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Merge Implementation of the mpio driver with selection I/O. #3360

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merged 4 commits into from
Aug 8, 2023
Merged

Merge Implementation of the mpio driver with selection I/O. #3360

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f89d5ec
Fix for the bug exposed from running test/set_extent.c when selection…
vchoi-hdfgroup Aug 4, 2023
a549e2e
test(parallel): verify FALSE case (#3356)
hyoklee Aug 5, 2023
a178141
Implementation of the mpio driver with selection I/O. (#3222)
vchoi-hdfgroup Aug 7, 2023
7418bd0
Revert "test(parallel): verify FALSE case (#3356)"
lrknox Aug 8, 2023
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44 changes: 32 additions & 12 deletions src/H5Dchunk.c
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Original file line number Diff line number Diff line change
Expand Up @@ -2731,11 +2731,20 @@ H5D__chunk_read(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info)
}
} /* end if */
else if (!skip_missing_chunks) {
/* Set up nonexistent dataset info for (fill value) read from nonexistent chunk */
nonexistent_dset_info.layout_io_info.contig_piece_info = chunk_info;
nonexistent_dset_info.file_space = chunk_info->fspace;
nonexistent_dset_info.mem_space = chunk_info->mspace;
nonexistent_dset_info.nelmts = chunk_info->piece_points;

/* Set request_nelmts. This is not normally set by the upper layers because selection I/O
* usually does not use strip mining (H5D__scatgath_write), and instead allocates buffers
* large enough for the entire I/O. Set request_nelmts to be large enough for all selected
* elements in this chunk because it must be at least that large */
nonexistent_dset_info.type_info.request_nelmts = nonexistent_dset_info.nelmts;

/* Perform the actual read operation from the nonexistent chunk
*/
nonexistent_dset_info.file_space = chunk_info->fspace;
nonexistent_dset_info.mem_space = chunk_info->mspace;
nonexistent_dset_info.nelmts = chunk_info->piece_points;
if ((dset_info->io_ops.single_read)(&nonexistent_io_info, &nonexistent_dset_info) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "chunked read failed");
} /* end if */
Expand Down Expand Up @@ -2866,9 +2875,10 @@ H5D__chunk_read(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info)

/* Perform the actual read operation */
assert(chk_io_info->count == 1);
chk_io_info->dsets_info[0].file_space = chunk_info->fspace;
chk_io_info->dsets_info[0].mem_space = chunk_info->mspace;
chk_io_info->dsets_info[0].nelmts = chunk_info->piece_points;
chk_io_info->dsets_info[0].layout_io_info.contig_piece_info = chunk_info;
chk_io_info->dsets_info[0].file_space = chunk_info->fspace;
chk_io_info->dsets_info[0].mem_space = chunk_info->mspace;
chk_io_info->dsets_info[0].nelmts = chunk_info->piece_points;
if ((dset_info->io_ops.single_read)(chk_io_info, &chk_io_info->dsets_info[0]) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "chunked read failed");

Expand Down Expand Up @@ -3055,10 +3065,19 @@ H5D__chunk_write(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info)
/* Set up the storage buffer information for this chunk */
cpt_store.compact.buf = chunk;

/* Set up compact dataset info for write to cached chunk */
cpt_dset_info.layout_io_info.contig_piece_info = chunk_info;
cpt_dset_info.file_space = chunk_info->fspace;
cpt_dset_info.mem_space = chunk_info->mspace;
cpt_dset_info.nelmts = chunk_info->piece_points;

/* Set request_nelmts. This is not normally set by the upper layers because selection I/O
* usually does not use strip mining (H5D__scatgath_write), and instead allocates buffers
* large enough for the entire I/O. Set request_nelmts to be large enough for all selected
* elements in this chunk because it must be at least that large */
cpt_dset_info.type_info.request_nelmts = cpt_dset_info.nelmts;

/* Perform the actual write operation */
cpt_dset_info.file_space = chunk_info->fspace;
cpt_dset_info.mem_space = chunk_info->mspace;
cpt_dset_info.nelmts = chunk_info->piece_points;
if ((dset_info->io_ops.single_write)(&cpt_io_info, &cpt_dset_info) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "chunked write failed");

Expand Down Expand Up @@ -3253,9 +3272,10 @@ H5D__chunk_write(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info)

/* Perform the actual write operation */
assert(chk_io_info->count == 1);
chk_io_info->dsets_info[0].file_space = chunk_info->fspace;
chk_io_info->dsets_info[0].mem_space = chunk_info->mspace;
chk_io_info->dsets_info[0].nelmts = chunk_info->piece_points;
chk_io_info->dsets_info[0].layout_io_info.contig_piece_info = chunk_info;
chk_io_info->dsets_info[0].file_space = chunk_info->fspace;
chk_io_info->dsets_info[0].mem_space = chunk_info->mspace;
chk_io_info->dsets_info[0].nelmts = chunk_info->piece_points;
if ((dset_info->io_ops.single_write)(chk_io_info, &chk_io_info->dsets_info[0]) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "chunked write failed");

Expand Down
5 changes: 3 additions & 2 deletions src/H5Dcompact.c
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Original file line number Diff line number Diff line change
Expand Up @@ -233,8 +233,9 @@ H5D__compact_io_init(H5D_io_info_t *io_info, H5D_dset_io_info_t *dinfo)
{
FUNC_ENTER_PACKAGE_NOERR

dinfo->store->compact.buf = dinfo->dset->shared->layout.storage.u.compact.buf;
dinfo->store->compact.dirty = &dinfo->dset->shared->layout.storage.u.compact.dirty;
dinfo->store->compact.buf = dinfo->dset->shared->layout.storage.u.compact.buf;
dinfo->store->compact.dirty = &dinfo->dset->shared->layout.storage.u.compact.dirty;
dinfo->layout_io_info.contig_piece_info = NULL;

/* Disable selection I/O */
io_info->use_select_io = H5D_SELECTION_IO_MODE_OFF;
Expand Down
3 changes: 3 additions & 0 deletions src/H5Defl.c
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Expand Up @@ -198,6 +198,9 @@ H5D__efl_io_init(H5D_io_info_t *io_info, H5D_dset_io_info_t *dinfo)

H5MM_memcpy(&dinfo->store->efl, &(dinfo->dset->shared->dcpl_cache.efl), sizeof(H5O_efl_t));

/* No "pieces" selected */
dinfo->layout_io_info.contig_piece_info = NULL;

/* Disable selection I/O */
io_info->use_select_io = H5D_SELECTION_IO_MODE_OFF;
io_info->no_selection_io_cause |= H5D_SEL_IO_NOT_CONTIGUOUS_OR_CHUNKED_DATASET;
Expand Down
30 changes: 16 additions & 14 deletions src/H5Dio.c
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Expand Up @@ -415,8 +415,14 @@ H5D__read(size_t count, H5D_dset_io_info_t *dset_info)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get MPI-I/O transfer mode");

/* Only report the collective I/O mode if we're actually performing collective I/O */
if (xfer_mode == H5FD_MPIO_COLLECTIVE)
if (xfer_mode == H5FD_MPIO_COLLECTIVE) {
H5CX_set_mpio_actual_io_mode(io_info.actual_io_mode);

/* If we did selection I/O, report that we used "link chunk" mode, since that's the most
* analogous to what selection I/O does */
if (io_info.use_select_io == H5D_SELECTION_IO_MODE_ON)
H5CX_set_mpio_actual_chunk_opt(H5D_MPIO_LINK_CHUNK);
}
}
#endif /* H5_HAVE_PARALLEL */
}
Expand Down Expand Up @@ -1131,20 +1137,16 @@ H5D__typeinfo_init_phase2(H5D_io_info_t *io_info)
assert(io_info);

/* If selection I/O mode is default (auto), enable it here if the VFD supports it (it will be turned off
* later if something else conflicts), otherwise disable it. If we're using the MPIO VFD, the automatic
* selection will happen in H5D__mpio_opt_possible() inside H5D__ioinfo_adjust(). */
#ifdef H5_HAVE_PARALLEL
if (!io_info->using_mpi_vfd)
#endif /* H5_HAVE_PARALLEL */
if (io_info->use_select_io == H5D_SELECTION_IO_MODE_DEFAULT) {
if (H5F_has_vector_select_io(io_info->dsets_info[0].dset->oloc.file,
io_info->op_type == H5D_IO_OP_WRITE))
io_info->use_select_io = H5D_SELECTION_IO_MODE_ON;
else {
io_info->use_select_io = H5D_SELECTION_IO_MODE_OFF;
io_info->no_selection_io_cause |= H5D_SEL_IO_DEFAULT_OFF;
}
* later if something else conflicts), otherwise disable it */
if (io_info->use_select_io == H5D_SELECTION_IO_MODE_DEFAULT) {
if (H5F_has_vector_select_io(io_info->dsets_info[0].dset->oloc.file,
io_info->op_type == H5D_IO_OP_WRITE))
io_info->use_select_io = H5D_SELECTION_IO_MODE_ON;
else {
io_info->use_select_io = H5D_SELECTION_IO_MODE_OFF;
io_info->no_selection_io_cause |= H5D_SEL_IO_DEFAULT_OFF;
}
}

/* If we're doing type conversion and we might be doing selection I/O, check if the buffers are large
* enough to handle the whole I/O */
Expand Down
22 changes: 3 additions & 19 deletions src/H5Dmpio.c
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Expand Up @@ -622,6 +622,9 @@ H5D__mpio_opt_possible(H5D_io_info_t *io_info)
if (!H5FD_mpi_opt_types_g)
local_cause[0] |= H5D_MPIO_MPI_OPT_TYPES_ENV_VAR_DISABLED;

/* Decision on whether to use selection I/O should have been made by now */
assert(io_info->use_select_io != H5D_SELECTION_IO_MODE_DEFAULT);

/* Datatype conversions and transformations are allowed with selection I/O. If the selection I/O mode
* is auto (default), disable collective for now and re-enable later if we can */
if (io_info->use_select_io != H5D_SELECTION_IO_MODE_ON) {
Expand Down Expand Up @@ -731,25 +734,6 @@ H5D__mpio_opt_possible(H5D_io_info_t *io_info)
HMPI_GOTO_ERROR(FAIL, "MPI_Allreduce failed", mpi_code)
} /* end else */

/* If the selection I/O mode is default (auto), decide here whether it should be on or off */
if (io_info->use_select_io == H5D_SELECTION_IO_MODE_DEFAULT) {
/* If the only reason(s) we've disabled collective are type conversions and/or transforms, enable
* selection I/O and re-enable collective I/O since it's supported by selection I/O */
if (global_cause[0] && !(global_cause[0] & ~((unsigned)H5D_MPIO_DATATYPE_CONVERSION |
(unsigned)H5D_MPIO_DATA_TRANSFORMS))) {
assert(!(local_cause[0] &
~((unsigned)H5D_MPIO_DATATYPE_CONVERSION | (unsigned)H5D_MPIO_DATA_TRANSFORMS)));
local_cause[0] = 0;
global_cause[0] = 0;
io_info->use_select_io = H5D_SELECTION_IO_MODE_ON;
}
else {
/* Otherwise, there's currently no benefit to selection I/O, so leave it off */
io_info->use_select_io = H5D_SELECTION_IO_MODE_OFF;
io_info->no_selection_io_cause |= H5D_SEL_IO_DEFAULT_OFF;
}
}

/* Set the local & global values of no-collective-cause in the API context */
H5CX_set_mpio_local_no_coll_cause(local_cause[0]);
H5CX_set_mpio_global_no_coll_cause(global_cause[0]);
Expand Down
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