Onion VFD: Sync with develop (#1685)

* 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.

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>

4 files changed, 42 insertions, 29 deletions

diff --git a/test/cross_read.c b/test/cross_read.c
index cb71996..b8a2b46 100644
--- a/test/cross_read.c
+++ b/test/cross_read.c
@@ -229,8 +229,10 @@ check_file(char *filename)
 #endif
 
     /* Open the file. */
-    if ((fid = H5Fopen(pathname, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0)
+    if ((fid = H5Fopen(pathname, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0) {
+        nerrors++;
         FAIL_STACK_ERROR;
+    }
 
     TESTING("regular dataset of LE DOUBLE");
     nerrors += check_data_f(DATASETNAME, fid);
@@ -357,6 +359,14 @@ main(void)
 
     h5_reset();
 
+    /*
+     * Skip tests for VFDs that need modified filenames.
+     */
+    if (h5_driver_uses_modified_filename()) {
+        HDputs(" -- SKIPPED for incompatible VFD --");
+        HDexit(EXIT_SUCCESS);
+    }
+
     HDputs("\n");
     HDputs("Testing reading data created on Linux");
     h5_fixname(FILENAME[1], H5P_DEFAULT, filename, sizeof(filename));
diff --git a/test/mirror_vfd.c b/test/mirror_vfd.c
index 7047146..f66e6fc 100644
--- a/test/mirror_vfd.c
+++ b/test/mirror_vfd.c
@@ -2183,8 +2183,9 @@ test_on_disk_zoo(void)
     if (pass) {
         validate_zoo(file_id, grp_name, 0); /* sanity-check */
     }
+
     if (!pass) {
-        HDprintf(failure_mssg);
+        HDprintf("%s", failure_mssg);
         TEST_ERROR;
     }
 
@@ -2250,12 +2251,11 @@ static int
 test_vanishing_datasets(void)
 {
     struct mirrortest_filenames names;
-    hid_t                       file_id        = H5I_INVALID_HID;
-    hid_t                       fapl_id        = H5I_INVALID_HID;
-    hid_t                       dset_id        = H5I_INVALID_HID;
-    hid_t                       dspace_id      = H5I_INVALID_HID;
-    hid_t                       mirror_fapl_id = H5I_INVALID_HID;
-    hsize_t                     dims[2]        = {DATABUFFER_SIZE, DATABUFFER_SIZE};
+    hid_t                       file_id   = H5I_INVALID_HID;
+    hid_t                       fapl_id   = H5I_INVALID_HID;
+    hid_t                       dset_id   = H5I_INVALID_HID;
+    hid_t                       dspace_id = H5I_INVALID_HID;
+    hsize_t                     dims[2]   = {DATABUFFER_SIZE, DATABUFFER_SIZE};
     uint32_t                    buf[DATABUFFER_SIZE][DATABUFFER_SIZE]; /* consider malloc? */
     H5G_info_t                  group_info;
     unsigned int                i, j, k;
@@ -2333,7 +2333,7 @@ test_vanishing_datasets(void)
     file_id = H5I_INVALID_HID;
 
     /* verify there are no datasets in file */
-    file_id = H5Fopen(names.rw, H5F_ACC_RDONLY, H5P_DEFAULT);
+    file_id = H5Fopen(names.rw, H5F_ACC_RDONLY, fapl_id);
     if (file_id < 0) {
         TEST_ERROR;
     }
@@ -2348,7 +2348,7 @@ test_vanishing_datasets(void)
     if (H5Fclose(file_id) < 0) {
         TEST_ERROR;
     }
-    file_id = H5Fopen(names.wo, H5F_ACC_RDONLY, H5P_DEFAULT);
+    file_id = H5Fopen(names.wo, H5F_ACC_RDONLY, fapl_id);
     if (file_id < 0) {
         TEST_ERROR;
     }
@@ -2384,9 +2384,6 @@ test_vanishing_datasets(void)
 error:
     H5E_BEGIN_TRY
     {
-        if (mirror_fapl_id != H5I_INVALID_HID) {
-            H5Pclose(mirror_fapl_id);
-        }
         if (fapl_id != H5I_INVALID_HID) {
             H5Pclose(fapl_id);
         }
diff --git a/test/test_mirror.sh.in b/test/test_mirror.sh.in
index b3e75c6..9713f89 100644
--- a/test/test_mirror.sh.in
+++ b/test/test_mirror.sh.in
@@ -45,7 +45,9 @@ done
 RUN_DIR=mirror_vfd_test
 MIRROR_UTILS=../utils/mirror_vfd # TODO: presupposes from test/
 
-mkdir $RUN_DIR
+if [[ ! -d $RUN_DIR ]] ; then
+    mkdir $RUN_DIR
+fi
 
 # Copy program files into dedicated test directory
 for FILE in $MIRROR_UTILS/mirror_* ; do
@@ -61,6 +63,10 @@ cp mirror_vfd $RUN_DIR
 # wrapper script. Copy these libs builds if appropriate.
 if [ -f $MIRROR_UTILS/.libs/mirror_server ] ; then
     RUN_LIBS=$RUN_DIR/.libs
+    # Delete previous .libs directory, to remove any generated libtool files
+    if [[ -d $RUN_LIBS ]] ; then
+        rm -rf $RUN_LIBS
+    fi
     mkdir $RUN_LIBS
     for FILE in $MIRROR_UTILS/.libs/mirror_* ; do
         case "$FILE" in
diff --git a/test/test_swmr.sh.in b/test/test_swmr.sh.in
index 771fe4a..d61fdbb 100644
--- a/test/test_swmr.sh.in
+++ b/test/test_swmr.sh.in
@@ -170,7 +170,7 @@ do
         echo "###############################################################################"
         # Launch the Generator without SWMR_WRITE
         echo launch the swmr_generator
-        $testdir/swmr_generator $compress $index_type
+        $testdir/swmr_generator -q $compress $index_type
         if test $? -ne 0; then
             echo generator had error
             nerrors=`expr $nerrors + 1`
@@ -178,7 +178,7 @@ do
 
         # Launch the Generator with SWMR_WRITE
         echo launch the swmr_generator with SWMR_WRITE
-        $testdir/swmr_generator -s $compress $index_type
+        $testdir/swmr_generator -q -s $compress $index_type
         if test $? -ne 0; then
             echo generator had error
             nerrors=`expr $nerrors + 1`
@@ -202,7 +202,7 @@ do
         # Launch the Writer
         echo launch the swmr_start_writer
         seed="" # Put -r <random seed> command here
-        $testdir/swmr_start_write $compress $index_type $Nrecords $seed 2>&1 |tee swmr_writer.out &
+        $testdir/swmr_start_write -q $compress $index_type $Nrecords $seed 2>&1 |tee swmr_writer.out &
         pid_writer=$!
         $DPRINT pid_writer=$pid_writer
 
@@ -218,7 +218,7 @@ do
         while [ $n -lt $Nreaders ]; do
             #seed="-r ${seeds[$n]}"
             seed=""
-            $testdir/swmr_reader $Nsecs_add $seed 2>&1 |tee swmr_reader.out.$n &
+            $testdir/swmr_reader -q $Nsecs_add $seed 2>&1 |tee swmr_reader.out.$n &
             pid_readers="$pid_readers $!"
             n=`expr $n + 1`
         done
@@ -263,7 +263,7 @@ do
 
         # Launch the Generator
         echo launch the swmr_generator
-        $testdir/swmr_generator -s $compress $index_type
+        $testdir/swmr_generator -q -s $compress $index_type
         if test $? -ne 0; then
             echo generator had error
             nerrors=`expr $nerrors + 1`
@@ -275,7 +275,7 @@ do
         # Launch the Writer
         echo launch the swmr_writer
         seed="" # Put -r <random seed> command here
-        $testdir/swmr_writer -o $Nrecords $seed 2>&1 |tee swmr_writer.out &
+        $testdir/swmr_writer -q -o $Nrecords $seed 2>&1 |tee swmr_writer.out &
         pid_writer=$!
         $DPRINT pid_writer=$pid_writer
 
@@ -290,7 +290,7 @@ do
         while [ $n -lt $Nreaders ]; do
             #seed="-r ${seeds[$n]}"
             seed=""
-            $testdir/swmr_reader $Nsecs_add $seed 2>&1 |tee swmr_reader.out.$n &
+            $testdir/swmr_reader -q $Nsecs_add $seed 2>&1 |tee swmr_reader.out.$n &
             pid_readers="$pid_readers $!"
             n=`expr $n + 1`
         done
@@ -338,7 +338,7 @@ do
         # Launch the Remove Writer
         echo launch the swmr_remove_writer
         seed="" # Put -r <random seed> command here
-        $testdir/swmr_remove_writer -o $Nrecs_rem $seed 2>&1 |tee swmr_writer.out &
+        $testdir/swmr_remove_writer -q -o $Nrecs_rem $seed 2>&1 |tee swmr_writer.out &
         pid_writer=$!
         $DPRINT pid_writer=$pid_writer
 
@@ -353,7 +353,7 @@ do
         while [ $n -lt $Nreaders ]; do
             #seed="-r ${seeds[$n]}"
             seed=""
-            $testdir/swmr_remove_reader $Nsecs_rem $seed 2>&1 |tee swmr_reader.out.$n &
+            $testdir/swmr_remove_reader -q $Nsecs_rem $seed 2>&1 |tee swmr_reader.out.$n &
             pid_readers="$pid_readers $!"
             n=`expr $n + 1`
         done
@@ -398,7 +398,7 @@ do
 
         # Launch the Generator
         echo launch the swmr_generator
-        $testdir/swmr_generator $compress $index_type
+        $testdir/swmr_generator -q $compress $index_type
         if test $? -ne 0; then
             echo generator had error
             nerrors=`expr $nerrors + 1`
@@ -407,7 +407,7 @@ do
         # Launch the Writer (not in parallel - just to rebuild the datasets)
         echo launch the swmr_writer
         seed="" # Put -r <random seed> command here
-        $testdir/swmr_writer $Nrecords $seed
+        $testdir/swmr_writer -q $Nrecords $seed
         if test $? -ne 0; then
             echo writer had error
             nerrors=`expr $nerrors + 1`
@@ -419,7 +419,7 @@ do
         # Launch the Add/Remove Writer
         echo launch the swmr_addrem_writer
         seed="" # Put -r <random seed> command here
-        $testdir/swmr_addrem_writer $Nrecords $seed 2>&1 |tee swmr_writer.out &
+        $testdir/swmr_addrem_writer -q $Nrecords $seed 2>&1 |tee swmr_writer.out &
         pid_writer=$!
         $DPRINT pid_writer=$pid_writer
 
@@ -434,7 +434,7 @@ do
         while [ $n -lt $Nreaders ]; do
             #seed="-r ${seeds[$n]}"
             seed=""
-            $testdir/swmr_remove_reader $Nsecs_addrem $seed 2>&1 |tee swmr_reader.out.$n &
+            $testdir/swmr_remove_reader -q $Nsecs_addrem $seed 2>&1 |tee swmr_reader.out.$n &
             pid_readers="$pid_readers $!"
             n=`expr $n + 1`
         done
@@ -482,7 +482,7 @@ do
         #       created by the generator.
         echo launch the swmr_generator
         seed="" # Put -r <random seed> command here
-        $testdir/swmr_generator $compress $index_type $seed
+        $testdir/swmr_generator -q $compress $index_type $seed
         if test $? -ne 0; then
             echo generator had error
             nerrors=`expr $nerrors + 1`
@@ -492,7 +492,7 @@ do
         rm -f $WRITER_MESSAGE
         # Launch the Sparse writer
         echo launch the swmr_sparse_writer
-        nice -n 20 $testdir/swmr_sparse_writer $Nrecs_spa 2>&1 |tee swmr_writer.out &
+        nice -n 20 $testdir/swmr_sparse_writer -q $Nrecs_spa 2>&1 |tee swmr_writer.out &
         pid_writer=$!
         $DPRINT pid_writer=$pid_writer