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 * Cleans up some POSIX header bits in H5private.h (#783) * Removes outdated checks for ways inline might be defined (#781) These are obsolete now that we require C99.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>
HDFGroup · Jul 12, 2021 · eebaee6 · eebaee6
1 parent b9dbabc
commit eebaee6
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Showing 38 changed files with 698 additions and 324 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,11 +1,5 @@
 # .gitignore file for HDF5
 
-# ctags
-**/tags
-
-# vim swap files
-**/.*.swp
-
 # Makefile.in files
 **/Makefile.in
 

diff --git a/config/cmake/H5pubconf.h.in b/config/cmake/H5pubconf.h.in
@@ -394,9 +394,6 @@
 /* Define if your system has window style path name. */
 #cmakedefine H5_HAVE_WINDOW_PATH @H5_HAVE_WINDOW_PATH@
 
-/* Define to 1 if you have the <winsock2.h> header file. */
-#cmakedefine H5_HAVE_WINSOCK2_H @H5_HAVE_WINSOCK2_H@
-
 /* Define to 1 if you have the <zlib.h> header file. */
 #cmakedefine H5_HAVE_ZLIB_H @H5_HAVE_ZLIB_H@
 

diff --git a/config/cmake_ext_mod/ConfigureChecks.cmake b/config/cmake_ext_mod/ConfigureChecks.cmake
@@ -53,7 +53,6 @@ if (MINGW)
   set (${HDF_PREFIX}_HAVE_MINGW 1)
   set (WINDOWS 1) # MinGW tries to imitate Windows
   set (CMAKE_REQUIRED_FLAGS "-DWIN32_LEAN_AND_MEAN=1 -DNOGDI=1")
-  set (${HDF_PREFIX}_HAVE_WINSOCK2_H 1)
   set (__USE_MINGW_ANSI_STDIO 1)
 endif ()
 
@@ -117,11 +116,6 @@ CHECK_INCLUDE_FILE_CONCAT ("features.h"      ${HDF_PREFIX}_HAVE_FEATURES_H)
 CHECK_INCLUDE_FILE_CONCAT ("dirent.h"        ${HDF_PREFIX}_HAVE_DIRENT_H)
 CHECK_INCLUDE_FILE_CONCAT ("unistd.h"        ${HDF_PREFIX}_HAVE_UNISTD_H)
 
-# Windows
-if (NOT CYGWIN)
-  CHECK_INCLUDE_FILE_CONCAT ("winsock2.h"      ${HDF_PREFIX}_HAVE_WINSOCK2_H)
-endif ()
-
 CHECK_INCLUDE_FILE_CONCAT ("globus/common.h" ${HDF_PREFIX}_HAVE_GLOBUS_COMMON_H)
 CHECK_INCLUDE_FILE_CONCAT ("pdb.h"           ${HDF_PREFIX}_HAVE_PDB_H)
 CHECK_INCLUDE_FILE_CONCAT ("pthread.h"       ${HDF_PREFIX}_HAVE_PTHREAD_H)

diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c
@@ -604,8 +604,6 @@ H5D__get_chunk_storage_size(H5D_t *dset, const hsize_t *offset, hsize_t *storage
     HDassert(offset);
     HDassert(storage_size);
 
-    *storage_size = 0;
-
     /* Allocate dataspace and initialize it if it hasn't been. */
     if (!(*layout->ops->is_space_alloc)(&layout->storage))
         HGOTO_DONE(SUCCEED)
@@ -5031,7 +5029,7 @@ H5D__chunk_collective_fill(const H5D_t *dset, H5D_chunk_coll_info_t *chunk_info,
          * order of offset in the file.
          */
         if (need_addr_sort)
-            HDqsort(chunk_disp_array, blocks, sizeof(MPI_Aint), H5D__chunk_cmp_addr);
+            HDqsort(chunk_disp_array, (size_t)blocks, sizeof(MPI_Aint), H5D__chunk_cmp_addr);
 
         /* MSC - should use this if MPI_type_create_hindexed block is working:
          * mpi_code = MPI_Type_create_hindexed_block(blocks, block_len, chunk_disp_array, MPI_BYTE,
@@ -6066,6 +6064,7 @@ H5D__chunk_copy_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
 
         if (udata->chunk_in_cache) {
             HDassert(H5F_addr_defined(chunk_rec->chunk_addr));
+            HDassert(ent);
             HDassert(H5F_addr_defined(ent->chunk_block.offset));
 
             H5_CHECKED_ASSIGN(nbytes, size_t, shared_fo->layout.u.chunk.size, uint32_t);
@@ -7498,6 +7497,36 @@ H5D__get_chunk_info_by_coord(const H5D_t *dset, const hsize_t *offset, unsigned
     FUNC_LEAVE_NOAPI_TAG(ret_value)
 } /* end H5D__get_chunk_info_by_coord() */
 
+/*-------------------------------------------------------------------------
+ * Function:    H5D__chunk_iter_cb
+ *
+ * Purpose:     Call the user-defined function with the chunk data. The iterator continues if
+ *              the user-defined function returns H5_ITER_CONT, and stops if H5_ITER_STOP is
+ *              returned.
+ *
+ * Return:      Success:    H5_ITER_CONT or H5_ITER_STOP
+ *              Failure:    Negative (H5_ITER_ERROR)
+ *
+ * Programmer:  Gaute Hope
+ *              August 2020
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+H5D__chunk_iter_cb(const H5D_chunk_rec_t *chunk_rec, void *udata)
+{
+    int ret_value = 0;
+
+    FUNC_ENTER_STATIC_NOERR
+
+    const H5D_chunk_iter_cb_data_t *data = (H5D_chunk_iter_cb_data_t *)udata;
+
+    ret_value = (data->cb)(chunk_rec->scaled, chunk_rec->filter_mask, chunk_rec->chunk_addr,
+                           chunk_rec->nbytes, data->op_data);
+
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D__chunk_iter_cb */
+
 /*-------------------------------------------------------------------------
  * Function:    H5D__chunk_iter
  *
@@ -7537,7 +7566,7 @@ H5D__chunk_iter(const H5D_t *dset, H5D_chunk_iter_op_t cb, void *op_data)
     for (ent = rdcc->head; ent; ent = ent->next)
         /* Flush the chunk out to disk, to make certain the size is correct later */
         if (H5D__chunk_flush_entry(dset, ent, FALSE) < 0)
-            HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot flush indexed storage buffer")
+            HGOTO_ERROR(H5E_DATASET, H5E_CANTFLUSH, FAIL, "cannot flush indexed storage buffer")
 
     /* Compose chunked index info struct */
     idx_info.f       = dset->oloc.file;
@@ -7559,33 +7588,3 @@ H5D__chunk_iter(const H5D_t *dset, H5D_chunk_iter_op_t cb, void *op_data)
 done:
     FUNC_LEAVE_NOAPI_TAG(ret_value)
 } /* end H5D__chunk_iter() */
-
-/*-------------------------------------------------------------------------
- * Function:    H5D__chunk_iter_cb
- *
- * Purpose:     Call the user-defined function with the chunk data. The iterator continues if
- *              the user-defined function returns H5_ITER_CONT, and stops if H5_ITER_STOP is
- *              returned.
- *
- * Return:      Success:    H5_ITER_CONT or H5_ITER_STOP
- *              Failure:    Negative (H5_ITER_ERROR)
- *
- * Programmer:  Gaute Hope
- *              August 2020
- *
- *-------------------------------------------------------------------------
- */
-static int
-H5D__chunk_iter_cb(const H5D_chunk_rec_t *chunk_rec, void *udata)
-{
-    int ret_value = 0;
-
-    FUNC_ENTER_STATIC_NOERR
-
-    const H5D_chunk_iter_cb_data_t *data = (H5D_chunk_iter_cb_data_t *)udata;
-
-    ret_value = (data->cb)(chunk_rec->scaled, chunk_rec->filter_mask, chunk_rec->chunk_addr,
-                           chunk_rec->nbytes, data->op_data);
-
-    FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5D__chunk_iter_cb */
diff --git a/src/H5Dprivate.h b/src/H5Dprivate.h
@@ -79,11 +79,12 @@
 #define H5D_MPIO_LOCAL_NO_COLLECTIVE_CAUSE_NAME                                                              \
     "local_no_collective_cause" /* cause of broken collective I/O in each process */
 #define H5D_MPIO_GLOBAL_NO_COLLECTIVE_CAUSE_NAME                                                             \
-    "global_no_collective_cause"                 /* cause of broken collective I/O in all processes */
-#define H5D_XFER_EDC_NAME       "err_detect"     /* EDC */
-#define H5D_XFER_FILTER_CB_NAME "filter_cb"      /* Filter callback function */
-#define H5D_XFER_CONV_CB_NAME   "type_conv_cb"   /* Type conversion callback function */
-#define H5D_XFER_XFORM_NAME     "data_transform" /* Data transform */
+    "global_no_collective_cause"                      /* cause of broken collective I/O in all processes */
+#define H5D_XFER_EDC_NAME         "err_detect"        /* EDC */
+#define H5D_XFER_FILTER_CB_NAME   "filter_cb"         /* Filter callback function */
+#define H5D_XFER_CONV_CB_NAME     "type_conv_cb"      /* Type conversion callback function */
+#define H5D_XFER_XFORM_NAME       "data_transform"    /* Data transform */
+#define H5D_XFER_DSET_IO_SEL_NAME "dset_io_selection" /* Dataset I/O selection */
 #ifdef H5_HAVE_INSTRUMENTED_LIBRARY
 /* Collective chunk instrumentation properties */
 #define H5D_XFER_COLL_CHUNK_LINK_HARD_NAME        "coll_chunk_link_hard"

diff --git a/src/H5Oattribute.c b/src/H5Oattribute.c
@@ -1901,48 +1901,3 @@ H5O__attr_bh_info(H5F_t *f, H5O_t *oh, H5_ih_info_t *bh_info)
 
     FUNC_LEAVE_NOAPI(ret_value)
 } /* H5O__attr_bh_info() */
-
-#ifndef H5_NO_DEPRECATED_SYMBOLS
-
-/*-------------------------------------------------------------------------
- * Function:    H5O__attr_count
- *
- * Purpose:     Determine the # of attributes on an object
- *
- * Return:      SUCCEED/FAIL
- *
- * Programmer:	Quincey Koziol
- *		Monday, December 11, 2006
- *
- *-------------------------------------------------------------------------
- */
-int
-H5O__attr_count(const H5O_loc_t *loc)
-{
-    H5O_t * oh = NULL;      /* Pointer to actual object header */
-    hsize_t nattrs;         /* Number of attributes */
-    int     ret_value = -1; /* Return value */
-
-    FUNC_ENTER_PACKAGE
-
-    /* Check arguments */
-    HDassert(loc);
-
-    /* Protect the object header to iterate over */
-    if (NULL == (oh = H5O_protect(loc, H5AC__READ_ONLY_FLAG, FALSE)))
-        HGOTO_ERROR(H5E_ATTR, H5E_CANTPROTECT, FAIL, "unable to load object header")
-
-    /* Retrieve # of attributes on object */
-    if (H5O__attr_count_real(loc->file, oh, &nattrs) < 0)
-        HGOTO_ERROR(H5E_ATTR, H5E_CANTGET, FAIL, "can't retrieve attribute count")
-
-    /* Set return value */
-    ret_value = (int)nattrs;
-
-done:
-    if (oh && H5O_unprotect(loc, oh, H5AC__NO_FLAGS_SET) < 0)
-        HDONE_ERROR(H5E_ATTR, H5E_CANTUNPROTECT, FAIL, "unable to release object header")
-
-    FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5O__attr_count */
-#endif /* H5_NO_DEPRECATED_SYMBOLS */