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Implement support for big I/O for independent reads (#1446)

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* Implement big I/O support for independent reads. Add test for this.

* Committing clang-format changes

* Update big I/O code in H5FD__mpio_write() to match that in
H5FD__mpio_read().

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
This commit is contained in:
Neil Fortner 2022-02-18 09:27:05 -06:00 committed by GitHub
parent cfe4198b6c
commit feda52b084
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2 changed files with 64 additions and 23 deletions
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50
src/H5FDmpio.c
View File

@ -1172,6 +1172,7 @@ H5FD__mpio_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU
int n; int n;
#endif #endif
hbool_t use_view_this_time = FALSE; hbool_t use_view_this_time = FALSE;
hbool_t derived_type = FALSE;
hbool_t rank0_bcast = FALSE; /* If read-with-rank0-and-bcast flag was used */ hbool_t rank0_bcast = FALSE; /* If read-with-rank0-and-bcast flag was used */
#ifdef H5FDmpio_DEBUG #ifdef H5FDmpio_DEBUG
hbool_t H5FD_mpio_debug_t_flag = (H5FD_mpio_debug_flags_s[(int)'t'] && H5FD_MPIO_TRACE_THIS_RANK(file)); hbool_t H5FD_mpio_debug_t_flag = (H5FD_mpio_debug_flags_s[(int)'t'] && H5FD_MPIO_TRACE_THIS_RANK(file));
@ -1199,8 +1200,6 @@ H5FD__mpio_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU
if (H5FD_mpi_haddr_to_MPIOff(addr, &mpi_off /*out*/) < 0) if (H5FD_mpi_haddr_to_MPIOff(addr, &mpi_off /*out*/) < 0)
HGOTO_ERROR(H5E_INTERNAL, H5E_BADRANGE, FAIL, "can't convert from haddr to MPI off") HGOTO_ERROR(H5E_INTERNAL, H5E_BADRANGE, FAIL, "can't convert from haddr to MPI off")
size_i = (int)size; size_i = (int)size;
if ((hsize_t)size_i != size)
HGOTO_ERROR(H5E_INTERNAL, H5E_BADRANGE, FAIL, "can't convert from size to size_i")
/* Only look for MPI views for raw data transfers */ /* Only look for MPI views for raw data transfers */
if (type == H5FD_MEM_DRAW) { if (type == H5FD_MEM_DRAW) {
@ -1304,6 +1303,21 @@ H5FD__mpio_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU
HMPI_GOTO_ERROR(FAIL, "MPI_File_set_view failed", mpi_code) HMPI_GOTO_ERROR(FAIL, "MPI_File_set_view failed", mpi_code)
} /* end if */ } /* end if */
else { else {
if (size != (hsize_t)size_i) {
/* If HERE, then we need to work around the integer size limit
* of 2GB. The input size_t size variable cannot fit into an integer,
* but we can get around that limitation by creating a different datatype
* and then setting the integer size (or element count) to 1 when using
* the derived_type.
*/
if (H5_mpio_create_large_type(size, 0, MPI_BYTE, &buf_type) < 0)
HGOTO_ERROR(H5E_INTERNAL, H5E_CANTGET, FAIL, "can't create MPI-I/O datatype")
derived_type = TRUE;
size_i = 1;
}
#ifdef H5FDmpio_DEBUG #ifdef H5FDmpio_DEBUG
if (H5FD_mpio_debug_r_flag) if (H5FD_mpio_debug_r_flag)
HDfprintf(stderr, "%s: (%d) doing MPI independent IO\n", __func__, file->mpi_rank); HDfprintf(stderr, "%s: (%d) doing MPI independent IO\n", __func__, file->mpi_rank);
@ -1377,6 +1391,9 @@ H5FD__mpio_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU
HDmemset((char *)buf + bytes_read, 0, (size_t)n); HDmemset((char *)buf + bytes_read, 0, (size_t)n);
done: done:
if (derived_type)
MPI_Type_free(&buf_type);
#ifdef H5FDmpio_DEBUG #ifdef H5FDmpio_DEBUG
if (H5FD_mpio_debug_t_flag) if (H5FD_mpio_debug_t_flag)
HDfprintf(stderr, "%s: (%d) Leaving\n", __func__, file->mpi_rank); HDfprintf(stderr, "%s: (%d) Leaving\n", __func__, file->mpi_rank);
@ -1489,20 +1506,6 @@ H5FD__mpio_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, h
*/ */
mpi_off = 0; mpi_off = 0;
} /* end if */ } /* end if */
else if (size != (hsize_t)size_i) {
/* If HERE, then we need to work around the integer size limit
* of 2GB. The input size_t size variable cannot fit into an integer,
* but we can get around that limitation by creating a different datatype
* and then setting the integer size (or element count) to 1 when using
* the derived_type.
*/
if (H5_mpio_create_large_type(size, 0, MPI_BYTE, &buf_type) < 0)
HGOTO_ERROR(H5E_INTERNAL, H5E_CANTGET, FAIL, "can't create MPI-I/O datatype")
derived_type = TRUE;
size_i = 1;
}
/* Write the data. */ /* Write the data. */
if (use_view_this_time) { if (use_view_this_time) {
@ -1548,6 +1551,21 @@ H5FD__mpio_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, h
HMPI_GOTO_ERROR(FAIL, "MPI_File_set_view failed", mpi_code) HMPI_GOTO_ERROR(FAIL, "MPI_File_set_view failed", mpi_code)
} /* end if */ } /* end if */
else { else {
if (size != (hsize_t)size_i) {
/* If HERE, then we need to work around the integer size limit
* of 2GB. The input size_t size variable cannot fit into an integer,
* but we can get around that limitation by creating a different datatype
* and then setting the integer size (or element count) to 1 when using
* the derived_type.
*/
if (H5_mpio_create_large_type(size, 0, MPI_BYTE, &buf_type) < 0)
HGOTO_ERROR(H5E_INTERNAL, H5E_CANTGET, FAIL, "can't create MPI-I/O datatype")
derived_type = TRUE;
size_i = 1;
}
#ifdef H5FDmpio_DEBUG #ifdef H5FDmpio_DEBUG
if (H5FD_mpio_debug_w_flag) if (H5FD_mpio_debug_w_flag)
HDfprintf(stderr, "%s: (%d) doing MPI independent IO\n", __func__, file->mpi_rank); HDfprintf(stderr, "%s: (%d) doing MPI independent IO\n", __func__, file->mpi_rank);

37
testpar/t_bigio.c
View File

@ -1107,13 +1107,15 @@ single_rank_independent_io(void)
HDprintf("\nSingle Rank Independent I/O\n"); HDprintf("\nSingle Rank Independent I/O\n");
if (MAIN_PROCESS) { if (MAIN_PROCESS) {
hsize_t dims[] = {LARGE_DIM}; hsize_t dims[] = {LARGE_DIM};
hid_t file_id = -1; hid_t file_id = -1;
hid_t fapl_id = -1; hid_t fapl_id = -1;
hid_t dset_id = -1; hid_t dset_id = -1;
hid_t fspace_id = -1; hid_t fspace_id = -1;
hid_t mspace_id = -1; hid_t mspace_id = -1;
void * data = NULL; herr_t ret;
int * data = NULL;
uint64_t i;
fapl_id = H5Pcreate(H5P_FILE_ACCESS); fapl_id = H5Pcreate(H5P_FILE_ACCESS);
VRFY_G((fapl_id >= 0), "H5P_FILE_ACCESS"); VRFY_G((fapl_id >= 0), "H5P_FILE_ACCESS");
@ -1135,6 +1137,10 @@ single_rank_independent_io(void)
data = malloc(LARGE_DIM * sizeof(int)); data = malloc(LARGE_DIM * sizeof(int));
/* Initialize data */
for (i = 0; i < LARGE_DIM; i++)
data[i] = (int)(i % (uint64_t)DXFER_BIGCOUNT);
if (mpi_rank_g == 0) if (mpi_rank_g == 0)
H5Sselect_all(fspace_id); H5Sselect_all(fspace_id);
else else
@ -1143,7 +1149,24 @@ single_rank_independent_io(void)
dims[0] = LARGE_DIM; dims[0] = LARGE_DIM;
mspace_id = H5Screate_simple(1, dims, NULL); mspace_id = H5Screate_simple(1, dims, NULL);
VRFY_G((mspace_id >= 0), "H5Screate_simple mspace_id succeeded"); VRFY_G((mspace_id >= 0), "H5Screate_simple mspace_id succeeded");
/* Write data */
H5Dwrite(dset_id, H5T_NATIVE_INT, mspace_id, fspace_id, H5P_DEFAULT, data); H5Dwrite(dset_id, H5T_NATIVE_INT, mspace_id, fspace_id, H5P_DEFAULT, data);
VRFY_G((ret >= 0), "H5Dwrite succeeded");
/* Wipe buffer */
HDmemset(data, 0, LARGE_DIM * sizeof(int));
/* Read data back */
H5Dread(dset_id, H5T_NATIVE_INT, mspace_id, fspace_id, H5P_DEFAULT, data);
VRFY_G((ret >= 0), "H5Dread succeeded");
/* Verify data */
for (i = 0; i < LARGE_DIM; i++)
if (data[i] != (int)(i % (uint64_t)DXFER_BIGCOUNT)) {
HDfprintf(stderr, "verify failed\n");
exit(1);
}
free(data); free(data);
H5Sclose(mspace_id); H5Sclose(mspace_id);