Merge branch 'develop' into release

.github/workflows/cmake-ctest.yml

@@ -413,9 +413,6 @@ jobs:
           compiler: intel
           version: '2024.1'
 
-      - name: Enable Developer Command Prompt
-        uses: ilammy/[email protected]
-
       - name: Set file base name (Windows_intel)
         id: set-file-base
         run: |

.github/workflows/vol_log.yml

@@ -58,7 +58,7 @@ jobs:
       - name: Checkout Log-based VOL
         uses: actions/[email protected]
         with:
-          repository: DataLib-ECP/vol-log-based
+          repository: HDFGroup/vol-log-based
           path: vol-log-based
 
       - name: Build HDF5 Log-based VOL connector and test with external tests 

doxygen/dox/IntroParHDF5.dox

@@ -23,8 +23,13 @@ Implementation requirements were to:
 \li Not have a reserved process, as this might interfere with parallel algorithms.
 \li Not spawn any processes, as this is not even commonly supported now.
 
-The following shows the Parallel HDF5 implementation layers.
+The following shows the Parallel HDF5 implementation layers:
 
+<table>
+<tr><td>
+\image html pimplayer.gif
+</td></tr>
+</table>
 
 \subsection subsec_pintro_prog Parallel Programming with HDF5
 This tutorial assumes that you are somewhat familiar with parallel programming with MPI (Message Passing Interface).

fortran/src/Makefile.am

@@ -155,7 +155,7 @@ H5Iff.lo:            $(srcdir)/H5Iff.F90 H5f90global.lo
 H5Lff.lo:            $(srcdir)/H5Lff.F90 H5f90global.lo
 H5Off.lo:            $(srcdir)/H5Off.F90 H5f90global.lo
 H5Pff.lo:            $(srcdir)/H5Pff.F90 H5f90global.lo H5fortkit.lo
-H5Rff.lo:            $(srcdir)/H5Rff.F90 H5f90global.lo
+H5Rff.lo:            $(srcdir)/H5Rff.F90 H5f90global.lo H5fortkit.lo
 H5Sff.lo:            $(srcdir)/H5Sff.F90 H5f90global.lo
 H5Tff.lo:            $(srcdir)/H5Tff.F90 H5f90global.lo
 H5VLff.lo:           $(srcdir)/H5VLff.F90 H5f90global.lo H5fortkit.lo

src/H5Fsuper.c

@@ -583,13 +583,10 @@ H5F__super_read(H5F_t *f, H5P_genplist_t *fa_plist, bool initial_read)
 
     if (H5F_INTENT(f) & H5F_ACC_SWMR_READ) {
         /*
-         * When the file is opened for SWMR read access, skip the check if:
-         * --the file is already marked for SWMR writing and
-         * --the file has version 3 superblock for SWMR support
+         * When the file is opened for SWMR read access, skip the check if
+         * the file has a version 3 superblock capable of SWMR support
          */
-        if ((sblock->status_flags & H5F_SUPER_SWMR_WRITE_ACCESS) &&
-            (sblock->status_flags & H5F_SUPER_WRITE_ACCESS) &&
-            sblock->super_vers >= HDF5_SUPERBLOCK_VERSION_3)
+        if (sblock->super_vers >= HDF5_SUPERBLOCK_VERSION_3)
             skip_eof_check = true;
     }
     if (!skip_eof_check && initial_read) {

src/H5Gint.c

@@ -506,7 +506,8 @@ static herr_t
 H5G__open_oid(H5G_t *grp)
 {
     bool   obj_opened = false;
-    herr_t ret_value  = SUCCEED;
+    htri_t msg_exists;
+    herr_t ret_value = SUCCEED;
 
     FUNC_ENTER_PACKAGE
 
@@ -523,8 +524,14 @@ H5G__open_oid(H5G_t *grp)
     obj_opened = true;
 
     /* Check if this object has the right message(s) to be treated as a group */
-    if ((H5O_msg_exists(&(grp->oloc), H5O_STAB_ID) <= 0) && (H5O_msg_exists(&(grp->oloc), H5O_LINFO_ID) <= 0))
-        HGOTO_ERROR(H5E_SYM, H5E_CANTOPENOBJ, FAIL, "not a group");
+    if ((msg_exists = H5O_msg_exists(&(grp->oloc), H5O_STAB_ID)) < 0)
+        HGOTO_ERROR(H5E_SYM, H5E_CANTGET, FAIL, "can't check if symbol table message exists");
+    if (!msg_exists) {
+        if ((msg_exists = H5O_msg_exists(&(grp->oloc), H5O_LINFO_ID)) < 0)
+            HGOTO_ERROR(H5E_SYM, H5E_CANTGET, FAIL, "can't check if link info message exists");
+        if (!msg_exists)
+            HGOTO_ERROR(H5E_SYM, H5E_CANTOPENOBJ, FAIL, "not a group");
+    }
 
 done:
     if (ret_value < 0) {

src/H5Odbg.c

@@ -87,6 +87,10 @@ H5O__assert(const H5O_t *oh)
 
     FUNC_ENTER_PACKAGE_NOERR
 
+    assert(oh);
+    assert(oh->chunk || oh->nchunks == 0);
+    assert(oh->mesg || oh->nmesgs == 0);
+
     /* Initialize the tracking variables */
     hdr_size   = 0;
     meta_space = (size_t)H5O_SIZEOF_HDR(oh) + (size_t)(H5O_SIZEOF_CHKHDR_OH(oh) * (oh->nchunks - 1));
@@ -140,6 +144,8 @@ H5O__assert(const H5O_t *oh)
         uint8_t H5_ATTR_NDEBUG_UNUSED *curr_hdr;      /* Start of current message header */
         size_t                         curr_tot_size; /* Total size of current message (including header) */
 
+        assert(curr_msg->type);
+
         curr_hdr      = curr_msg->raw - H5O_SIZEOF_MSGHDR_OH(oh);
         curr_tot_size = curr_msg->raw_size + (size_t)H5O_SIZEOF_MSGHDR_OH(oh);
 

src/H5Oint.c

@@ -1113,7 +1113,9 @@ H5O_protect(const H5O_loc_t *loc, unsigned prot_flags, bool pin_all_chunks)
         if (cont_msg_info.msgs)
             cont_msg_info.msgs = (H5O_cont_t *)H5FL_SEQ_FREE(H5O_cont_t, cont_msg_info.msgs);
 
-        if (H5O_unprotect(loc, oh, H5AC__NO_FLAGS_SET) < 0)
+        /* Unprotect the ohdr and delete it from cache since if we failed to load it it's in an inconsistent
+         * state */
+        if (H5O_unprotect(loc, oh, H5AC__DELETED_FLAG) < 0)
             HDONE_ERROR(H5E_OHDR, H5E_CANTUNPROTECT, NULL, "unable to release object header");
     }
 
@@ -1234,10 +1236,21 @@ H5O_unprotect(const H5O_loc_t *loc, H5O_t *oh, unsigned oh_flags)
             } /* end if */
         }     /* end for */
 
-        /* Reet the flag from the unprotect */
+        /* Reset the flag from the unprotect */
         oh->chunks_pinned = false;
     } /* end if */
 
+    /* Remove the other chunks if we're removing the ohdr (due to a failure) */
+    if (oh_flags & H5AC__DELETED_FLAG) {
+        unsigned u; /* Local index variable */
+
+        /* Iterate over chunks > 0 */
+        for (u = 1; u < oh->nchunks; u++)
+            /* Expunge chunk proxy from cache */
+            if (H5AC_expunge_entry(loc->file, H5AC_OHDR_CHK, oh->chunk[u].addr, H5AC__NO_FLAGS_SET) < 0)
+                HGOTO_ERROR(H5E_OHDR, H5E_CANTUNPIN, FAIL, "unable to expunge object header chunk");
+    } /* end if */
+
     /* Unprotect the object header */
     if (H5AC_unprotect(loc->file, H5AC_OHDR, oh->chunk[0].addr, oh, oh_flags) < 0)
         HGOTO_ERROR(H5E_OHDR, H5E_CANTUNPROTECT, FAIL, "unable to release object header");