1 files changed, 153 insertions, 113 deletions

diff --git a/src/H5Farray.c b/src/H5Farray.c
index 67c0446..6019f1e 100644
--- a/src/H5Farray.c
+++ b/src/H5Farray.c
@@ -15,10 +15,15 @@
 #include <H5Dprivate.h>
 #include <H5Eprivate.h>
 #include <H5Fprivate.h>
+#include <H5Iprivate.h>
 #include <H5MFprivate.h>
 #include <H5Oprivate.h>
+#include <H5Pprivate.h>
 #include <H5Vprivate.h>
 
+/* MPIO driver functions are needed for some special checks */
+#include <H5FDmpio.h>
+
 /* Interface initialization */
 #define PABLO_MASK	H5Farray_mask
 #define INTERFACE_INIT	NULL
@@ -51,14 +56,14 @@ H5F_arr_create (H5F_t *f, struct H5O_layout_t *layout/*in,out*/)
     /* check args */
     assert (f);
     assert (layout);
-    layout->addr = H5F_ADDR_UNDEF; /*just in case we fail*/
+    layout->addr = HADDR_UNDEF; /*just in case we fail*/
    
     switch (layout->type) {
     case H5D_CONTIGUOUS:
 	/* Reserve space in the file for the entire array */
 	for (i=0, nbytes=1; i<layout->ndims; i++) nbytes *= layout->dim[i];
 	assert (nbytes>0);
-	if (H5MF_alloc (f, H5MF_RAW, nbytes, &(layout->addr)/*out*/)<0) {
+	if (HADDR_UNDEF==(layout->addr=H5MF_alloc(f, H5FD_MEM_DRAW, nbytes))) {
 	    HRETURN_ERROR (H5E_IO, H5E_NOSPACE, FAIL,
 			   "unable to reserve file space");
 	}
@@ -103,22 +108,24 @@ H5F_arr_create (H5F_t *f, struct H5O_layout_t *layout/*in,out*/)
  *              Friday, January 16, 1998
  *
  * Modifications:
- *		June 2, 1998	Albert Cheng
+ *		Albert Cheng, 1998-06-02
  *		Added xfer_mode argument
  *
- * 		Sep 28, 1998	Robb Matzke
+ * 		Robb Matzke, 1998-09-28
  *		Added the `xfer' argument and removed the `xfer_mode'
  *		argument since it's a field of `xfer'.
  *
+ * 		Robb Matzke, 1999-08-02
+ *		Data transfer properties are passed by ID since that's how
+ *		the virtual file layer wants them.
  *-------------------------------------------------------------------------
  */
 herr_t
-H5F_arr_read (H5F_t *f, const H5F_xfer_t *xfer,
-	      const struct H5O_layout_t *layout,
-	      const struct H5O_pline_t *pline, const H5O_fill_t *fill,
-	      const struct H5O_efl_t *efl, const hsize_t _hslab_size[],
-	      const hsize_t mem_size[], const hssize_t mem_offset[],
-	      const hssize_t file_offset[], void *_buf/*out*/)
+H5F_arr_read(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout,
+	     const struct H5O_pline_t *pline, const H5O_fill_t *fill,
+	     const struct H5O_efl_t *efl, const hsize_t _hslab_size[],
+	     const hsize_t mem_size[], const hssize_t mem_offset[],
+	     const hssize_t file_offset[], void *_buf/*out*/)
 {
     uint8_t	*buf = (uint8_t*)_buf;		/*cast for arithmetic	*/
     hssize_t	file_stride[H5O_LAYOUT_NDIMS];	/*strides through file	*/
@@ -133,27 +140,43 @@ H5F_arr_read (H5F_t *f, const H5F_xfer_t *xfer,
     haddr_t	addr;				/*address in file	*/
     intn	i, j;				/*counters		*/
     hbool_t	carray;				/*carry for subtraction	*/
+#ifdef HAVE_PARALLEL
+    H5FD_mpio_xfer_t xfer_mode=H5FD_MPIO_INDEPENDENT;
+#endif
    
-    FUNC_ENTER (H5F_arr_read, FAIL);
+    FUNC_ENTER(H5F_arr_read, FAIL);
 
     /* Check args */
-    assert (f);
-    assert (layout);
-    assert (_hslab_size);
-    assert (file_offset);
-    assert (mem_offset);
-    assert (mem_size);
-    assert (buf);
+    assert(f);
+    assert(layout);
+    assert(_hslab_size);
+    assert(file_offset);
+    assert(mem_offset);
+    assert(mem_size);
+    assert(buf);
 
     /* Make a local copy of size so we can modify it */
-    H5V_vector_cpy (layout->ndims, hslab_size, _hslab_size);
+    H5V_vector_cpy(layout->ndims, hslab_size, _hslab_size);
 
 #ifdef HAVE_PARALLEL
-    if (xfer->xfer_mode==H5D_XFER_COLLECTIVE){
-	if (layout->type != H5D_CONTIGUOUS)
-	    HRETURN_ERROR (H5E_DATASET, H5E_READERROR, FAIL,
-			   "collective access on non-contiguous datasets not "
-			   "supported yet");
+    {
+	/* Get the transfer mode */
+	H5F_xfer_t *dxpl;
+	H5FD_mpio_dxpl_t *dx;
+	if (H5P_DEFAULT!=dxpl_id && (dxpl=H5I_object(dxpl_id)) &&
+	    H5FD_MPIO==dxpl->driver_id && (dx=dxpl->driver_info) &&
+	    H5FD_MPIO_INDEPENDENT!=dx->xfer_mode) {
+	    xfer_mode = dx->xfer_mode;
+	}
+    }
+#endif
+    
+#ifdef HAVE_PARALLEL
+    /* Collective MPIO access is unsupported for non-contiguous datasets */
+    if (H5D_CONTIGUOUS!=layout->type && H5FD_MPIO_COLLECTIVE==xfer_mode) {
+	HRETURN_ERROR (H5E_DATASET, H5E_READERROR, FAIL,
+		       "collective access on non-contiguous datasets not "
+		       "supported yet");
     }
 #endif
 #ifdef QAK
@@ -177,8 +200,8 @@ H5F_arr_read (H5F_t *f, const H5F_xfer_t *xfer,
 	 */
 	for (i=0; i<ndims; i++) {
 	    if (mem_offset[i]<0 || file_offset[i]<0) {
-		HRETURN_ERROR (H5E_IO, H5E_READERROR, FAIL,
-			       "negative offsets are not valid");
+		HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL,
+			      "negative offsets are not valid");
 	    }
 	}
 
@@ -186,8 +209,8 @@ H5F_arr_read (H5F_t *f, const H5F_xfer_t *xfer,
 	 * Filters cannot be used for contiguous data.
 	 */
 	if (pline && pline->nfilters>0) {
-	    HRETURN_ERROR (H5E_IO, H5E_READERROR, FAIL,
-			   "filters are not allowed for contiguous data");
+	    HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL,
+			  "filters are not allowed for contiguous data");
 	}
 	
 	/*
@@ -195,12 +218,12 @@ H5F_arr_read (H5F_t *f, const H5F_xfer_t *xfer,
 	 * and memory. Optimize the strides to result in the fewest number of
 	 * I/O requests.
 	 */
-	mem_start = H5V_hyper_stride (ndims, hslab_size, mem_size,
-				      mem_offset, mem_stride/*out*/);
-	file_start = H5V_hyper_stride (ndims, hslab_size, layout->dim,
-				       file_offset, file_stride/*out*/);
-	H5V_stride_optimize2 (&ndims, &elmt_size, hslab_size,
-			      mem_stride, file_stride);
+	mem_start = H5V_hyper_stride(ndims, hslab_size, mem_size,
+				     mem_offset, mem_stride/*out*/);
+	file_start = H5V_hyper_stride(ndims, hslab_size, layout->dim,
+				      file_offset, file_stride/*out*/);
+	H5V_stride_optimize2(&ndims, &elmt_size, hslab_size,
+			     mem_stride, file_stride);
 
 	/*
 	 * Initialize loop variables.  The loop is a multi-dimensional loop
@@ -208,8 +231,8 @@ H5F_arr_read (H5F_t *f, const H5F_xfer_t *xfer,
 	 * element of IDX is treated as a digit with IDX[0] being the least
 	 * significant digit.
 	 */
-	H5V_vector_cpy (ndims, idx, hslab_size);
-	nelmts = H5V_vector_reduce_product (ndims, hslab_size);
+	H5V_vector_cpy(ndims, idx, hslab_size);
+	nelmts = H5V_vector_reduce_product(ndims, hslab_size);
 	if (efl && efl->nused>0) {
 	    addr = 0;
 	} else {
@@ -223,19 +246,20 @@ H5F_arr_read (H5F_t *f, const H5F_xfer_t *xfer,
 	 * memory.
 	 */
 #ifdef HAVE_PARALLEL
-	if (xfer->xfer_mode==H5D_XFER_COLLECTIVE){
-	    /* Currently supports same number of collective access.
-	     * Need to be changed LATER to combine all reads into one
-	     * collective MPIO call.
+	if (H5FD_MPIO_COLLECTIVE==xfer_mode){
+	    /*
+	     * Currently supports same number of collective access. Need to
+	     * be changed LATER to combine all reads into one collective MPIO
+	     * call.
 	     */
 	    unsigned long max, min, temp;
 
 	    temp = nelmts;
 	    assert(temp==nelmts);	/* verify no overflow */
 	    MPI_Allreduce(&temp, &max, 1, MPI_UNSIGNED_LONG, MPI_MAX,
-		f->shared->access_parms->u.mpio.comm);
+			  H5FD_mpio_communicator(f->shared->lf));
 	    MPI_Allreduce(&temp, &min, 1, MPI_UNSIGNED_LONG, MPI_MIN,
-		f->shared->access_parms->u.mpio.comm);
+			  H5FD_mpio_communicator(f->shared->lf));
 #ifdef AKC
 	    printf("nelmts=%lu, min=%lu, max=%lu\n", temp, min, max);
 #endif
@@ -250,18 +274,17 @@ H5F_arr_read (H5F_t *f, const H5F_xfer_t *xfer,
 
 	    /* Read from file */
 	    if (efl && efl->nused>0) {
-		if (H5O_efl_read (f, efl, addr, elmt_size, buf)<0) {
-		    HRETURN_ERROR (H5E_IO, H5E_READERROR, FAIL,
-				   "external data read failed");
+		if (H5O_efl_read(f, efl, addr, elmt_size, buf)<0) {
+		    HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL,
+				  "external data read failed");
 		}
-	    } else if (H5F_block_read (f, addr, elmt_size, xfer, buf)<0) {
-		HRETURN_ERROR (H5E_IO, H5E_READERROR, FAIL,
-			       "block read failed");
+	    } else if (H5F_block_read(f, addr, elmt_size, dxpl_id, buf)<0) {
+		HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL,
+			      "block read failed");
 	    }
 
 	    /* Decrement indices and advance pointers */
 	    for (j=ndims-1, carray=TRUE; j>=0 && carray; --j) {
-		
 		addr += file_stride[j];
 		buf += mem_stride[j];
 
@@ -277,29 +300,29 @@ H5F_arr_read (H5F_t *f, const H5F_xfer_t *xfer,
 	 * into a proper hyperslab.
 	 */
 	if (efl && efl->nused>0) {
-	    HRETURN_ERROR (H5E_IO, H5E_UNSUPPORTED, FAIL,
-			   "chunking and external files are mutually "
-			   "exclusive");
+	    HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL,
+			  "chunking and external files are mutually "
+			  "exclusive");
 	}
 	for (i=0; i<layout->ndims; i++) {
 	    if (0!=mem_offset[i] || hslab_size[i]!=mem_size[i]) {
-		HRETURN_ERROR (H5E_IO, H5E_UNSUPPORTED, FAIL,
-			       "unable to copy into a proper hyperslab");
+		HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL,
+			      "unable to copy into a proper hyperslab");
 	    }
 	}
-	if (H5F_istore_read (f, xfer, layout, pline, fill, file_offset,
+	if (H5F_istore_read(f, dxpl_id, layout, pline, fill, file_offset,
 			     hslab_size, buf)<0) {
-	    HRETURN_ERROR (H5E_IO, H5E_READERROR, FAIL, "chunked read failed");
+	    HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, "chunked read failed");
 	}
 	break;
 
     default:
-	assert ("not implemented yet" && 0);
-	HRETURN_ERROR (H5E_IO, H5E_UNSUPPORTED, FAIL,
-		       "unsupported storage layout");
+	assert("not implemented yet" && 0);
+	HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL,
+		      "unsupported storage layout");
     }
 
-    FUNC_LEAVE (SUCCEED);
+    FUNC_LEAVE(SUCCEED);
 }
 
 
@@ -324,23 +347,25 @@ H5F_arr_read (H5F_t *f, const H5F_xfer_t *xfer,
  *              Friday, January 16, 1998
  *
  * Modifications:
- *		June 2, 1998	Albert Cheng
+ *		Albert Cheng, 1998-06-02
  *		Added xfer_mode argument
  *
- * 		Sep 28, 1998	Robb Matzke
+ * 		Robb Matzke, 1998-09-28
  *		Added `xfer' argument, removed `xfer_mode' argument since it
  *		is a member of H5F_xfer_t.
  *
+ * 		Robb Matzke, 1999-08-02
+ *		Data transfer properties are passed by ID since that's how
+ *		the virtual file layer wants them.
  *-------------------------------------------------------------------------
  */
 herr_t
-H5F_arr_write (H5F_t *f, const H5F_xfer_t *xfer,
-	       const struct H5O_layout_t *layout,
-	       const struct H5O_pline_t *pline,
-	       const struct H5O_fill_t *fill, const struct H5O_efl_t *efl,
-	       const hsize_t _hslab_size[], const hsize_t mem_size[],
-	       const hssize_t mem_offset[], const hssize_t file_offset[],
-	       const void *_buf)
+H5F_arr_write(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout,
+	      const struct H5O_pline_t *pline,
+	      const struct H5O_fill_t *fill, const struct H5O_efl_t *efl,
+	      const hsize_t _hslab_size[], const hsize_t mem_size[],
+	      const hssize_t mem_offset[], const hssize_t file_offset[],
+	      const void *_buf)
 {
     const uint8_t *buf = (const uint8_t *)_buf;	/*cast for arithmetic	*/
     hssize_t	file_stride[H5O_LAYOUT_NDIMS];	/*strides through file	*/
@@ -355,8 +380,11 @@ H5F_arr_write (H5F_t *f, const H5F_xfer_t *xfer,
     haddr_t	addr;				/*address in file	*/
     intn	i, j;				/*counters		*/
     hbool_t	carray;				/*carry for subtraction	*/
+#ifdef HAVE_PARALLEL
+    H5FD_mpio_xfer_t xfer_mode=H5FD_MPIO_INDEPENDENT;
+#endif
    
-    FUNC_ENTER (H5F_arr_write, FAIL);
+    FUNC_ENTER(H5F_arr_write, FAIL);
 
     /* Check args */
     assert(f);
@@ -368,17 +396,29 @@ H5F_arr_write (H5F_t *f, const H5F_xfer_t *xfer,
     assert(buf);
 
     /* Make a local copy of _size so we can modify it */
-    H5V_vector_cpy (layout->ndims, hslab_size, _hslab_size);
+    H5V_vector_cpy(layout->ndims, hslab_size, _hslab_size);
 
 #ifdef HAVE_PARALLEL
-    if (xfer->xfer_mode==H5D_XFER_COLLECTIVE) {
-	if (layout->type != H5D_CONTIGUOUS) {
-	    HRETURN_ERROR (H5E_DATASET, H5E_WRITEERROR, FAIL,
-			   "collective access on non-contiguous datasets not "
-			   "supported yet");
+    {
+	/* Get the transfer mode */
+	H5F_xfer_t *dxpl;
+	H5FD_mpio_dxpl_t *dx;
+	if (H5P_DEFAULT!=dxpl_id && (dxpl=H5I_object(dxpl_id)) &&
+	    H5FD_MPIO==dxpl->driver_id && (dx=dxpl->driver_info) &&
+	    H5FD_MPIO_INDEPENDENT!=dx->xfer_mode) {
+	    xfer_mode = dx->xfer_mode;
 	}
     }
 #endif
+    
+#ifdef HAVE_PARALLEL
+    if (H5D_CONTIGUOUS!=layout->type && H5FD_MPIO_COLLECTIVE==xfer_mode) {
+	HRETURN_ERROR (H5E_DATASET, H5E_WRITEERROR, FAIL,
+		       "collective access on non-contiguous datasets not "
+		       "supported yet");
+    }
+#endif
+    
 #ifdef QAK
     {
 	extern int qak_debug;
@@ -403,8 +443,8 @@ H5F_arr_write (H5F_t *f, const H5F_xfer_t *xfer,
 	 */
 	for (i=0; i<ndims; i++) {
 	    if (mem_offset[i]<0 || file_offset[i]<0) {
-		HRETURN_ERROR (H5E_IO, H5E_WRITEERROR, FAIL,
-			       "negative offsets are not valid");
+		HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL,
+			      "negative offsets are not valid");
 	    }
 	}
 
@@ -412,8 +452,8 @@ H5F_arr_write (H5F_t *f, const H5F_xfer_t *xfer,
 	 * Filters cannot be used for contiguous data
 	 */
 	if (pline && pline->nfilters>0) {
-	    HRETURN_ERROR (H5E_IO, H5E_WRITEERROR, FAIL,
-			   "filters are not allowed for contiguous data");
+	    HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL,
+			  "filters are not allowed for contiguous data");
 	}
 	
 	/*
@@ -421,12 +461,12 @@ H5F_arr_write (H5F_t *f, const H5F_xfer_t *xfer,
 	 * Optimize the strides to result in the fewest number of I/O
 	 * requests.
 	 */
-	mem_start = H5V_hyper_stride (ndims, hslab_size, mem_size,
-				      mem_offset, mem_stride/*out*/);
-	file_start = H5V_hyper_stride (ndims, hslab_size, layout->dim,
-				       file_offset, file_stride/*out*/);
-	H5V_stride_optimize2 (&ndims, &elmt_size, hslab_size,
-			      mem_stride, file_stride);
+	mem_start = H5V_hyper_stride(ndims, hslab_size, mem_size,
+				     mem_offset, mem_stride/*out*/);
+	file_start = H5V_hyper_stride(ndims, hslab_size, layout->dim,
+				      file_offset, file_stride/*out*/);
+	H5V_stride_optimize2(&ndims, &elmt_size, hslab_size,
+			     mem_stride, file_stride);
 
 	/*
 	 * Initialize loop variables.  The loop is a multi-dimensional loop
@@ -434,8 +474,8 @@ H5F_arr_write (H5F_t *f, const H5F_xfer_t *xfer,
 	 * element of IDX is treated as a digit with IDX[0] being the least
 	 * significant digit.
 	 */
-	H5V_vector_cpy (ndims, idx, hslab_size);
-	nelmts = H5V_vector_reduce_product (ndims, hslab_size);
+	H5V_vector_cpy(ndims, idx, hslab_size);
+	nelmts = H5V_vector_reduce_product(ndims, hslab_size);
 	if (efl && efl->nused>0) {
 	    addr = 0;
 	} else {
@@ -449,19 +489,20 @@ H5F_arr_write (H5F_t *f, const H5F_xfer_t *xfer,
 	 * disk.
 	 */
 #ifdef HAVE_PARALLEL
-	if (xfer->xfer_mode==H5D_XFER_COLLECTIVE){
-	    /* Currently supports same number of collective access.
-	     * Need to be changed LATER to combine all writes into one
-	     * collective MPIO call.
+	if (H5FD_MPIO_COLLECTIVE==xfer_mode){
+	    /*
+	     * Currently supports same number of collective access. Need to
+	     * be changed LATER to combine all writes into one collective
+	     * MPIO call.
 	     */
 	    unsigned long max, min, temp;
 
 	    temp = nelmts;
 	    assert(temp==nelmts);	/* verify no overflow */
 	    MPI_Allreduce(&temp, &max, 1, MPI_UNSIGNED_LONG, MPI_MAX,
-		f->shared->access_parms->u.mpio.comm);
+			  H5FD_mpio_communicator(f->shared->lf));
 	    MPI_Allreduce(&temp, &min, 1, MPI_UNSIGNED_LONG, MPI_MIN,
-		f->shared->access_parms->u.mpio.comm);
+			  H5FD_mpio_communicator(f->shared->lf));
 #ifdef AKC
 	    printf("nelmts=%lu, min=%lu, max=%lu\n", temp, min, max);
 #endif
@@ -477,18 +518,17 @@ H5F_arr_write (H5F_t *f, const H5F_xfer_t *xfer,
 
 	    /* Write to file */
 	    if (efl && efl->nused>0) {
-		if (H5O_efl_write (f, efl, addr, elmt_size, buf)<0) {
-		    HRETURN_ERROR (H5E_IO, H5E_READERROR, FAIL,
-				   "external data write failed");
+		if (H5O_efl_write(f, efl, addr, elmt_size, buf)<0) {
+		    HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL,
+				  "external data write failed");
 		}
-	    } else if (H5F_block_write(f, addr, elmt_size, xfer, buf)<0) {
-		HRETURN_ERROR (H5E_IO, H5E_WRITEERROR, FAIL,
-			       "block write failed");
+	    } else if (H5F_block_write(f, addr, elmt_size, dxpl_id, buf)<0) {
+		HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL,
+			      "block write failed");
 	    }
 
 	    /* Decrement indices and advance pointers */
 	    for (j=ndims-1, carray=TRUE; j>=0 && carray; --j) {
-		
 		addr += file_stride[j];
 		buf += mem_stride[j];
 		
@@ -505,27 +545,27 @@ H5F_arr_write (H5F_t *f, const H5F_xfer_t *xfer,
 	 * from a proper hyperslab.
 	 */
 	if (efl && efl->nused>0) {
-	    HRETURN_ERROR (H5E_IO, H5E_UNSUPPORTED, FAIL,
-			   "chunking and external files are mutually "
-			   "exclusive");
+	    HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL,
+			  "chunking and external files are mutually "
+			  "exclusive");
 	}
 	for (i=0; i<layout->ndims; i++) {
 	    if (0!=mem_offset[i] || hslab_size[i]!=mem_size[i]) {
-		HRETURN_ERROR (H5E_IO, H5E_UNSUPPORTED, FAIL,
-			       "unable to copy from a proper hyperslab");
+		HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL,
+			      "unable to copy from a proper hyperslab");
 	    }
 	}
-	if (H5F_istore_write (f, xfer, layout, pline, fill, file_offset,
-			      hslab_size, buf)<0) {
-	    HRETURN_ERROR (H5E_IO, H5E_WRITEERROR, FAIL,
-			   "chunked write failed");
+	if (H5F_istore_write(f, dxpl_id, layout, pline, fill, file_offset,
+			     hslab_size, buf)<0) {
+	    HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL,
+			  "chunked write failed");
 	}
 	break;
 
     default:
-	assert ("not implemented yet" && 0);
-	HRETURN_ERROR (H5E_IO, H5E_UNSUPPORTED, FAIL,
-		       "unsupported storage layout");
+	assert("not implemented yet" && 0);
+	HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL,
+		      "unsupported storage layout");
     }
 
     FUNC_LEAVE (SUCCEED);