[svn-r22641] Dectris project: I revised the code per Quincey's and Neil's comments. I added a performance benchmark program dectris_perf.c in the test/ directory.

Tested on koala and jam.

10 files changed, 56 insertions, 54 deletions

diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c
index e9a50ef..7cde7b6 100644
--- a/src/H5Dchunk.c
+++ b/src/H5Dchunk.c
@@ -60,8 +60,6 @@
 #include "H5Iprivate.h"		/* IDs			  		*/
 #include "H5MMprivate.h"	/* Memory management			*/
 #include "H5Vprivate.h"		/* Vector and array functions		*/
-#include "H5Fprivate.h"
-#include "H5FDprivate.h"
 
 
 /****************/
@@ -298,8 +296,8 @@ H5FL_BLK_DEFINE_STATIC(chunk);
  *-------------------------------------------------------------------------
  */
 herr_t
-H5D__direct_write(const H5D_t *dset, hid_t dxpl_id, size_t *offset, size_t buf_size,
-	 const void *buf)
+H5D__chunk_direct_write(const H5D_t *dset, hid_t dxpl_id, unsigned filters, hsize_t *offset, 
+         size_t data_size, const void *buf)
 {
     const H5O_layout_t *layout = &(dset->shared->layout);       /* Dataset layout */
     H5D_chunk_ud_t udata;   /* User data for querying chunk info */
@@ -337,8 +335,12 @@ H5D__direct_write(const H5D_t *dset, hid_t dxpl_id, size_t *offset, size_t buf_s
 	    &udata) < 0)
         HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address")
 
-    /* If the chunk hasn't been allocated on disk, do so now. */
-    if(!H5F_addr_defined(udata.addr)) {
+    udata.filter_mask = filters;
+
+    /* Check if the chunk needs to be 'inserted' (could exist already and
+     *      the 'insert' operation could resize it)
+     */
+    {
 	H5D_chk_idx_info_t idx_info;        /* Chunked index info */
 
 	/* Compose chunked index info struct */
@@ -349,9 +351,11 @@ H5D__direct_write(const H5D_t *dset, hid_t dxpl_id, size_t *offset, size_t buf_s
 	idx_info.storage = &(dset->shared->layout.storage.u.chunk);
 
 	/* Set up the size of chunk for user data */
-	udata.nbytes = buf_size;
+	udata.nbytes = data_size;
 
-	/* Create the chunk */
+        /* Create the chunk it if it doesn't exist, or reallocate the chunk
+         *  if its size changed.
+         */
 	if((dset->shared->layout.storage.u.chunk.ops->insert)(&idx_info, &udata) < 0)
 	    HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert/resize chunk")
 
@@ -372,10 +376,10 @@ H5D__direct_write(const H5D_t *dset, hid_t dxpl_id, size_t *offset, size_t buf_s
 	    HGOTO_ERROR(H5E_DATASET, H5E_CANTREMOVE, FAIL, "unable to evict chunk")
     } /* end if */
 
-    /* Write the data to the file driver, instead of H5F_block_write */
-    lf = H5F_DRIVER(dset->oloc.file);
-    if(H5FD_write(lf, dxpl_id, H5FD_MEM_DRAW, udata.addr, buf_size, buf) < 0)
-	HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "file write failed")
+    /* Write the data to the file */
+    if(H5F_block_write(dset->oloc.file, H5FD_MEM_DRAW, udata.addr, data_size, dxpl_id, buf) < 0)
+        HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to write raw data to file")
+
 
 done:
     /*FUNC_LEAVE_NOAPI(ret_value)*/
diff --git a/src/H5Dio.c b/src/H5Dio.c
index accb948..9576177 100644
--- a/src/H5Dio.c
+++ b/src/H5Dio.c
@@ -28,6 +28,7 @@
 #include "H5Eprivate.h"		/* Error handling		  	*/
 #include "H5FLprivate.h"	/* Free Lists                           */
 #include "H5Iprivate.h"		/* IDs			  		*/
+#include "H5Sprivate.h"		/* Dataspace			  	*/
 
 #ifdef H5_HAVE_PARALLEL
 /* Remove this if H5R_DATASET_REGION is no longer used in this file */
@@ -284,10 +285,13 @@ done:
  *-------------------------------------------------------------------------
  */
 herr_t
-H5PSIdirect_write(hid_t dset_id, hid_t dxpl_id, size_t *offset, size_t buf_size,
-	 const void *buf)
+H5PSIdirect_write(hid_t dset_id, hid_t dxpl_id, unsigned filters, hsize_t *offset, 
+         size_t data_size, const void *buf)
 {
     H5D_t		   *dset = NULL;
+    int                     ndims;
+    hsize_t                *dims;
+    int                     i;
     herr_t                  ret_value = SUCCEED;  /* Return value */
 
     FUNC_ENTER_API(FAIL)
@@ -298,6 +302,9 @@ H5PSIdirect_write(hid_t dset_id, hid_t dxpl_id, size_t *offset, size_t buf_size,
     if(NULL == dset->oloc.file)
 	HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
 
+    if(H5D_CHUNKED != dset->shared->layout.type)
+	HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a chunked dataset")
+
     /* Get the default dataset transfer property list if the user didn't provide one */
     if(H5P_DEFAULT == dxpl_id)
         dxpl_id= H5P_DATASET_XFER_DEFAULT;
@@ -308,8 +315,26 @@ H5PSIdirect_write(hid_t dset_id, hid_t dxpl_id, size_t *offset, size_t buf_size,
     if(!buf)
 	HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer")
 
+    ndims = (int)H5S_GET_EXTENT_NDIMS(dset->shared->space);
+    dims = (hsize_t *)HDmalloc(ndims*sizeof(hsize_t));
+
+    if(H5S_get_simple_extent_dims(dset->shared->space, dims, NULL) < 0)
+        HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't retrieve dataspace extent dims")
+
+    /* Make sure the offset doesn't exceed the dataset's dimensions */
+    for(i=0; i<ndims; i++)
+        if(offset[i] > dims[i])
+            HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "offset exceeds dimensions of dataset")
+
+    /* Make sure the offset fall right on a chunk's boundary */
+    for(i=0; i<ndims; i++)
+        if(offset[i] % dset->shared->layout.u.chunk.dim[i])
+            HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "offset doesn't fall on chunks's boundary")
+   
+    HDfree(dims);
+
     /* write raw data */
-    if(H5D__direct_write(dset, dxpl_id, offset, buf_size, buf) < 0)
+    if(H5D__chunk_direct_write(dset, dxpl_id, filters, offset, data_size, buf) < 0)
 	HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data")
 
 done:
diff --git a/src/H5Dprivate.h b/src/H5Dprivate.h
index b52800b..342c284 100644
--- a/src/H5Dprivate.h
+++ b/src/H5Dprivate.h
@@ -176,8 +176,8 @@ H5_DLL herr_t H5D_chunk_idx_reset(H5O_storage_chunk_t *storage, hbool_t reset_ad
 H5_DLL herr_t H5D_btree_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE * stream,
 				int indent, int fwidth, unsigned ndims);
 
-H5_DLL herr_t H5D__direct_write(const H5D_t *dset, hid_t dxpl_id, size_t *offset, 
-         size_t buf_size, const void *buf);
+H5_DLL herr_t H5D__chunk_direct_write(const H5D_t *dset, hid_t dxpl_id, unsigned filters, 
+         hsize_t *offset, size_t data_size, const void *buf);
 
 #endif /* _H5Dprivate_H */
 
diff --git a/src/H5Dpublic.h b/src/H5Dpublic.h
index b072e64..58c2a2b 100644
--- a/src/H5Dpublic.h
+++ b/src/H5Dpublic.h
@@ -118,8 +118,8 @@ H5_DLL herr_t H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
 			hid_t file_space_id, hid_t plist_id, void *buf/*out*/);
 H5_DLL herr_t H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
 			 hid_t file_space_id, hid_t plist_id, const void *buf);
-H5_DLL herr_t H5PSIdirect_write(hid_t dset_id, hid_t dxpl_id, size_t *offset, size_t buf_size,
-	                 const void *buf);
+H5_DLL herr_t H5PSIdirect_write(hid_t dset_id, hid_t dxpl_id, unsigned filters, hsize_t *offset, 
+                         size_t data_size, const void *buf);
 H5_DLL herr_t H5Diterate(void *buf, hid_t type_id, hid_t space_id,
             H5D_operator_t op, void *operator_data);
 H5_DLL herr_t H5Dvlen_reclaim(hid_t type_id, hid_t space_id, hid_t plist_id, void *buf);
diff --git a/src/H5F.c b/src/H5F.c
index 5d13ea6..b1f052d 100644
--- a/src/H5F.c
+++ b/src/H5F.c
@@ -1251,7 +1251,7 @@ H5F_open(const char *name, unsigned flags, hid_t fcpl_id, hid_t fapl_id,
      * way for us to detect it here anyway).
      */
     if(drvr->cmp)
-	tent_flags = flags & ~(H5F_ACC_CREAT|H5F_ACC_TRUNC|H5F_ACC_EXCL);
+	tent_flags = flags & ~(H5F_ACC_CREAT|H5F_ACC_TRUNC|H5F_ACC_EXCL|H5F_ACC_SYNC);
     else
 	tent_flags = flags;
 
@@ -1454,9 +1454,9 @@ H5Fcreate(const char *filename, unsigned flags, hid_t fcpl_id, hid_t fapl_id)
     if(!filename || !*filename)
 	HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid file name")
     /* In this routine, we only accept the following flags:
-     *          H5F_ACC_EXCL, H5F_ACC_TRUNC and H5F_ACC_DEBUG
+     *          H5F_ACC_SYNC, H5F_ACC_EXCL, H5F_ACC_TRUNC and H5F_ACC_DEBUG
      */
-    if(flags & ~(H5F_ACC_EXCL | H5F_ACC_TRUNC | H5F_ACC_DEBUG))
+    if(flags & ~(H5F_ACC_SYNC | H5F_ACC_EXCL | H5F_ACC_TRUNC | H5F_ACC_DEBUG))
 	HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid flags")
     /* The H5F_ACC_EXCL and H5F_ACC_TRUNC flags are mutually exclusive */
     if((flags & H5F_ACC_EXCL) && (flags & H5F_ACC_TRUNC))
diff --git a/src/H5FDsec2.c b/src/H5FDsec2.c
index 4201e07..085465c 100644
--- a/src/H5FDsec2.c
+++ b/src/H5FDsec2.c
@@ -357,6 +357,8 @@ H5FD_sec2_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr)
         o_flags |= O_CREAT;
     if(H5F_ACC_EXCL & flags)
         o_flags |= O_EXCL;
+    if(H5F_ACC_SYNC & flags)
+        o_flags |= O_SYNC;
 
     /* Open the file */
     if((fd = HDopen(name, o_flags, 0666)) < 0) {
diff --git a/src/H5Fpkg.h b/src/H5Fpkg.h
index 334879c..2d4678b 100644
--- a/src/H5Fpkg.h
+++ b/src/H5Fpkg.h
@@ -63,7 +63,8 @@
 #define H5F_SUPER_ALL_FLAGS             (H5F_SUPER_WRITE_ACCESS | H5F_SUPER_FILE_OK)
 
 /* Mask for removing private file access flags */
-#define H5F_ACC_PUBLIC_FLAGS 	        0x001fu
+/* #define H5F_ACC_PUBLIC_FLAGS 	        0x001fu */
+#define H5F_ACC_PUBLIC_FLAGS 	        0x003fu
 
 /* Free space section+aggregator merge flags */
 #define H5F_FS_MERGE_METADATA           0x01    /* Section can merge with metadata aggregator */
diff --git a/src/H5Fprivate.h b/src/H5Fprivate.h
index 3b3af49..1ef40b0 100644
--- a/src/H5Fprivate.h
+++ b/src/H5Fprivate.h
@@ -234,7 +234,6 @@ typedef struct H5F_blk_aggr_t H5F_blk_aggr_t;
 #define H5F_FILE_ID(F)          ((F)->file_id)
 #define H5F_PARENT(F)           ((F)->parent)
 #define H5F_NMOUNTS(F)          ((F)->nmounts)
-#define H5F_DRIVER(F)           ((F)->shared->lf)
 #define H5F_DRIVER_ID(F)        ((F)->shared->lf->driver_id)
 #define H5F_GET_FILENO(F,FILENUM) ((FILENUM) = (F)->shared->lf->fileno)
 #define H5F_HAS_FEATURE(F,FL)   ((F)->shared->lf->feature_flags & (FL))
@@ -277,7 +276,6 @@ typedef struct H5F_blk_aggr_t H5F_blk_aggr_t;
 #define H5F_FILE_ID(F)          (H5F_get_file_id(F))
 #define H5F_PARENT(F)           (H5F_get_parent(F))
 #define H5F_NMOUNTS(F)          (H5F_get_nmounts(F))
-#define H5F_DRIVER(F)           (H5F_get_driver(F))
 #define H5F_DRIVER_ID(F)        (H5F_get_driver_id(F))
 #define H5F_GET_FILENO(F,FILENUM) (H5F_get_fileno((F), &(FILENUM)))
 #define H5F_HAS_FEATURE(F,FL)   (H5F_has_feature(F,FL))
diff --git a/src/H5Fpublic.h b/src/H5Fpublic.h
index f32b3e0..7b7acb4 100644
--- a/src/H5Fpublic.h
+++ b/src/H5Fpublic.h
@@ -48,6 +48,7 @@
 #define H5F_ACC_EXCL	(H5CHECK 0x0004u)	/*fail if file already exists*/
 #define H5F_ACC_DEBUG	(H5CHECK 0x0008u)	/*print debug info	     */
 #define H5F_ACC_CREAT	(H5CHECK 0x0010u)	/*create non-existing files  */
+#define H5F_ACC_SYNC	(H5CHECK 0x0020u)	/*no filesystem caching      */
 
 /* Value passed to H5Pset_elink_acc_flags to cause flags to be taken from the
  * parent file. */
diff --git a/src/H5Fquery.c b/src/H5Fquery.c
index 1be5c50..c04ba24 100644
--- a/src/H5Fquery.c
+++ b/src/H5Fquery.c
@@ -919,35 +919,6 @@ H5F_get_driver_id(const H5F_t *f)
 
 
 /*-------------------------------------------------------------------------
- * Function:	H5F_get_driver
- *
- * Purpose:	Quick and dirty routine to retrieve the file's 'driver' structure 
- *          (Mainly added to stop non-file routines from poking about in the
- *          H5F_t data structure)
- *
- * Return:	'driver' structure on success/abort on failure (shouldn't fail)
- *
- * Programmer:	Raymond Lu
- *		30 July 2012
- *
- *-------------------------------------------------------------------------
- */
-H5FD_t *
-H5F_get_driver(const H5F_t *f)
-{
-    /* Use FUNC_ENTER_NOAPI_NOINIT_NOERR here to avoid performance issues */
-    FUNC_ENTER_NOAPI_NOINIT_NOERR
-
-    HDassert(f);
-    HDassert(f->shared);
-    HDassert(f->shared->lf);
-
-    FUNC_LEAVE_NOAPI(f->shared->lf)
-} /* end H5F_get_driver() */
-
-
-
-/*-------------------------------------------------------------------------
  * Function:	H5F_get_fileno
  *
  * Purpose:	Quick and dirty routine to retrieve the file's 'fileno' value