Merge pull request open-mpi#5 from markalle/romio341_refresh_mpich_ad…

…ditions

mpich additions for Romio341 refresh

3rd-party/romio341/adio/ad_gpfs/ad_gpfs.h

@@ -11,11 +11,11 @@
 #ifndef AD_GPFS_H_INCLUDED
 #define AD_GPFS_H_INCLUDED
 
+#include "adio.h"
 #include <unistd.h>
 #include <stdlib.h>
 #include <sys/types.h>
 #include <fcntl.h>
-#include "adio.h"
 
 #ifdef HAVE_SIGNAL_H
 #include <signal.h>

3rd-party/romio341/adio/ad_gpfs/ad_gpfs_aggrs.c

@@ -705,6 +705,7 @@ void ADIOI_GPFS_Calc_others_req(ADIO_File fd, int count_my_req_procs,
         } else {
             others_req[i].count = 0;
             others_req[i].offsets = NULL;
+            others_req[i].mem_ptrs = NULL;
             others_req[i].lens = NULL;
         }
     }

3rd-party/romio341/adio/ad_gpfs/ad_gpfs_rdcoll.c

@@ -425,8 +425,12 @@ void ADIOI_GPFS_ReadStridedColl(ADIO_File fd, void *buf, int count,
     GPFSMPIO_T_CIO_REPORT(0, fd, myrank, nprocs);
 
     /* free all memory allocated for collective I/O */
-    ADIOI_Free(others_req[0].offsets);
-    ADIOI_Free(others_req[0].mem_ptrs);
+    if (others_req[0].offsets) {
+        ADIOI_Free(others_req[0].offsets);
+    }
+    if (others_req[0].mem_ptrs) {
+        ADIOI_Free(others_req[0].mem_ptrs);
+    }
     ADIOI_Free(others_req);
 
     ADIOI_Free(buf_idx);

3rd-party/romio341/adio/ad_gpfs/ad_gpfs_wrcoll.c

@@ -360,7 +360,7 @@ void ADIOI_GPFS_WriteStridedColl(ADIO_File fd, const void *buf, int count,
             ADIOI_OneSidedWriteAggregation(fd, offset_list, len_list, contig_access_count, buf,
                                            datatype, error_code, firstFileOffset, lastFileOffset,
                                            currentValidDataIndex, fd_start, fd_end, &holeFound,
-                                           noStripeParms);
+                                           &noStripeParms);
             romio_onesided_no_rmw = prev_romio_onesided_no_rmw;
             GPFSMPIO_T_CIO_REPORT(1, fd, myrank, nprocs);
             ADIOI_Free(offset_list);
@@ -447,8 +447,12 @@ void ADIOI_GPFS_WriteStridedColl(ADIO_File fd, const void *buf, int count,
     GPFSMPIO_T_CIO_REPORT(1, fd, myrank, nprocs);
 
     /* free all memory allocated for collective I/O */
-    ADIOI_Free(others_req[0].offsets);
-    ADIOI_Free(others_req[0].mem_ptrs);
+    if (others_req[0].offsets) {
+        ADIOI_Free(others_req[0].offsets);
+    }
+    if (others_req[0].mem_ptrs) {
+        ADIOI_Free(others_req[0].mem_ptrs);
+    }
     ADIOI_Free(others_req);
 
     ADIOI_Free(buf_idx);
@@ -1541,7 +1545,7 @@ static void ADIOI_W_Exchange_data_alltoallv(ADIO_File fd, const void *buf, char
         for (i = 0; i < nprocs; i++) {
             if (send_size[i]) {
                 sbuf_ptr = all_send_buf + sdispls[i];
-                memcpy(sbuf_ptr, buf + buf_idx[i], send_size[i]);
+                memcpy(sbuf_ptr, (char *) buf + buf_idx[i], send_size[i]);
                 buf_idx[i] += send_size[i];
             }
         }

3rd-party/romio341/adio/ad_lustre/ad_lustre.h

@@ -9,6 +9,7 @@
 /* temp*/
 #define HAVE_ASM_TYPES_H 1
 
+#include "adio.h"
 #define _GNU_SOURCE 1
 #include <stdlib.h>
 #include <sys/types.h>
@@ -30,7 +31,6 @@
 
 #include <sys/ioctl.h>
 
-#include "adio.h"
 #include "ad_tuning.h"
 
 #ifdef HAVE_LUSTRE_LUSTRE_USER_H

3rd-party/romio341/adio/ad_lustre/ad_lustre_wrstr.c

@@ -13,7 +13,7 @@
                 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,     \
@@ -30,7 +30,7 @@
             writebuf_len = (unsigned) MPL_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,                       \
@@ -53,7 +53,7 @@
         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,         \
@@ -70,7 +70,7 @@
             writebuf_len = (unsigned) MPL_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,                       \
@@ -213,8 +213,9 @@ 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++) {
@@ -231,7 +232,7 @@ 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, start_off, SEEK_SET, bufsize);
         if (*error_code != MPI_SUCCESS) {
             ADIOI_Free(writebuf);
@@ -311,8 +312,12 @@ 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
@@ -362,8 +367,9 @@ void ADIOI_LUSTRE_WriteStrided(ADIO_File fd, const void *buf, int count,
             fwr_size = MPL_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;
@@ -481,12 +487,12 @@ void ADIOI_LUSTRE_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)
                 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);

3rd-party/romio341/adio/ad_panfs/ad_panfs.h

@@ -6,10 +6,10 @@
 #ifndef AD_PANFS_H_INCLUDED
 #define AD_PANFS_H_INCLUDED
 
+#include "adio.h"
 #include <unistd.h>
 #include <sys/types.h>
 #include <fcntl.h>
-#include "adio.h"
 
 #ifndef NO_AIO
 #ifdef AIO_SUN

3rd-party/romio341/adio/ad_pvfs2/ad_pvfs2_io_dtype.c

@@ -3,8 +3,8 @@
  *     See COPYRIGHT in top-level directory
  */
 
-#include <assert.h>
 #include "adio.h"
+#include <assert.h>
 #include "adio_extern.h"
 #include "ad_pvfs2.h"
 #include "ad_pvfs2_io.h"

3rd-party/romio341/adio/ad_pvfs2/ad_pvfs2_io_list.c

@@ -3,8 +3,8 @@
  *     See COPYRIGHT in top-level directory
  */
 
-#include <assert.h>
 #include "adio.h"
+#include <assert.h>
 #include "adio_extern.h"
 #include "ad_pvfs2.h"
 #include "ad_pvfs2_io.h"

3rd-party/romio341/adio/ad_xfs/ad_xfs.h

@@ -6,10 +6,10 @@
 #ifndef AD_XFS_H_INCLUDED
 #define AD_XFS_H_INCLUDED
 
+#include "adio.h"
 #include <unistd.h>
 #include <sys/types.h>
 #include <fcntl.h>
-#include "adio.h"
 
 #if defined(MPISGI)
 #include "xfs/xfs_fs.h"

3rd-party/romio341/adio/common/ad_darray.c

@@ -196,6 +196,13 @@ static int MPIOI_Type_block(int *array_of_gsizes, int dim, int ndims, int nprocs
     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;
 }
 
@@ -293,5 +300,11 @@ 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_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;
 }

3rd-party/romio341/adio/common/ad_write_str.c

@@ -12,7 +12,8 @@
             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, \
@@ -23,7 +24,8 @@
             }                                                           \
             writebuf_off = req_off;                                     \
             writebuf_len = (unsigned) (MPL_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) {                           \
@@ -40,7 +42,8 @@
         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, \
@@ -52,7 +55,8 @@
             userbuf_off += write_sz;                                    \
             writebuf_off += writebuf_len;                               \
             writebuf_len = (unsigned) (MPL_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) {                           \
@@ -184,8 +188,9 @@ void ADIOI_GEN_WriteStrided(ADIO_File fd, const void *buf, int count,
         writebuf = (char *) ADIOI_Malloc(max_bufsize);
         writebuf_len = (unsigned) (MPL_MIN(max_bufsize, end_offset - writebuf_off + 1));
 
-/* 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);
 
         for (j = 0; j < count; j++) {
@@ -204,7 +209,7 @@ void ADIOI_GEN_WriteStrided(ADIO_File fd, const void *buf, int count,
                              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)
@@ -280,8 +285,10 @@ 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
@@ -330,8 +337,9 @@ void ADIOI_GEN_WriteStrided(ADIO_File fd, const void *buf, int count,
             fwr_size = MPL_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;
@@ -451,12 +459,12 @@ 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)