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authorNeil Fortner <fortnern@gmail.com>2022-10-19 16:13:15 (GMT)
committerGitHub <noreply@github.com>2022-10-19 16:13:15 (GMT)
commit93754cae33d4ed45850745664ce5e59f270f38f8 (patch)
treeac3154f44fe7969dacb452474c32fcaeb84e620d /fortran/src
parenta898cef6c2e277f74cc99302a3c49c39a7428b5b (diff)
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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 'fortran/src')
-rw-r--r--fortran/src/H5Dff.F90104
-rw-r--r--fortran/src/hdf5_fortrandll.def.in2
2 files changed, 105 insertions, 1 deletions
diff --git a/fortran/src/H5Dff.F90 b/fortran/src/H5Dff.F90
index d15e59e..1e88399 100644
--- a/fortran/src/H5Dff.F90
+++ b/fortran/src/H5Dff.F90
@@ -1098,7 +1098,7 @@ CONTAINS
!>
!! \ingroup FH5D
!!
-!! \brief Writes raw data from a dataset into a buffer.
+!! \brief Writes raw data from a buffer to a dataset.
!!
!! \attention \fortran_approved
!!
@@ -1762,6 +1762,108 @@ CONTAINS
CALL h5dfill_ptr(f_ptr_fill_value, fill_type_id, f_ptr_buf, mem_type_id, space_id, hdferr)
END SUBROUTINE h5dfill_char
+!>
+!! \ingroup FH5D
+!!
+!! \brief Reads data from a file to memory buffers for multiple datasets.
+!!
+!! \param count Number of datasets to write to.
+!! \param dset_id Identifier of the dataset to write to.
+!! \param mem_type_id Identifier of the memory datatype.
+!! \param mem_space_id Identifier of the memory dataspace.
+!! \param file_space_id Identifier of the dataset&apos;s dataspace in the file.
+!! \param buf Buffer with data to be written to the file.
+!! \param hdferr \fortran_error
+!! \param xfer_prp Identifier of a transfer property list for this I/O operation.
+!!
+ SUBROUTINE H5Dread_multi_f(count, dset_id, mem_type_id, mem_space_id, file_space_id, buf, hdferr, xfer_prp)
+ IMPLICIT NONE
+
+ INTEGER(SIZE_T), INTENT(IN) :: count
+ INTEGER(HID_T), INTENT(IN), DIMENSION(*) :: dset_id
+ INTEGER(HID_T), INTENT(IN), DIMENSION(*) :: mem_type_id
+ INTEGER(HID_T), INTENT(IN), DIMENSION(*) :: mem_space_id
+ INTEGER(HID_T), INTENT(IN), DIMENSION(*) :: file_space_id
+ TYPE(C_PTR), DIMENSION(*) :: buf
+ INTEGER, INTENT(OUT) :: hdferr
+ INTEGER(HID_T), INTENT(IN), OPTIONAL :: xfer_prp
+
+ INTEGER(HID_T) :: xfer_prp_default
+
+ INTERFACE
+ INTEGER FUNCTION H5Dread_multi(count, dset_id, mem_type_id, mem_space_id, file_space_id, xfer_prp, buf) &
+ BIND(C, NAME='H5Dread_multi')
+ IMPORT :: SIZE_T
+ IMPORT :: HID_T
+ IMPORT :: C_PTR
+ IMPLICIT NONE
+ INTEGER(SIZE_T), VALUE :: count
+ INTEGER(HID_T), DIMENSION(*) :: dset_id
+ INTEGER(HID_T), DIMENSION(*) :: mem_type_id
+ INTEGER(HID_T), DIMENSION(*) :: mem_space_id
+ INTEGER(HID_T), DIMENSION(*) :: file_space_id
+ INTEGER(HID_T), VALUE :: xfer_prp
+ TYPE(C_PTR), DIMENSION(*) :: buf
+ END FUNCTION H5Dread_multi
+ END INTERFACE
+
+ xfer_prp_default = H5P_DEFAULT_F
+ IF (PRESENT(xfer_prp)) xfer_prp_default = xfer_prp
+
+ hdferr = H5Dread_multi(count, dset_id, mem_type_id, mem_space_id, file_space_id, xfer_prp_default, buf)
+
+ END SUBROUTINE H5Dread_multi_f
+!>
+!! \ingroup FH5D
+!!
+!! \brief Writes data in memory to a file for multiple datasets.
+!!
+!! \param count Number of datasets to write to.
+!! \param dset_id Identifier of the dataset to write to.
+!! \param mem_type_id Identifier of the memory datatype.
+!! \param mem_space_id Identifier of the memory dataspace.
+!! \param file_space_id Identifier of the dataset&apos;s dataspace in the file.
+!! \param buf Buffer with data to be written to the file.
+!! \param hdferr \fortran_error
+!! \param xfer_prp Identifier of a transfer property list for this I/O operation.
+!!
+ SUBROUTINE H5Dwrite_multi_f(count, dset_id, mem_type_id, mem_space_id, file_space_id, buf, hdferr, xfer_prp)
+ IMPLICIT NONE
+
+ INTEGER(SIZE_T), INTENT(IN) :: count
+ INTEGER(HID_T), INTENT(IN), DIMENSION(*) :: dset_id
+ INTEGER(HID_T), INTENT(IN), DIMENSION(*) :: mem_type_id
+ INTEGER(HID_T), INTENT(IN), DIMENSION(*) :: mem_space_id
+ INTEGER(HID_T), INTENT(IN), DIMENSION(*) :: file_space_id
+ TYPE(C_PTR), DIMENSION(*) :: buf
+ INTEGER, INTENT(OUT) :: hdferr
+ INTEGER(HID_T), INTENT(IN), OPTIONAL :: xfer_prp
+
+ INTEGER(HID_T) :: xfer_prp_default
+
+ INTERFACE
+ INTEGER FUNCTION H5Dwrite_multi(count, dset_id, mem_type_id, mem_space_id, file_space_id, xfer_prp, buf) &
+ BIND(C, NAME='H5Dwrite_multi')
+ IMPORT :: SIZE_T
+ IMPORT :: HID_T
+ IMPORT :: C_PTR
+ IMPLICIT NONE
+ INTEGER(SIZE_T), VALUE :: count
+ INTEGER(HID_T), DIMENSION(*) :: dset_id
+ INTEGER(HID_T), DIMENSION(*) :: mem_type_id
+ INTEGER(HID_T), DIMENSION(*) :: mem_space_id
+ INTEGER(HID_T), DIMENSION(*) :: file_space_id
+ INTEGER(HID_T), VALUE :: xfer_prp
+ TYPE(C_PTR), DIMENSION(*) :: buf
+ END FUNCTION H5Dwrite_multi
+ END INTERFACE
+
+ xfer_prp_default = H5P_DEFAULT_F
+ IF (PRESENT(xfer_prp)) xfer_prp_default = xfer_prp
+
+ hdferr = H5Dwrite_multi(count, dset_id, mem_type_id, mem_space_id, file_space_id, xfer_prp_default, buf)
+
+ END SUBROUTINE H5Dwrite_multi_f
#endif
diff --git a/fortran/src/hdf5_fortrandll.def.in b/fortran/src/hdf5_fortrandll.def.in
index dee56ac..4fa6f6a 100644
--- a/fortran/src/hdf5_fortrandll.def.in
+++ b/fortran/src/hdf5_fortrandll.def.in
@@ -80,6 +80,8 @@ H5D_mp_H5DGET_ACCESS_PLIST_F
H5D_mp_H5DWRITE_PTR
H5D_mp_H5DREAD_PTR
H5D_mp_H5DVLEN_RECLAIM_F
+H5D_mp_H5DREAD_MULTI_F
+H5D_mp_H5DWRITE_MULTI_F
; H5E
H5E_mp_H5ECLEAR_F
H5E_mp_H5EPRINT_F