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-rw-r--r--src/H5Dmpio.c302
-rw-r--r--src/H5Dprivate.h2
-rw-r--r--src/H5Ppublic.h3
-rw-r--r--src/H5trace.c4
-rw-r--r--testpar/t_coll_chunk.c36
-rw-r--r--testpar/t_dset.c104
-rw-r--r--testpar/testphdf5.c2
-rw-r--r--testpar/testphdf5.h9
8 files changed, 117 insertions, 345 deletions
diff --git a/src/H5Dmpio.c b/src/H5Dmpio.c
index c2d964e..900ad6a 100644
--- a/src/H5Dmpio.c
+++ b/src/H5Dmpio.c
@@ -105,10 +105,9 @@ static herr_t H5D__chunk_collective_io(H5D_io_info_t *io_info,
static herr_t H5D__multi_chunk_collective_io(H5D_io_info_t *io_info,
const H5D_type_info_t *type_info, H5D_chunk_map_t *fm,
H5P_genplist_t *dx_plist);
-static herr_t H5D__multi_chunk_collective_io_no_opt(H5D_io_info_t *io_info,
- const H5D_type_info_t *type_info, H5D_chunk_map_t *fm, H5P_genplist_t *dx_plist);
static herr_t H5D__link_chunk_collective_io(H5D_io_info_t *io_info,
- const H5D_type_info_t *type_info, H5D_chunk_map_t *fm, int sum_chunk);
+ const H5D_type_info_t *type_info, H5D_chunk_map_t *fm, int sum_chunk,
+ H5P_genplist_t *dx_plist);
static herr_t H5D__inter_collective_io(H5D_io_info_t *io_info,
const H5D_type_info_t *type_info, const H5S_t *file_space,
const H5S_t *mem_space);
@@ -586,6 +585,12 @@ done:
* Programmer: Muqun Yang
* Monday, Feb. 13th, 2006
*
+ * Modification:
+ * - Refctore to remove multi-chunk-without-opimization feature and update for
+ * multi-chunk-io accordingly
+ * Programmer: Jonathan Kim
+ * Date: 2012-10-10
+ *
*-------------------------------------------------------------------------
*/
static herr_t
@@ -594,8 +599,6 @@ H5D__chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_inf
{
H5P_genplist_t *dx_plist; /* Pointer to DXPL */
H5FD_mpio_chunk_opt_t chunk_opt_mode;
- H5D_mpio_actual_chunk_opt_mode_t actual_chunk_opt_mode;
- H5D_mpio_actual_io_mode_t actual_io_mode;
int io_option = H5D_MULTI_CHUNK_IO_MORE_OPT;
int sum_chunk = -1;
#ifdef H5_HAVE_INSTRUMENTED_LIBRARY
@@ -617,10 +620,12 @@ H5D__chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_inf
/* Check the optional property list on what to do with collective chunk IO. */
chunk_opt_mode = (H5FD_mpio_chunk_opt_t)H5P_peek_unsigned(dx_plist, H5D_XFER_MPIO_CHUNK_OPT_HARD_NAME);
- if(chunk_opt_mode == H5FD_MPIO_CHUNK_ONE_IO)
+ if(H5FD_MPIO_CHUNK_ONE_IO == chunk_opt_mode)
io_option = H5D_ONE_LINK_CHUNK_IO; /*no opt*/
- else if(chunk_opt_mode == H5FD_MPIO_CHUNK_MULTI_IO)
- io_option = H5D_MULTI_CHUNK_IO; /*no opt */
+ /* direct request to multi-chunk-io */
+ else if(H5FD_MPIO_CHUNK_MULTI_IO == chunk_opt_mode)
+ io_option = H5D_MULTI_CHUNK_IO;
+ /* via default path. branch by num threshold */
else {
unsigned one_link_chunk_io_threshold; /* Threshhold to use single collective I/O for all chunks */
int mpi_size; /* Number of processes in MPI job */
@@ -649,7 +654,7 @@ H5D__chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_inf
/*** Test collective chunk user-input optimization APIs. ***/
check_prop = H5Pexist(io_info->dxpl_id, H5D_XFER_COLL_CHUNK_LINK_HARD_NAME);
if(check_prop > 0) {
- if(io_option == H5D_ONE_LINK_CHUNK_IO) {
+ if(H5D_ONE_LINK_CHUNK_IO == io_option) {
new_value = 0;
if(H5Pset(io_info->dxpl_id, H5D_XFER_COLL_CHUNK_LINK_HARD_NAME, &new_value) < 0)
HGOTO_ERROR(H5E_IO, H5E_CANTSET, FAIL, "unable to set property value")
@@ -657,7 +662,7 @@ H5D__chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_inf
} /* end if */
check_prop = H5Pexist(io_info->dxpl_id, H5D_XFER_COLL_CHUNK_MULTI_HARD_NAME);
if(check_prop > 0) {
- if(io_option == H5D_MULTI_CHUNK_IO) {
+ if(H5D_MULTI_CHUNK_IO == io_option) {
new_value = 0;
if(H5Pset(io_info->dxpl_id, H5D_XFER_COLL_CHUNK_MULTI_HARD_NAME, &new_value) < 0)
HGOTO_ERROR(H5E_IO, H5E_CANTSET, FAIL, "unable to set property value")
@@ -665,7 +670,7 @@ H5D__chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_inf
} /* end if */
check_prop = H5Pexist(io_info->dxpl_id, H5D_XFER_COLL_CHUNK_LINK_NUM_TRUE_NAME);
if(check_prop > 0) {
- if(io_option == H5D_ONE_LINK_CHUNK_IO_MORE_OPT) {
+ if(H5D_ONE_LINK_CHUNK_IO_MORE_OPT == io_option) {
new_value = 0;
if(H5Pset(io_info->dxpl_id, H5D_XFER_COLL_CHUNK_LINK_NUM_TRUE_NAME, &new_value) < 0)
HGOTO_ERROR(H5E_IO, H5E_CANTSET, FAIL, "unable to set property value")
@@ -682,39 +687,16 @@ H5D__chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_inf
#endif
/* step 2: Go ahead to do IO.*/
- if(io_option == H5D_ONE_LINK_CHUNK_IO || io_option == H5D_ONE_LINK_CHUNK_IO_MORE_OPT) {
- /* set the actual io mode properties to the correct values for link chunk io.
- * Link chunk I/O does not break to independent, so we can set the actual_io mode
- * as well as the optimisation mode. */
- actual_chunk_opt_mode = H5D_MPIO_LINK_CHUNK;
- actual_io_mode = H5D_MPIO_CHUNK_COLLECTIVE;
-
- /* Set the actual chunk opt mode property. */
- if(H5P_set(dx_plist, H5D_MPIO_ACTUAL_CHUNK_OPT_MODE_NAME, &actual_chunk_opt_mode) < 0)
- HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "couldn't set actual chunk opt mode property")
-
- if(H5D__link_chunk_collective_io(io_info, type_info, fm, sum_chunk) < 0)
+ if(H5D_ONE_LINK_CHUNK_IO == io_option || H5D_ONE_LINK_CHUNK_IO_MORE_OPT == io_option) {
+ if(H5D__link_chunk_collective_io(io_info, type_info, fm, sum_chunk, dx_plist) < 0)
HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "couldn't finish linked chunk MPI-IO")
-
- /* Set the actual io mode property. */
- if(H5P_set(dx_plist, H5D_MPIO_ACTUAL_IO_MODE_NAME, &actual_io_mode) < 0)
- HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "couldn't set actual io mode property")
} /* end if */
- else
- if(io_option == H5D_MULTI_CHUNK_IO) {
- /* Set the actual chunk opt mode property */
- actual_chunk_opt_mode = H5D_MPIO_MULTI_CHUNK_NO_OPT;
- if(H5P_set(dx_plist, H5D_MPIO_ACTUAL_CHUNK_OPT_MODE_NAME, &actual_chunk_opt_mode) < 0)
- HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "couldn't set actual chunk opt mode property")
-
- if(H5D__multi_chunk_collective_io_no_opt(io_info, type_info, fm, dx_plist) < 0)
- HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "couldn't finish multiple chunk MPI-IO")
+ /* direct request to multi-chunk-io */
+ else if(H5D_MULTI_CHUNK_IO == io_option) {
+ if(H5D__multi_chunk_collective_io(io_info, type_info, fm, dx_plist) < 0)
+ HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "couldn't finish optimized multiple chunk MPI-IO")
} /* end if */
- else { /*multiple chunk IOs with opt */
- actual_chunk_opt_mode = H5D_MPIO_MULTI_CHUNK;
- if(H5P_set(dx_plist, H5D_MPIO_ACTUAL_CHUNK_OPT_MODE_NAME, &actual_chunk_opt_mode) < 0)
- HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "couldn't set actual chunk opt mode property")
-
+ else { /* multiple chunk IO via threshold */
if(H5D__multi_chunk_collective_io(io_info, type_info, fm, dx_plist) < 0)
HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "couldn't finish optimized multiple chunk MPI-IO")
} /* end else */
@@ -801,11 +783,16 @@ done:
* Programmer: Muqun Yang
* Monday, Feb. 13th, 2006
*
+ * Modification:
+ * - Set H5D_MPIO_ACTUAL_CHUNK_OPT_MODE_NAME and H5D_MPIO_ACTUAL_IO_MODE_NAME
+ * dxpl in this.
+ * Programmer: Jonathan Kim
+ * Date: 2012-10-10
*-------------------------------------------------------------------------
*/
static herr_t
H5D__link_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
- H5D_chunk_map_t *fm, int sum_chunk)
+ H5D_chunk_map_t *fm, int sum_chunk, H5P_genplist_t *dx_plist)
{
H5D_chunk_addr_info_t *chunk_addr_info_array = NULL;
MPI_Datatype chunk_final_mtype; /* Final memory MPI datatype for all chunks with seletion */
@@ -824,10 +811,21 @@ H5D__link_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *typ
int *chunk_mpi_file_counts = NULL; /* Count of MPI file datatype for each chunk */
int *chunk_mpi_mem_counts = NULL; /* Count of MPI memory datatype for each chunk */
int mpi_code; /* MPI return code */
+ H5D_mpio_actual_chunk_opt_mode_t actual_chunk_opt_mode = H5D_MPIO_LINK_CHUNK;
+ H5D_mpio_actual_io_mode_t actual_io_mode = H5D_MPIO_CHUNK_COLLECTIVE;
herr_t ret_value = SUCCEED;
FUNC_ENTER_STATIC
+ /* Set the actual-chunk-opt-mode property. */
+ if(H5P_set(dx_plist, H5D_MPIO_ACTUAL_CHUNK_OPT_MODE_NAME, &actual_chunk_opt_mode) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "couldn't set actual chunk opt mode property")
+
+ /* Set the actual-io-mode property.
+ * Link chunk I/O does not break to independent, so can set right away */
+ if(H5P_set(dx_plist, H5D_MPIO_ACTUAL_IO_MODE_NAME, &actual_io_mode) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "couldn't set actual io mode property")
+
/* Get the sum # of chunks, if not already available */
if(sum_chunk < 0) {
if(H5D__mpio_get_sum_chunk(io_info, fm, &sum_chunk) < 0)
@@ -1075,6 +1073,12 @@ if(H5DEBUG(D))
* Programmer: Muqun Yang
* Monday, Feb. 13th, 2006
*
+ * Modification:
+ * - Set H5D_MPIO_ACTUAL_CHUNK_OPT_MODE_NAME dxpl in this to go along with
+ * setting H5D_MPIO_ACTUAL_IO_MODE_NAME dxpl at the bottom.
+ * Programmer: Jonathan Kim
+ * Date: 2012-10-10
+ *
*-------------------------------------------------------------------------
*/
static herr_t
@@ -1096,11 +1100,16 @@ H5D__multi_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *ty
int mpi_rank;
#endif
size_t u; /* Local index variable */
+ H5D_mpio_actual_chunk_opt_mode_t actual_chunk_opt_mode = H5D_MPIO_MULTI_CHUNK; /* actual chunk optimization mode */
H5D_mpio_actual_io_mode_t actual_io_mode = H5D_MPIO_NO_COLLECTIVE; /* Local variable for tracking the I/O mode used. */
herr_t ret_value = SUCCEED;
FUNC_ENTER_STATIC
+ /* Set the actual chunk opt mode property */
+ if(H5P_set(dx_plist, H5D_MPIO_ACTUAL_CHUNK_OPT_MODE_NAME, &actual_chunk_opt_mode) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "couldn't set actual chunk opt mode property")
+
#ifdef H5Dmpio_DEBUG
mpi_rank = H5F_mpi_get_rank(io_info->dset->oloc.file);
#endif
@@ -1263,210 +1272,6 @@ done:
} /* end H5D__multi_chunk_collective_io */
-/*-------------------------------------------------------------------------
- * Function: H5D__multi_chunk_collective_io_no_opt
- *
- * Purpose: To do collective IO without any optimization per chunk base
- * The internal independent IO inside HDF5 cannot handle
- * non-contiguous(or with holes) storage efficiently.
- * Under this case, the one independent IO call may consist of
- * many small disk IOs. So we may use independent IO with derived datatype
- * to replace the independent IO when we find this chunk is not good to
- * do collective IO. However, according to our performance study,
- * this approach may not overcome the overhead caused by MPI gather/scatter.
- * So we decide to leave the original collective IO per chunk approach as
- * an option for users. NO MPI gather/scatter calls are used.
- * HDF5 will try to collective IO if possible.
- * If users choose to use
- * H5Pset_dxpl_mpio_chunk_opt(dxpl_id,H5FD_MPIO_OPT_MULTI_IO),
- * this function will be called.
- * The HDF5 library won't do any IO management but leave it to MPI-IO to figure
- * out.
- *
- * Return: Non-negative on success/Negative on failure
- *
- * Programmer: Muqun Yang
- * Monday, Feb. 13th, 2006
- *
- *-------------------------------------------------------------------------
- */
-static herr_t
-H5D__multi_chunk_collective_io_no_opt(H5D_io_info_t *io_info,
- const H5D_type_info_t *type_info, H5D_chunk_map_t *fm, H5P_genplist_t *dx_plist)
-{
- H5SL_node_t *chunk_node; /* Current node in chunk skip list */
- H5D_io_info_t ctg_io_info; /* Contiguous I/O info object */
- H5D_storage_t ctg_store; /* Chunk storage information as contiguous dataset */
- H5D_io_info_t cpt_io_info; /* Compact I/O info object */
- H5D_storage_t cpt_store; /* Chunk storage information as compact dataset */
- hbool_t cpt_dirty; /* Temporary placeholder for compact storage "dirty" flag */
- int min_chunk = -1; /* Minimum # of chunks all processes will operate on */
- int count_chunk; /* How many chunks have we operated on? */
- H5D_storage_t store; /* union of EFL and chunk pointer in file space */
- H5D_mpio_actual_io_mode_t actual_io_mode = H5D_MPIO_NO_COLLECTIVE; /*Local variable for tracking the I/O modes used. */
- herr_t ret_value = SUCCEED;
-
- FUNC_ENTER_STATIC
-
-#ifdef H5D_DEBUG
-if(H5DEBUG(D)) {
- int mpi_rank;
-
- mpi_rank = H5F_mpi_get_rank(io_info->dset->oloc.file);
- HDfprintf(H5DEBUG(D), "Rank %d: coming to multi_chunk_collective_io_no_opt\n", mpi_rank);
-}
-#endif
-
- /* Set up contiguous I/O info object */
- HDmemcpy(&ctg_io_info, io_info, sizeof(ctg_io_info));
- ctg_io_info.store = &ctg_store;
- ctg_io_info.layout_ops = *H5D_LOPS_CONTIG;
-
- /* Initialize temporary contiguous storage info */
- ctg_store.contig.dset_size = (hsize_t)io_info->dset->shared->layout.u.chunk.size;
-
- /* Set up compact I/O info object */
- HDmemcpy(&cpt_io_info, io_info, sizeof(cpt_io_info));
- cpt_io_info.store = &cpt_store;
- cpt_io_info.layout_ops = *H5D_LOPS_COMPACT;
-
- /* Initialize temporary compact storage info */
- cpt_store.compact.dirty = &cpt_dirty;
-
- /* Set dataset storage for I/O info */
- io_info->store = &store;
-
- /* Get the min. # of chunks */
- if(H5D__mpio_get_min_chunk(io_info, fm, &min_chunk) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get minimum number of chunk")
- HDassert(min_chunk >= 0);
-
- /* Get first node in chunk skip list */
- chunk_node = H5SL_first(fm->sel_chunks);
- count_chunk = 0;
-
- /* Iterate through chunks to be operated on */
- while(chunk_node) {
- H5D_chunk_info_t *chunk_info; /* chunk information */
- H5D_chunk_ud_t udata; /* B-tree pass-through */
- hbool_t make_ind, make_coll; /* Flags to indicate that the MPI mode should change */
-
- /* Get the actual chunk information from the skip list node */
- chunk_info = H5SL_item(chunk_node);
-
- /* Pass in chunk's coordinates in a union. */
- store.chunk.offset = chunk_info->coords;
- store.chunk.index = chunk_info->index;
-
- /* Reset flags for changing parallel I/O mode */
- make_ind = make_coll = FALSE;
-
- count_chunk++;
-
- /* If the number of chunk is greater than minimum number of chunk,
- * Do independent read.
- */
- if(count_chunk > min_chunk)
- /* Switch to independent I/O (permanently) */
- make_ind = TRUE;
-
- /* Retrieve the chunk's address */
- if(H5D__chunk_lookup(io_info->dset, io_info->dxpl_id, chunk_info->coords,
- chunk_info->index, &udata) < 0)
- HGOTO_ERROR(H5E_STORAGE, H5E_CANTGET, FAIL, "couldn't get chunk info from skipped list")
-
- /* Independent I/O */
- if(make_ind) {
- void *chunk; /* Pointer to the data chunk in cache */
- H5D_io_info_t *chk_io_info; /* Pointer to I/O info object for this chunk */
- uint32_t accessed_bytes = 0; /* Total accessed size in a chunk */
- htri_t cacheable; /* Whether the chunk is cacheable */
-
- /* Switch to independent I/O */
- if(H5D__ioinfo_xfer_mode(io_info, dx_plist, H5FD_MPIO_INDEPENDENT) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't switch to independent I/O")
-
- /* Update the local variable tracking the dxpl's actual io mode */
- actual_io_mode = actual_io_mode | H5D_MPIO_CHUNK_INDEPENDENT;
-
- /* Load the chunk into cache and lock it. */
- if((cacheable = H5D__chunk_cacheable(io_info, udata.addr,
- io_info->op_type == H5D_IO_OP_WRITE)) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't tell if chunk is cacheable")
- if(cacheable) {
- hbool_t entire_chunk = TRUE; /* Whether whole chunk is selected */
-
- /* Compute # of bytes accessed in chunk */
- accessed_bytes = chunk_info->chunk_points * type_info->src_type_size;
-
- /* Determine if we will access all the data in the chunk */
- if(((io_info->op_type == H5D_IO_OP_WRITE) && (accessed_bytes != ctg_store.contig.dset_size))
- || (io_info->op_type != H5D_IO_OP_WRITE))
- entire_chunk = FALSE;
-
- /* Lock the chunk into the cache */
- if(NULL == (chunk = H5D__chunk_lock(io_info, &udata, entire_chunk)))
- HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk")
-
- /* Set up the storage buffer information for this chunk */
- cpt_store.compact.buf = chunk;
-
- /* Point I/O info at contiguous I/O info for this chunk */
- chk_io_info = &cpt_io_info;
- } /* end if */
- else {
- /* Set up the storage address information for this chunk */
- ctg_store.contig.dset_addr = udata.addr;
-
- /* No chunk cached */
- chunk = NULL;
-
- /* Point I/O info at temporary I/O info for this chunk */
- chk_io_info = &ctg_io_info;
- } /* end else */
-
- if(io_info->op_type == H5D_IO_OP_WRITE) {
- if((io_info->io_ops.single_write)(chk_io_info, type_info,
- (hsize_t)chunk_info->chunk_points, chunk_info->fspace, chunk_info->mspace) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "optimized write failed")
- } /* end if */
- else {
- if((io_info->io_ops.single_read)(chk_io_info, type_info,
- (hsize_t)chunk_info->chunk_points, chunk_info->fspace, chunk_info->mspace) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "optimized read failed")
- } /* end ese */
-
- /* Release the cache lock on the chunk. */
- if(chunk)
- if(H5D__chunk_unlock(io_info, &udata, (io_info->op_type == H5D_IO_OP_WRITE), chunk, accessed_bytes) < 0)
- HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to unlock raw data chunk")
- } /* end if */
- else { /*collective I/O */
- /* Set up the storage address information for this chunk */
- ctg_store.contig.dset_addr = udata.addr;
-
- /* Update the local variable tracking the dxpl's actual io Mode. */
- actual_io_mode = actual_io_mode | H5D_MPIO_CHUNK_COLLECTIVE;
-
- if(H5D__inter_collective_io(&ctg_io_info, type_info, chunk_info->fspace, chunk_info->mspace) < 0)
- HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL,"couldn't finish shared collective MPI-IO")
- } /* end else */
-
- if(make_coll)
- if(H5D__ioinfo_xfer_mode(io_info, dx_plist, H5FD_MPIO_COLLECTIVE) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't switch to independent I/O")
-
- /* Get the next chunk node in the skip list */
- chunk_node = H5SL_next(chunk_node);
- } /* end while */
-
- /* Write the local value of actual io mode to the DXPL. */
- if(H5P_set(dx_plist, H5D_MPIO_ACTUAL_IO_MODE_NAME, &actual_io_mode) < 0)
- HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "couldn't set actual io mode property")
-
-done:
- FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5D__multi_chunk_collective_io_no_opt */
/*-------------------------------------------------------------------------
@@ -1794,7 +1599,6 @@ H5D__obtain_mpio_mode(H5D_io_info_t* io_info, H5D_chunk_map_t *fm,
{
int total_chunks;
unsigned percent_nproc_per_chunk, threshold_nproc_per_chunk;
- H5FD_mpio_chunk_opt_t chunk_opt_mode;
uint8_t* io_mode_info = NULL;
uint8_t* recv_io_mode_info = NULL;
uint8_t* mergebuf = NULL;
@@ -1827,8 +1631,8 @@ H5D__obtain_mpio_mode(H5D_io_info_t* io_info, H5D_chunk_map_t *fm,
/* Setup parameters */
H5_ASSIGN_OVERFLOW(total_chunks, fm->layout->u.chunk.nchunks, hsize_t, int);
percent_nproc_per_chunk = H5P_peek_unsigned(dx_plist, H5D_XFER_MPIO_CHUNK_OPT_RATIO_NAME);
- chunk_opt_mode = (H5FD_mpio_chunk_opt_t)H5P_peek_unsigned(dx_plist, H5D_XFER_MPIO_CHUNK_OPT_HARD_NAME);
- if((chunk_opt_mode == H5FD_MPIO_CHUNK_MULTI_IO) || (percent_nproc_per_chunk == 0)) {
+ /* if ratio is 0, perform collective io */
+ if(0 == percent_nproc_per_chunk) {
if(H5D__chunk_addrmap(io_info, chunk_addr) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get chunk address");
for(ic = 0; ic < total_chunks; ic++)
diff --git a/src/H5Dprivate.h b/src/H5Dprivate.h
index 02c2138..5acf43f 100644
--- a/src/H5Dprivate.h
+++ b/src/H5Dprivate.h
@@ -87,8 +87,6 @@
#define H5D_XFER_COLL_CHUNK_LINK_NUM_FALSE_NAME "coll_chunk_link_false"
#define H5D_XFER_COLL_CHUNK_MULTI_RATIO_COLL_NAME "coll_chunk_multi_coll"
#define H5D_XFER_COLL_CHUNK_MULTI_RATIO_IND_NAME "coll_chunk_multi_ind"
-#define H5D_XFER_COLL_CHUNK_LINK_TO_MULTI "coll_chunk_link_mul"/* Internal transferring from link to multiple chunk */
-#define H5D_XFER_COLL_CHUNK_LINK_TO_MULTI_OPT "coll_chunk_link_mul_opt"/* Internal transferring from link opt to multiple chunk opt*/
/* Definitions for all collective chunk instrumentation properties */
#define H5D_XFER_COLL_CHUNK_SIZE sizeof(unsigned)
diff --git a/src/H5Ppublic.h b/src/H5Ppublic.h
index 507bbb6..6b17e0b 100644
--- a/src/H5Ppublic.h
+++ b/src/H5Ppublic.h
@@ -131,8 +131,7 @@ typedef enum H5D_mpio_actual_chunk_opt_mode_t {
*/
H5D_MPIO_NO_CHUNK_OPTIMIZATION = 0,
H5D_MPIO_LINK_CHUNK,
- H5D_MPIO_MULTI_CHUNK,
- H5D_MPIO_MULTI_CHUNK_NO_OPT
+ H5D_MPIO_MULTI_CHUNK
} H5D_mpio_actual_chunk_opt_mode_t;
typedef enum H5D_mpio_actual_io_mode_t {
diff --git a/src/H5trace.c b/src/H5trace.c
index 2dab8ec..92736d4 100644
--- a/src/H5trace.c
+++ b/src/H5trace.c
@@ -612,10 +612,6 @@ H5_trace(const double *returning, const char *func, const char *type, ...)
fprintf(out, "H5D_MPIO_MULTI_CHUNK");
break;
- case H5D_MPIO_MULTI_CHUNK_NO_OPT:
- fprintf(out, "H5D_MPIO_MULTI_CHUNK_NO_OPT");
- break;
-
default:
fprintf(out, "%ld", (long)chunk_opt_mode);
break;
diff --git a/testpar/t_coll_chunk.c b/testpar/t_coll_chunk.c
index 61e7bfd..73e7f09 100644
--- a/testpar/t_coll_chunk.c
+++ b/testpar/t_coll_chunk.c
@@ -258,8 +258,10 @@ coll_chunk5(void)
/*-------------------------------------------------------------------------
* Function: coll_chunk6
*
- * Purpose: Wrapper to test the collective chunk IO for regular JOINT
- selection with at least number of 2*mpi_size chunks
+ * Purpose: Test direct request for multi-chunk-io.
+ * Wrapper to test the collective chunk IO for regular JOINT
+ * selection with at least number of 2*mpi_size chunks
+ * Test for direct to Multi Chunk I/O.
*
* Return: Success: 0
*
@@ -489,6 +491,12 @@ coll_chunk10(void)
*
* Failure: -1
*
+ * Modifications:
+ * Remove invalid temporary property checkings for API_LINK_HARD and
+ * API_LINK_TRUE cases.
+ * Programmer: Jonathan Kim
+ * Date: 2012-10-10
+ *
* Programmer: Unknown
* July 12th, 2004
*
@@ -634,11 +642,6 @@ coll_chunktest(const char* filename,
NULL, NULL, NULL, NULL, NULL, NULL);
VRFY((status >= 0),"testing property list inserted succeeded");
- prop_value = H5D_XFER_COLL_CHUNK_FIX;
- status = H5Pinsert2(xfer_plist, H5D_XFER_COLL_CHUNK_LINK_TO_MULTI, H5D_XFER_COLL_CHUNK_SIZE, &prop_value,
- NULL, NULL, NULL, NULL, NULL, NULL);
- VRFY((status >= 0),"testing property list inserted succeeded");
-
break;
case API_MULTI_HARD:
@@ -654,11 +657,6 @@ coll_chunktest(const char* filename,
NULL, NULL, NULL, NULL, NULL, NULL);
VRFY((status >= 0),"testing property list inserted succeeded");
- prop_value = H5D_XFER_COLL_CHUNK_FIX;
- status = H5Pinsert2(xfer_plist, H5D_XFER_COLL_CHUNK_LINK_TO_MULTI_OPT, H5D_XFER_COLL_CHUNK_SIZE, &prop_value,
- NULL, NULL, NULL, NULL, NULL, NULL);
- VRFY((status >= 0),"testing property list inserted succeeded");
-
break;
case API_LINK_FALSE:
@@ -699,25 +697,17 @@ coll_chunktest(const char* filename,
case API_LINK_HARD:
status = H5Pget(xfer_plist,H5D_XFER_COLL_CHUNK_LINK_HARD_NAME,&prop_value);
VRFY((status >= 0),"testing property list get succeeded");
- if(prop_value !=0){/*double check if the option is switched to multiple chunk internally.*/
- status = H5Pget(xfer_plist,H5D_XFER_COLL_CHUNK_LINK_TO_MULTI, &prop_value);
- VRFY((status >= 0),"testing property list get succeeded");
- VRFY((prop_value == 1),"API to set LINK COLLECTIVE IO without optimization succeeded");
- }
+ VRFY((prop_value == 0),"API to set LINK COLLECTIVE IO directly succeeded");
break;
case API_MULTI_HARD:
status = H5Pget(xfer_plist,H5D_XFER_COLL_CHUNK_MULTI_HARD_NAME,&prop_value);
VRFY((status >= 0),"testing property list get succeeded");
- VRFY((prop_value == 0),"API to set MULTI-CHUNK COLLECTIVE IO without optimization succeeded");
+ VRFY((prop_value == 0),"API to set MULTI-CHUNK COLLECTIVE IO optimization succeeded");
break;
case API_LINK_TRUE:
status = H5Pget(xfer_plist,H5D_XFER_COLL_CHUNK_LINK_NUM_TRUE_NAME,&prop_value);
VRFY((status >= 0),"testing property list get succeeded");
- if(prop_value !=0){/*double check if the option is switched to multiple chunk internally.*/
- status = H5Pget(xfer_plist,H5D_XFER_COLL_CHUNK_LINK_TO_MULTI_OPT, &prop_value);
- VRFY((status >= 0),"testing property list get succeeded");
- VRFY((prop_value == 1),"API to set LINK COLLECTIVE IO without optimization succeeded");
- }
+ VRFY((prop_value == 0),"API to set LINK COLLECTIVE IO succeeded");
break;
case API_LINK_FALSE:
status = H5Pget(xfer_plist,H5D_XFER_COLL_CHUNK_LINK_NUM_FALSE_NAME,&prop_value);
diff --git a/testpar/t_dset.c b/testpar/t_dset.c
index 22eefbc..79a5555 100644
--- a/testpar/t_dset.c
+++ b/testpar/t_dset.c
@@ -2523,12 +2523,12 @@ none_selection_chunk(void)
* H5D_mpi_chunk_collective_io, processes disagree. The root reports
* collective, the rest report independent I/O
*
- * TEST_ACTUAL_IO_MULTI_CHUNK_NO_OPT_COL:
- * H5D_mpi_chunk_collective_io_no_opt, each process reports collective I/O
- *
- * TEST_ACTUAL_IO_MULTI_CHUNK_NO_OPT_MIX_DISAGREE:
- * H5D_mpi_chunk_collective_io_no_opt, processes disagree
- * (collective and mixed I/O)
+ * TEST_ACTUAL_IO_DIRECT_MULTI_CHUNK_IND:
+ * Same test TEST_ACTUAL_IO_MULTI_CHUNK_IND.
+ * Set directly go to multi-chunk-io without num threshold calc.
+ * TEST_ACTUAL_IO_DIRECT_MULTI_CHUNK_COL:
+ * Same test TEST_ACTUAL_IO_MULTI_CHUNK_COL.
+ * Set directly go to multi-chunk-io without num threshold calc.
*
* TEST_ACTUAL_IO_LINK_CHUNK:
* H5D_link_chunk_collective_io, processes report linked chunk I/O
@@ -2547,10 +2547,17 @@ none_selection_chunk(void)
* (The most complex case that works on all builds) and then performs
* an independent read and write with the same dxpls.
*
- * It may seem like TEST_ACTUAL_IO_MULTI_CHUNK_NO_OPT_IND and
- * TEST_ACTUAL_IO_MULTI_CHUNK_NO_OPT_MIX have been accidentally
- * left out. This is intentional; the other test cases sufficiently
- * cover all cases for Multi Chunk No Opt I/O.
+ * Note: DIRECT_MULTI_CHUNK_MIX and DIRECT_MULTI_CHUNK_MIX_DISAGREE
+ * is not needed as they are covered by DIRECT_CHUNK_MIX and
+ * MULTI_CHUNK_MIX_DISAGREE cases. _DIRECT_ cases are only for testing
+ * path way to multi-chunk-io by H5FD_MPIO_CHUNK_MULTI_IO insted of num-threshold.
+ *
+ * Modification:
+ * - Refctore to remove multi-chunk-without-opimization test and update for
+ * testing direct to multi-chunk-io
+ * Programmer: Jonathan Kim
+ * Date: 2012-10-10
+ *
*
* Programmer: Jacob Gruber
* Date: 2011-04-06
@@ -2565,8 +2572,8 @@ test_actual_io_mode(int selection_mode) {
H5D_mpio_actual_io_mode_t actual_io_mode_expected = -1;
const char * filename;
const char * test_name;
- hbool_t multi_chunk_no_opt;
- hbool_t multi_chunk_with_opt;
+ hbool_t direct_multi_chunk_io;
+ hbool_t multi_chunk_io;
hbool_t is_chunked;
hbool_t is_collective;
int mpi_size = -1;
@@ -2593,18 +2600,18 @@ test_actual_io_mode(int selection_mode) {
hsize_t count[RANK];
hsize_t block[RANK];
hbool_t use_gpfs = FALSE;
+ char message[256];
herr_t ret;
/* Set up some flags to make some future if statements slightly more readable */
- multi_chunk_no_opt = (
- selection_mode == TEST_ACTUAL_IO_MULTI_CHUNK_NO_OPT_IND ||
- selection_mode == TEST_ACTUAL_IO_MULTI_CHUNK_NO_OPT_COL ||
- selection_mode == TEST_ACTUAL_IO_MULTI_CHUNK_NO_OPT_MIX_DISAGREE );
+ direct_multi_chunk_io = (
+ selection_mode == TEST_ACTUAL_IO_DIRECT_MULTI_CHUNK_IND ||
+ selection_mode == TEST_ACTUAL_IO_DIRECT_MULTI_CHUNK_COL );
/* Note: RESET performs the same tests as MULTI_CHUNK_MIX_DISAGREE and then
* tests independent I/O
*/
- multi_chunk_with_opt = (
+ multi_chunk_io = (
selection_mode == TEST_ACTUAL_IO_MULTI_CHUNK_IND ||
selection_mode == TEST_ACTUAL_IO_MULTI_CHUNK_COL ||
selection_mode == TEST_ACTUAL_IO_MULTI_CHUNK_MIX ||
@@ -2673,6 +2680,7 @@ test_actual_io_mode(int selection_mode) {
/* Independent I/O with optimization */
case TEST_ACTUAL_IO_MULTI_CHUNK_IND:
+ case TEST_ACTUAL_IO_DIRECT_MULTI_CHUNK_IND:
/* Since the dataset is chunked by row and each process selects a row,
* each process writes to a different chunk. This forces all I/O to be
* independent.
@@ -2686,6 +2694,7 @@ test_actual_io_mode(int selection_mode) {
/* Collective I/O with optimization */
case TEST_ACTUAL_IO_MULTI_CHUNK_COL:
+ case TEST_ACTUAL_IO_DIRECT_MULTI_CHUNK_COL:
/* The dataset is chunked by rows, so each process takes a column which
* spans all chunks. Since the processes write non-overlapping regular
* selections to each chunk, the operation is purely collective.
@@ -2779,39 +2788,6 @@ test_actual_io_mode(int selection_mode) {
break;
- /* Collective I/O without optimization */
- case TEST_ACTUAL_IO_MULTI_CHUNK_NO_OPT_COL:
- /* The dataset is chunked by rows, so when each process takes a column, its
- * selection spans all chunks. Since no process writes more chunks than any
- * other, colective I/O is never broken. */
- slab_set(mpi_rank, mpi_size, start, count, stride, block, BYCOL);
-
- test_name = "Multi Chunk No Opt - Collective";
- actual_chunk_opt_mode_expected = H5D_MPIO_MULTI_CHUNK_NO_OPT;
- actual_io_mode_expected = H5D_MPIO_CHUNK_COLLECTIVE;
- break;
-
-
- /* Mixed I/O without optimization with disagreement */
- case TEST_ACTUAL_IO_MULTI_CHUNK_NO_OPT_MIX_DISAGREE:
- /* Each process takes a column, but the root's column is shortened so that
- * it only reads the first chunk. Since all the other processes are writing
- * to more chunks, they will break collective after the first chunk.
- */
- slab_set(mpi_rank, mpi_size, start, count, stride, block, BYCOL);
- if(mpi_rank == 0)
- block[0] = block[0] / mpi_size;
-
- test_name = "Multi Chunk No Opt - Mixed (Disagreement)";
- actual_chunk_opt_mode_expected = H5D_MPIO_MULTI_CHUNK_NO_OPT;
-
- if(mpi_rank == 0)
- actual_io_mode_expected = H5D_MPIO_CHUNK_COLLECTIVE;
- else
- actual_io_mode_expected = H5D_MPIO_CHUNK_MIXED;
-
- break;
-
/* Linked Chunk I/O */
case TEST_ACTUAL_IO_LINK_CHUNK:
/* Nothing special; link chunk I/O is forced in the dxpl settings. */
@@ -2887,20 +2863,25 @@ test_actual_io_mode(int selection_mode) {
ret = H5Pset_dxpl_mpio(dxpl_write, H5FD_MPIO_COLLECTIVE);
VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
- /* Set the threshold number of processes per chunk for link chunk I/O
- * to twice mpi_size. This will prevent the threshold from ever being
- * met, thus forcing multi chunk io instead of link chunk io.
+ /* Set the threshold number of processes per chunk to twice mpi_size.
+ * This will prevent the threshold from ever being met, thus forcing
+ * multi chunk io instead of link chunk io.
+ * This is via deault.
*/
- if(multi_chunk_with_opt) {
+ if(multi_chunk_io) {
+ /* force multi-chunk-io by threshold */
ret = H5Pset_dxpl_mpio_chunk_opt_num(dxpl_write, (unsigned) mpi_size*2);
VRFY((ret >= 0), "H5Pset_dxpl_mpio_chunk_opt_num succeeded");
+ /* set this to manipulate testing senario about allocating processes
+ * to chunks */
ret = H5Pset_dxpl_mpio_chunk_opt_ratio(dxpl_write, (unsigned) 99);
VRFY((ret >= 0), "H5Pset_dxpl_mpio_chunk_opt_ratio succeeded");
}
- /* Request multi chunk I/O without optimization */
- if(multi_chunk_no_opt) {
+ /* Set directly go to multi-chunk-io without threshold calc. */
+ if(direct_multi_chunk_io) {
+ /* set for multi chunk io by property*/
ret = H5Pset_dxpl_mpio_chunk_opt(dxpl_write, H5FD_MPIO_CHUNK_MULTI_IO);
VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
}
@@ -2943,7 +2924,6 @@ test_actual_io_mode(int selection_mode) {
/* Test values */
if(actual_chunk_opt_mode_expected != (unsigned) -1 && actual_io_mode_expected != (unsigned) -1) {
- char message[100];
sprintf(message, "Actual Chunk Opt Mode has the correct value for %s.\n",test_name);
VRFY((actual_chunk_opt_mode_write == actual_chunk_opt_mode_expected), message);
sprintf(message, "Actual IO Mode has the correct value for %s.\n",test_name);
@@ -3027,6 +3007,9 @@ actual_io_mode_tests(void) {
test_actual_io_mode(TEST_ACTUAL_IO_NO_COLLECTIVE);
+ /*
+ * Test multi-chunk-io via proc_num threshold
+ */
test_actual_io_mode(TEST_ACTUAL_IO_MULTI_CHUNK_IND);
test_actual_io_mode(TEST_ACTUAL_IO_MULTI_CHUNK_COL);
@@ -3038,8 +3021,11 @@ actual_io_mode_tests(void) {
test_actual_io_mode(TEST_ACTUAL_IO_MULTI_CHUNK_MIX_DISAGREE);
- test_actual_io_mode(TEST_ACTUAL_IO_MULTI_CHUNK_NO_OPT_COL);
- test_actual_io_mode(TEST_ACTUAL_IO_MULTI_CHUNK_NO_OPT_MIX_DISAGREE);
+ /*
+ * Test multi-chunk-io via setting direct property
+ */
+ test_actual_io_mode(TEST_ACTUAL_IO_DIRECT_MULTI_CHUNK_IND);
+ test_actual_io_mode(TEST_ACTUAL_IO_DIRECT_MULTI_CHUNK_COL);
test_actual_io_mode(TEST_ACTUAL_IO_LINK_CHUNK);
test_actual_io_mode(TEST_ACTUAL_IO_CONTIGUOUS);
diff --git a/testpar/testphdf5.c b/testpar/testphdf5.c
index 97a377e..784892a 100644
--- a/testpar/testphdf5.c
+++ b/testpar/testphdf5.c
@@ -440,7 +440,7 @@ int main(int argc, char **argv)
"linked chunk collective IO without optimization",PARATESTFILE);
AddTest((mpi_size < 3)? "-cchunk6" : "cchunk6",
coll_chunk6,NULL,
- "multi-chunk collective IO without optimization",PARATESTFILE);
+ "multi-chunk collective IO with direct request",PARATESTFILE);
AddTest((mpi_size < 3)? "-cchunk7" : "cchunk7",
coll_chunk7,NULL,
"linked chunk collective IO with optimization",PARATESTFILE);
diff --git a/testpar/testphdf5.h b/testpar/testphdf5.h
index 2219dc9..fa83697 100644
--- a/testpar/testphdf5.h
+++ b/testpar/testphdf5.h
@@ -169,11 +169,10 @@ enum H5TEST_COLL_CHUNK_API {API_NONE=0,API_LINK_HARD,
#define TEST_ACTUAL_IO_MULTI_CHUNK_COL 3
#define TEST_ACTUAL_IO_MULTI_CHUNK_MIX 4
#define TEST_ACTUAL_IO_MULTI_CHUNK_MIX_DISAGREE 5
-#define TEST_ACTUAL_IO_MULTI_CHUNK_NO_OPT_IND 6
-#define TEST_ACTUAL_IO_MULTI_CHUNK_NO_OPT_COL 7
-#define TEST_ACTUAL_IO_MULTI_CHUNK_NO_OPT_MIX_DISAGREE 8
-#define TEST_ACTUAL_IO_LINK_CHUNK 9
-#define TEST_ACTUAL_IO_CONTIGUOUS 10
+#define TEST_ACTUAL_IO_DIRECT_MULTI_CHUNK_IND 6
+#define TEST_ACTUAL_IO_DIRECT_MULTI_CHUNK_COL 7
+#define TEST_ACTUAL_IO_LINK_CHUNK 8
+#define TEST_ACTUAL_IO_CONTIGUOUS 9
/* Definitions of the selection mode for the no_collective_cause_tests function. */
#define TEST_COLLECTIVE 0x001