Merge1 issue 839 PRs to hdf5 1 12 (#904)

* Fixes for a couple of trivial warnings (#676)

* Committing clang-format changes

* Trivial warning fixes:

* Removes an unused done target in H5Tbit.c
* Add (void) to quiet "ignored return value" warnings in the generators
  (which generally ignore errors)

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

* Removes alternative function enter/leave macro scheme (#678)

* Committing clang-format changes

* Converted BEGIN_FUNC, etc. macros to FUNC_ENTER

* Rips out the BEGIN_FUNC, etc. macros

* Removes 'end if', etc. comments from H5HL package

* Committing clang-format changes

* Fixes an H5EA iterate issue

* Fixes an issue in the H5FA iterator code

* Further cleanup in bin/trace after macro removal

* Iterator changes in H5EA and H5FA

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

* Various CMake changes (#679)

* Committing clang-format changes

* Several CMake updates:

* Removes unused HDF5_ENABLE_HSIZET
* Switches TEST_SHELL_SCRIPTS to ON
* Sets SH_PROGRAM to bash instead of sh

* Set default build type back to RelWithDebInfo

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

* err_compat test cleanup (#681)

* Committing clang-format changes

* Cleans up err_compat test and output

* Formatted source

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

* CMake fix for sporadic flush2 failures (#692)

* Committing clang-format changes

* Runs the flush1/flush2 tests in their own directory

Avoids file deletions by other tests.

* Revert "Runs the flush1/flush2 tests in their own directory"

This reverts commit 746c04882434cb502e4231de8f7dd5acb4949f54.

Also pulls the flush files from the clean list, which is a simpler fix.

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

* Ubsan fixes (#498)

* Fixed use of null pointer identified by UBSan

UBSan warned:
runtime error: member access within null pointer of type 'named_dt_t' (aka 'struct named_dt_t')

with these two tests:
H5REPACK-committed_dt_DFF
H5REPACK-committed_dt

Reformulated per @gnuoyd suggestion.

* Fixed undefined float -> unsigned char conversion in HL_test_image

* Removed dead skip_overflow_tests_g global

The global `skip_overflow_tests_g` was being set but never read.

* Don't treat 2d array as 1d array, fixing UBSan complaint in `CPP_testhdf5`

* Committing clang-format changes

* Remove extra ']' in line 730.

* Committing clang-format changes

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

* BUG: DataSet assignment operator is missing (#503)

* BUG: DataSet assignment operator is missing

* Some compilers complain if the copy constructor is given explicitly
  but the assignment operator is implicitly set to default.

* Explicitly defining the assignment operator allows us to properly
  handle reference counters for shared resources.

* BUG: DataSet assignment operator is missing.

* Mimicking code of H5DataType::operator() as suggested by @bmribler.

* Added test

Description:
    Added test for DataSet::operator= that Leengit added
Platform tested:
    Linux/64 (jelly)

* Removed Author field.

* Commit clang format changes.

* Entry for Leengit's github PR #503

* Removed lines left by mistake

Co-authored-by: Binh-Minh Ribler <bmribler@hdfgroup.org>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>

* Hdf5 merge pr7 (#516)

* Modify temporary rpath for testing in java example scripts.

* Update URL in source file Copyright headers for web copy of COPYING (license) file.

* Add release_docs/code-conventions.md file.

* Add script to test h5py.

* Fix script error.

* Add file h5pytest.yml.

* Test declaration of counter variables in for loops.

* Committing clang-format changes

* Committing clang-format changes

* Added [] to line 126 of H5LTanalyze.l.
Ran bin/genparser with flex v2.6.4 and Bison v3.0.4 on jelly.

* Revert "Added [] to line 126 of H5LTanalyze.l."

This reverts commit e4a9cee441efa75b16a8ee030c86189e186dd266.

* Revert extra commits to match canonical develop.

* Add cmake variable HDF5_LIB_INFIX (#7)

* Add cmake variable HDF5_LIB_INFIX

This infix is added to all library names after 'hdf5'.
e.g. the infix '_openmpi' results in the library name 'libhdf5_openmpi.so'
This name is used in packages on debian based systems.
(see https://packages.debian.org/jessie/amd64/libhdf5-openmpi-8/filelist)

This option is useful when testing projects on debian based systems with
custom builds of hdf5 while trying to minimize differences between the
custom setup and the environment created by installing system packages.

* Added RELEASE.txt entry for HDF5_LIB_INFIX.

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

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

* Fixes a segfault when H5Pset_mdc_log_options is called multiple times on a fapl (#601)

* Committing clang-format changes

* Fixes a segfault when H5Pset_mdc_log_options() is called multiple times

An internal string is incorrectly freed when the API call is invoked
multiple times on a property list, which will usually cause a segfault
to occur. On the first call the log location is NULL so the problem
doesn't occur.

Fixes HDFFV-11239

* Fixes typos

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

* Fix for a segfault when H5Pset_fapl_log is passed an invalid fapl ID (#607)

* Committing clang-format changes

* Fixes an issue where H5Pset_fapl_log sefaults when passed an invalid
fapl ID

This was due to a pointer-containing struct being memset after the first
internal API call. If the first call failed, the error condition would
check if the pointer was not NULL and then attempt to free it if not.
This would lead to the freeing of a wild pointer if an invalid fapl ID
were passed in.

This was fixed by reordering the memset and adding a test to ensure the
problem stays fixed.

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

* Fixes crashes when size_hint > UINT32_MAX is passed to H5Gcreate1 (#611)

* Committing clang-format changes

* Fixes incorrect size_hint handling in H5Gcreate1

* Updates the size hint type for group creation

* Updates the RELEASE.txt note

* Revert "Updates the RELEASE.txt note"

This reverts commit 3df386acca806d652bbe2209f7c4503b30f068ff.

* Reverts previous behavior to use a uint32_t struct field

* Updates RELEASE.txt

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

Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Sean McBride <sean@rogue-research.com>
Co-authored-by: Lee Newberg <35611400+Leengit@users.noreply.github.com>
Co-authored-by: Binh-Minh Ribler <bmribler@hdfgroup.org>
Co-authored-by: Raphael Grimm <barcode@users.noreply.github.com>

1 files changed, 74 insertions, 47 deletions

diff --git a/src/H5FAdblkpage.c b/src/H5FAdblkpage.c
index 0f5ee29..1dca0fb 100644
--- a/src/H5FAdblkpage.c
+++ b/src/H5FAdblkpage.c
@@ -84,21 +84,25 @@ H5FL_BLK_DEFINE(page_elmts);
  *
  *-------------------------------------------------------------------------
  */
-BEGIN_FUNC(PKG, ERR, H5FA_dblk_page_t *, NULL, NULL, H5FA__dblk_page_alloc(H5FA_hdr_t *hdr, size_t nelmts))
-
-    /* Local variables */
+H5FA_dblk_page_t *
+H5FA__dblk_page_alloc(H5FA_hdr_t *hdr, size_t nelmts)
+{
     H5FA_dblk_page_t *dblk_page = NULL; /* Fixed array data block page */
+    H5FA_dblk_page_t *ret_value = NULL;
+
+    FUNC_ENTER_PACKAGE
 
     /* Check arguments */
     HDassert(hdr);
 
     /* Allocate memory for the data block */
     if (NULL == (dblk_page = H5FL_CALLOC(H5FA_dblk_page_t)))
-        H5E_THROW(H5E_CANTALLOC, "memory allocation failed for fixed array data block page")
+        HGOTO_ERROR(H5E_FARRAY, H5E_CANTALLOC, NULL,
+                    "memory allocation failed for fixed array data block page")
 
     /* Share common array information */
     if (H5FA__hdr_incr(hdr) < 0)
-        H5E_THROW(H5E_CANTINC, "can't increment reference count on shared array header")
+        HGOTO_ERROR(H5E_FARRAY, H5E_CANTINC, NULL, "can't increment reference count on shared array header")
     dblk_page->hdr = hdr;
 
     /* Set non-zero internal fields */
@@ -106,37 +110,41 @@ BEGIN_FUNC(PKG, ERR, H5FA_dblk_page_t *, NULL, NULL, H5FA__dblk_page_alloc(H5FA_
 
     /* Allocate buffer for elements in data block page */
     if (NULL == (dblk_page->elmts = H5FL_BLK_MALLOC(page_elmts, nelmts * hdr->cparam.cls->nat_elmt_size)))
-        H5E_THROW(H5E_CANTALLOC, "memory allocation failed for data block page element buffer")
+        HGOTO_ERROR(H5E_FARRAY, H5E_CANTALLOC, NULL,
+                    "memory allocation failed for data block page element buffer")
 
     /* Set the return value */
     ret_value = dblk_page;
 
-    CATCH
+done:
 
     if (!ret_value)
         if (dblk_page && H5FA__dblk_page_dest(dblk_page) < 0)
-            H5E_THROW(H5E_CANTFREE, "unable to destroy fixed array data block page")
+            HDONE_ERROR(H5E_FARRAY, H5E_CANTFREE, NULL, "unable to destroy fixed array data block page")
 
-END_FUNC(PKG) /* end H5FA__dblk_page_alloc() */
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5FA__dblk_page_alloc() */
 
 /*-------------------------------------------------------------------------
  * Function:    H5FA__dblk_page_create
  *
  * Purpose:     Creates a new fixed array data block page in the file
  *
- * Return:      Valid file address on success/HADDR_UNDEF on failure
+ * Return:      SUCCEED/FAIL
  *
  * Programmer:  Vailin Choi
  *              Thursday, April 30, 2009
  *
  *-------------------------------------------------------------------------
  */
-BEGIN_FUNC(PKG, ERR, herr_t, SUCCEED, FAIL,
-           H5FA__dblk_page_create(H5FA_hdr_t *hdr, haddr_t addr, size_t nelmts))
-
-    /* Local variables */
+herr_t
+H5FA__dblk_page_create(H5FA_hdr_t *hdr, haddr_t addr, size_t nelmts)
+{
     H5FA_dblk_page_t *dblk_page = NULL;  /* Fixed array data block page */
     hbool_t           inserted  = FALSE; /* Whether the header was inserted into cache */
+    herr_t            ret_value = SUCCEED;
+
+    FUNC_ENTER_PACKAGE
 
 #ifdef H5FA_DEBUG
     HDfprintf(stderr, "%s: Called, addr = %a\n", FUNC, addr);
@@ -147,7 +155,8 @@ BEGIN_FUNC(PKG, ERR, herr_t, SUCCEED, FAIL,
 
     /* Allocate the data block page */
     if (NULL == (dblk_page = H5FA__dblk_page_alloc(hdr, nelmts)))
-        H5E_THROW(H5E_CANTALLOC, "memory allocation failed for fixed array data block page")
+        HGOTO_ERROR(H5E_FARRAY, H5E_CANTALLOC, FAIL,
+                    "memory allocation failed for fixed array data block page")
 
     /* Set info about data block page on disk */
     dblk_page->addr = addr;
@@ -158,34 +167,38 @@ BEGIN_FUNC(PKG, ERR, herr_t, SUCCEED, FAIL,
 
     /* Clear any elements in data block page to fill value */
     if ((hdr->cparam.cls->fill)(dblk_page->elmts, nelmts) < 0)
-        H5E_THROW(H5E_CANTSET, "can't set fixed array data block page elements to class's fill value")
+        HGOTO_ERROR(H5E_FARRAY, H5E_CANTSET, FAIL,
+                    "can't set fixed array data block page elements to class's fill value")
 
     /* Cache the new fixed array data block page */
     if (H5AC_insert_entry(hdr->f, H5AC_FARRAY_DBLK_PAGE, dblk_page->addr, dblk_page, H5AC__NO_FLAGS_SET) < 0)
-        H5E_THROW(H5E_CANTINSERT, "can't add fixed array data block page to cache")
+        HGOTO_ERROR(H5E_FARRAY, H5E_CANTINSERT, FAIL, "can't add fixed array data block page to cache")
     inserted = TRUE;
 
     /* Add data block page as child of 'top' proxy */
     if (hdr->top_proxy) {
         if (H5AC_proxy_entry_add_child(hdr->top_proxy, hdr->f, dblk_page) < 0)
-            H5E_THROW(H5E_CANTSET, "unable to add fixed array entry as child of array proxy")
+            HGOTO_ERROR(H5E_FARRAY, H5E_CANTSET, FAIL,
+                        "unable to add fixed array entry as child of array proxy")
         dblk_page->top_proxy = hdr->top_proxy;
     } /* end if */
 
-    CATCH
+done:
     if (ret_value < 0)
         if (dblk_page) {
             /* Remove from cache, if inserted */
             if (inserted)
                 if (H5AC_remove_entry(dblk_page) < 0)
-                    H5E_THROW(H5E_CANTREMOVE, "unable to remove fixed array data block page from cache")
+                    HDONE_ERROR(H5E_FARRAY, H5E_CANTREMOVE, FAIL,
+                                "unable to remove fixed array data block page from cache")
 
             /* Destroy data block page */
             if (H5FA__dblk_page_dest(dblk_page) < 0)
-                H5E_THROW(H5E_CANTFREE, "unable to destroy fixed array data block page")
+                HDONE_ERROR(H5E_FARRAY, H5E_CANTFREE, FAIL, "unable to destroy fixed array data block page")
         } /* end if */
 
-END_FUNC(PKG) /* end H5FA__dblk_page_create() */
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5FA__dblk_page_create() */
 
 /*-------------------------------------------------------------------------
  * Function:    H5FA__dblk_page_protect
@@ -200,13 +213,14 @@ END_FUNC(PKG) /* end H5FA__dblk_page_create() */
  *
  *-------------------------------------------------------------------------
  */
-BEGIN_FUNC(PKG, ERR, H5FA_dblk_page_t *, NULL, NULL,
-           H5FA__dblk_page_protect(H5FA_hdr_t *hdr, haddr_t dblk_page_addr, size_t dblk_page_nelmts,
-                                   unsigned flags))
-
-    /* Local variables */
+H5FA_dblk_page_t *
+H5FA__dblk_page_protect(H5FA_hdr_t *hdr, haddr_t dblk_page_addr, size_t dblk_page_nelmts, unsigned flags)
+{
     H5FA_dblk_page_t *        dblk_page = NULL; /* Fixed array data block page */
     H5FA_dblk_page_cache_ud_t udata;            /* Information needed for loading data block page */
+    H5FA_dblk_page_t *        ret_value = NULL;
+
+    FUNC_ENTER_PACKAGE
 
 #ifdef H5FA_DEBUG
     HDfprintf(stderr, "%s: Called\n", FUNC);
@@ -227,32 +241,36 @@ BEGIN_FUNC(PKG, ERR, H5FA_dblk_page_t *, NULL, NULL,
     /* Protect the data block page */
     if (NULL == (dblk_page = (H5FA_dblk_page_t *)H5AC_protect(hdr->f, H5AC_FARRAY_DBLK_PAGE, dblk_page_addr,
                                                               &udata, flags)))
-        H5E_THROW(H5E_CANTPROTECT, "unable to protect fixed array data block page, address = %llu",
-                  (unsigned long long)dblk_page_addr)
+        HGOTO_ERROR(H5E_FARRAY, H5E_CANTPROTECT, NULL,
+                    "unable to protect fixed array data block page, address = %llu",
+                    (unsigned long long)dblk_page_addr)
 
     /* Create top proxy, if it doesn't exist */
     if (hdr->top_proxy && NULL == dblk_page->top_proxy) {
         /* Add data block page as child of 'top' proxy */
         if (H5AC_proxy_entry_add_child(hdr->top_proxy, hdr->f, dblk_page) < 0)
-            H5E_THROW(H5E_CANTSET, "unable to add fixed array entry as child of array proxy")
+            HGOTO_ERROR(H5E_FARRAY, H5E_CANTSET, NULL,
+                        "unable to add fixed array entry as child of array proxy")
         dblk_page->top_proxy = hdr->top_proxy;
     } /* end if */
 
     /* Set return value */
     ret_value = dblk_page;
 
-    CATCH
+done:
 
     /* Clean up on error */
     if (!ret_value) {
         /* Release the data block page, if it was protected */
         if (dblk_page &&
             H5AC_unprotect(hdr->f, H5AC_FARRAY_DBLK_PAGE, dblk_page->addr, dblk_page, H5AC__NO_FLAGS_SET) < 0)
-            H5E_THROW(H5E_CANTUNPROTECT, "unable to unprotect fixed array data block page, address = %llu",
-                      (unsigned long long)dblk_page->addr)
+            HDONE_ERROR(H5E_FARRAY, H5E_CANTUNPROTECT, NULL,
+                        "unable to unprotect fixed array data block page, address = %llu",
+                        (unsigned long long)dblk_page->addr)
     } /* end if */
 
-END_FUNC(PKG) /* end H5FA__dblk_page_protect() */
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5FA__dblk_page_protect() */
 
 /*-------------------------------------------------------------------------
  * Function:    H5FA__dblk_page_unprotect
@@ -267,10 +285,12 @@ END_FUNC(PKG) /* end H5FA__dblk_page_protect() */
  *
  *-------------------------------------------------------------------------
  */
-BEGIN_FUNC(PKG, ERR, herr_t, SUCCEED, FAIL,
-           H5FA__dblk_page_unprotect(H5FA_dblk_page_t *dblk_page, unsigned cache_flags))
+herr_t
+H5FA__dblk_page_unprotect(H5FA_dblk_page_t *dblk_page, unsigned cache_flags)
+{
+    herr_t ret_value = SUCCEED;
 
-/* Local variables */
+    FUNC_ENTER_PACKAGE
 
 #ifdef H5FA_DEBUG
     HDfprintf(stderr, "%s: Called\n", FUNC);
@@ -281,12 +301,13 @@ BEGIN_FUNC(PKG, ERR, herr_t, SUCCEED, FAIL,
 
     /* Unprotect the data block page */
     if (H5AC_unprotect(dblk_page->hdr->f, H5AC_FARRAY_DBLK_PAGE, dblk_page->addr, dblk_page, cache_flags) < 0)
-        H5E_THROW(H5E_CANTUNPROTECT, "unable to unprotect fixed array data block page, address = %llu",
-                  (unsigned long long)dblk_page->addr)
-
-    CATCH
+        HGOTO_ERROR(H5E_FARRAY, H5E_CANTUNPROTECT, FAIL,
+                    "unable to unprotect fixed array data block page, address = %llu",
+                    (unsigned long long)dblk_page->addr)
 
-END_FUNC(PKG) /* end H5FA__dblk_page_unprotect() */
+done:
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5FA__dblk_page_unprotect() */
 
 /*-------------------------------------------------------------------------
  * Function:    H5FA__dblk_page_dest
@@ -300,7 +321,12 @@ END_FUNC(PKG) /* end H5FA__dblk_page_unprotect() */
  *
  *-------------------------------------------------------------------------
  */
-BEGIN_FUNC(PKG, ERR, herr_t, SUCCEED, FAIL, H5FA__dblk_page_dest(H5FA_dblk_page_t *dblk_page))
+herr_t
+H5FA__dblk_page_dest(H5FA_dblk_page_t *dblk_page)
+{
+    herr_t ret_value = SUCCEED;
+
+    FUNC_ENTER_PACKAGE
 
     /* Sanity check */
     HDassert(dblk_page);
@@ -315,7 +341,8 @@ BEGIN_FUNC(PKG, ERR, herr_t, SUCCEED, FAIL, H5FA__dblk_page_dest(H5FA_dblk_page_
 
         /* Decrement reference count on shared info */
         if (H5FA__hdr_decr(dblk_page->hdr) < 0)
-            H5E_THROW(H5E_CANTDEC, "can't decrement reference count on shared array header")
+            HGOTO_ERROR(H5E_FARRAY, H5E_CANTDEC, FAIL,
+                        "can't decrement reference count on shared array header")
         dblk_page->hdr = NULL;
     } /* end if */
 
@@ -325,6 +352,6 @@ BEGIN_FUNC(PKG, ERR, herr_t, SUCCEED, FAIL, H5FA__dblk_page_dest(H5FA_dblk_page_
     /* Free the data block page itself */
     dblk_page = H5FL_FREE(H5FA_dblk_page_t, dblk_page);
 
-    CATCH
-
-END_FUNC(PKG) /* end H5FA__dblk_page_dest() */
+done:
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5FA__dblk_page_dest() */