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authorQuincey Koziol <koziol@lbl.gov>2018-03-21 05:09:16 (GMT)
committerQuincey Koziol <koziol@lbl.gov>2018-03-21 05:09:16 (GMT)
commit4766d282ff21bf7dad3852696b33869beff12415 (patch)
treeaf070d6361070fa1dab466f9efdd9c4ab9e294f8
parentc5db36c7df19f27d65b29364596e81f7d5c8434d (diff)
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Corrections for parallel I/O & tests.
-rw-r--r--src/H5CX.c1
-rw-r--r--src/H5Dio.c9
-rw-r--r--src/H5Dmpio.c69
-rw-r--r--testpar/t_cache.c6
-rw-r--r--testpar/t_dset.c48
5 files changed, 58 insertions, 75 deletions
diff --git a/src/H5CX.c b/src/H5CX.c
index 0f98a15..dd1d74f 100644
--- a/src/H5CX.c
+++ b/src/H5CX.c
@@ -2723,6 +2723,7 @@ H5CX__pop_common(void)
H5CX_SET_PROP(H5D_XFER_COLL_CHUNK_LINK_NUM_TRUE_NAME, mpio_coll_chunk_link_num_true)
H5CX_SET_PROP(H5D_XFER_COLL_CHUNK_LINK_NUM_FALSE_NAME, mpio_coll_chunk_link_num_false)
H5CX_SET_PROP(H5D_XFER_COLL_CHUNK_MULTI_RATIO_COLL_NAME, mpio_coll_chunk_multi_ratio_coll)
+ H5CX_SET_PROP(H5D_XFER_COLL_CHUNK_MULTI_RATIO_IND_NAME, mpio_coll_chunk_multi_ratio_ind)
#endif /* H5_HAVE_PARALLEL */
/* Pop the top context node from the stack */
diff --git a/src/H5Dio.c b/src/H5Dio.c
index 334f18f..cd6b627 100644
--- a/src/H5Dio.c
+++ b/src/H5Dio.c
@@ -57,8 +57,7 @@ static herr_t H5D__typeinfo_init(const H5D_t *dset, hid_t mem_type_id,
hbool_t do_write, H5D_type_info_t *type_info);
#ifdef H5_HAVE_PARALLEL
static herr_t H5D__ioinfo_adjust(H5D_io_info_t *io_info, const H5D_t *dset,
- const H5S_t *file_space, const H5S_t *mem_space, const H5D_type_info_t *type_info,
- const H5D_chunk_map_t *fm);
+ const H5S_t *file_space, const H5S_t *mem_space, const H5D_type_info_t *type_info);
#endif /* H5_HAVE_PARALLEL */
static herr_t H5D__typeinfo_term(const H5D_type_info_t *type_info);
@@ -562,7 +561,7 @@ H5D__read(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space,
#ifdef H5_HAVE_PARALLEL
/* Adjust I/O info for any parallel I/O */
- if(H5D__ioinfo_adjust(&io_info, dataset, file_space, mem_space, &type_info, fm) < 0)
+ if(H5D__ioinfo_adjust(&io_info, dataset, file_space, mem_space, &type_info) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to adjust I/O info for parallel I/O")
#endif /*H5_HAVE_PARALLEL*/
@@ -789,7 +788,7 @@ H5D__write(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space,
#ifdef H5_HAVE_PARALLEL
/* Adjust I/O info for any parallel I/O */
- if(H5D__ioinfo_adjust(&io_info, dataset, file_space, mem_space, &type_info, fm) < 0)
+ if(H5D__ioinfo_adjust(&io_info, dataset, file_space, mem_space, &type_info) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to adjust I/O info for parallel I/O")
#endif /*H5_HAVE_PARALLEL*/
@@ -1091,7 +1090,7 @@ done:
static herr_t
H5D__ioinfo_adjust(H5D_io_info_t *io_info, const H5D_t *dset,
const H5S_t *file_space, const H5S_t *mem_space,
- const H5D_type_info_t *type_info, const H5D_chunk_map_t *fm)
+ const H5D_type_info_t *type_info)
{
herr_t ret_value = SUCCEED; /* Return value */
diff --git a/src/H5Dmpio.c b/src/H5Dmpio.c
index 669da68..eb7aad9 100644
--- a/src/H5Dmpio.c
+++ b/src/H5Dmpio.c
@@ -37,12 +37,13 @@
#include "H5Eprivate.h" /* Error handling */
#include "H5Fprivate.h" /* File access */
#include "H5FDprivate.h" /* File drivers */
+#include "H5FDmpi.h" /* MPI-based file drivers */
#include "H5Iprivate.h" /* IDs */
#include "H5MMprivate.h" /* Memory management */
#include "H5Oprivate.h" /* Object headers */
#include "H5Pprivate.h" /* Property lists */
#include "H5Sprivate.h" /* Dataspaces */
-#include "H5VMprivate.h" /* Vector */
+#include "H5VMprivate.h" /* Vector */
#ifdef H5_HAVE_PARALLEL
@@ -77,13 +78,11 @@
*/
/* Macros to represent different IO modes(NONE, Independent or collective)for multiple chunk IO case */
-#define H5D_CHUNK_IO_MODE_IND 0
#define H5D_CHUNK_IO_MODE_COL 1
/* Macros to represent the regularity of the selection for multiple chunk IO case. */
#define H5D_CHUNK_SELECT_REG 1
-#define H5D_CHUNK_SELECT_IRREG 2
-#define H5D_CHUNK_SELECT_NONE 0
+
/******************/
/* Local Typedefs */
@@ -225,8 +224,6 @@ static herr_t H5D__sort_chunk(H5D_io_info_t *io_info, const H5D_chunk_map_t *fm,
H5D_chunk_addr_info_t chunk_addr_info_array[], int many_chunk_opt);
static herr_t H5D__obtain_mpio_mode(H5D_io_info_t *io_info, H5D_chunk_map_t *fm,
uint8_t assign_io_mode[], haddr_t chunk_addr[]);
-static herr_t H5D__mpio_get_min_chunk(const H5D_io_info_t *io_info,
- const H5D_chunk_map_t *fm, int *min_chunkf);
static herr_t H5D__mpio_get_sum_chunk(const H5D_io_info_t *io_info,
const H5D_chunk_map_t *fm, int *sum_chunkf);
static herr_t H5D__construct_filtered_io_info_list(const H5D_io_info_t *io_info,
@@ -280,8 +277,8 @@ H5D__mpio_opt_possible(const H5D_io_info_t *io_info, const H5S_t *file_space,
const H5S_t *mem_space, const H5D_type_info_t *type_info)
{
H5FD_mpio_xfer_t io_xfer_mode; /* MPI I/O transfer mode */
- int local_cause = 0; /* Local reason(s) for breaking collective mode */
- int global_cause = 0; /* Global reason(s) for breaking collective mode */
+ unsigned local_cause = 0; /* Local reason(s) for breaking collective mode */
+ unsigned global_cause = 0; /* Global reason(s) for breaking collective mode */
htri_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_PACKAGE
@@ -342,7 +339,7 @@ H5D__mpio_opt_possible(const H5D_io_info_t *io_info, const H5S_t *file_space,
/* Form consensus opinion among all processes about whether to perform
* collective I/O
*/
- if(MPI_SUCCESS != (mpi_code = MPI_Allreduce(&local_cause, &global_cause, 1, MPI_INT, MPI_BOR, io_info->comm)))
+ if(MPI_SUCCESS != (mpi_code = MPI_Allreduce(&local_cause, &global_cause, 1, MPI_UNSIGNED, MPI_BOR, io_info->comm)))
HMPI_GOTO_ERROR(FAIL, "MPI_Allreduce failed", mpi_code)
} /* end else */
@@ -525,41 +522,6 @@ done:
/*-------------------------------------------------------------------------
- * Function: H5D__mpio_get_min_chunk
- *
- * Purpose: Routine for obtaining minimum number of chunks to cover
- * hyperslab selection selected by all processors.
- *
- * Return: Non-negative on success/Negative on failure
- *
- * Programmer: Muqun Yang
- * Monday, Feb. 13th, 2006
- *
- *-------------------------------------------------------------------------
- */
-static herr_t
-H5D__mpio_get_min_chunk(const H5D_io_info_t *io_info, const H5D_chunk_map_t *fm,
- int *min_chunkf)
-{
- int num_chunkf; /* Number of chunks to iterate over */
- int mpi_code; /* MPI return code */
- herr_t ret_value = SUCCEED;
-
- FUNC_ENTER_STATIC
-
- /* Get the number of chunks to perform I/O on */
- H5_CHECKED_ASSIGN(num_chunkf, int, H5SL_count(fm->sel_chunks), size_t)
-
- /* Determine the minimum # of chunks for all processes */
- if(MPI_SUCCESS != (mpi_code = MPI_Allreduce(&num_chunkf, min_chunkf, 1, MPI_INT, MPI_MIN, io_info->comm)))
- HMPI_GOTO_ERROR(FAIL, "MPI_Allreduce failed", mpi_code)
-
-done:
- FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5D__mpio_get_min_chunk() */
-
-
-/*-------------------------------------------------------------------------
* Function: H5D__mpio_get_sum_chunk
*
* Purpose: Routine for obtaining total number of chunks to cover
@@ -3070,19 +3032,34 @@ H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io_info_t *chunk
* read from the file and unfiltered.
*/
if(!chunk_entry->full_overwrite || io_info->op_type == H5D_IO_OP_READ) {
+ H5FD_mpio_xfer_t xfer_mode; /* Parallel transfer for this request */
+
chunk_entry->chunk_states.new_chunk.length = chunk_entry->chunk_states.chunk_current.length;
/* Currently, these chunk reads are done independently and will likely
* cause issues with collective metadata reads enabled. In the future,
* this should be refactored to use collective chunk reads - JTH */
+
+ /* Get the original state of parallel I/O transfer mode */
+ if(H5CX_get_io_xfer_mode(&xfer_mode) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get MPI-I/O transfer mode")
+
+ /* Change the xfer_mode to independent for handling the I/O */
+ if(H5CX_set_io_xfer_mode(H5FD_MPIO_INDEPENDENT) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set MPI-I/O transfer mode")
+
if(H5F_block_read(io_info->dset->oloc.file, H5FD_MEM_DRAW, chunk_entry->chunk_states.chunk_current.offset,
chunk_entry->chunk_states.new_chunk.length, chunk_entry->buf) < 0)
- HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk")
+ HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "unable to read raw data chunk")
+
+ /* Return to the original I/O transfer mode setting */
+ if(H5CX_set_io_xfer_mode(xfer_mode) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set MPI-I/O transfer mode")
if(H5Z_pipeline(&io_info->dset->shared->dcpl_cache.pline, H5Z_FLAG_REVERSE,
&filter_mask, err_detect, filter_cb, (size_t *)&chunk_entry->chunk_states.new_chunk.length,
&buf_size, &chunk_entry->buf) < 0)
- HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, FAIL, "couldn't unfilter chunk for modifying")
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTFILTER, FAIL, "couldn't unfilter chunk for modifying")
} /* end if */
else {
chunk_entry->chunk_states.new_chunk.length = true_chunk_size;
diff --git a/testpar/t_cache.c b/testpar/t_cache.c
index 63b6ac7..caa578e 100644
--- a/testpar/t_cache.c
+++ b/testpar/t_cache.c
@@ -4075,6 +4075,9 @@ setup_cache_for_test(hid_t * fid_ptr,
fid = H5Fcreate(filenames[0], H5F_ACC_TRUNC, H5P_DEFAULT, fapl);
+ /* Push API context */
+ H5CX_push();
+
if ( fid < 0 ) {
nerrors++;
if ( verbose ) {
@@ -4556,6 +4559,9 @@ take_down_cache(hid_t fid, H5C_t * cache_ptr)
}
+ /* Pop API context */
+ H5CX_pop();
+
if ( success ) {
if ( world_mpi_rank == world_server_mpi_rank ) {
diff --git a/testpar/t_dset.c b/testpar/t_dset.c
index 65d1bb4..b315772 100644
--- a/testpar/t_dset.c
+++ b/testpar/t_dset.c
@@ -679,8 +679,8 @@ dataset_writeAll(void)
ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
- ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
- VRFY((ret>= 0),"set independent IO collectively succeeded");
+ ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
+ VRFY((ret>= 0),"set independent IO collectively succeeded");
}
@@ -748,8 +748,8 @@ dataset_writeAll(void)
ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
VRFY((ret >= 0), "H5Pcreate xfer succeeded");
if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
- ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
- VRFY((ret>= 0),"set independent IO collectively succeeded");
+ ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
+ VRFY((ret>= 0),"set independent IO collectively succeeded");
}
@@ -819,8 +819,8 @@ dataset_writeAll(void)
ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
VRFY((ret >= 0), "H5Pcreate xfer succeeded");
if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
- ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
- VRFY((ret>= 0),"set independent IO collectively succeeded");
+ ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
+ VRFY((ret>= 0),"set independent IO collectively succeeded");
}
@@ -884,8 +884,8 @@ dataset_writeAll(void)
ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
VRFY((ret >= 0), "H5Pcreate xfer succeeded");
if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
- ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
- VRFY((ret>= 0),"set independent IO collectively succeeded");
+ ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
+ VRFY((ret>= 0),"set independent IO collectively succeeded");
}
/* write data collectively */
@@ -1184,8 +1184,8 @@ dataset_readAll(void)
ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
VRFY((ret >= 0), "H5Pcreate xfer succeeded");
if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
- ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
- VRFY((ret>= 0),"set independent IO collectively succeeded");
+ ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
+ VRFY((ret>= 0),"set independent IO collectively succeeded");
}
@@ -1252,8 +1252,8 @@ dataset_readAll(void)
ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
VRFY((ret >= 0), "H5Pcreate xfer succeeded");
if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
- ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
- VRFY((ret>= 0),"set independent IO collectively succeeded");
+ ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
+ VRFY((ret>= 0),"set independent IO collectively succeeded");
}
@@ -1335,8 +1335,8 @@ dataset_readAll(void)
ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
VRFY((ret >= 0), "H5Pcreate xfer succeeded");
if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
- ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
- VRFY((ret>= 0),"set independent IO collectively succeeded");
+ ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
+ VRFY((ret>= 0),"set independent IO collectively succeeded");
}
/* read data collectively */
@@ -2200,8 +2200,8 @@ extend_writeAll(void)
ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
- ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
- VRFY((ret>= 0),"set independent IO collectively succeeded");
+ ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
+ VRFY((ret>= 0),"set independent IO collectively succeeded");
}
@@ -2240,8 +2240,8 @@ extend_writeAll(void)
ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
- ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
- VRFY((ret>= 0),"set independent IO collectively succeeded");
+ ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
+ VRFY((ret>= 0),"set independent IO collectively succeeded");
}
@@ -2414,8 +2414,8 @@ extend_readAll(void)
ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
- ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
- VRFY((ret>= 0),"set independent IO collectively succeeded");
+ ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
+ VRFY((ret>= 0),"set independent IO collectively succeeded");
}
@@ -2461,8 +2461,8 @@ extend_readAll(void)
ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
- ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
- VRFY((ret>= 0),"set independent IO collectively succeeded");
+ ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
+ VRFY((ret>= 0),"set independent IO collectively succeeded");
}
@@ -2634,8 +2634,8 @@ compress_readAll(void)
ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
- ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
- VRFY((ret>= 0),"set independent IO collectively succeeded");
+ ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
+ VRFY((ret>= 0),"set independent IO collectively succeeded");
}