also includes a discussion on potential ways to mitigate
+      this issue.
 
 
 Support for new platforms, languages and compilers
@@ -840,6 +849,15 @@ Bug Fixes since HDF5-1.14.0 release
       and H5VLget_connector_id_by_value should be closed to avoid resource
       leaks.
 
+    - Fixed a memory leak in H5F__accum_write()
+
+      The memory was allocated in H5F__accum_write() and was to be freed in
+      H5F__accum_reset() during the closing process but a failure occurred just
+      before the deallocation, leaving the memory un-freed.  The problem is
+      now fixed.
+
+      Fixes GitHub #4585
+
     - Fixed an incorrect returned value by H5LTfind_dataset()
 
       H5LTfind_dataset() returned true for non-existing datasets because it only

src/H5Faccum.c

@@ -725,7 +725,7 @@ H5F__accum_write(H5F_shared_t *f_sh, H5FD_mem_t map_type, haddr_t addr, size_t s
             /* Make certain that data in accumulator is visible before new write */
             if ((H5F_SHARED_INTENT(f_sh) & H5F_ACC_SWMR_WRITE) > 0)
                 /* Flush if dirty and reset accumulator */
-                if (H5F__accum_reset(f_sh, true) < 0)
+                if (H5F__accum_reset(f_sh, true, false) < 0)
                     HGOTO_ERROR(H5E_IO, H5E_CANTRESET, FAIL, "can't reset accumulator");
 
             /* Write the data */
@@ -776,7 +776,7 @@ H5F__accum_write(H5F_shared_t *f_sh, H5FD_mem_t map_type, haddr_t addr, size_t s
                     }      /* end if */
                     else { /* Access covers whole accumulator */
                         /* Reset accumulator, but don't flush */
-                        if (H5F__accum_reset(f_sh, false) < 0)
+                        if (H5F__accum_reset(f_sh, false, false) < 0)
                             HGOTO_ERROR(H5E_IO, H5E_CANTRESET, FAIL, "can't reset accumulator");
                     }                    /* end else */
                 }                        /* end if */
@@ -1039,7 +1039,7 @@ H5F__accum_flush(H5F_shared_t *f_sh)
  *-------------------------------------------------------------------------
  */
 herr_t
-H5F__accum_reset(H5F_shared_t *f_sh, bool flush)
+H5F__accum_reset(H5F_shared_t *f_sh, bool flush, bool force)
 {
     herr_t ret_value = SUCCEED; /* Return value */
 
@@ -1050,8 +1050,11 @@ H5F__accum_reset(H5F_shared_t *f_sh, bool flush)
 
     /* Flush any dirty data in accumulator, if requested */
     if (flush)
-        if (H5F__accum_flush(f_sh) < 0)
-            HGOTO_ERROR(H5E_FILE, H5E_CANTFLUSH, FAIL, "can't flush metadata accumulator");
+        if (H5F__accum_flush(f_sh) < 0) {
+            HDONE_ERROR(H5E_FILE, H5E_CANTFLUSH, FAIL, "can't flush metadata accumulator");
+            if (!force)
+                HGOTO_DONE(FAIL);
+        }
 
     /* Check if we need to reset the metadata accumulator information */
     if (f_sh->feature_flags & H5FD_FEAT_ACCUMULATE_METADATA) {

src/H5Fint.c

@@ -1555,7 +1555,7 @@ H5F__dest(H5F_t *f, bool flush, bool free_on_failure)
         } /* end if */
 
         /* Destroy other components of the file */
-        if (H5F__accum_reset(f->shared, true) < 0)
+        if (H5F__accum_reset(f->shared, true, true) < 0)
             /* Push error, but keep going*/
             HDONE_ERROR(H5E_FILE, H5E_CANTRELEASE, FAIL, "problems closing file");
         if (H5FO_dest(f) < 0)
@@ -3888,7 +3888,7 @@ H5F__start_swmr_write(H5F_t *f)
     }     /* end if */
 
     /* Flush and reset the accumulator */
-    if (H5F__accum_reset(f->shared, true) < 0)
+    if (H5F__accum_reset(f->shared, true, false) < 0)
         HGOTO_ERROR(H5E_IO, H5E_CANTRESET, FAIL, "can't reset accumulator");
 
     /* Turn on SWMR write in shared file open flags */

src/H5Fio.c

@@ -422,7 +422,7 @@ H5F_flush_tagged_metadata(H5F_t *f, haddr_t tag)
         HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "unable to flush tagged metadata");
 
     /* Flush and reset the accumulator */
-    if (H5F__accum_reset(f->shared, true) < 0)
+    if (H5F__accum_reset(f->shared, true, false) < 0)
         HGOTO_ERROR(H5E_IO, H5E_CANTRESET, FAIL, "can't reset accumulator");
 
     /* Flush file buffers to disk. */

src/H5Fpkg.h

@@ -444,7 +444,7 @@ H5_DLL herr_t H5F__accum_write(H5F_shared_t *f_sh, H5FD_mem_t type, haddr_t addr
                                const void *buf);
 H5_DLL herr_t H5F__accum_free(H5F_shared_t *f, H5FD_mem_t type, haddr_t addr, hsize_t size);
 H5_DLL herr_t H5F__accum_flush(H5F_shared_t *f_sh);
-H5_DLL herr_t H5F__accum_reset(H5F_shared_t *f_sh, bool flush);
+H5_DLL herr_t H5F__accum_reset(H5F_shared_t *f_sh, bool flush, bool force);
 
 /* Shared file list related routines */
 H5_DLL herr_t        H5F__sfile_add(H5F_shared_t *shared);

test/accum.c

@@ -61,7 +61,7 @@ void accum_printf(const H5F_t *f);
 #define accum_read(a, s, b)  H5F_block_read(f, H5FD_MEM_DEFAULT, (haddr_t)(a), (size_t)(s), (b))
 #define accum_free(f, a, s)  H5F__accum_free(f->shared, H5FD_MEM_DEFAULT, (haddr_t)(a), (hsize_t)(s))
 #define accum_flush(f)       H5F__accum_flush(f->shared)
-#define accum_reset(f)       H5F__accum_reset(f->shared, true)
+#define accum_reset(f)       H5F__accum_reset(f->shared, true, false)
 
 /* ================= */
 /* Main Test Routine */