VFD SWMR: sync with develop (#830)

* Normalization with develop

* Removes checks and work-arounds for strtoll and strtoull (#769)

* Removes checks for (v)snprintf, which are C99 (#772)

* Update missing release note info. (#776)

* Replaces the H5_OVERRIDE macro with override (#773)

The macro is no longer necessary now that we require C++11.

* Cleans up some POSIX header bits in H5private.h (#783)

* Removes outdated checks for ways inline might be defined (#781)

These are obsolete now that we require C99.

* Removes checks for system(), which is C89/90 (#782)

* Removes C++ dependency on H5private.h (#774)

* Removes C++ dependency on H5private.h

Most C API calls have been removed, aside from a few uses of free,
where we just dropped the 'HD'. A couple of H5_ATTR_UNUSED macros
were also replaced with (void) statements.

* Committing clang-format changes

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

* Further simplifies Autotools type size checks (#789)

Also fixes an issue where clock_gettime and difftime are not detected
due to earlier simplifications of this code.

* Release Note (#784)

* Normalization of CMake H5pubconf.h with Autotools (#791)

Mostly just moving things around and changing the comments to keep the
delta small. The only symbol change is that for curl/curl.h which I
changed to H5_HAVE_CURL_CURL_H to match the Autotools. This symbol
is not used in the library and is just an artifact of the checks.

* Fix tools test (#794)

* Removes ancient Autotools cruft (#790)

* Reorganization of C and POSIX headers in H5public.h & H5private.h (#793)

* Reorganization of C and POSIX headers in H5public.h & H5private.h

Consolidated and removed duplicates

* It turns out Windows has sys/types.h

Co-authored-by: Larry Knox <lrknox@hdfgroup.org>

* Removes checks for signal and set/longjmp, which are C89 (#798)

Also removes checks for setjmp.h and stddef.h

* Assume frexpl/f and fabsl/f, which are C99 (#799)

* Assume the library has C99 types in C++ type code (#806)

* Assume the library has C99 types in C++ type code

* Committing clang-format changes

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

* Removes obsolete equivalents of C99's __func__ (#800)

* Cleans up POSIX/C bits in H5private.h (#804)

* Cleans up POSIX/C bits in H5private.h

* Assume difftime exists (C89)
* Reorg AC_CHECK_HEADERS so headers are in alphabetical order
* Split off networking-related AC_CHECK_HEADERS
* Remove unused UNAME_CYGWIN from configure.ac
* Remove checks for unused sys/timeb.h
* Tidying pass over H5private.h HD prefix macros
* Tidy H5win32defs.h
* Add HD prefix to various scanf calls

* Committing clang-format changes

* Fixes to the alarm(2) code used in the tests to make Windows happy

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

* Brings the tools getopt(3) replacement into the main library (#803)

* Moves get_option from the tools library to the C library

* Adds H5 prefix to get_option call and variables

* Renames the H5_get_option long options struct and enum

* Removes type guesses when C99 types are missing (#807)

* Assume C99 types exist in H5detect.c (#808)

* Fixes parallel issues from recent C99 changes

* Adds MPE FUNC --> __func__ changes missed in earlier PRs

* Fix typo

* Fixes parallel issues from recent C99 changes (#809)

* Fixes parallel issues from recent C99 changes

* Adds MPE FUNC --> __func__ changes missed in earlier PRs

* Even more missed FUNC --> __func__ macros

* Removes remaining H5_TIME_WITH_SYS_TIME cruft (#810)

Mostly from CMake

* Merges with develop

* Committing clang-format changes

* Normalization with develop

* direct_chunk test and H5Dget_chunk_storage_size changes
* Removes unused H5O call

* Brings some dataspace changes from the combo branch merge

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>

1 files changed, 136 insertions, 18 deletions

diff --git a/src/H5VLnative_dataset.c b/src/H5VLnative_dataset.c
index 978ecb3..3a7f105 100644
--- a/src/H5VLnative_dataset.c
+++ b/src/H5VLnative_dataset.c
@@ -49,6 +49,10 @@
 /* Local Prototypes */
 /********************/
 
+/* Helper routines for read/write API calls */
+static herr_t H5VL__native_dataset_io_setup(H5D_t *dset, hid_t dxpl_id, hid_t file_space_id,
+                                            hid_t mem_space_id, H5S_t **file_space, H5S_t **mem_space);
+
 /*********************/
 /* Package Variables */
 /*********************/
@@ -62,6 +66,100 @@
 /*******************/
 
 /*-------------------------------------------------------------------------
+ * Function:    H5VL__native_dataset_io_setup
+ *
+ * Purpose:     Set up file and memory dataspaces for dataset I/O operation
+ *
+ * Return:      SUCCEED/FAIL
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5VL__native_dataset_io_setup(H5D_t *dset, hid_t dxpl_id, hid_t file_space_id, hid_t mem_space_id,
+                              H5S_t **file_space, H5S_t **mem_space)
+{
+    herr_t ret_value = SUCCEED; /* Return value */
+
+    FUNC_ENTER_STATIC
+
+    /* Sanity checks */
+    HDassert(dset);
+    HDassert(file_space && NULL == *file_space);
+    HDassert(mem_space && NULL == *mem_space);
+
+    /* Set up file dataspace */
+    if (H5S_ALL == file_space_id)
+        /* Use dataspace for dataset */
+        *file_space = dset->shared->space;
+    else if (H5S_BLOCK == file_space_id)
+        HGOTO_ERROR(H5E_DATASET, H5E_BADTYPE, FAIL, "H5S_BLOCK is not allowed for file dataspace")
+    else if (H5S_PLIST == file_space_id) {
+        H5P_genplist_t *plist; /* Property list pointer */
+        H5S_t *         space; /* Dataspace to hold selection */
+
+        /* Get the plist structure */
+        if (NULL == (plist = H5P_object_verify(dxpl_id, H5P_DATASET_XFER)))
+            HGOTO_ERROR(H5E_DATASET, H5E_BADID, FAIL, "bad dataset transfer property list")
+
+        /* See if a dataset I/O selection is already set, and free it if it is */
+        if (H5P_peek(plist, H5D_XFER_DSET_IO_SEL_NAME, &space) < 0)
+            HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error getting dataset I/O selection")
+
+        /* Use dataspace for dataset */
+        *file_space = dset->shared->space;
+
+        /* Copy, but share, selection from property list to dataset's dataspace */
+        if (H5S_SELECT_COPY(*file_space, space, TRUE) < 0)
+            HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "can't copy dataset I/O selection")
+    } /* end else-if */
+    else {
+        /* Get the dataspace pointer */
+        if (NULL == (*file_space = (H5S_t *)H5I_object_verify(file_space_id, H5I_DATASPACE)))
+            HGOTO_ERROR(H5E_DATASET, H5E_BADTYPE, FAIL, "file_space_id is not a dataspace ID")
+    } /* end else */
+
+    /* Get dataspace for memory buffer */
+    if (H5S_ALL == mem_space_id)
+        *mem_space = *file_space;
+    else if (H5S_BLOCK == mem_space_id) {
+        hsize_t nelmts; /* # of selected elements in file */
+
+        /* Get the # of elements selected */
+        nelmts = H5S_GET_SELECT_NPOINTS(*file_space);
+
+        /* Check for any elements */
+        if (nelmts > 0) {
+            /* Create a 1-D dataspace of the same # of elements */
+            if (NULL == (*mem_space = H5S_create_simple(1, &nelmts, NULL)))
+                HGOTO_ERROR(H5E_DATASET, H5E_CANTCREATE, FAIL, "unable to create simple memory dataspace")
+        } /* end if */
+        else {
+            /* Create a NULL dataspace of the same # of elements */
+            if (NULL == (*mem_space = H5S_create(H5S_NULL)))
+                HGOTO_ERROR(H5E_DATASET, H5E_CANTCREATE, FAIL, "unable to create NULL memory dataspace")
+        } /* end else */
+    }     /* end if */
+    else if (H5S_PLIST == mem_space_id)
+        HGOTO_ERROR(H5E_DATASET, H5E_BADTYPE, FAIL, "H5S_PLIST is not allowed for memory dataspace")
+    else {
+        /* Get the dataspace pointer */
+        if (NULL == (*mem_space = (H5S_t *)H5I_object_verify(mem_space_id, H5I_DATASPACE)))
+            HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "mem_space_id is not a dataspace ID")
+    } /* end else */
+
+    /* Check for valid selections */
+    if (H5S_SELECT_VALID(*file_space) != TRUE)
+        HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL,
+                    "selection + offset not within extent for file dataspace")
+    if (H5S_SELECT_VALID(*mem_space) != TRUE)
+        HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL,
+                    "selection + offset not within extent for memory dataspace")
+
+done:
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5VL__native_dataset_io_setup() */
+
+/*-------------------------------------------------------------------------
  * Function:    H5VL__native_dataset_create
  *
  * Purpose:     Handles the dataset create callback
@@ -172,10 +270,10 @@ herr_t
 H5VL__native_dataset_read(void *obj, hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_id,
                           hid_t dxpl_id, void *buf, void H5_ATTR_UNUSED **req)
 {
-    H5D_t *      dset       = (H5D_t *)obj;
-    const H5S_t *mem_space  = NULL;
-    const H5S_t *file_space = NULL;
-    herr_t       ret_value  = SUCCEED; /* Return value */
+    H5D_t *dset       = (H5D_t *)obj;
+    H5S_t *mem_space  = NULL;
+    H5S_t *file_space = NULL;
+    herr_t ret_value  = SUCCEED; /* Return value */
 
     FUNC_ENTER_PACKAGE
 
@@ -183,11 +281,10 @@ H5VL__native_dataset_read(void *obj, hid_t mem_type_id, hid_t mem_space_id, hid_
     if (NULL == dset->oloc.file)
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "dataset is not associated with a file")
 
-    /* Get validated dataspace pointers */
-    if (H5S_get_validated_dataspace(mem_space_id, &mem_space) < 0)
-        HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "could not get a validated dataspace from mem_space_id")
-    if (H5S_get_validated_dataspace(file_space_id, &file_space) < 0)
-        HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "could not get a validated dataspace from file_space_id")
+    /* Get file & memory dataspaces */
+    if (H5VL__native_dataset_io_setup(dset, dxpl_id, file_space_id, mem_space_id, &file_space, &mem_space) <
+        0)
+        HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to set up file and memory dataspaces")
 
     /* Set DXPL for operation */
     H5CX_set_dxpl(dxpl_id);
@@ -197,6 +294,17 @@ H5VL__native_dataset_read(void *obj, hid_t mem_type_id, hid_t mem_space_id, hid_
         HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data")
 
 done:
+    /* Clean up */
+    if (H5S_BLOCK == mem_space_id && mem_space) {
+        if (H5S_close(mem_space) < 0)
+            HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL,
+                        "unable to release temporary memory dataspace for H5S_BLOCK")
+    } /* end if */
+    else if (H5S_PLIST == file_space_id && file_space)
+        if (H5S_select_all(file_space, TRUE) < 0)
+            HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL,
+                        "unable to release file dataspace selection for H5S_PLIST")
+
     FUNC_LEAVE_NOAPI(ret_value)
 } /* end H5VL__native_dataset_read() */
 
@@ -213,10 +321,10 @@ herr_t
 H5VL__native_dataset_write(void *obj, hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_id,
                            hid_t dxpl_id, const void *buf, void H5_ATTR_UNUSED **req)
 {
-    H5D_t *      dset       = (H5D_t *)obj;
-    const H5S_t *mem_space  = NULL;
-    const H5S_t *file_space = NULL;
-    herr_t       ret_value  = SUCCEED; /* Return value */
+    H5D_t *dset       = (H5D_t *)obj;
+    H5S_t *mem_space  = NULL;
+    H5S_t *file_space = NULL;
+    herr_t ret_value  = SUCCEED; /* Return value */
 
     FUNC_ENTER_PACKAGE
 
@@ -224,11 +332,10 @@ H5VL__native_dataset_write(void *obj, hid_t mem_type_id, hid_t mem_space_id, hid
     if (NULL == dset->oloc.file)
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "dataset is not associated with a file")
 
-    /* Get validated dataspace pointers */
-    if (H5S_get_validated_dataspace(mem_space_id, &mem_space) < 0)
-        HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "could not get a validated dataspace from mem_space_id")
-    if (H5S_get_validated_dataspace(file_space_id, &file_space) < 0)
-        HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "could not get a validated dataspace from file_space_id")
+    /* Get file & memory dataspaces */
+    if (H5VL__native_dataset_io_setup(dset, dxpl_id, file_space_id, mem_space_id, &file_space, &mem_space) <
+        0)
+        HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to set up file and memory dataspaces")
 
     /* Set DXPL for operation */
     H5CX_set_dxpl(dxpl_id);
@@ -238,6 +345,17 @@ H5VL__native_dataset_write(void *obj, hid_t mem_type_id, hid_t mem_space_id, hid
         HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data")
 
 done:
+    /* Clean up */
+    if (H5S_BLOCK == mem_space_id && mem_space) {
+        if (H5S_close(mem_space) < 0)
+            HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL,
+                        "unable to release temporary memory dataspace for H5S_BLOCK")
+    } /* end if */
+    else if (H5S_PLIST == file_space_id && file_space)
+        if (H5S_select_all(file_space, TRUE) < 0)
+            HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL,
+                        "unable to release file dataspace selection for H5S_PLIST")
+
     FUNC_LEAVE_NOAPI(ret_value)
 } /* end H5VL__native_dataset_write() */