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authorJohn Mainzer <mainzer@hdfgroup.org>2010-10-17 07:52:19 (GMT)
committerJohn Mainzer <mainzer@hdfgroup.org>2010-10-17 07:52:19 (GMT)
commit93b2b7cf0782943085e2e9cb87459ed60d10c97b (patch)
treec279ed3cf00e85662cbc201c51050aebd2e4f479
parent1c14d3e96d8e4ab0b504ca98fdd3958c9cc451ea (diff)
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[svn-r19621] Port fo fix for the round robin parallel flush bug caused by the failure
of the H5Ocache.c code to update its image of the on disk representation of the object header on a call to clear callback. This wasn't an issue as long as all flushes of the object header were made from the same process, but if an object header is modified, and then flushed on one process and cleared on the rest, the changes were not be reflected in the images of the on disk representation on all processes where the object header was cleared rather than flushed. If one of these processes did the next flush, the changes were lost in the on disk representation. Fixed this by causing all dirty messages and to be written to the copy of the on disk image maintained by the object header code on both flush and clear. Also added associated test code in t_mdset.c. Also checking in some cache debug code developed while chasing this bug. Commit tested and tested (parallel) on phoenix.
-rw-r--r--src/H5AC.c34
-rw-r--r--src/H5ACprivate.h2
-rw-r--r--src/H5C.c131
-rw-r--r--src/H5Cprivate.h3
-rw-r--r--src/H5Ocache.c74
-rw-r--r--testpar/t_mdset.c512
-rw-r--r--testpar/testphdf5.c7
-rw-r--r--testpar/testphdf5.h1
8 files changed, 764 insertions, 0 deletions
diff --git a/src/H5AC.c b/src/H5AC.c
index 4f85303..042eb8e 100644
--- a/src/H5AC.c
+++ b/src/H5AC.c
@@ -1710,6 +1710,40 @@ done:
/*-------------------------------------------------------------------------
+ * Function: H5AC_dump_cache
+ *
+ * Purpose: Dumps a summary of the contents of the metadata cache
+ * to stdout.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: John Mainzer
+ * Sunday, October 10, 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5AC_dump_cache(const H5F_t *f)
+{
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI(H5AC_dump_cache, FAIL)
+
+ HDassert(f);
+ HDassert(f->shared);
+ HDassert(f->shared->cache);
+
+ if ( H5C_dump_cache(f->shared->cache, H5F_OPEN_NAME(f)) < 0 ) {
+
+ HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "H5C_dump_cache() failed.")
+ }
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* H5AC_dump_cache() */
+
+
+/*-------------------------------------------------------------------------
* Function: H5AC_get_cache_auto_resize_config
*
* Purpose: Wrapper function for H5C_get_cache_auto_resize_config().
diff --git a/src/H5ACprivate.h b/src/H5ACprivate.h
index 1c37d41..359b576 100644
--- a/src/H5ACprivate.h
+++ b/src/H5ACprivate.h
@@ -339,6 +339,8 @@ H5_DLL herr_t H5AC_set_write_done_callback(H5C_t * cache_ptr,
void (* write_done)(void));
H5_DLL herr_t H5AC_stats(const H5F_t *f);
+H5_DLL herr_t H5AC_dump_cache(const H5F_t *f);
+
H5_DLL herr_t H5AC_get_cache_auto_resize_config(const H5AC_t * cache_ptr,
H5AC_cache_config_t *config_ptr);
diff --git a/src/H5C.c b/src/H5C.c
index a92f694..a13bcd6 100644
--- a/src/H5C.c
+++ b/src/H5C.c
@@ -4878,6 +4878,137 @@ H5C_stats__reset(H5C_t UNUSED * cache_ptr)
/*-------------------------------------------------------------------------
+ * Function: H5C_dump_cache
+ *
+ * Purpose: Print a summary of the contents of the metadata cache for
+ * debugging purposes.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: John Mainzer
+ * 10/10/10
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5C_dump_cache(H5C_t * cache_ptr,
+ const char * cache_name)
+{
+ herr_t ret_value = SUCCEED; /* Return value */
+ int i;
+ H5C_cache_entry_t * entry_ptr = NULL;
+ H5SL_t * slist_ptr = NULL;
+ H5SL_node_t * node_ptr = NULL;
+
+ FUNC_ENTER_NOAPI(H5C_dump_cache, FAIL)
+
+ HDassert(cache_ptr != NULL);
+ HDassert(cache_ptr->magic == H5C__H5C_T_MAGIC);
+ HDassert(cache_name != NULL );
+
+ /* First, create a skip list */
+ slist_ptr = H5SL_create(H5SL_TYPE_HADDR);
+
+ if ( slist_ptr == NULL ) {
+
+ HGOTO_ERROR(H5E_CACHE, H5E_CANTCREATE, FAIL, "can't create skip list.")
+ }
+
+ /* Next, scan the index, and insert all entries in the skip list.
+ * Do this, as we want to display cache entries in increasing address
+ * order.
+ */
+ for ( i = 0; i < H5C__HASH_TABLE_LEN; i++ ) {
+
+ entry_ptr = cache_ptr->index[i];
+
+ while ( entry_ptr != NULL ) {
+
+ HDassert( entry_ptr->magic == H5C__H5C_CACHE_ENTRY_T_MAGIC );
+
+ if ( H5SL_insert(slist_ptr, entry_ptr, &(entry_ptr->addr)) < 0 ) {
+
+ HGOTO_ERROR(H5E_CACHE, H5E_BADVALUE, FAIL, \
+ "Can't insert entry in skip list")
+ }
+
+ entry_ptr = entry_ptr->ht_next;
+ }
+ }
+
+ /* If we get this far, all entries in the cache are listed in the
+ * skip list -- scan the skip list generating the desired output.
+ */
+
+ HDfprintf(stdout, "\n\nDump of metadata cache \"%s\".\n", cache_name);
+ HDfprintf(stdout,
+ "Num: Addr: Len: Type: Prot: Pinned: Dirty:\n");
+
+ i = 0;
+
+ node_ptr = H5SL_first(slist_ptr);
+
+ if ( node_ptr != NULL ) {
+
+ entry_ptr = (H5C_cache_entry_t *)H5SL_item(node_ptr);
+
+ } else {
+
+ entry_ptr = NULL;
+ }
+
+ while ( entry_ptr != NULL ) {
+
+ HDassert( entry_ptr->magic == H5C__H5C_CACHE_ENTRY_T_MAGIC );
+
+ HDfprintf(stdout,
+ "%s%d 0x%08llx 0x%3llx %2d %d %d %d\n",
+ cache_ptr->prefix, i,
+ (long long)(entry_ptr->addr),
+ (long long)(entry_ptr->size),
+ (int)(entry_ptr->type->id),
+ (int)(entry_ptr->is_protected),
+ (int)(entry_ptr->is_pinned),
+ (int)(entry_ptr->is_dirty));
+
+ /* increment node_ptr before we delete its target */
+ node_ptr = H5SL_next(node_ptr);
+
+ /* remove the first item in the skip list */
+ if ( H5SL_remove(slist_ptr, &(entry_ptr->addr)) != entry_ptr ) {
+
+ HGOTO_ERROR(H5E_CACHE, H5E_BADVALUE, FAIL, \
+ "Can't delete entry from skip list.")
+ }
+
+ if ( node_ptr != NULL ) {
+
+ entry_ptr = (H5C_cache_entry_t *)H5SL_item(node_ptr);
+
+ } else {
+
+ entry_ptr = NULL;
+ }
+
+ i++;
+ }
+
+ HDfprintf(stdout, "\n\n");
+
+ /* Finally, discard the skip list */
+
+ HDassert( H5SL_count(slist_ptr) == 0 );
+
+ H5SL_close(slist_ptr);
+
+done:
+
+ FUNC_LEAVE_NOAPI(ret_value)
+
+} /* H5C_dump_cache() */
+
+
+/*-------------------------------------------------------------------------
* Function: H5C_unpin_entry()
*
* Purpose: Unpin a cache entry. The entry must be unprotected at
diff --git a/src/H5Cprivate.h b/src/H5Cprivate.h
index 2ad6909..389cf5d 100644
--- a/src/H5Cprivate.h
+++ b/src/H5Cprivate.h
@@ -1121,6 +1121,9 @@ H5_DLL herr_t H5C_stats(H5C_t * cache_ptr,
H5_DLL void H5C_stats__reset(H5C_t * cache_ptr);
+H5_DLL herr_t H5C_dump_cache(H5C_t * cache_ptr,
+ const char * cache_name);
+
H5_DLL herr_t H5C_unpin_entry(void *thing);
H5_DLL herr_t H5C_unprotect(H5F_t * f,
diff --git a/src/H5Ocache.c b/src/H5Ocache.c
index fd8be18..a89da1f 100644
--- a/src/H5Ocache.c
+++ b/src/H5Ocache.c
@@ -558,6 +558,21 @@ done:
* koziol@ncsa.uiuc.edu
* Mar 20 2003
*
+ * Changes: In the parallel case, there is the possibility that the
+ * the object header may be flushed by different processes
+ * over the life of the computation. Thus we must ensure
+ * that the chunk images are up to date before we mark the
+ * messages clean -- as otherwise we may overwrite valid
+ * data with a blank section of a chunk image.
+ *
+ * To deal with this, I have added code to call
+ * H5O_chunk_serialize() for all chunks before we
+ * mark all messages as clean if we are not destroying the
+ * object. Do this in the parallel case only, as the problem
+ * can only occur in this context.
+ *
+ * JRM -- 10/12/10
+ *
*-------------------------------------------------------------------------
*/
static herr_t
@@ -571,6 +586,30 @@ H5O_clear(H5F_t *f, H5O_t *oh, hbool_t destroy)
/* check args */
HDassert(oh);
+#ifdef H5_HAVE_PARALLEL
+ if ( ( oh->cache_info.is_dirty ) && ( ! destroy ) ) {
+
+ size_t i;
+
+ /* scan through all chunks associated with the object header,
+ * and cause them to update their images for all entries currently
+ * marked dirty. Must do this in the parallel case, as it is possible
+ * that this processor may clear this object header several times
+ * before flushing it -- thus causing undefined sections of the image
+ * to be written to disk overwriting valid data.
+ */
+
+ for ( i = 0; i < oh->nchunks; i++ ) {
+
+ if ( H5O_chunk_serialize(f, oh, i) < 0 ) {
+
+ HGOTO_ERROR(H5E_OHDR, H5E_CANTSERIALIZE, FAIL,
+ "unable to serialize object header chunk")
+ }
+ }
+ }
+#endif /* H5_HAVE_PARALLEL */
+
/* Mark messages as clean */
for(u = 0; u < oh->nmesgs; u++)
oh->mesg[u].dirty = FALSE;
@@ -828,6 +867,30 @@ done:
* koziol@hdfgroup.org
* July 12, 2008
*
+ * Changes: In the parallel case, there is the possibility that the
+ * the object header chunk may be flushed by different
+ * processes over the life of the computation. Thus we must
+ * ensure that the chunk image is up to date before we mark its
+ * messages clean -- as otherwise we may overwrite valid
+ * data with a blank section of a chunk image.
+ *
+ * To deal with this, I have added code to call
+ * H5O_chunk_serialize() for this chunk before we
+ * mark all messages as clean if we are not destroying the
+ * chunk.
+ *
+ * Do this in the parallel case only, as the problem
+ * can only occur in this context.
+ *
+ * Note that at present at least, it seems that this fix
+ * is not necessary, as we don't seem to be able to
+ * generate a dirty chunk without creating a dirty object
+ * header. However, the object header code will be changing
+ * a lot in the near future, so I'll leave this fix in
+ * for now, unless Quincey requests otherwise.
+ *
+ * JRM -- 10/12/10
+ *
*-------------------------------------------------------------------------
*/
static herr_t
@@ -841,6 +904,17 @@ H5O_cache_chk_clear(H5F_t *f, H5O_chunk_proxy_t *chk_proxy, hbool_t destroy)
/* check args */
HDassert(chk_proxy);
+#ifdef H5_HAVE_PARALLEL
+ if ( ( chk_proxy->oh->cache_info.is_dirty ) && ( ! destroy ) ) {
+
+ if ( H5O_chunk_serialize(f, chk_proxy->oh, chk_proxy->chunkno) < 0 ) {
+
+ HGOTO_ERROR(H5E_OHDR, H5E_CANTSERIALIZE, FAIL,
+ "unable to serialize object header chunk")
+ }
+ }
+#endif /* H5_HAVE_PARALLEL */
+
/* Mark messages in chunk as clean */
for(u = 0; u < chk_proxy->oh->nmesgs; u++)
if(chk_proxy->oh->mesg[u].chunkno == chk_proxy->chunkno)
diff --git a/testpar/t_mdset.c b/testpar/t_mdset.c
index 51f06d7..779c681 100644
--- a/testpar/t_mdset.c
+++ b/testpar/t_mdset.c
@@ -1671,6 +1671,518 @@ void io_mode_confusion(void)
#undef N
+/*
+ * At present, the object header code maintains an image of its on disk
+ * representation, which is updates as necessary instead of generating on
+ * request.
+ *
+ * Prior to the fix that this test in designed to verify, the image of the
+ * on disk representation was only updated on flush -- not when the object
+ * header was marked clean.
+ *
+ * This worked perfectly well as long as all writes of a given object
+ * header were written from a single process. However, with the implementation
+ * of round robin metadata data writes in parallel HDF5, this is no longer
+ * the case -- it is possible for a given object header to be flushed from
+ * several different processes, with the object header simply being marked
+ * clean in all other processes on each flush. This resulted in NULL or
+ * out of data object header information being written to disk.
+ *
+ * To repair this, I modified the object header code to update its
+ * on disk image both on flush on when marked clean.
+ *
+ * This test is directed at verifying that the fix performs as expected.
+ *
+ * The test functions by creating a HDF5 file with several small datasets,
+ * and then flushing the file. This should result of at least one of
+ * the associated object headers being flushed by a process other than
+ * process 0.
+ *
+ * Then for each data set, add an attribute and flush the file again.
+ *
+ * Close the file and re-open it.
+ *
+ * Open the each of the data sets in turn. If all opens are successful,
+ * the test passes. Otherwise the test fails.
+ *
+ * Note that this test will probably become irrelevent shortly, when we
+ * land the journaling modifications on the trunk -- at which point all
+ * cache clients will have to construct on disk images on demand.
+ *
+ * JRM -- 10/13/10
+ *
+ * Changes: None.
+ */
+
+#define NUM_DATA_SETS 4
+#define LOCAL_DATA_SIZE 4
+#define LARGE_ATTR_SIZE 256
+
+void rr_obj_hdr_flush_confusion(void)
+{
+ const char * dataset_name[NUM_DATA_SETS] =
+ {
+ "dataset_0",
+ "dataset_1",
+ "dataset_2",
+ "dataset_3"
+ };
+ const char * att_name[NUM_DATA_SETS] =
+ {
+ "attribute_0",
+ "attribute_1",
+ "attribute_2",
+ "attribute_3"
+ };
+ const char * lg_att_name[NUM_DATA_SETS] =
+ {
+ "large_attribute_0",
+ "large_attribute_1",
+ "large_attribute_2",
+ "large_attribute_3"
+ };
+ int i;
+ int j;
+ hid_t file_id = -1;
+ hid_t fapl_id = -1;
+ hid_t dxpl_id = -1;
+ hid_t att_id[NUM_DATA_SETS];
+ hid_t att_space[NUM_DATA_SETS];
+ hid_t lg_att_id[NUM_DATA_SETS];
+ hid_t lg_att_space[NUM_DATA_SETS];
+ hid_t disk_space[NUM_DATA_SETS];
+ hid_t mem_space[NUM_DATA_SETS];
+ hid_t dataset[NUM_DATA_SETS];
+ hsize_t att_size[1];
+ hsize_t lg_att_size[1];
+ hsize_t disk_count[1];
+ hsize_t disk_size[1];
+ hsize_t disk_start[1];
+ hsize_t mem_count[1];
+ hsize_t mem_size[1];
+ hsize_t mem_start[1];
+ herr_t err;
+ double data[LOCAL_DATA_SIZE];
+ double att[LOCAL_DATA_SIZE];
+ double lg_att[LARGE_ATTR_SIZE];
+
+ /* MPI variables */
+ int mpi_size;
+ int mpi_rank;
+
+ /* test bed related variables */
+ const char * fcn_name = "rr_obj_hdr_flush_confusion";
+ const hbool_t verbose = FALSE;
+ const H5Ptest_param_t * pt;
+ char * filename;
+
+ /*
+ * setup test bed related variables:
+ */
+
+ pt = GetTestParameters();
+ filename = pt->name;
+
+ MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
+ MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
+
+ /*
+ * Set up file access property list with parallel I/O access
+ */
+
+ if(verbose )
+ HDfprintf(stdout, "%0d:%s: Setting up property list.\n",
+ mpi_rank, fcn_name);
+
+ fapl_id = H5Pcreate(H5P_FILE_ACCESS);
+ VRFY((fapl_id != -1), "H5Pcreate(H5P_FILE_ACCESS) failed");
+
+ err = H5Pset_fapl_mpio(fapl_id, MPI_COMM_WORLD, MPI_INFO_NULL);
+ VRFY((err >= 0 ), "H5Pset_fapl_mpio() failed");
+
+
+ /*
+ * Create a new file collectively and release property list identifier.
+ */
+
+ if(verbose )
+ HDfprintf(stdout, "%0d:%s: Creating new file \"%s\".\n",
+ mpi_rank, fcn_name, filename);
+
+ file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id);
+ VRFY((file_id >= 0 ), "H5Fcreate() failed");
+
+ err = H5Pclose(fapl_id);
+ VRFY((err >= 0 ), "H5Pclose(fapl_id) failed");
+
+
+ /*
+ * create the data sets.
+ */
+
+ if(verbose )
+ HDfprintf(stdout, "%0d:%s: Creating the datasets.\n",
+ mpi_rank, fcn_name);
+
+ disk_size[0] = (hsize_t)(LOCAL_DATA_SIZE * mpi_size);
+ mem_size[0] = (hsize_t)(LOCAL_DATA_SIZE);
+
+ for ( i = 0; i < NUM_DATA_SETS; i++ ) {
+
+ disk_space[i] = H5Screate_simple(1, disk_size, NULL);
+ VRFY((disk_space[i] >= 0), "H5Screate_simple(1) failed.\n");
+
+ dataset[i] = H5Dcreate(file_id, dataset_name[i], H5T_NATIVE_DOUBLE,
+ disk_space[i], H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+
+ VRFY((dataset[i] >= 0), "H5Dcreate(1) failed.\n");
+ }
+
+
+ /*
+ * setup data transfer property list
+ */
+
+ if(verbose )
+ HDfprintf(stdout, "%0d:%s: Setting up dxpl.\n", mpi_rank, fcn_name);
+
+ dxpl_id = H5Pcreate(H5P_DATASET_XFER);
+ VRFY((dxpl_id != -1), "H5Pcreate(H5P_DATASET_XFER) failed.\n");
+
+ err = H5Pset_dxpl_mpio(dxpl_id, H5FD_MPIO_COLLECTIVE);
+ VRFY((err >= 0),
+ "H5Pset_dxpl_mpio(dxpl_id, H5FD_MPIO_COLLECTIVE) failed.\n");
+
+ /*
+ * write data to the data sets
+ */
+
+ if(verbose )
+ HDfprintf(stdout, "%0d:%s: Writing datasets.\n", mpi_rank, fcn_name);
+
+ disk_count[0] = (hsize_t)(LOCAL_DATA_SIZE);
+ disk_start[0] = (hsize_t)(LOCAL_DATA_SIZE * mpi_rank);
+ mem_count[0] = (hsize_t)(LOCAL_DATA_SIZE);
+ mem_start[0] = (hsize_t)(0);
+
+ for ( j = 0; j < LOCAL_DATA_SIZE; j++ ) {
+
+ data[j] = (double)(mpi_rank + 1);
+ }
+
+ for ( i = 0; i < NUM_DATA_SETS; i++ ) {
+
+ err = H5Sselect_hyperslab(disk_space[i], H5S_SELECT_SET, disk_start,
+ NULL, disk_count, NULL);
+ VRFY((err >= 0), "H5Sselect_hyperslab(1) failed.\n");
+
+ mem_space[i] = H5Screate_simple(1, mem_size, NULL);
+ VRFY((mem_space[i] >= 0), "H5Screate_simple(2) failed.\n");
+
+ err = H5Sselect_hyperslab(mem_space[i], H5S_SELECT_SET,
+ mem_start, NULL, mem_count, NULL);
+ VRFY((err >= 0), "H5Sselect_hyperslab(2) failed.\n");
+
+ err = H5Dwrite(dataset[i], H5T_NATIVE_DOUBLE, mem_space[i],
+ disk_space[i], dxpl_id, data);
+ VRFY((err >= 0), "H5Dwrite(1) failed.\n");
+
+ for ( j = 0; j < LOCAL_DATA_SIZE; j++ ) data[j] *= 10.0;
+ }
+
+ /*
+ * close the data spaces
+ */
+
+ if(verbose )
+ HDfprintf(stdout, "%0d:%s: closing dataspaces.\n", mpi_rank, fcn_name);
+
+ for ( i = 0; i < NUM_DATA_SETS; i++ ) {
+
+ err = H5Sclose(disk_space[i]);
+ VRFY((err >= 0), "H5Sclose(disk_space[i]) failed.\n");
+
+ err = H5Sclose(mem_space[i]);
+ VRFY((err >= 0), "H5Sclose(mem_space[i]) failed.\n");
+ }
+
+ /*
+ * flush the metadata cache
+ */
+
+ if(verbose )
+ HDfprintf(stdout, "%0d:%s: flushing metadata cache.\n",
+ mpi_rank, fcn_name);
+ err = H5Fflush(file_id, H5F_SCOPE_GLOBAL);
+ VRFY((err >= 0), "H5Fflush(1) failed.\n");
+
+
+ /*
+ * write attributes to each dataset
+ */
+
+ if(verbose )
+ HDfprintf(stdout, "%0d:%s: writing attributes.\n", mpi_rank, fcn_name);
+
+ att_size[0] = (hsize_t)(LOCAL_DATA_SIZE);
+
+ for ( j = 0; j < LOCAL_DATA_SIZE; j++ ) {
+
+ att[j] = (double)(j + 1);
+ }
+
+ for ( i = 0; i < NUM_DATA_SETS; i++ ) {
+
+ att_space[i] = H5Screate_simple(1, att_size, NULL);
+ VRFY((att_space[i] >= 0), "H5Screate_simple(3) failed.\n");
+
+ att_id[i] = H5Acreate(dataset[i], att_name[i], H5T_NATIVE_DOUBLE,
+ att_space[i], H5P_DEFAULT, H5P_DEFAULT);
+ VRFY((att_id[i] >= 0), "H5Acreate(1) failed.\n");
+
+
+ err = H5Awrite(att_id[i], H5T_NATIVE_DOUBLE, att);
+ VRFY((err >= 0), "H5Awrite(1) failed.\n");
+
+ for ( j = 0; j < LOCAL_DATA_SIZE; j++ ) {
+
+ att[j] /= 10.0;
+ }
+ }
+
+ /*
+ * close attribute IDs and spaces
+ */
+
+ if(verbose )
+ HDfprintf(stdout, "%0d:%s: closing attr ids and spaces .\n",
+ mpi_rank, fcn_name);
+
+ for ( i = 0; i < NUM_DATA_SETS; i++ ) {
+
+ err = H5Sclose(att_space[i]);
+ VRFY((err >= 0), "H5Sclose(att_space[i]) failed.\n");
+
+ err = H5Aclose(att_id[i]);
+ VRFY((err >= 0), "H5Aclose(att_id[i]) failed.\n");
+ }
+
+ /*
+ * flush the metadata cache again
+ */
+
+ if(verbose )
+ HDfprintf(stdout, "%0d:%s: flushing metadata cache.\n",
+ mpi_rank, fcn_name);
+ err = H5Fflush(file_id, H5F_SCOPE_GLOBAL);
+ VRFY((err >= 0), "H5Fflush(2) failed.\n");
+
+
+ /*
+ * write large attributes to each dataset
+ */
+
+ if(verbose )
+ HDfprintf(stdout, "%0d:%s: writing large attributes.\n",
+ mpi_rank, fcn_name);
+
+ lg_att_size[0] = (hsize_t)(LARGE_ATTR_SIZE);
+
+ for ( j = 0; j < LARGE_ATTR_SIZE; j++ ) {
+
+ lg_att[j] = (double)(j + 1);
+ }
+
+ for ( i = 0; i < NUM_DATA_SETS; i++ ) {
+
+ lg_att_space[i] = H5Screate_simple(1, lg_att_size, NULL);
+ VRFY((lg_att_space[i] >= 0), "H5Screate_simple(4) failed.\n");
+
+ lg_att_id[i] = H5Acreate(dataset[i], lg_att_name[i], H5T_NATIVE_DOUBLE,
+ lg_att_space[i], H5P_DEFAULT, H5P_DEFAULT);
+ VRFY((lg_att_id[i] >= 0), "H5Acreate(2) failed.\n");
+
+
+ err = H5Awrite(lg_att_id[i], H5T_NATIVE_DOUBLE, lg_att);
+ VRFY((err >= 0), "H5Awrite(2) failed.\n");
+
+ for ( j = 0; j < LARGE_ATTR_SIZE; j++ ) {
+
+ lg_att[j] /= 10.0;
+ }
+ }
+
+ /*
+ * flush the metadata cache yet again to clean the object headers.
+ *
+ * This is an attempt to crate a situation where we have dirty
+ * object header continuation chunks, but clean opject headers
+ * to verify a speculative bug fix -- it doesn't seem to work,
+ * but I will leave the code in anyway, as the object header
+ * code is going to change a lot in the near future.
+ */
+
+ if(verbose )
+ HDfprintf(stdout, "%0d:%s: flushing metadata cache.\n",
+ mpi_rank, fcn_name);
+ err = H5Fflush(file_id, H5F_SCOPE_GLOBAL);
+ VRFY((err >= 0), "H5Fflush(3) failed.\n");
+
+
+ /*
+ * write different large attributes to each dataset
+ */
+
+ if(verbose )
+ HDfprintf(stdout, "%0d:%s: writing different large attributes.\n",
+ mpi_rank, fcn_name);
+
+ for ( j = 0; j < LARGE_ATTR_SIZE; j++ ) {
+
+ lg_att[j] = (double)(j + 2);
+ }
+
+ for ( i = 0; i < NUM_DATA_SETS; i++ ) {
+
+ err = H5Awrite(lg_att_id[i], H5T_NATIVE_DOUBLE, lg_att);
+ VRFY((err >= 0), "H5Awrite(2) failed.\n");
+
+ for ( j = 0; j < LARGE_ATTR_SIZE; j++ ) {
+
+ lg_att[j] /= 10.0;
+ }
+ }
+
+
+ /*
+ * close large attribute IDs and spaces
+ */
+
+ if(verbose )
+ HDfprintf(stdout, "%0d:%s: closing large attr ids and spaces .\n",
+ mpi_rank, fcn_name);
+
+ for ( i = 0; i < NUM_DATA_SETS; i++ ) {
+
+ err = H5Sclose(lg_att_space[i]);
+ VRFY((err >= 0), "H5Sclose(lg_att_space[i]) failed.\n");
+
+ err = H5Aclose(lg_att_id[i]);
+ VRFY((err >= 0), "H5Aclose(lg_att_id[i]) failed.\n");
+ }
+
+
+ /*
+ * close the data sets
+ */
+
+ if(verbose )
+ HDfprintf(stdout, "%0d:%s: closing datasets .\n", mpi_rank, fcn_name);
+
+ for ( i = 0; i < NUM_DATA_SETS; i++ ) {
+
+ err = H5Dclose(dataset[i]);
+ VRFY((err >= 0), "H5Dclose(dataset[i])1 failed.\n");
+ }
+
+ /*
+ * close the data transfer property list.
+ */
+
+ if(verbose )
+ HDfprintf(stdout, "%0d:%s: closing dxpl .\n", mpi_rank, fcn_name);
+
+ err = H5Pclose(dxpl_id);
+ VRFY((err >= 0), "H5Pclose(dxpl_id) failed.\n");
+
+
+ /*
+ * Close file.
+ */
+
+ if(verbose )
+ HDfprintf(stdout, "%0d:%s: closing file.\n", mpi_rank, fcn_name);
+
+ err = H5Fclose(file_id);
+ VRFY((err >= 0 ), "H5Fclose(1) failed");
+
+ /*
+ * Must now open file and attempt to read data sets -- do this on process
+ * zero only. Test passes if we are able to do this, and fails otherwise.
+ */
+
+ if ( mpi_rank == 0 ) {
+
+ /*
+ * Re-open the file
+ */
+ if(verbose)
+ HDfprintf(stdout, "%0d:%s: re-opening file.\n", mpi_rank, fcn_name);
+ file_id = H5Fopen(filename, H5F_ACC_RDONLY, H5P_DEFAULT);
+ VRFY((file_id >= 0 ), "H5Fopen() failed");
+
+ /*
+ * Attempt to open the data sets
+ */
+
+ if(verbose )
+ HDfprintf(stdout, "%0d:%s: opening datasets.\n",
+ mpi_rank, fcn_name);
+
+ for ( i = 0; i < NUM_DATA_SETS; i++ ) {
+
+ dataset[i] = -1;
+ }
+
+ for ( i = 0; i < NUM_DATA_SETS; i++ ) {
+
+ dataset[i] = H5Dopen1(file_id, dataset_name[i]);
+
+ if ( dataset[i] < 0 ) {
+
+ nerrors++;
+ }
+ }
+
+ /*
+ * Close the data sets
+ */
+
+ if(verbose )
+ HDfprintf(stdout, "%0d:%s: closing datasets again.\n",
+ mpi_rank, fcn_name);
+
+ for ( i = 0; i < NUM_DATA_SETS; i++ ) {
+
+ if ( dataset[i] >= 0 ) {
+
+ err = H5Dclose(dataset[i]);
+ VRFY((err >= 0), "H5Dclose(dataset[i])1 failed.\n");
+ }
+ }
+
+ /*
+ * Close the file
+ */
+ if(verbose)
+ HDfprintf(stdout, "%0d:%s: closing file again.\n",
+ mpi_rank, fcn_name);
+ err = H5Fclose(file_id);
+ VRFY((err >= 0 ), "H5Fclose(1) failed");
+
+ }
+
+ if(verbose )
+ HDfprintf(stdout, "%0d:%s: Done.\n", mpi_rank, fcn_name);
+
+ return;
+
+} /* rr_obj_hdr_flush_confusion() */
+
+#undef NUM_DATA_SETS
+#undef LOCAL_DATA_SIZE
+#undef LARGE_ATTR_SIZE
+
/*=============================================================================
* End of t_mdset.c
*===========================================================================*/
diff --git a/testpar/testphdf5.c b/testpar/testphdf5.c
index 0864b11..44415e4 100644
--- a/testpar/testphdf5.c
+++ b/testpar/testphdf5.c
@@ -317,6 +317,7 @@ int main(int argc, char **argv)
H5Ptest_param_t ndsets_params, ngroups_params;
H5Ptest_param_t collngroups_params;
H5Ptest_param_t io_mode_confusion_params;
+ H5Ptest_param_t rr_obj_flush_confusion_params;
/* Un-buffer the stdout and stderr */
setbuf(stderr, NULL);
@@ -472,6 +473,12 @@ int main(int argc, char **argv)
"I/O mode confusion test -- hangs quickly on failure",
&io_mode_confusion_params);
+ rr_obj_flush_confusion_params.name = PARATESTFILE;
+ rr_obj_flush_confusion_params.count = 0; /* value not used */
+ AddTest("rrobjflushconf", rr_obj_hdr_flush_confusion, NULL,
+ "round robin object header flush confusion test",
+ &rr_obj_flush_confusion_params);
+
AddTest("tldsc",
lower_dim_size_comp_test, NULL,
"test lower dim size comp in span tree to mpi derived type",
diff --git a/testpar/testphdf5.h b/testpar/testphdf5.h
index ba46e4d..609db05 100644
--- a/testpar/testphdf5.h
+++ b/testpar/testphdf5.h
@@ -237,6 +237,7 @@ void coll_irregular_simple_chunk_write(void);
void coll_irregular_complex_chunk_read(void);
void coll_irregular_complex_chunk_write(void);
void io_mode_confusion(void);
+void rr_obj_hdr_flush_confusion(void);
void lower_dim_size_comp_test(void);
void link_chunk_collective_io_test(void);
void contig_hyperslab_dr_pio_test(void);