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Implementation of the mpio driver with selection I/O. #3222

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merged 30 commits into from
Aug 7, 2023
Merged

Implementation of the mpio driver with selection I/O. #3222

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25c434e
Implementation of the mpio driver with selection I/O.
vchoi-hdfgroup Jul 3, 2023
45e0709
Committing clang-format changes
github-actions[bot] Jul 3, 2023
a8c0351
Add comments for the changes. Minor modifications to the mpio driver …
vchoi-hdfgroup Jul 6, 2023
c3fee29
Committing clang-format changes
github-actions[bot] Jul 6, 2023
f75cbd3
Correct spelling error.
vchoi-hdfgroup Jul 6, 2023
db37097
Merge branch 'HDFGroup:develop' into new_mpio_develop
vchoi-hdfgroup Jul 11, 2023
d1d5abf
Merge branch 'HDFGroup:develop' into new_mpio_develop
vchoi-hdfgroup Jul 14, 2023
b6cc695
Merge branch 'HDFGroup:develop' into new_mpio_develop
vchoi-hdfgroup Jul 17, 2023
a39f805
Merge branch 'HDFGroup:develop' into new_mpio_develop
vchoi-hdfgroup Jul 19, 2023
56e0ca3
Add tests for the three bugs found when setting H5D_SELECTION_IO_MODE…
vchoi-hdfgroup Jul 19, 2023
41f68d4
Committing clang-format changes
github-actions[bot] Jul 19, 2023
eddb315
Correct spelling error.
vchoi-hdfgroup Jul 19, 2023
6604ad4
Merge branch 'HDFGroup:develop' into new_mpio_develop
vchoi-hdfgroup Jul 24, 2023
accb22f
Merge branch 'HDFGroup:develop' into new_mpio_develop
vchoi-hdfgroup Jul 26, 2023
8b080ec
Merge branch 'HDFGroup:develop' into new_mpio_develop
vchoi-hdfgroup Jul 27, 2023
5f20722
Add tests for selection I/O which are derived from test/vfd.c and mod…
vchoi-hdfgroup Jul 27, 2023
efbe96c
Committing clang-format changes
github-actions[bot] Jul 27, 2023
40c3d64
Correct spelling errors.
vchoi-hdfgroup Jul 27, 2023
83ab87d
Committing clang-format changes
github-actions[bot] Jul 27, 2023
ab7746c
Merge branch 'HDFGroup:develop' into new_mpio_develop
vchoi-hdfgroup Aug 1, 2023
eeb29b2
Merge branch 'develop' into new_mpio_develop
vchoi-hdfgroup Aug 3, 2023
1fadf80
Committing clang-format changes
github-actions[bot] Aug 3, 2023
340cf6b
Merge branch 'HDFGroup:develop' into new_mpio_develop
vchoi-hdfgroup Aug 3, 2023
a1fd1f4
Fix CI failures due ot ";" after macros.
vchoi-hdfgroup Aug 3, 2023
de6a7fd
Committing clang-format changes
github-actions[bot] Aug 3, 2023
8e42490
This changes the default selection I/O to on for MPIO.
vchoi-hdfgroup Aug 4, 2023
dc886ee
Merge branch 'HDFGroup:develop' into new_mpio_develop
vchoi-hdfgroup Aug 5, 2023
d61facc
Fixes for the two issues in PR review:
vchoi-hdfgroup Aug 5, 2023
2621bbb
Committing clang-format changes
github-actions[bot] Aug 5, 2023
3bf430f
Address spelling/grammar errors from PR review.
vchoi-hdfgroup Aug 6, 2023
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402 changes: 398 additions & 4 deletions src/H5FD.c
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20 changes: 16 additions & 4 deletions src/H5FDdevelop.h
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Original file line number Diff line number Diff line change
Expand Up @@ -196,12 +196,12 @@ typedef struct H5FD_class_t {
size_t sizes[], void *bufs[]);
herr_t (*write_vector)(H5FD_t *file, hid_t dxpl, uint32_t count, H5FD_mem_t types[], haddr_t addrs[],
size_t sizes[], const void *bufs[]);
herr_t (*read_selection)(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, size_t count, hid_t mem_spaces[],
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I understand we want to keep things consistent but if we're going to change the API to keep the count parameter the same type we should change it to size_t. I think we should just lave it alone for now though.

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So I will keep as size_t for read_selection() and write_selection()? But as uint32_t for write_vector and read_vector?

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Yeah I don't think we should change it now, it's already part of the API

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Just want to double-check:
as size_t will be used for all APIs and the related intermediate routines:
H5FDread/write_selection(), H5FDread/write_vector_from_selection(), H5FDread/write_from_selection()

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correction to previous comment: "count" as size_t

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Don't change any APIs right now, thanks, just revert the type change to the H5FD_class_t struct

herr_t (*read_selection)(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, uint32_t count, hid_t mem_spaces[],
hid_t file_spaces[], haddr_t offsets[], size_t element_sizes[],
void *bufs[] /*out*/);
herr_t (*write_selection)(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, size_t count, hid_t mem_spaces[],
hid_t file_spaces[], haddr_t offsets[], size_t element_sizes[],
const void *bufs[] /*in*/);
herr_t (*write_selection)(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, uint32_t count,
hid_t mem_spaces[], hid_t file_spaces[], haddr_t offsets[],
size_t element_sizes[], const void *bufs[] /*in*/);
herr_t (*flush)(H5FD_t *file, hid_t dxpl_id, hbool_t closing);
herr_t (*truncate)(H5FD_t *file, hid_t dxpl_id, hbool_t closing);
herr_t (*lock)(H5FD_t *file, hbool_t rw);
Expand Down Expand Up @@ -281,6 +281,18 @@ H5_DLL herr_t H5FDread_selection(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id,
H5_DLL herr_t H5FDwrite_selection(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, uint32_t count,
hid_t mem_spaces[], hid_t file_spaces[], haddr_t offsets[],
size_t element_sizes[], const void *bufs[]);
H5_DLL herr_t H5FDread_vector_from_selection(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, uint32_t count,
hid_t mem_spaces[], hid_t file_spaces[], haddr_t offsets[],
size_t element_sizes[], void *bufs[] /* out */);
H5_DLL herr_t H5FDwrite_vector_from_selection(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, uint32_t count,
hid_t mem_spaces[], hid_t file_spaces[], haddr_t offsets[],
size_t element_sizes[], const void *bufs[] /* in */);
H5_DLL herr_t H5FDread_from_selection(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, uint32_t count,
hid_t mem_space_ids[], hid_t file_space_ids[], haddr_t offsets[],
size_t element_sizes[], void *bufs[] /* out */);
H5_DLL herr_t H5FDwrite_from_selection(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, uint32_t count,
hid_t mem_space_ids[], hid_t file_space_ids[], haddr_t offsets[],
size_t element_sizes[], const void *bufs[] /* in */);
H5_DLL herr_t H5FDflush(H5FD_t *file, hid_t dxpl_id, hbool_t closing);
H5_DLL herr_t H5FDtruncate(H5FD_t *file, hid_t dxpl_id, hbool_t closing);
H5_DLL herr_t H5FDlock(H5FD_t *file, hbool_t rw);
Expand Down
709 changes: 592 additions & 117 deletions src/H5FDint.c
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1,025 changes: 980 additions & 45 deletions src/H5FDmpio.c
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36 changes: 31 additions & 5 deletions src/H5FDprivate.h
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Original file line number Diff line number Diff line change
Expand Up @@ -77,6 +77,10 @@ typedef struct {
} \
}

#define SKIP_NO_CB 0x00u
#define SKIP_SELECTION_CB 0x01u
#define SKIP_VECTOR_CB 0x02u

/* Define structure to hold driver ID, info & configuration string for FAPLs */
typedef struct {
hid_t driver_id; /* Driver's ID */
Expand Down Expand Up @@ -149,12 +153,27 @@ H5_DLL herr_t H5FD_read_selection(H5FD_t *file, H5FD_mem_t type, uint32_t count
H5_DLL herr_t H5FD_write_selection(H5FD_t *file, H5FD_mem_t type, uint32_t count, struct H5S_t **mem_spaces,
struct H5S_t **file_spaces, haddr_t offsets[], size_t element_sizes[],
const void *bufs[]);
H5_DLL herr_t H5FD_read_selection_id(H5FD_t *file, H5FD_mem_t type, uint32_t count, hid_t mem_space_ids[],
hid_t file_space_ids[], haddr_t offsets[], size_t element_sizes[],
void *bufs[] /* out */);
H5_DLL herr_t H5FD_write_selection_id(H5FD_t *file, H5FD_mem_t type, uint32_t count, hid_t mem_space_ids[],
H5_DLL herr_t H5FD_read_selection_id(uint32_t skip_cb, H5FD_t *file, H5FD_mem_t type, uint32_t count,
hid_t mem_space_ids[], hid_t file_space_ids[], haddr_t offsets[],
size_t element_sizes[], void *bufs[] /* out */);
H5_DLL herr_t H5FD_write_selection_id(uint32_t skip_cb, H5FD_t *file, H5FD_mem_t type, uint32_t count,
hid_t mem_space_ids[], hid_t file_space_ids[], haddr_t offsets[],
size_t element_sizes[], const void *bufs[]);
H5_DLL herr_t H5FD_read_vector_from_selection(H5FD_t *file, H5FD_mem_t type, uint32_t count,
hid_t mem_space_ids[], hid_t file_space_ids[],
haddr_t offsets[], size_t element_sizes[], void *bufs[]);

H5_DLL herr_t H5FD_write_vector_from_selection(H5FD_t *file, H5FD_mem_t type, uint32_t count,
hid_t mem_space_ids[], hid_t file_space_ids[],
haddr_t offsets[], size_t element_sizes[], const void *bufs[]);

H5_DLL herr_t H5FD_read_from_selection(H5FD_t *file, H5FD_mem_t type, uint32_t count, hid_t mem_space_ids[],
hid_t file_space_ids[], haddr_t offsets[], size_t element_sizes[],
const void *bufs[]);
void *bufs[]);

H5_DLL herr_t H5FD_write_from_selection(H5FD_t *file, H5FD_mem_t type, uint32_t count, hid_t mem_space_ids[],
hid_t file_space_ids[], haddr_t offsets[], size_t element_sizes[],
const void *bufs[]);
H5_DLL herr_t H5FD_flush(H5FD_t *file, hbool_t closing);
H5_DLL herr_t H5FD_truncate(H5FD_t *file, hbool_t closing);
H5_DLL herr_t H5FD_lock(H5FD_t *file, hbool_t rw);
Expand All @@ -171,6 +190,13 @@ H5_DLL herr_t H5FD_sort_vector_io_req(hbool_t *vector_was_sorted, uint32_t count
haddr_t addrs[], size_t sizes[], H5_flexible_const_ptr_t bufs[],
H5FD_mem_t **s_types_ptr, haddr_t **s_addrs_ptr, size_t **s_sizes_ptr,
H5_flexible_const_ptr_t **s_bufs_ptr);

H5_DLL herr_t H5FD_sort_selection_io_req(hbool_t *selection_was_sorted, uint32_t _count,
hid_t mem_space_ids[], hid_t file_space_ids[], haddr_t offsets[],
size_t element_sizes[], H5_flexible_const_ptr_t bufs[],
hid_t **s_mem_space_ids, hid_t **s_file_space_ids,
haddr_t **s_offsets_ptr, size_t **s_element_sizes_ptr,
H5_flexible_const_ptr_t **s_bufs_ptr);
H5_DLL herr_t H5FD_init(void);

/* Function prototypes for MPI based VFDs*/
Expand Down
24 changes: 20 additions & 4 deletions test/select_io_dset.c
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Original file line number Diff line number Diff line change
Expand Up @@ -2751,9 +2751,6 @@ test_set_get_select_io_mode(hid_t fid)
if (H5Pget_selection_io(dxpl, &selection_io_mode) < 0)
TEST_ERROR;

if (selection_io_mode != H5D_SELECTION_IO_MODE_DEFAULT)
TEST_ERROR;

/* Disable case */
if (H5Pset_selection_io(dxpl, H5D_SELECTION_IO_MODE_OFF) < 0)
TEST_ERROR;
Expand Down Expand Up @@ -3063,11 +3060,29 @@ static herr_t
test_get_no_selection_io_cause(const char *filename, hid_t fapl)
{

int errs = 0;
hid_t dxpl = H5I_INVALID_HID;
H5D_selection_io_mode_t selection_io_mode;
int errs = 0;

printf("\n");
TESTING("H5Pget_no_selection_io_cause()");

if ((dxpl = H5Pcreate(H5P_DATASET_XFER)) < 0)
FAIL_STACK_ERROR;

if (H5Pget_selection_io(dxpl, &selection_io_mode) < 0)
TEST_ERROR;

if (H5Pclose(dxpl) < 0)
FAIL_STACK_ERROR;

/* The following tests are based on H5D_SELECTION_IO_MODE_DEFAULT as the
default setting in the library; skip the tests if that is not true */
if (selection_io_mode != H5D_SELECTION_IO_MODE_DEFAULT) {
SKIPPED();
return SUCCEED;
}

errs += test_no_selection_io_cause_mode(filename, fapl, TEST_DISABLE_BY_API);
errs += test_no_selection_io_cause_mode(filename, fapl, TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET);
errs += test_no_selection_io_cause_mode(filename, fapl, TEST_CONTIGUOUS_SIEVE_BUFFER);
Expand All @@ -3083,6 +3098,7 @@ test_get_no_selection_io_cause(const char *filename, hid_t fapl)
errs += test_no_selection_io_cause_mode(filename, fapl, TEST_PAGE_BUFFER);
#endif

error:
if (errs) {
printf(" FAILED\n");
return FAIL;
Expand Down
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