Onion VFD: Misc cleanup (#1693)

* Removes unused definitions from module headers (#1624)

* Fix these Doxygen warnings #1581 (#1589)

* Fixes a typo in H5.c (#1639)

* free MPI_Group/MPI_Comm/MPI_Datatype objects (#1638)

* free MPI_Group/MPI_Comm/MPI_Datatype objects

* fix clang-format style

* Adds build and license shields to README.md (#1641)

* First stab at a Github status bar

* Adds a .tokeignore file for counting lines of code accurately

* Yanks lines of code calculation since it wildly overcounts

* not depend on doIO to free an MPI_Comm object (#1642)

* free MPI datatypes previously created (#1637)

* Retrieve MPI-IO hints used by MPI library after file open (#1636)

H5Pget_fapl_mpio() should return an MPI info object containing all the
MPI-IO hints used by the MPI library underneath, after the file is
opened. Some hints, such as cb_nodes (number of I/O aggregators), are
useful for HDF5 applications and I/O libraries built on top of HDF5.

* OESS-168: Remove clang warnings. (#1309)

* OESS-168: Remove clang warnings.

* OESS-168: Address @lrknox review.

* OESS-168: Remove clang warnings. (#1376)

* Remove H5_NO_ALIGNMENT_RESTRICTIONS (#1426)

* Do not conditionally compile code that uses a pointer dereference
and assignment to copy a potentially unaligned variable to aligned
automatic storage, or vice versa.  Instead, always use naked `memcpy(3)`s.
Disassembling the generated code reveals that the `memcpy(3)`s optimize
(`-O3`) to a single `mov` instruction for x86_64, which is not strict
about alignment.

This change reduces the size of code and scripts by 143 lines, eases
our way to cross-compilation, and avoids invoking undefined behavior.

* Committing clang-format changes

* Per discussion, use HD and add comments.

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

* Cleans up some HL library code that inappropriately returns htri_t values cast to herr_t (#1651)

* Cleans up some HL library code that inappropriately returns
htri_t values cast to herr_t

* Committing clang-format changes

* Formatted source

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

* Mirror vfd test fixes (#1629)

* Use the FAPL that was created earlier in the test (and delete an unused
variable).   This allows 'make check-vfd' to pass with --enable-mirror-vfd.

* Check for testing directory before creating, to avoid warning from bash.
Clean out .libs directory before re-using it (after a failed test), to
remove any files generated by libtool.

* Committing clang-format changes

* Increment error count on failed file open and skip tests for VFDs that need
modified filenames.

* Skip the mirror VFD for 'make check-vfd' - the mirror VFD requires networking
configuration parameters and can't be provided for an automated test that
is configured with an environment variable.

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

* Removes HDF Group paths, adds shellcheck fixes (#1656)

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...
  https://www.shellcheck.net/wiki/SC2230 -- which is non-standard. Use builti...
  https://www.shellcheck.net/wiki/SC2006 -- Use $(...) notation instead of le...

* HDFFV-11306 Fixed (#1657)

* HDFFV-11306,
 * Fixed it so both h5open_f and h5close_f can be called multiple times.
 * Fixed an issue with open objects remaining after h5close_f was called.
 * Added additional tests.

* comments clean-up

* Develop clang format java (#1653)

* added HDFFV-11306 entry (#1662)

* Adds the -q flag to all swmr test programs, quieting noisy output (#1665)

* Adds paths-ignore to the Github pull request workflow (#1663)

* Changes Github action `hdf5 dev CI` to `PR hdf5 dev CI` (#1666)

So the PR action name is not the same as the one in main.yml

* Replace H5detect's build-time detection of C99 integer properties with a (#1400)

* Replace H5detect's build-time detection of C99 integer properties with a
table-driven routine, `H5T__init_native_int()`, that is run at library
initialization time.

* Improve handling of copying of dynamic libraries and clean them up after (#1681)

test finishes.

* Warnings fixes (#1680)

* Clean stack size warnings in sio_engine (#1687)

* Fixes stack size warnings in tcoords.c (#1688)

* Minor things noticed while bringing VFD SWMR in line with develop (#1691)

* Removed dead code, weird formatting, and other badness

* Fixed remaining stack size warnings in onion VFD

* Committing clang-format changes

Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: Wei-keng Liao <wkliao@users.noreply.github.com>
Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
Co-authored-by: David Young <dyoung@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Quincey Koziol <koziol@lbl.gov>
Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org>

1 files changed, 35 insertions, 20 deletions

diff --git a/tools/src/h5perf/sio_engine.c b/tools/src/h5perf/sio_engine.c
index bdd2c08..abf8b9a 100644
--- a/tools/src/h5perf/sio_engine.c
+++ b/tools/src/h5perf/sio_engine.c
@@ -123,7 +123,6 @@ static hid_t    h5dxpl          = H5I_INVALID_HID; /* Dataset transfer property
  * Purpose:         SIO Engine where IO are executed.
  * Return:          results
  * Programmer:      Christian Chilan, April, 2008
- * Modifications:
  */
 void
 do_sio(parameters param, results *res)
@@ -134,18 +133,20 @@ do_sio(parameters param, results *res)
     iotype     iot;                /* API type */
     char       base_name[256];     /* test file base name */
     /* return codes */
-    herr_t ret_code = 0; /*return code                           */
+    herr_t ret_code = 0; /* return code */
 
-    char fname[FILENAME_MAX]; /* test file name */
-    int  i;
-    /* HDF5 variables */
-    herr_t hrc; /*HDF5 return code              */
+    char *fname = NULL;
+    int   i;
 
-    /* Sanity check parameters */
+    /* HDF5 variables */
+    herr_t hrc; /* HDF5 return code */
 
     /* IO type */
     iot = param.io_type;
 
+    if (NULL == (fname = HDcalloc(FILENAME_MAX, sizeof(char))))
+        GOTOERROR(FAIL);
+
     switch (iot) {
         case POSIXIO:
             fd.posixfd  = -1;
@@ -267,8 +268,8 @@ done:
     }
 
     /* release generic resources */
-    if (buffer)
-        free(buffer);
+    HDfree(buffer);
+    HDfree(fname);
 
     res->ret_code = ret_code;
 }
@@ -1125,7 +1126,6 @@ done:
  * Purpose:     Sets file driver.
  * Return:      SUCCESS or FAIL
  * Programmer:  Christian Chilan, April, 2008
- * Modifications:
  */
 
 hid_t
@@ -1164,9 +1164,11 @@ set_vfd(parameters *param)
         H5FD_mem_t  memb_map[H5FD_MEM_NTYPES];
         hid_t       memb_fapl[H5FD_MEM_NTYPES];
         const char *memb_name[H5FD_MEM_NTYPES];
-        char        sv[H5FD_MEM_NTYPES][1024];
         haddr_t     memb_addr[H5FD_MEM_NTYPES];
         H5FD_mem_t  mt;
+        struct {
+            char arr[H5FD_MEM_NTYPES][1024];
+        } *sv = NULL;
 
         HDmemset(memb_map, 0, sizeof memb_map);
         HDmemset(memb_fapl, 0, sizeof memb_fapl);
@@ -1174,16 +1176,22 @@ set_vfd(parameters *param)
         HDmemset(memb_addr, 0, sizeof memb_addr);
 
         HDassert(HDstrlen(multi_letters) == H5FD_MEM_NTYPES);
+
+        if (NULL == (sv = HDcalloc(1, sizeof(*sv))))
+            return -1;
         for (mt = H5FD_MEM_DEFAULT; mt < H5FD_MEM_NTYPES; mt++) {
             memb_fapl[mt] = H5P_DEFAULT;
-            HDsprintf(sv[mt], "%%s-%c.h5", multi_letters[mt]);
-            memb_name[mt] = sv[mt];
+            HDsprintf(sv->arr[mt], "%%s-%c.h5", multi_letters[mt]);
+            memb_name[mt] = sv->arr[mt];
             memb_addr[mt] = (haddr_t)MAX(mt - 1, 0) * (HADDR_MAX / 10);
         }
 
         if (H5Pset_fapl_multi(my_fapl, memb_map, memb_fapl, memb_name, memb_addr, FALSE) < 0) {
+            HDfree(sv);
             return -1;
         }
+
+        HDfree(sv);
     }
     else if (vfd == family) {
         hsize_t fam_size = 1 * 1024 * 1024; /*100 MB*/
@@ -1262,14 +1270,18 @@ done:
  * Purpose:     Cleanup temporary file unless HDF5_NOCLEANUP is set.
  * Return:      void
  * Programmer:  Albert Cheng 2001/12/12
- * Modifications: Support for file drivers. Christian Chilan, April, 2008
  */
 static void
 do_cleanupfile(iotype iot, char *filename)
 {
-    char  temp[4096 + sizeof("-?.h5")];
-    int   j;
-    hid_t driver;
+    char * temp = NULL;
+    size_t temp_sz;
+    int    j;
+    hid_t  driver;
+
+    temp_sz = (4096 + sizeof("-?.h5")) * sizeof(char);
+    if (NULL == (temp = HDcalloc(1, temp_sz)))
+        goto done;
 
     if (clean_file_g == -1)
         clean_file_g = (HDgetenv(HDF5_NOCLEANUP) == NULL) ? 1 : 0;
@@ -1286,7 +1298,7 @@ do_cleanupfile(iotype iot, char *filename)
 
                 if (driver == H5FD_FAMILY) {
                     for (j = 0; /*void*/; j++) {
-                        HDsnprintf(temp, sizeof temp, filename, j);
+                        HDsnprintf(temp, temp_sz, filename, j);
 
                         if (HDaccess(temp, F_OK) < 0)
                             break;
@@ -1305,10 +1317,10 @@ do_cleanupfile(iotype iot, char *filename)
                 }
                 else if (driver == H5FD_MULTI) {
                     H5FD_mem_t mt;
-                    assert(HDstrlen(multi_letters) == H5FD_MEM_NTYPES);
+                    HDassert(HDstrlen(multi_letters) == H5FD_MEM_NTYPES);
 
                     for (mt = H5FD_MEM_DEFAULT; mt < H5FD_MEM_NTYPES; mt++) {
-                        HDsnprintf(temp, sizeof temp, "%s-%c.h5", filename, multi_letters[mt]);
+                        HDsnprintf(temp, temp_sz, "%s-%c.h5", filename, multi_letters[mt]);
                         HDremove(temp); /*don't care if it fails*/
                     }
                 }
@@ -1325,4 +1337,7 @@ do_cleanupfile(iotype iot, char *filename)
                 break;
         }
     }
+
+done:
+    HDfree(temp);
 }