diff options
author | Neil Fortner <fortnern@gmail.com> | 2022-10-19 16:13:15 (GMT) |
---|---|---|
committer | GitHub <noreply@github.com> | 2022-10-19 16:13:15 (GMT) |
commit | 93754cae33d4ed45850745664ce5e59f270f38f8 (patch) | |
tree | ac3154f44fe7969dacb452474c32fcaeb84e620d /src/H5Dselect.c | |
parent | a898cef6c2e277f74cc99302a3c49c39a7428b5b (diff) | |
download | hdf5-93754cae33d4ed45850745664ce5e59f270f38f8.zip hdf5-93754cae33d4ed45850745664ce5e59f270f38f8.tar.gz hdf5-93754cae33d4ed45850745664ce5e59f270f38f8.tar.bz2 |
Multi Dataset (#2120)
* Fix bug with cross platform compatibility of references within vlens.
No testing yet.
* Merge from multi_rd_wd_coll_io to a more recent branch from develop.
Untested, probably does not work yet.
* Committing clang-format changes
* Committing clang-format changes
* Fix many bugs in multi dataset branch. Mostly works, some issues in
SWMR tests.
* Committing clang-format changes
* Disable test in swmr.c that was failing due to bug in HDF5 unrelated to
multi dataset.
* Committing clang-format changes
* Fixed fortran multi-dataset tests
* Fixed xlf errors
* Added benchmark code for multi-datasets
* loops over datasets
* added missing error arg.
* Added gnuplot formatting
* Jonathan Kim original MD benchmarking code
* updated MD benchmarking code
* code clean-up
* Only make files in feature test mode
* misc clean-up
* removed TEST_MDSET_NO_LAST_DSET_2ND_PROC option
* Committing clang-format changes
* Change multi dataset API to use arrays of individual parameters instead
of the parameter struct.
* Committing clang-format changes
* Update to new multi dataset Fortran API and tests. (#1724)
* Update to new multi dataset Fortran API and tests.
* Sync Fortran with develop.
* skipping h5pget_mpio_actual_io_mode_f for now
* Fixed issue with dxpl_id, changed to variable size dim. (#1770)
* Remove "is_coll_broken" field from H5D_io_info_t struct
* Committing clang-format changes
* Minor cleanup in multi dataset code.
* Committing clang-format changes
* Clean up in multi dataset code.
* Committing clang-format changes
* Committing clang-format changes
* Fix speeling
* Fix bug in parallel compression. Switch base_maddr in io_info to be a
union.
* Committing clang-format changes
* Implement selection I/O support with multi dataset. Will be broken in
parallel until PR 1803 is merged to develop then the MDS branch.
* Committing clang-format changes
* Spelling
* Fix bug in multi dataset that could cause errors when only some of the
datasets in the multi dataset I/O used type conversion.
* Committing clang-format changes
* Integrate multi dataset APIs with VOL layer. Add async versions of
multi dataset APIs.
* Committing clang-format changes
* Spelling fixes
* Fix bug in non-parallel HDF5 compilation.
* Committing clang-format changes
* Fix potential memory/free list error. Minor performance fix. Other minor
changes.
* Committing clang-format changes
* Fix memory leak with memory dataspace for I/O.
* Committing clang-format changes
* Fix stack variables too large. Rename H5D_dset_info_t to
H5D_dset_io_info_t.
* Committing clang-format changes
* Remove mem_space_alloc field from H5D_dset_io_info_t. Each function is
now responsible for freeing any spaces it adds to dset_info.
* Committing clang-format changes
* fixed _multi Fortran declaration
* Refactor various things in (mostly) the serial I/O code path to make
things more maintainable.
* Committing clang-format changes
* updated to array based, doxygen, and examples
* Reinstate H5D_chunk_map_t, stored (via pointer) inside
H5D_dset_io_info_t.
* Change from calloc to malloc for H5D_dset_io_info_t and H5D_chunk_map_t.
Switch temporary dset_infos to be local stack variables.
* Committing clang-format changes
* format cleanup
* format cleanup
* added coll and ind
* Modify all parallel I/O paths to take dset_info instead of assuming
dset_info[0].
* Committing clang-format changes
* fixed output
* Rework parallel I/O code to work properly with multi dataset in more
cases. Fix bug in parallel compression.
* Committing clang-format changes
* Prevent H5D__multi_chunk_collective_io() from messing up collective opt
property for other datasets in I/O. Other minor cleanup. Add new test
case to t_pmulti_dset.c for H5FD_MPIO_INDIVIDUAL_IO, disabled for now
due to failures apparently unrelated to multi dataset code.
* Fix spelling
* Committing clang-format changes
* Replace N log N algorithm for finding chunk in
H5D__multi_chunk_collective_io() with O(N) algorithm, and remove use of
io_info->sel_pieces in that function.
* Committing clang-format changes
* Replace sel_pieces skiplist in io_info with flat array of pointers, use
qsort in I/O routine only when necessary.
* Committing clang-format changes
* Add new test case to mdset.c
* Committing clang-format changes
* Fix spelling
* Very minor fix in H5VL__native_dataset_read()
* Fix bug that could affect filtered parallel multi-dataset I/O.
* Add RM entries for H5Dread_multi(), H5Dread_multi_async(),
H5Dwrite_multi(), and H5Dwrite_multi_async()
* Unskip test in swmr.c
* Committing clang-format changes
* Eliminate H5D__pre_read and H5D__pre_write
* Remove examples/ph5mdsettest.c. Will fix and re-add as a test.
* Enable hyperslab combinations in mdset test
* Committing clang-format changes
* Clarify H5Dread/write_multi documentation.
* Fix bugs in multi-dataset I/O. Expand serial multi dataset test.
Update macro in parallel multi dataset test.
* Committing clang-format changes
* Spelling
* Remove obsolete entry in bin/trace
* Rework type conversion buffer allocation. Only one buffer is shared
between datasets in mdset mode, and it is malloced instead of calloced.
* Committing clang-format changes
* Fix bug in error handling in H5D__read/write
* added multi-dataset fortran check with optional dataset creation id (#2150)
* removed dup. dll entry
* Address comments from code review.
* Remove spurious changes in H5Fmpi.c
* Fix issue with reading unallocated datasets in multi-dataset mode.
Address other comments from code review.
* Committing clang-format changes
* Delay chunk index lookup from io_init to mdio_init so it doesn't add
overhead to single dataset I/O.
* Committing clang-format changes
* Fix inappropriate use of piece_count
* updated copyright on new file, removed benchmark from testing dir.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: M. Scot Breitenfeld <brtnfld@hdfgroup.org>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Diffstat (limited to 'src/H5Dselect.c')
-rw-r--r-- | src/H5Dselect.c | 62 |
1 files changed, 31 insertions, 31 deletions
diff --git a/src/H5Dselect.c b/src/H5Dselect.c index b16dd5a..1d1b5f2 100644 --- a/src/H5Dselect.c +++ b/src/H5Dselect.c @@ -44,8 +44,8 @@ /* Local Prototypes */ /********************/ -static herr_t H5D__select_io(const H5D_io_info_t *io_info, size_t elmt_size, size_t nelmts, H5S_t *file_space, - H5S_t *mem_space); +static herr_t H5D__select_io(const H5D_io_info_t *io_info, const H5D_dset_io_info_t *dset_info, + size_t elmt_size); /*********************/ /* Package Variables */ @@ -77,8 +77,7 @@ H5FL_EXTERN(H5S_sel_iter_t); *------------------------------------------------------------------------- */ static herr_t -H5D__select_io(const H5D_io_info_t *io_info, size_t elmt_size, size_t nelmts, H5S_t *file_space, - H5S_t *mem_space) +H5D__select_io(const H5D_io_info_t *io_info, const H5D_dset_io_info_t *dset_info, size_t elmt_size) { H5S_sel_iter_t *mem_iter = NULL; /* Memory selection iteration info */ hbool_t mem_iter_init = FALSE; /* Memory selection iteration info has been initialized */ @@ -95,19 +94,23 @@ H5D__select_io(const H5D_io_info_t *io_info, size_t elmt_size, size_t nelmts, H5 size_t dxpl_vec_size; /* Vector length from API context's DXPL */ size_t vec_size; /* Vector length */ ssize_t tmp_file_len; /* Temporary number of bytes in file sequence */ + size_t nelmts; /* Number of elements to process */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE /* Check args */ HDassert(io_info); - HDassert(io_info->dset); - HDassert(io_info->store); - HDassert(io_info->u.rbuf); + HDassert(dset_info->dset); + HDassert(dset_info->store); + HDassert(dset_info->buf.vp); if (elmt_size == 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADVALUE, FAIL, "invalid elmt_size of 0") + /* Initialize nelmts */ + nelmts = dset_info->nelmts; + /* Check for only one element in selection */ if (nelmts == 1) { hsize_t single_mem_off; /* Offset in memory */ @@ -116,9 +119,9 @@ H5D__select_io(const H5D_io_info_t *io_info, size_t elmt_size, size_t nelmts, H5 size_t single_file_len; /* Length in the file */ /* Get offset of first element in selections */ - if (H5S_SELECT_OFFSET(file_space, &single_file_off) < 0) + if (H5S_SELECT_OFFSET(dset_info->file_space, &single_file_off) < 0) HGOTO_ERROR(H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "can't retrieve file selection offset") - if (H5S_SELECT_OFFSET(mem_space, &single_mem_off) < 0) + if (H5S_SELECT_OFFSET(dset_info->mem_space, &single_mem_off) < 0) HGOTO_ERROR(H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "can't retrieve memory selection offset") /* Set up necessary information for I/O operation */ @@ -130,16 +133,16 @@ H5D__select_io(const H5D_io_info_t *io_info, size_t elmt_size, size_t nelmts, H5 /* Perform I/O on memory and file sequences */ if (io_info->op_type == H5D_IO_OP_READ) { - if ((tmp_file_len = (*io_info->layout_ops.readvv)( - io_info, file_nseq, &curr_file_seq, &single_file_len, &single_file_off, mem_nseq, - &curr_mem_seq, &single_mem_len, &single_mem_off)) < 0) + if ((tmp_file_len = (*dset_info->layout_ops.readvv)( + io_info, dset_info, file_nseq, &curr_file_seq, &single_file_len, &single_file_off, + mem_nseq, &curr_mem_seq, &single_mem_len, &single_mem_off)) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_READERROR, FAIL, "read error") } /* end if */ else { HDassert(io_info->op_type == H5D_IO_OP_WRITE); - if ((tmp_file_len = (*io_info->layout_ops.writevv)( - io_info, file_nseq, &curr_file_seq, &single_file_len, &single_file_off, mem_nseq, - &curr_mem_seq, &single_mem_len, &single_mem_off)) < 0) + if ((tmp_file_len = (*dset_info->layout_ops.writevv)( + io_info, dset_info, file_nseq, &curr_file_seq, &single_file_len, &single_file_off, + mem_nseq, &curr_mem_seq, &single_mem_len, &single_mem_off)) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_WRITEERROR, FAIL, "write error") } /* end else */ @@ -175,12 +178,13 @@ H5D__select_io(const H5D_io_info_t *io_info, size_t elmt_size, size_t nelmts, H5 HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate file iterator") /* Initialize file iterator */ - if (H5S_select_iter_init(file_iter, file_space, elmt_size, H5S_SEL_ITER_GET_SEQ_LIST_SORTED) < 0) + if (H5S_select_iter_init(file_iter, dset_info->file_space, elmt_size, + H5S_SEL_ITER_GET_SEQ_LIST_SORTED) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator") file_iter_init = 1; /* File selection iteration info has been initialized */ /* Initialize memory iterator */ - if (H5S_select_iter_init(mem_iter, mem_space, elmt_size, 0) < 0) + if (H5S_select_iter_init(mem_iter, dset_info->mem_space, elmt_size, 0) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator") mem_iter_init = 1; /* Memory selection iteration info has been initialized */ @@ -214,16 +218,16 @@ H5D__select_io(const H5D_io_info_t *io_info, size_t elmt_size, size_t nelmts, H5 /* Perform I/O on memory and file sequences */ if (io_info->op_type == H5D_IO_OP_READ) { - if ((tmp_file_len = - (*io_info->layout_ops.readvv)(io_info, file_nseq, &curr_file_seq, file_len, file_off, - mem_nseq, &curr_mem_seq, mem_len, mem_off)) < 0) + if ((tmp_file_len = (*dset_info->layout_ops.readvv)( + io_info, dset_info, file_nseq, &curr_file_seq, file_len, file_off, mem_nseq, + &curr_mem_seq, mem_len, mem_off)) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_READERROR, FAIL, "read error") } /* end if */ else { HDassert(io_info->op_type == H5D_IO_OP_WRITE); - if ((tmp_file_len = (*io_info->layout_ops.writevv)(io_info, file_nseq, &curr_file_seq, - file_len, file_off, mem_nseq, - &curr_mem_seq, mem_len, mem_off)) < 0) + if ((tmp_file_len = (*dset_info->layout_ops.writevv)( + io_info, dset_info, file_nseq, &curr_file_seq, file_len, file_off, mem_nseq, + &curr_mem_seq, mem_len, mem_off)) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_WRITEERROR, FAIL, "write error") } /* end else */ @@ -452,16 +456,14 @@ done: *------------------------------------------------------------------------- */ herr_t -H5D__select_read(const H5D_io_info_t *io_info, const H5D_type_info_t *type_info, hsize_t nelmts, - H5S_t *file_space, H5S_t *mem_space) +H5D__select_read(const H5D_io_info_t *io_info, const H5D_dset_io_info_t *dset_info) { herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE /* Call generic selection operation */ - H5_CHECK_OVERFLOW(nelmts, hsize_t, size_t); - if (H5D__select_io(io_info, type_info->src_type_size, (size_t)nelmts, file_space, mem_space) < 0) + if (H5D__select_io(io_info, dset_info, dset_info->type_info.src_type_size) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_READERROR, FAIL, "read error") done: @@ -481,16 +483,14 @@ done: *------------------------------------------------------------------------- */ herr_t -H5D__select_write(const H5D_io_info_t *io_info, const H5D_type_info_t *type_info, hsize_t nelmts, - H5S_t *file_space, H5S_t *mem_space) +H5D__select_write(const H5D_io_info_t *io_info, const H5D_dset_io_info_t *dset_info) { herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE /* Call generic selection operation */ - H5_CHECK_OVERFLOW(nelmts, hsize_t, size_t); - if (H5D__select_io(io_info, type_info->dst_type_size, (size_t)nelmts, file_space, mem_space) < 0) + if (H5D__select_io(io_info, dset_info, dset_info->type_info.dst_type_size) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_WRITEERROR, FAIL, "write error") done: |