Fix bugs in test/vfd.c (#1538)

* Added support for vector I/O calls to the VFD layer, and
associated test code.  Note that this includes the optimization
to allow shortened sizes and types arrays to allow more space
efficient representations of vectors in which all entries are
of the same size and/or type.  See the Selection I/o RFC for
further details.

Tested serial and parallel, debug and production on Charis.
       serial and parallel debug only on Jelly.

* ran code formatter

quick serial build and test on jelly

* Add H5FD_read_selection() and H5FD_write_selection().  Currently only
translate to scalar calls.  Fix const buf in H5FD_write_vector().

* Format source

* Fix comments

* Added vector read / write support to the MPIO VFD, with associated
test code (see testpar/t_vfd.c).

Note that this implementation does NOT support vector entries of
size greater than 2 GB.  This must be repaired before release,
but it should be good enough for correctness testing.

As MPIO requires vector I/O requests to be sorted in increasing
address order, also added a vector sort utility in H5FDint.c  This
function is tested in passing by the MPIO vector I/O extension.

In passing, repaired a bug in size / type vector extension management
in H5FD_read/write_vector()

Tested parallel debug and production on charis and Jelly.

* Ran source code formatter

* Minor optimization to vector I/O request sort routine.

Tested parallel / debug on Jelly.

* Add selection I/O to chunk code, used when: not using chunk cache, no
datatype conversion, no I/O filters, no page buffer, not using collective
I/O.  Requires global variable H5_use_selection_io_g be set to TRUE.
Implemented selection to vector I/O transaltion at the file driver
layer.

* Fix formatting unrelated to previous change to stop github from
complaining.

* Add full API support for selection I/O.  Add tests for this.

* Added "ctl" callback to the VFD interfance, and the associated
H5FDctl() and H5FD_ctl() calls.

Modified the MPIO VFD accordingly -- specifically:

Added ctl() call with op-code support to expose rank, size,
and communicator.

Modified H5FD_mpi_get_rank(), H5FD_mpi_get_size(),
and H5FD_mpi_get_comm() to use the new ctl() callback.  In passing
removed the const qualifier from the file parameter of these
functions, as the file parameter of the ctl callback is not
const.

Deleted the old  H5FD__mpio_mpi_rank(), H5FD__mpio_mpi_size(), and
H5FD__mpio_communicator() calls from the MPIO VFD.

Deleted H5FD_class_mpi_t from H5FDprivate.h, and modified the
MPIO VFD accordingly.  Note that all VFDs now use H5FD_class_t,
with no special class for VFDs that that support MPI.

Some minor touch ups to the Neil's selection I/O mods in passing.

Tested serial and parallel, debug and production on charis and
jelly.

* Implement selection I/O for contiguous datasets.  Fix bug in selection
I/O translation.  Add const qualifiers to some internal selection I/O
routines to maintain const-correctness while avoiding memcpys.

* Add support for independent parallel I/O with selection I/O.  Add
HDF5_USE_SELECTION_IO env var to control selection I/O (default off).

* Implement parallel collective support for selection I/O.

* Fix comments and run formatter.

* Committing clang-format changes

* Run formatter

* Update selection IO branch with develop (#1215)

Merged branch 'develop' into selection_io

* Sync with develop (#1262)

Updated the branch with develop changes.

* Committing clang-format changes

* fixed spelling (#1353)

* Implement big I/O support for vector I/O requests in the MPIO file
driver.

* Committing clang-format changes

* Update dummy file driver in h5test.c to match new struct.

* Fix another outdated H5FD_class_t struct.

* Free arrays in H5FD__mpio_read/write_vector() as soon as they're not
needed, to cut down on memory usage during I/O.

* Committing clang-format changes

* Address comments from code review.  Fix const warnings with
H5S_SEL_ITER_INIT().

* Committing clang-format changes

* Fix warnings in selection I/O code

* Refactor H5FD__mpio_read/write_vector() to bring common code for
constructing MPI Datatype into a shared function.

* Committing clang-format changes

* Fix bugs in selection I/O code.

* Fix bugs in selection I/O code

* Address comments from review.  Add "version" field to H5FD_class_t
struct and accompanying H5FD_CLASS_VERSION macro.

* Committing clang-format changes

* Committing clang-format changes

* Address comments from selection I/O PR

* Committing clang-format changes

* Fix spelling

* Fix bugs int test/vfd.c

Co-authored-by: mainzer <mainzer#hdfgroup.org>
Co-authored-by: jrmainzer <72230804+jrmainzer@users.noreply.github.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>

1 files changed, 8 insertions, 3 deletions

diff --git a/test/vfd.c b/test/vfd.c
index 74889fd..1b83228 100644
--- a/test/vfd.c
+++ b/test/vfd.c
@@ -4399,7 +4399,6 @@ test_vector_io__verify_v(uint32_t count, H5FD_mem_t types[], size_t sizes[], voi
     hbool_t     verbose    = TRUE;
     uint32_t    i;
     size_t      j;
-    uint32_t    buf_size;
     char *      w_buf;
     char *      r_buf;
     const char *mem_type_names[7] = {"H5FD_MEM_DEFAULT", "H5FD_MEM_SUPER", "H5FD_MEM_BTREE", "H5FD_MEM_DRAW",
@@ -4429,7 +4428,7 @@ test_vector_io__verify_v(uint32_t count, H5FD_mem_t types[], size_t sizes[], voi
 
                     HDfprintf(stdout, "\n\nread/write buf mismatch in vector/entry");
                     HDfprintf(stdout, "\"%s\"/%u at offset %llu/%llu w/r = %c/%c type = %s\n\n", name,
-                              (unsigned)i, (long long unsigned)j, (long long unsigned)buf_size, w_buf[j],
+                              (unsigned)i, (long long unsigned)j, (long long unsigned)size, w_buf[j],
                               r_buf[j], mem_type_names[type]);
                 }
             }
@@ -5521,6 +5520,7 @@ test_selection_io(const char *vfd_name)
         /* Update file buf */
         for (i = 0, i2 = 1, j2 = 0; i < SEL_IO_DIM0; i++)
             for (j = 1; j < SEL_IO_DIM1; j += 2) {
+                HDassert(i2 < SEL_IO_DIM0);
                 fbuf2[i2][j2] = wbuf2[i][j];
                 if (++j2 == SEL_IO_DIM1) {
                     i2 += 2;
@@ -5582,9 +5582,10 @@ test_selection_io(const char *vfd_name)
 
         /* Update file buf */
         for (i = 1, i2 = 0, j2 = 1; i < (SEL_IO_DIM0 * SEL_IO_DIM1); i += 2) {
+            HDassert(i2 < SEL_IO_DIM0);
             fbuf2[i2][j2] = wbuf1[i];
             j2 += 2;
-            if (j2 == SEL_IO_DIM1) {
+            if (j2 >= SEL_IO_DIM1) {
                 i2++;
                 j2 = 1;
             }
@@ -5643,6 +5644,7 @@ test_selection_io(const char *vfd_name)
         /* Update file buf */
         for (i = 0, i2 = 0; i < SEL_IO_DIM0; i += 2)
             for (j = 0; j < SEL_IO_DIM1; j++) {
+                HDassert(i2 < (SEL_IO_DIM0 * SEL_IO_DIM1));
                 fbuf1[i2] = wbuf2[i][j];
                 i2 += 2;
             }
@@ -5726,6 +5728,7 @@ test_selection_io(const char *vfd_name)
                 fbuf1[(2 * i) + 1] = wbuf1[2 * i];
             for (i = 1, i2 = 0, j2 = 1; i < SEL_IO_DIM0; i += 2)
                 for (j = 0; j < SEL_IO_DIM1; j++) {
+                    HDassert(i2 < SEL_IO_DIM0);
                     fbuf2[i2][j2] = wbuf2[i][j];
                     j2 += 2;
                     if (j2 >= SEL_IO_DIM1) {
@@ -5834,6 +5837,7 @@ test_selection_io(const char *vfd_name)
              * find 1D index into 2D array */
             for (i = 0, i2 = 0, j2 = 0; i < SEL_IO_DIM0; i += 2)
                 for (j = 0; j < SEL_IO_DIM1; j++) {
+                    HDassert(i2 < SEL_IO_DIM0);
                     fbuf1[(i2 * SEL_IO_DIM1) + j2] = wbuf2[i][j];
                     j2 += 2;
                     if (j2 >= SEL_IO_DIM1) {
@@ -5843,6 +5847,7 @@ test_selection_io(const char *vfd_name)
                 }
             for (i = 1, i2 = 0, j2 = 1; i < SEL_IO_DIM0; i += 2)
                 for (j = 0; j < SEL_IO_DIM1; j++) {
+                    HDassert(i2 < SEL_IO_DIM0);
                     fbuf2[i2][j2] = wbuf2[i][j];
                     j2 += 2;
                     if (j2 >= SEL_IO_DIM1) {