Sync with develop (#3764)

* Add missing test files to distclean target (#3734)

Cleans up new files in Autotools `make distclean` in the test directory

* Add tools/libtest to Autotools builds (#3735)

This was only added to CMake many years ago and tests the tools
library.

* Clean up onion VFD files in tools `make clean` (#3739)

Cleans up h5dump and h5diff *.onion files in the Autotools when
runing `make clean`.

* Clean Java test files on Autotools (#3740)

Removes generated HDF5 and text output files when running `make clean`.

* Clean the flushrefresh test dir on Autotools (#3741)

The flushrefresh_test directory was not being cleaned up w/
`make clean` under the Autotools

* Fix file names in tfile.c (#3743)

Some tests in tfile.c use h5_fileaccess to get a VFD-dependent file
name but use the scheme from testhdf5, reusing the FILE1 and FILE8
names. This leads to files like test1.h5.h5 which are unintended
and not cleaned up.

This changes the filename scheme for a few tests to work with h5test,
resulting in more informative names and allowing the files to
be cleaned up at the end of the test. The test files have also
been added to the `make clean` target for the Autotools.

* Clean Autotools files in parallel tests (#3744)

Adds missing files to `make clean` for parallel, including Fortran.

* Add native VOL checks to deprecated functions (#3647)

* Add native VOL checks to deprecated functions

* Remove unneeded native VOL checks

* Move native checks to top level calls

* Fix buffer overflow in cache debugging code (#3691)

* update stat arg for apple (#3726)

* update stat arg for apple

* use H5_HAVE_DARWIN for Apple ifdef

* fix typo

* removed duplicate H5_ih_info_t

* added fortran async test to cmake

* Fix windows cpack error in WiX package. (#3747)

* Add a simple cache to the ros3 VFD (#3753)

Adds a small cache of the first N bytes of a file opened with the
read-only S3 (ros3) VFD, where N is 4kiB or the size of the file,
whichever is smaller. This avoids a lot of small I/O operations
on file open.

Addresses GitHub issue #3381

* Update Autotools to correctly configure oneAPI (#3751)

* Update Autotools to correctly configure oneAPI

Splits the Intel config files under the Autotools into 'classic'
Intel and oneAPI versions, fixing 'unsupported option' messages.

Also turns off `-check uninit` (new in 2023) in Fortran, which kills
the H5_buildiface program due to false positives.

* Enable Fortran in oneAPI CI workflow

* Turn on Fortran in CMake, update LD_LIBRARY_PATH

* Go back to disabling Fortran w/ Intel

For some reason there's a linking problem w/ Fortran

error while loading shared libraries: libifport.so.5: cannot open shared object file: No such file or directory

* Add h5pget_actual_selection_io_mode fortran wrapper (#3746)

* added h5pget_actual_selection_io_mode_f test

* added tests for h5pget_actual_selection_io_mode_f

* fixed int_f type conversion

* Update fortran action step (#3748)

* Added missing DLL for H5PGET_ACTUAL_SELECTION_IO_MODE_F (#3760)

* add missing H5PGET_ACTUAL_SELECTION_IO_MODE_F dll

* Bump the ros3 VFD cache to 16 MiB (#3759)

* Fix hangs during collective I/O with independent metadata writes (#3693)

* Fix some issues with collective metadata reads for chunked datasets (#3716)

Add functions/callbacks for explicit control over chunk index open/close

Add functions/callbacks to check if chunk index is open or not so
that it can be opened if necessary before temporarily disabling
collective metadata reads in the library

Add functions/callbacks for requesting loading of additional chunk
index metadata beyond the chunk index itself

* Fix failure in t_select_io_dset when run with more than 10 ranks (#3758)

* Fix H5Pset_evict_on_close failing regardless of actual parallel use (#3761)

Allow H5Pset_evict_on_close to be called regardless of whether a parallel build of HDF5 is being used

Fail during file opens if H5Pset_evict_on_close has been set to true on the given File Access Property List and the size of the MPI communicator being used is greater than 1

1 files changed, 169 insertions, 65 deletions

diff --git a/src/H5Dfarray.c b/src/H5Dfarray.c
index 450d466..8d06de4 100644
--- a/src/H5Dfarray.c
+++ b/src/H5Dfarray.c
@@ -37,6 +37,8 @@
 /* Local Macros */
 /****************/
 
+#define H5D_FARRAY_IDX_IS_OPEN(idx_info) (NULL != (idx_info)->storage->u.btree2.bt2)
+
 /* Value to fill unset array elements with */
 #define H5D_FARRAY_FILL HADDR_UNDEF
 #define H5D_FARRAY_FILT_FILL                                                                                 \
@@ -105,10 +107,14 @@ static herr_t H5D__farray_filt_debug(FILE *stream, int indent, int fwidth, hsize
 static herr_t H5D__farray_idx_init(const H5D_chk_idx_info_t *idx_info, const H5S_t *space,
                                    haddr_t dset_ohdr_addr);
 static herr_t H5D__farray_idx_create(const H5D_chk_idx_info_t *idx_info);
+static herr_t H5D__farray_idx_open(const H5D_chk_idx_info_t *idx_info);
+static herr_t H5D__farray_idx_close(const H5D_chk_idx_info_t *idx_info);
+static herr_t H5D__farray_idx_is_open(const H5D_chk_idx_info_t *idx_info, bool *is_open);
 static bool   H5D__farray_idx_is_space_alloc(const H5O_storage_chunk_t *storage);
 static herr_t H5D__farray_idx_insert(const H5D_chk_idx_info_t *idx_info, H5D_chunk_ud_t *udata,
                                      const H5D_t *dset);
 static herr_t H5D__farray_idx_get_addr(const H5D_chk_idx_info_t *idx_info, H5D_chunk_ud_t *udata);
+static herr_t H5D__farray_idx_load_metadata(const H5D_chk_idx_info_t *idx_info);
 static int    H5D__farray_idx_iterate(const H5D_chk_idx_info_t *idx_info, H5D_chunk_cb_func_t chunk_cb,
                                       void *chunk_udata);
 static herr_t H5D__farray_idx_remove(const H5D_chk_idx_info_t *idx_info, H5D_chunk_common_ud_t *udata);
@@ -123,7 +129,6 @@ static herr_t H5D__farray_idx_dump(const H5O_storage_chunk_t *storage, FILE *str
 static herr_t H5D__farray_idx_dest(const H5D_chk_idx_info_t *idx_info);
 
 /* Generic fixed array routines */
-static herr_t H5D__farray_idx_open(const H5D_chk_idx_info_t *idx_info);
 static herr_t H5D__farray_idx_depend(const H5D_chk_idx_info_t *idx_info);
 
 /*********************/
@@ -135,9 +140,13 @@ const H5D_chunk_ops_t H5D_COPS_FARRAY[1] = {{
     true,                           /* Fixed array indices support SWMR access */
     H5D__farray_idx_init,           /* init */
     H5D__farray_idx_create,         /* create */
+    H5D__farray_idx_open,           /* open */
+    H5D__farray_idx_close,          /* close */
+    H5D__farray_idx_is_open,        /* is_open */
     H5D__farray_idx_is_space_alloc, /* is_space_alloc */
     H5D__farray_idx_insert,         /* insert */
     H5D__farray_idx_get_addr,       /* get_addr */
+    H5D__farray_idx_load_metadata,  /* load_metadata */
     NULL,                           /* resize */
     H5D__farray_idx_iterate,        /* iterate */
     H5D__farray_idx_remove,         /* remove */
@@ -727,55 +736,6 @@ H5D__farray_idx_init(const H5D_chk_idx_info_t *idx_info, const H5S_t H5_ATTR_UNU
 } /* end H5D__farray_idx_init() */
 
 /*-------------------------------------------------------------------------
- * Function:    H5D__farray_idx_open
- *
- * Purpose:     Opens an existing fixed array and initializes
- *              the layout struct with information about the storage.
- *
- * Return:      Success:    non-negative
- *              Failure:    negative
- *
- *-------------------------------------------------------------------------
- */
-static herr_t
-H5D__farray_idx_open(const H5D_chk_idx_info_t *idx_info)
-{
-    H5D_farray_ctx_ud_t udata;               /* User data for fixed array open call */
-    herr_t              ret_value = SUCCEED; /* Return value */
-
-    FUNC_ENTER_PACKAGE
-
-    /* Check args */
-    assert(idx_info);
-    assert(idx_info->f);
-    assert(idx_info->pline);
-    assert(idx_info->layout);
-    assert(H5D_CHUNK_IDX_FARRAY == idx_info->layout->idx_type);
-    assert(idx_info->storage);
-    assert(H5D_CHUNK_IDX_FARRAY == idx_info->storage->idx_type);
-    assert(H5_addr_defined(idx_info->storage->idx_addr));
-    assert(NULL == idx_info->storage->u.farray.fa);
-
-    /* Set up the user data */
-    udata.f          = idx_info->f;
-    udata.chunk_size = idx_info->layout->size;
-
-    /* Open the fixed array for the chunk index */
-    if (NULL ==
-        (idx_info->storage->u.farray.fa = H5FA_open(idx_info->f, idx_info->storage->idx_addr, &udata)))
-        HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't open fixed array");
-
-    /* Check for SWMR writes to the file */
-    if (H5F_INTENT(idx_info->f) & H5F_ACC_SWMR_WRITE)
-        if (H5D__farray_idx_depend(idx_info) < 0)
-            HGOTO_ERROR(H5E_DATASET, H5E_CANTDEPEND, FAIL,
-                        "unable to create flush dependency on object header");
-
-done:
-    FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5D__farray_idx_open() */
-
-/*-------------------------------------------------------------------------
  * Function:    H5D__farray_idx_create
  *
  * Purpose:     Creates a new indexed-storage fixed array and initializes
@@ -854,11 +814,114 @@ done:
 } /* end H5D__farray_idx_create() */
 
 /*-------------------------------------------------------------------------
+ * Function:    H5D__farray_idx_open
+ *
+ * Purpose:     Opens an existing fixed array and initializes
+ *              the layout struct with information about the storage.
+ *
+ * Return:      Success:    non-negative
+ *              Failure:    negative
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__farray_idx_open(const H5D_chk_idx_info_t *idx_info)
+{
+    H5D_farray_ctx_ud_t udata;               /* User data for fixed array open call */
+    herr_t              ret_value = SUCCEED; /* Return value */
+
+    FUNC_ENTER_PACKAGE
+
+    /* Check args */
+    assert(idx_info);
+    assert(idx_info->f);
+    assert(idx_info->pline);
+    assert(idx_info->layout);
+    assert(H5D_CHUNK_IDX_FARRAY == idx_info->layout->idx_type);
+    assert(idx_info->storage);
+    assert(H5D_CHUNK_IDX_FARRAY == idx_info->storage->idx_type);
+    assert(H5_addr_defined(idx_info->storage->idx_addr));
+    assert(NULL == idx_info->storage->u.farray.fa);
+
+    /* Set up the user data */
+    udata.f          = idx_info->f;
+    udata.chunk_size = idx_info->layout->size;
+
+    /* Open the fixed array for the chunk index */
+    if (NULL ==
+        (idx_info->storage->u.farray.fa = H5FA_open(idx_info->f, idx_info->storage->idx_addr, &udata)))
+        HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't open fixed array");
+
+    /* Check for SWMR writes to the file */
+    if (H5F_INTENT(idx_info->f) & H5F_ACC_SWMR_WRITE)
+        if (H5D__farray_idx_depend(idx_info) < 0)
+            HGOTO_ERROR(H5E_DATASET, H5E_CANTDEPEND, FAIL,
+                        "unable to create flush dependency on object header");
+
+done:
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D__farray_idx_open() */
+
+/*-------------------------------------------------------------------------
+ * Function:    H5D__farray_idx_close
+ *
+ * Purpose:     Closes an existing fixed array.
+ *
+ * Return:      Success:    non-negative
+ *              Failure:    negative
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__farray_idx_close(const H5D_chk_idx_info_t *idx_info)
+{
+    herr_t ret_value = SUCCEED; /* Return value */
+
+    FUNC_ENTER_PACKAGE
+
+    assert(idx_info);
+    assert(idx_info->storage);
+    assert(H5D_CHUNK_IDX_FARRAY == idx_info->storage->idx_type);
+    assert(idx_info->storage->u.farray.fa);
+
+    if (H5FA_close(idx_info->storage->u.farray.fa) < 0)
+        HGOTO_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to close fixed array");
+    idx_info->storage->u.farray.fa = NULL;
+
+done:
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D__farray_idx_close() */
+
+/*-------------------------------------------------------------------------
+ * Function:    H5D__farray_idx_is_open
+ *
+ * Purpose:     Query if the index is opened or not
+ *
+ * Return:      SUCCEED (can't fail)
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__farray_idx_is_open(const H5D_chk_idx_info_t *idx_info, bool *is_open)
+{
+    FUNC_ENTER_PACKAGE_NOERR
+
+    assert(idx_info);
+    assert(idx_info->storage);
+    assert(H5D_CHUNK_IDX_FARRAY == idx_info->storage->idx_type);
+    assert(is_open);
+
+    *is_open = H5D_FARRAY_IDX_IS_OPEN(idx_info);
+
+    FUNC_LEAVE_NOAPI(SUCCEED)
+} /* end H5D__farray_idx_is_open() */
+
+/*-------------------------------------------------------------------------
  * Function:    H5D__farray_idx_is_space_alloc
  *
  * Purpose:     Query if space is allocated for index method
  *
- * Return:      Non-negative on success/Negative on failure
+ * Return:      true/false
  *
  *-------------------------------------------------------------------------
  */
@@ -901,7 +964,7 @@ H5D__farray_idx_insert(const H5D_chk_idx_info_t *idx_info, H5D_chunk_ud_t *udata
     assert(udata);
 
     /* Check if the fixed array is open yet */
-    if (NULL == idx_info->storage->u.farray.fa) {
+    if (!H5D_FARRAY_IDX_IS_OPEN(idx_info)) {
         /* Open the fixed array in file */
         if (H5D__farray_idx_open(idx_info) < 0)
             HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open fixed array");
@@ -969,7 +1032,7 @@ H5D__farray_idx_get_addr(const H5D_chk_idx_info_t *idx_info, H5D_chunk_ud_t *uda
     assert(udata);
 
     /* Check if the fixed array is open yet */
-    if (NULL == idx_info->storage->u.farray.fa) {
+    if (!H5D_FARRAY_IDX_IS_OPEN(idx_info)) {
         /* Open the fixed array in file */
         if (H5D__farray_idx_open(idx_info) < 0)
             HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open fixed array");
@@ -1017,6 +1080,50 @@ done:
 } /* H5D__farray_idx_get_addr() */
 
 /*-------------------------------------------------------------------------
+ * Function:    H5D__farray_idx_load_metadata
+ *
+ * Purpose:     Load additional chunk index metadata beyond the chunk index
+ *              itself.
+ *
+ * Return:      Non-negative on success/Negative on failure
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__farray_idx_load_metadata(const H5D_chk_idx_info_t *idx_info)
+{
+    H5D_chunk_ud_t chunk_ud;
+    hsize_t        scaled[H5O_LAYOUT_NDIMS] = {0};
+    herr_t         ret_value                = SUCCEED;
+
+    FUNC_ENTER_PACKAGE
+
+    /*
+     * After opening a dataset that uses a fixed array, the
+     * fixed array data block will generally not be read in
+     * until an element is looked up for the first time. Since
+     * there isn't currently a good way of controlling that
+     * explicitly, perform a fake lookup of a chunk to cause
+     * it to be read in.
+     */
+    chunk_ud.common.layout  = idx_info->layout;
+    chunk_ud.common.storage = idx_info->storage;
+    chunk_ud.common.scaled  = scaled;
+
+    chunk_ud.chunk_block.offset = HADDR_UNDEF;
+    chunk_ud.chunk_block.length = 0;
+    chunk_ud.filter_mask        = 0;
+    chunk_ud.new_unfilt_chunk   = false;
+    chunk_ud.idx_hint           = UINT_MAX;
+
+    if (H5D__farray_idx_get_addr(idx_info, &chunk_ud) < 0)
+        HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't load fixed array data block");
+
+done:
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* H5D__farray_idx_load_metadata() */
+
+/*-------------------------------------------------------------------------
  * Function:    H5D__farray_idx_iterate_cb
  *
  * Purpose:     Callback routine for fixed array element iteration.
@@ -1102,7 +1209,7 @@ H5D__farray_idx_iterate(const H5D_chk_idx_info_t *idx_info, H5D_chunk_cb_func_t
     assert(chunk_udata);
 
     /* Check if the fixed array is open yet */
-    if (NULL == idx_info->storage->u.farray.fa) {
+    if (!H5D_FARRAY_IDX_IS_OPEN(idx_info)) {
         /* Open the fixed array in file */
         if (H5D__farray_idx_open(idx_info) < 0)
             HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open fixed array");
@@ -1171,7 +1278,7 @@ H5D__farray_idx_remove(const H5D_chk_idx_info_t *idx_info, H5D_chunk_common_ud_t
     assert(udata);
 
     /* Check if the fixed array is open yet */
-    if (NULL == idx_info->storage->u.farray.fa) {
+    if (!H5D_FARRAY_IDX_IS_OPEN(idx_info)) {
         /* Open the fixed array in file */
         if (H5D__farray_idx_open(idx_info) < 0)
             HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open fixed array");
@@ -1302,9 +1409,8 @@ H5D__farray_idx_delete(const H5D_chk_idx_info_t *idx_info)
             HGOTO_ERROR(H5E_DATASET, H5E_BADITER, FAIL, "unable to iterate over chunk addresses");
 
         /* Close fixed array */
-        if (H5FA_close(idx_info->storage->u.farray.fa) < 0)
+        if (H5D__farray_idx_close(idx_info) < 0)
             HGOTO_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to close fixed array");
-        idx_info->storage->u.farray.fa = NULL;
 
         /* Set up the user data */
         ctx_udata.f          = idx_info->f;
@@ -1352,10 +1458,11 @@ H5D__farray_idx_copy_setup(const H5D_chk_idx_info_t *idx_info_src, const H5D_chk
     assert(!H5_addr_defined(idx_info_dst->storage->idx_addr));
 
     /* Check if the source fixed array is open yet */
-    if (NULL == idx_info_src->storage->u.farray.fa)
+    if (!H5D_FARRAY_IDX_IS_OPEN(idx_info_src)) {
         /* Open the fixed array in file */
         if (H5D__farray_idx_open(idx_info_src) < 0)
             HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open fixed array");
+    }
 
     /* Set copied metadata tag */
     H5_BEGIN_TAG(H5AC__COPIED_TAG)
@@ -1450,9 +1557,8 @@ H5D__farray_idx_size(const H5D_chk_idx_info_t *idx_info, hsize_t *index_size)
 
 done:
     if (idx_info->storage->u.farray.fa) {
-        if (H5FA_close(idx_info->storage->u.farray.fa) < 0)
-            HGOTO_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to close fixed array");
-        idx_info->storage->u.farray.fa = NULL;
+        if (H5D__farray_idx_close(idx_info) < 0)
+            HDONE_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to close fixed array");
     } /* end if */
 
     FUNC_LEAVE_NOAPI(ret_value)
@@ -1528,16 +1634,14 @@ H5D__farray_idx_dest(const H5D_chk_idx_info_t *idx_info)
     assert(idx_info->storage);
 
     /* Check if the fixed array is open */
-    if (idx_info->storage->u.farray.fa) {
-
+    if (H5D_FARRAY_IDX_IS_OPEN(idx_info)) {
         /* Patch the top level file pointer contained in fa if needed */
         if (H5FA_patch_file(idx_info->storage->u.farray.fa, idx_info->f) < 0)
             HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't patch fixed array file pointer");
 
         /* Close fixed array */
-        if (H5FA_close(idx_info->storage->u.farray.fa) < 0)
+        if (H5D__farray_idx_close(idx_info) < 0)
             HGOTO_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to close fixed array");
-        idx_info->storage->u.farray.fa = NULL;
     } /* end if */
 
 done: