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Merged
merged 5 commits into from
Oct 11, 2021
Merged

Romio fixes from mpich v41x #8371

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c9c1ec6
[from mpich] romio: avoid freeing NULLs in gpfs
markalle Aug 10, 2021
4de4fd3
[from mpich] romio GPFS: missing initialization
markalle Aug 10, 2021
3e317d7
[from mpich] darray (romio) needs a resize in the block()/cyclic() su…
markalle Dec 17, 2020
adda190
[from mpich] romio flatten has flat->count consistency problems
markalle Dec 17, 2020
ecd3e05
[from mpich] make ADIOI_GEN_WriteStrided not step on itself
markalle Jan 12, 2021
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1 change: 1 addition & 0 deletions ompi/mca/io/romio321/romio/adio/ad_gpfs/ad_gpfs_aggrs.c
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Original file line number Diff line number Diff line change
Expand Up @@ -719,6 +719,7 @@ void ADIOI_GPFS_Calc_others_req(ADIO_File fd, int count_my_req_procs,
others_req[i].count = 0;
others_req[i].offsets = NULL;
others_req[i].lens = NULL;
others_req[i].mem_ptrs = NULL;
}
}

Expand Down
10 changes: 5 additions & 5 deletions ompi/mca/io/romio321/romio/adio/ad_gpfs/ad_gpfs_rdcoll.c
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Original file line number Diff line number Diff line change
Expand Up @@ -444,8 +444,8 @@ void ADIOI_GPFS_ReadStridedColl(ADIO_File fd, void *buf, int count,
ADIOI_Free(count_my_req_per_proc);
for (i=0; i<nprocs; i++) {
if (my_req[i].count) {
ADIOI_Free(my_req[i].offsets);
ADIOI_Free(my_req[i].lens);
if (my_req[i].offsets) { ADIOI_Free(my_req[i].offsets); }
if (my_req[i].lens) { ADIOI_Free(my_req[i].lens); }
}
}
ADIOI_Free(my_req);
Expand All @@ -469,9 +469,9 @@ void ADIOI_GPFS_ReadStridedColl(ADIO_File fd, void *buf, int count,
/* free all memory allocated for collective I/O */
for (i=0; i<nprocs; i++) {
if (others_req[i].count) {
ADIOI_Free(others_req[i].offsets);
ADIOI_Free(others_req[i].lens);
ADIOI_Free(others_req[i].mem_ptrs);
if (others_req[i].offsets) { ADIOI_Free(others_req[i].offsets); }
if (others_req[i].lens) { ADIOI_Free(others_req[i].lens); }
if (others_req[i].mem_ptrs) { ADIOI_Free(others_req[i].mem_ptrs); }
}
}
ADIOI_Free(others_req);
Expand Down
10 changes: 5 additions & 5 deletions ompi/mca/io/romio321/romio/adio/ad_gpfs/ad_gpfs_wrcoll.c
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Original file line number Diff line number Diff line change
Expand Up @@ -453,8 +453,8 @@ void ADIOI_GPFS_WriteStridedColl(ADIO_File fd, const void *buf, int count,
ADIOI_Free(count_my_req_per_proc);
for (i=0; i < nprocs; i++) {
if (my_req[i].count) {
ADIOI_Free(my_req[i].offsets);
ADIOI_Free(my_req[i].lens);
if (my_req[i].offsets) { ADIOI_Free(my_req[i].offsets); }
if (my_req[i].lens) { ADIOI_Free(my_req[i].lens); }
}
}
ADIOI_Free(my_req);
Expand All @@ -475,9 +475,9 @@ void ADIOI_GPFS_WriteStridedColl(ADIO_File fd, const void *buf, int count,

for (i=0; i<nprocs; i++) {
if (others_req[i].count) {
ADIOI_Free(others_req[i].offsets);
ADIOI_Free(others_req[i].lens);
ADIOI_Free(others_req[i].mem_ptrs);
if (others_req[i].offsets) { ADIOI_Free(others_req[i].offsets); }
if (others_req[i].lens) { ADIOI_Free(others_req[i].lens); }
if (others_req[i].mem_ptrs) { ADIOI_Free(others_req[i].mem_ptrs); }
}
}
ADIOI_Free(others_req);
Expand Down
28 changes: 17 additions & 11 deletions ompi/mca/io/romio321/romio/adio/ad_lustre/ad_lustre_wrstr.c
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@
ADIO_WriteContig(fd, writebuf, writebuf_len, MPI_BYTE, \
ADIO_EXPLICIT_OFFSET, writebuf_off, \
&status1, error_code); \
if (!(fd->atomicity)) \
if (!fd->atomicity && fd->hints->ds_write == ADIOI_HINT_DISABLE) \
ADIOI_UNLOCK(fd, writebuf_off, SEEK_SET, writebuf_len); \
if (*error_code != MPI_SUCCESS) { \
*error_code = MPIO_Err_create_code(*error_code, \
Expand All @@ -35,7 +35,7 @@
writebuf_len = (unsigned) ADIOI_MIN(end_offset - writebuf_off + 1, \
(writebuf_off / stripe_size + 1) * \
stripe_size - writebuf_off); \
if (!(fd->atomicity)) \
if (!fd->atomicity && fd->hints->ds_write == ADIOI_HINT_DISABLE) \
ADIOI_WRITE_LOCK(fd, writebuf_off, SEEK_SET, writebuf_len); \
ADIO_ReadContig(fd, writebuf, writebuf_len, MPI_BYTE, \
ADIO_EXPLICIT_OFFSET, \
Expand All @@ -58,7 +58,7 @@
while (write_sz != req_len) { \
ADIO_WriteContig(fd, writebuf, writebuf_len, MPI_BYTE, \
ADIO_EXPLICIT_OFFSET, writebuf_off, &status1, error_code); \
if (!(fd->atomicity)) \
if (!fd->atomicity && fd->hints->ds_write == ADIOI_HINT_DISABLE) \
ADIOI_UNLOCK(fd, writebuf_off, SEEK_SET, writebuf_len); \
if (*error_code != MPI_SUCCESS) { \
*error_code = MPIO_Err_create_code(*error_code, \
Expand All @@ -75,7 +75,7 @@
writebuf_len = (unsigned) ADIOI_MIN(end_offset - writebuf_off + 1, \
(writebuf_off / stripe_size + 1) * \
stripe_size - writebuf_off); \
if (!(fd->atomicity)) \
if (!fd->atomicity && fd->hints->ds_write == ADIOI_HINT_DISABLE) \
ADIOI_WRITE_LOCK(fd, writebuf_off, SEEK_SET, writebuf_len); \
ADIO_ReadContig(fd, writebuf, writebuf_len, MPI_BYTE, \
ADIO_EXPLICIT_OFFSET, \
Expand Down Expand Up @@ -221,8 +221,9 @@ void ADIOI_LUSTRE_WriteStrided(ADIO_File fd, const void *buf, int count,
writebuf_off = 0;
writebuf_len = 0;

/* if atomicity is true, lock the region to be accessed */
if (fd->atomicity)
/* if atomicity is true or data sieving is not disable, lock the region
* to be accessed */
if (fd->atomicity || fd->hints->ds_write != ADIOI_HINT_DISABLE)
ADIOI_WRITE_LOCK(fd, start_off, SEEK_SET, bufsize);

for (j = 0; j < count; j++) {
Expand All @@ -241,7 +242,7 @@ void ADIOI_LUSTRE_WriteStrided(ADIO_File fd, const void *buf, int count,
ADIO_EXPLICIT_OFFSET, writebuf_off, &status1,
error_code);

if (fd->atomicity)
if (fd->atomicity || fd->hints->ds_write != ADIOI_HINT_DISABLE)
ADIOI_UNLOCK(fd, start_off, SEEK_SET, bufsize);
if (*error_code != MPI_SUCCESS) {
ADIOI_Free(writebuf);
Expand Down Expand Up @@ -325,9 +326,13 @@ void ADIOI_LUSTRE_WriteStrided(ADIO_File fd, const void *buf, int count,
userbuf_off = 0;
ADIOI_BUFFERED_WRITE_WITHOUT_READ
/* write the buffer out finally */
if (fd->hints->ds_write != ADIOI_HINT_DISABLE)
ADIOI_WRITE_LOCK(fd, writebuf_off, SEEK_SET, writebuf_len);
ADIO_WriteContig(fd, writebuf, writebuf_len, MPI_BYTE,
ADIO_EXPLICIT_OFFSET, writebuf_off, &status1,
error_code);
if (fd->hints->ds_write != ADIOI_HINT_DISABLE)
ADIOI_UNLOCK(fd, writebuf_off, SEEK_SET, writebuf_len);

if (file_ptr_type == ADIO_INDIVIDUAL) {
/* update MPI-IO file pointer to point to the first byte
Expand Down Expand Up @@ -378,8 +383,9 @@ void ADIOI_LUSTRE_WriteStrided(ADIO_File fd, const void *buf, int count,
fwr_size = ADIOI_MIN(flat_file->blocklens[j], bufsize-i_offset);
}

/* if atomicity is true, lock the region to be accessed */
if (fd->atomicity)
/* if atomicity is true or data sieving is not disable, lock the region
* to be accessed */
if (fd->atomicity || fd->hints->ds_write != ADIOI_HINT_DISABLE)
ADIOI_WRITE_LOCK(fd, start_off, SEEK_SET, end_offset-start_off+1);

writebuf_off = 0;
Expand Down Expand Up @@ -502,11 +508,11 @@ void ADIOI_LUSTRE_WriteStrided(ADIO_File fd, const void *buf, int count,
ADIO_WriteContig(fd, writebuf, writebuf_len, MPI_BYTE,
ADIO_EXPLICIT_OFFSET,
writebuf_off, &status1, error_code);
if (!(fd->atomicity))
if (!fd->atomicity && fd->hints->ds_write == ADIOI_HINT_DISABLE)
ADIOI_UNLOCK(fd, writebuf_off, SEEK_SET, writebuf_len);
if (*error_code != MPI_SUCCESS) return;
}
if (fd->atomicity)
if (fd->atomicity || fd->hints->ds_write != ADIOI_HINT_DISABLE)
ADIOI_UNLOCK(fd, start_off, SEEK_SET, end_offset-start_off+1);

ADIOI_Free(writebuf);
Expand Down
14 changes: 14 additions & 0 deletions ompi/mca/io/romio321/romio/adio/common/ad_darray.c
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Original file line number Diff line number Diff line change
Expand Up @@ -199,6 +199,13 @@ static int MPIOI_Type_block(int *array_of_gsizes, int dim, int ndims, int nprocs
/* in terms of no. of elements of type oldtype in this dimension */
if (mysize == 0) *st_offset = 0;

MPI_Aint ex;
MPI_Type_extent(type_old, &ex);
MPI_Datatype type_tmp;
MPI_Type_create_resized(*type_new, 0, array_of_gsizes[dim] * ex, &type_tmp);
MPI_Type_free(type_new);
*type_new = type_tmp;

return MPI_SUCCESS;
}

Expand Down Expand Up @@ -287,5 +294,12 @@ static int MPIOI_Type_cyclic(int *array_of_gsizes, int dim, int ndims, int nproc

if (local_size == 0) *st_offset = 0;

MPI_Aint ex;
MPI_Type_extent(type_old, &ex);
MPI_Datatype type_tmp2;
MPI_Type_create_resized(*type_new, 0, array_of_gsizes[dim] * ex, &type_tmp2);
MPI_Type_free(type_new);
*type_new = type_tmp2;

return MPI_SUCCESS;
}
34 changes: 21 additions & 13 deletions ompi/mca/io/romio321/romio/adio/common/ad_write_str.c
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,8 @@
if (writebuf_len) { \
ADIO_WriteContig(fd, writebuf, writebuf_len, MPI_BYTE, \
ADIO_EXPLICIT_OFFSET, writebuf_off, &status1, error_code); \
if (!(fd->atomicity)) ADIOI_UNLOCK(fd, writebuf_off, SEEK_SET, writebuf_len); \
if (!fd->atomicity && fd->hints->ds_write == ADIOI_HINT_DISABLE) \
ADIOI_UNLOCK(fd, writebuf_off, SEEK_SET, writebuf_len); \
if (*error_code != MPI_SUCCESS) { \
*error_code = MPIO_Err_create_code(*error_code, \
MPIR_ERR_RECOVERABLE, myname, \
Expand All @@ -25,7 +26,8 @@
} \
writebuf_off = req_off; \
writebuf_len = (unsigned) (ADIOI_MIN(max_bufsize,end_offset-writebuf_off+1));\
if (!(fd->atomicity)) ADIOI_WRITE_LOCK(fd, writebuf_off, SEEK_SET, writebuf_len); \
if (!fd->atomicity && fd->hints->ds_write == ADIOI_HINT_DISABLE) \
ADIOI_WRITE_LOCK(fd, writebuf_off, SEEK_SET, writebuf_len); \
ADIO_ReadContig(fd, writebuf, writebuf_len, MPI_BYTE, \
ADIO_EXPLICIT_OFFSET, writebuf_off, &status1, error_code); \
if (*error_code != MPI_SUCCESS) { \
Expand All @@ -42,7 +44,8 @@
while (write_sz != req_len) { \
ADIO_WriteContig(fd, writebuf, writebuf_len, MPI_BYTE, \
ADIO_EXPLICIT_OFFSET, writebuf_off, &status1, error_code); \
if (!(fd->atomicity)) ADIOI_UNLOCK(fd, writebuf_off, SEEK_SET, writebuf_len); \
if (!fd->atomicity && fd->hints->ds_write == ADIOI_HINT_DISABLE) \
ADIOI_UNLOCK(fd, writebuf_off, SEEK_SET, writebuf_len); \
if (*error_code != MPI_SUCCESS) { \
*error_code = MPIO_Err_create_code(*error_code, \
MPIR_ERR_RECOVERABLE, myname, \
Expand All @@ -54,7 +57,8 @@
userbuf_off += write_sz; \
writebuf_off += writebuf_len; \
writebuf_len = (unsigned) (ADIOI_MIN(max_bufsize,end_offset-writebuf_off+1));\
if (!(fd->atomicity)) ADIOI_WRITE_LOCK(fd, writebuf_off, SEEK_SET, writebuf_len); \
if (!fd->atomicity && fd->hints->ds_write == ADIOI_HINT_DISABLE) \
ADIOI_WRITE_LOCK(fd, writebuf_off, SEEK_SET, writebuf_len); \
ADIO_ReadContig(fd, writebuf, writebuf_len, MPI_BYTE, \
ADIO_EXPLICIT_OFFSET, writebuf_off, &status1, error_code); \
if (*error_code != MPI_SUCCESS) { \
Expand Down Expand Up @@ -191,9 +195,10 @@ void ADIOI_GEN_WriteStrided(ADIO_File fd, const void *buf, int count,
writebuf = (char *) ADIOI_Malloc(max_bufsize);
writebuf_len = (unsigned) (ADIOI_MIN(max_bufsize, end_offset-writebuf_off+1));

/* if atomicity is true, lock the region to be accessed */
if (fd->atomicity)
ADIOI_WRITE_LOCK(fd, start_off, SEEK_SET, end_offset-start_off+1);
/* if atomicity is true or data sieving is not disable, lock the region
* to be accessed */
if (fd->atomicity || fd->hints->ds_write != ADIOI_HINT_DISABLE)
ADIOI_WRITE_LOCK(fd, start_off, SEEK_SET, end_offset - start_off + 1);

for (j=0; j<count; j++)
{
Expand All @@ -210,7 +215,7 @@ void ADIOI_GEN_WriteStrided(ADIO_File fd, const void *buf, int count,
ADIO_WriteContig(fd, writebuf, writebuf_len, MPI_BYTE, ADIO_EXPLICIT_OFFSET,
writebuf_off, &status1, error_code);

if (fd->atomicity)
if (fd->atomicity || fd->hints->ds_write != ADIOI_HINT_DISABLE)
ADIOI_UNLOCK(fd, start_off, SEEK_SET, end_offset-start_off+1);

if (*error_code != MPI_SUCCESS) goto fn_exit;
Expand Down Expand Up @@ -287,8 +292,10 @@ void ADIOI_GEN_WriteStrided(ADIO_File fd, const void *buf, int count,
* datatypes, instead of a count of bytes (which might overflow)
* Other WriteContig calls in this path are operating on data
* sieving buffer */
ADIOI_WRITE_LOCK(fd, offset, SEEK_SET, bufsize);
ADIO_WriteContig(fd, buf, count, datatype, ADIO_EXPLICIT_OFFSET,
offset, status, error_code);
ADIOI_UNLOCK(fd, offset, SEEK_SET, bufsize);

if (file_ptr_type == ADIO_INDIVIDUAL) {
/* update MPI-IO file pointer to point to the first byte
Expand Down Expand Up @@ -338,9 +345,10 @@ void ADIOI_GEN_WriteStrided(ADIO_File fd, const void *buf, int count,
fwr_size = ADIOI_MIN(flat_file->blocklens[j], bufsize-i_offset);
}

/* if atomicity is true, lock the region to be accessed */
if (fd->atomicity)
ADIOI_WRITE_LOCK(fd, start_off, SEEK_SET, end_offset-start_off+1);
/* if atomicity is true or data sieving is not disable, lock the region
* to be accessed */
if (fd->atomicity || fd->hints->ds_write != ADIOI_HINT_DISABLE)
ADIOI_WRITE_LOCK(fd, start_off, SEEK_SET, end_offset - start_off + 1);

writebuf_off = 0;
writebuf_len = 0;
Expand Down Expand Up @@ -460,11 +468,11 @@ void ADIOI_GEN_WriteStrided(ADIO_File fd, const void *buf, int count,
if (writebuf_len) {
ADIO_WriteContig(fd, writebuf, writebuf_len, MPI_BYTE, ADIO_EXPLICIT_OFFSET,
writebuf_off, &status1, error_code);
if (!(fd->atomicity))
if (!fd->atomicity && fd->hints->ds_write == ADIOI_HINT_DISABLE)
ADIOI_UNLOCK(fd, writebuf_off, SEEK_SET, writebuf_len);
if (*error_code != MPI_SUCCESS) goto fn_exit;
}
if (fd->atomicity)
if (fd->atomicity || fd->hints->ds_write != ADIOI_HINT_DISABLE)
ADIOI_UNLOCK(fd, start_off, SEEK_SET, end_offset-start_off+1);

if (file_ptr_type == ADIO_INDIVIDUAL) fd->fp_ind = off;
Expand Down
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