[svn-r14096] There're 3 changes in this checkin as below:

  1. In H5Dwrite and H5Dread, let the data buffer point to a fake address if the application passes
     in an empty buffer.  This is mainly for MPIO programs that some processes may not have any 
     data to write or read but still participate the I/O.  This solution solves some MPI's problem
     like the ChaMPIon on tungsten which doesn't support empty buffer.
  2. The ChaMPIon on tungsten doesn't support complex derived MPI data type correctly and collective
     I/O when some processes don't have any data to write or read correctly.  Detect the compiler
     "cmpicc" in the system-specific config file and set the variables for these two cases to false.
     The PHDF5 library already has set up a way to switch collective chunked I/O to independent 
     under these two cases.
  3. A bug fix - During the work of the optimization for compound data I/O, the case for switching
     collective chunked I/O to independent I/O was leftout.  Fixed it by adding I/O caching to it in
     H5D_multi_chunk_collective_io in H5Dmpio.c.

Tested on tungsten, cobalt, and kagiso for parallel; on linew and smirom for serial.
  

2 files changed, 104 insertions, 18 deletions

diff --git a/src/H5Dio.c b/src/H5Dio.c
index 6e75a93..259eb06 100644
--- a/src/H5Dio.c
+++ b/src/H5Dio.c
@@ -289,6 +289,7 @@ H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
     H5D_t		   *dset = NULL;
     const H5S_t		   *mem_space = NULL;
     const H5S_t		   *file_space = NULL;
+    char                    fake_char;
     herr_t                  ret_value=SUCCEED;  /* Return value */
 
     FUNC_ENTER_API(H5Dread, FAIL)
@@ -326,6 +327,13 @@ H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
     if (!buf && H5S_GET_SELECT_NPOINTS(file_space)!=0)
 	HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer")
 
+    /* If the buffer is nil, and 0 element is selected, make a fake buffer.
+     * This is for some MPI package like ChaMPIon on NCSA's tungsten which 
+     * doesn't support this feature. 
+     */ 
+    if (!buf)
+        buf = &fake_char;
+
     /* read raw data */
     if (H5D_read(dset, mem_type_id, mem_space, file_space, plist_id, buf/*out*/) < 0)
 	HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data")
@@ -373,6 +381,7 @@ H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
     H5D_t		   *dset = NULL;
     const H5S_t		   *mem_space = NULL;
     const H5S_t		   *file_space = NULL;
+    char                    fake_char;
     herr_t                  ret_value=SUCCEED;  /* Return value */
 
     FUNC_ENTER_API(H5Dwrite, FAIL)
@@ -409,6 +418,13 @@ H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
             HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms")
     if(!buf && H5S_GET_SELECT_NPOINTS(file_space)!=0)
 	HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer")
+    
+    /* If the buffer is nil, and 0 element is selected, make a fake buffer.
+     * This is for some MPI package like ChaMPIon on NCSA's tungsten which 
+     * doesn't support this feature. 
+     */ 
+    if (!buf)
+        buf = &fake_char;
 
     /* write raw data */
     if(H5D_write(dset, mem_type_id, mem_space, file_space, plist_id, buf) < 0)
@@ -788,6 +804,8 @@ H5D_contig_read(H5D_io_info_t *io_info, hsize_t nelmts,
 
     FUNC_ENTER_NOAPI_NOINIT(H5D_contig_read)
 
+    assert (buf);
+
     /* Initialize storage info for this dataset */
     if (dataset->shared->dcpl_cache.efl.nused > 0)
         HDmemcpy(&store.efl, &(dataset->shared->dcpl_cache.efl), sizeof(H5O_efl_t));
@@ -1066,6 +1084,8 @@ H5D_contig_write(H5D_io_info_t *io_info, hsize_t nelmts,
 
     FUNC_ENTER_NOAPI_NOINIT(H5D_contig_write)
 
+    assert (buf);
+
     /* Initialize storage info for this dataset */
     if(dataset->shared->dcpl_cache.efl.nused > 0)
         HDmemcpy(&store.efl, &(dataset->shared->dcpl_cache.efl), sizeof(H5O_efl_t));
@@ -1344,6 +1364,8 @@ H5D_chunk_read(H5D_io_info_t *io_info, hsize_t nelmts,
 
     FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_read)
 
+    assert (buf);
+
     /* Map elements between file and memory for each chunk*/
     if(H5D_create_chunk_map(dataset, mem_type, file_space, mem_space, &fm) < 0)
         HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't build chunk mapping")
@@ -1734,6 +1756,8 @@ H5D_chunk_write(H5D_io_info_t *io_info, hsize_t nelmts,
 
     FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_write)
 
+    assert (buf);
+
     /* Map elements between file and memory for each chunk*/
     if(H5D_create_chunk_map(dataset, mem_type, file_space, mem_space, &fm) < 0)
         HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't build chunk mapping")
diff --git a/src/H5Dmpio.c b/src/H5Dmpio.c
index 90f8974..a6981ee 100644
--- a/src/H5Dmpio.c
+++ b/src/H5Dmpio.c
@@ -988,6 +988,7 @@ H5D_link_chunk_collective_io(H5D_io_info_t *io_info,fm_map *fm,const void *buf,
 	for ( i = 0; i< num_chunk;i++){
 	  if (MPI_SUCCESS != (mpi_code= MPI_Type_free( chunk_mtype+i )))
             HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code);
+
 	  if (MPI_SUCCESS != (mpi_code= MPI_Type_free( chunk_ftype+i )))
             HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code);
 	}
@@ -1014,7 +1015,7 @@ H5D_link_chunk_collective_io(H5D_io_info_t *io_info,fm_map *fm,const void *buf,
   if(H5DEBUG(D))
     HDfprintf(H5DEBUG(D),"before coming to final collective IO\n");
 #endif
-      
+
       if(H5D_final_collective_io(io_info,&chunk_final_ftype,&chunk_final_mtype,&coll_info,buf,do_write)<0)
 	HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL,"couldn't finish MPI-IO");
 
@@ -1059,7 +1060,6 @@ done:
 static herr_t 
 H5D_multi_chunk_collective_io(H5D_io_info_t *io_info,fm_map *fm,const void *buf, hbool_t do_write) 
 {
-
       unsigned          i, total_chunk;
       hsize_t           ori_total_chunk;
       uint8_t          *chunk_io_option;
@@ -1070,6 +1070,16 @@ H5D_multi_chunk_collective_io(H5D_io_info_t *io_info,fm_map *fm,const void *buf,
       H5D_storage_t     store;                /* union of EFL and chunk pointer in file space */
       hbool_t           select_chunk;
       hbool_t 	        last_io_mode_coll = TRUE;
+
+      void             *chunk = NULL;         /* Pointer to the data chunk in cache */
+      H5D_t            *dataset=io_info->dset;/* Local pointer to dataset info */
+      H5D_istore_ud1_t  udata;		      /*B-tree pass-through	*/
+      haddr_t           caddr;                /* Address of the cached chunk */
+      size_t            accessed_bytes;       /*total accessed size in a chunk */
+      unsigned          idx_hint=0;           /* Cache index hint      */
+      hbool_t           dirty = TRUE;         /* Flag for cache flushing */
+      hbool_t           relax=TRUE;           /* Whether whole chunk is selected */
+
       herr_t            ret_value = SUCCEED;    
 #ifdef H5Dmpio_DEBUG
       int mpi_rank;
@@ -1167,18 +1177,41 @@ H5D_multi_chunk_collective_io(H5D_io_info_t *io_info,fm_map *fm,const void *buf,
                 if(H5D_ioinfo_make_ind(io_info) < 0)
                    HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't switch to independent I/O")
 
+            /* Load the chunk into cache.  But if the whole chunk is written,
+             * simply allocate space instead of load the chunk. */
+            if(HADDR_UNDEF==(caddr = H5D_istore_get_addr(io_info, &udata)))
+                HGOTO_ERROR(H5E_STORAGE, H5E_CANTGET, FAIL,"couldn't get chunk info from skipped list");
+
+            if (H5D_istore_if_load(dataset, caddr)) {
+                accessed_bytes = chunk_info->chunk_points * H5T_get_size(dataset->shared->type);
+                if((do_write && (accessed_bytes != dataset->shared->layout.u.chunk.size)) || !do_write)
+                    relax=FALSE;
+
+	        if(NULL == (chunk = H5D_istore_lock(io_info, &udata, relax, &idx_hint)))
+		    HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk")
+	    } else
+		chunk = NULL;
+ 
             if(do_write) {
                 if((io_info->ops.write)(io_info,
                          chunk_info->chunk_points,H5T_get_size(io_info->dset->shared->type),
-                         chunk_info->fspace,chunk_info->mspace,0, NULL, buf) < 0)
+                         chunk_info->fspace,chunk_info->mspace,caddr,chunk, buf) < 0)
                     HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "optimized write failed")
             }
             else {
                  if((io_info->ops.read)(io_info,
                           chunk_info->chunk_points,H5T_get_size(io_info->dset->shared->type),
-                          chunk_info->fspace,chunk_info->mspace,0, NULL, buf) < 0)
+                          chunk_info->fspace,chunk_info->mspace,caddr,chunk, buf) < 0)
                     HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "optimized read failed")
-              }
+            }
+
+            /* Release the cache lock on the chunk. */
+            if (H5D_istore_if_load(dataset, caddr)) {
+                if(!do_write) dirty = FALSE;
+
+	        if(H5D_istore_unlock(io_info, dirty, idx_hint, chunk, accessed_bytes) < 0)
+		    HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to unlock raw data chunk")
+	    }
 #else
             if(!last_io_mode_coll)
                 /* using independent I/O with file setview.*/
@@ -1250,6 +1283,16 @@ H5D_multi_chunk_collective_io_no_opt(H5D_io_info_t *io_info,fm_map *fm,const voi
       haddr_t           chunk_addr;
       H5SL_node_t      *chunk_node;           /* Current node in chunk skip list */
       H5D_storage_t     store;                /* union of EFL and chunk pointer in file space */
+      H5D_chunk_info_t *chunk_info;           /* chunk information */
+      hbool_t make_ind, make_coll;            /* Flags to indicate that the MPI mode should change */
+
+      void             *chunk = NULL;         /* Pointer to the data chunk in cache */
+      H5D_t            *dataset=io_info->dset;/* Local pointer to dataset info */
+      H5D_istore_ud1_t  udata;		      /*B-tree pass-through	*/
+      size_t            accessed_bytes;       /*total accessed size in a chunk */
+      unsigned          idx_hint=0;           /* Cache index hint      */
+      hbool_t           dirty = TRUE;         /* Flag for cache flushing */
+      hbool_t           relax=TRUE;           /* Whether whole chunk is selected */
       herr_t            ret_value = SUCCEED;    
 
 #ifdef H5Dmpio_DEBUG
@@ -1317,24 +1360,43 @@ H5D_multi_chunk_collective_io_no_opt(H5D_io_info_t *io_info,fm_map *fm,const voi
                 if(H5D_ioinfo_make_ind(io_info) < 0)
                     HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't switch to independent I/O")
 
+            if(HADDR_UNDEF==(chunk_addr = H5D_istore_get_addr(io_info, &udata)))
+                HGOTO_ERROR(H5E_STORAGE, H5E_CANTGET, FAIL,"couldn't get chunk info from skipped list");
+
             if(make_ind) {/*independent I/O */
-  
-              if(do_write) {
-                if((io_info->ops.write)(io_info,
+                /* Load the chunk into cache.  But if the whole chunk is written,
+                 * simply allocate space instead of load the chunk. */
+                if (H5D_istore_if_load(dataset, chunk_addr)) {
+                    accessed_bytes = chunk_info->chunk_points * H5T_get_size(dataset->shared->type);
+                    if((do_write && (accessed_bytes != dataset->shared->layout.u.chunk.size)) || !do_write)
+                        relax=FALSE;
+
+		    if(NULL == (chunk = H5D_istore_lock(io_info, &udata, relax, &idx_hint)))
+		        HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk")
+		} else
+		    chunk = NULL;
+ 
+                if(do_write) {
+                    if((io_info->ops.write)(io_info,
                          chunk_info->chunk_points,H5T_get_size(io_info->dset->shared->type),
-                         chunk_info->fspace,chunk_info->mspace, (hsize_t)0, NULL, buf) < 0)
-                    HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "optimized write failed")
-              }
-              else {
-                if((io_info->ops.read)(io_info,
+                         chunk_info->fspace,chunk_info->mspace, chunk_addr, chunk, buf) < 0)
+                        HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "optimized write failed")
+                } else {
+                    if((io_info->ops.read)(io_info,
                           chunk_info->chunk_points,H5T_get_size(io_info->dset->shared->type),
-                          chunk_info->fspace,chunk_info->mspace, (hsize_t)0, NULL, buf) < 0)
-                  HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "optimized read failed")
-              }
+                          chunk_info->fspace,chunk_info->mspace, chunk_addr, chunk, buf) < 0)
+                        HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "optimized read failed")
+                }
+
+                /* Release the cache lock on the chunk. */
+                if (H5D_istore_if_load(dataset, chunk_addr)) {
+                    if(!do_write) dirty = FALSE;
+
+		    if(H5D_istore_unlock(io_info, dirty, idx_hint, chunk, accessed_bytes) < 0)
+			HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to unlock raw data chunk")
+		}
             }
             else { /*collective I/O */
-              if(HADDR_UNDEF==(chunk_addr = H5D_istore_get_addr(io_info,NULL)))
-                  HGOTO_ERROR(H5E_STORAGE, H5E_CANTGET, FAIL,"couldn't get chunk info from skipped list");
               if(H5D_inter_collective_io(io_info,chunk_info->fspace,chunk_info->mspace,
                      chunk_addr,buf,do_write ) < 0)
                 HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL,"couldn't finish shared collective MPI-IO");