[svn-r321] Changes since 19980306

----------------------

./MANIFEST
./src/H5D.c
./src/H5S.c
./src/H5Sprivate.h
./src/H5Ssimp.c
./src/H5Tpkg.h
./src/H5Tprivate.h
./src/H5V.c
./test/Makefile.in
./test/iopipe.c			[NEW]
	Optimizations to the I/O pipeline.

./src/H5Fistore.c
./src/H5Oefl.c
	Fixed a few compiler warnings.

./MANIFEST
	Added entries for ./config/{intel-osf1,irix5.3}

10 files changed, 338 insertions, 23 deletions

diff --git a/src/H5D.c b/src/H5D.c
index ead898f..b417ca7 100644
--- a/src/H5D.c
+++ b/src/H5D.c
@@ -31,6 +31,12 @@ static char		RcsId[] = "@(#)$Revision$";
 #define PABLO_MASK	H5D_mask
 
 /*
+ * Define this to be zero or one depending on whether the I/O pipeline should
+ * be optimized.
+ */
+#define H5D_OPTIMIZE_PIPE 1
+
+/*
  * A dataset is the following struct.
  */
 struct H5D_t {
@@ -807,7 +813,7 @@ H5D_create(H5F_t *f, const char *name, const H5T_t *type, const H5S_t *space,
     }
 
     /* Create (open for write access) an object header */
-    if (H5O_create(f, 0, &(new_dset->ent)) < 0) {
+    if (H5O_create(f, 80, &(new_dset->ent)) < 0) {
 	HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL,
 		    "unable to create dataset object header");
     }
@@ -1090,6 +1096,7 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
     H5S_number_t	numbering;		/*element numbering info*/
     H5T_cdata_t		*cdata = NULL;		/*type conversion data	*/
     herr_t		ret_value = FAIL;
+    herr_t		status;
 
     FUNC_ENTER(H5D_read, FAIL);
 
@@ -1140,10 +1147,36 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
      * Compute the size of the request and allocate scratch buffers.
      */
     nelmts = H5S_get_npoints(mem_space);
+
+    /*
+     * If there is no type conversion then try reading directly into the
+     * application's buffer.
+     */
+    if (H5D_OPTIMIZE_PIPE &&
+	H5T_conv_noop==tconv_func &&
+	NULL!=sconv_func->read) {
+#ifndef NDEBUG
+	fprintf (stderr, "HDF5-DIAG: Trying I/O pipe optimization...\n");
+#endif
+	status = (sconv_func->read)(dataset->ent.file, &(dataset->layout),
+				    &(dataset->create_parms->efl),
+				    H5T_get_size (dataset->type), file_space,
+				    mem_space, buf/*out*/);
+	if (status>=0) goto succeed;
+#ifndef NDEBUG
+	fprintf (stderr, "HDF5-DIAG: I/O pipe optimization failed\n");
+#endif
+	H5E_clear ();
+    }
+    
+	
+    /*
+     * This is the general case.
+     */
 #ifndef LATER
     /*
      * Note: this prototype version allocates a buffer large enough to
-     *	     satisfy the entire request; strip mining is not implemented.
+     *	 satisfy the entire request; strip mining is not implemented.
      */
     {
 	size_t src_size = nelmts * H5T_get_size(dataset->type);
@@ -1152,7 +1185,6 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
 	if (cdata->need_bkg) bkg_buf = H5MM_xmalloc (dst_size);
     }
 #endif
-
     /*
      * Gather the data from disk into the data type conversion buffer. Also
      * gather data from application to background buffer (this step is not
@@ -1192,9 +1224,12 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
 			    &numbering, 0, nelmts, buf/*out*/)<0) {
 	HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL, "scatter failed");
     }
+
+    
+ succeed:
     ret_value = SUCCEED;
     
-  done:
+ done:
     if (src_id >= 0) H5A_dec_ref(src_id);
     if (dst_id >= 0) H5A_dec_ref(dst_id);
     tconv_buf = H5MM_xfree(tconv_buf);
@@ -1233,7 +1268,7 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
     const H5S_conv_t	*sconv_func = NULL;	/*space conversion funcs*/
     H5S_number_t	numbering;		/*element numbering info*/
     H5T_cdata_t		*cdata = NULL;		/*type conversion data	*/
-    herr_t		ret_value = FAIL;
+    herr_t		ret_value = FAIL, status;
 
     FUNC_ENTER(H5D_write, FAIL);
 
@@ -1284,6 +1319,32 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
      * Compute the size of the request and allocate scratch buffers.
      */
     nelmts = H5S_get_npoints(mem_space);
+
+    /*
+     * If there is no type conversion then try writing directly from
+     * application buffer to file.
+     */
+    if (H5D_OPTIMIZE_PIPE &&
+	H5T_conv_noop==tconv_func &&
+	NULL!=sconv_func->write) {
+#ifndef NDEBUG
+	fprintf (stderr, "HDF5-DIAG: Trying I/O pipe optimization...\n");
+#endif
+	status = (sconv_func->write)(dataset->ent.file, &(dataset->layout),
+				     &(dataset->create_parms->efl),
+				     H5T_get_size (dataset->type), file_space,
+				     mem_space, buf);
+	if (status>=0) goto succeed;
+#ifndef NDEBUG
+	fprintf (stderr, "HDF5-DIAG: I/O pipe optimization failed\n");
+#endif
+	H5E_clear ();
+    }
+
+
+    /*
+     * This is the general case.
+     */
 #ifndef LATER
     /*
      * Note: This prototype version allocates a buffer large enough to
@@ -1296,8 +1357,6 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
 	if (cdata->need_bkg) bkg_buf = H5MM_xmalloc (dst_size);
     }
 #endif
-
-
     /*
      * Gather data from application buffer into the data type conversion
      * buffer. Also gather data from the file into the background buffer
@@ -1338,9 +1397,11 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
 			    &numbering, 0, nelmts, tconv_buf)<0) {
 	HGOTO_ERROR (H5E_DATASET, H5E_WRITEERROR, FAIL, "scatter failed");
     }
+
+ succeed:
     ret_value = SUCCEED;
     
-  done:
+ done:
     if (src_id >= 0) H5A_dec_ref(src_id);
     if (dst_id >= 0) H5A_dec_ref(dst_id);
     tconv_buf = H5MM_xfree(tconv_buf);
diff --git a/src/H5Distore.c b/src/H5Distore.c
index eeed99c..25b81b2 100644
--- a/src/H5Distore.c
+++ b/src/H5Distore.c
@@ -835,7 +835,9 @@ herr_t
 H5F_istore_create(H5F_t *f, H5O_layout_t *layout /*out */ )
 {
     H5F_istore_ud1_t        udata;
+#ifndef NDEBUG
     int                     i;
+#endif
 
     FUNC_ENTER(H5F_istore_create, FAIL);
 
diff --git a/src/H5Fistore.c b/src/H5Fistore.c
index eeed99c..25b81b2 100644
--- a/src/H5Fistore.c
+++ b/src/H5Fistore.c
@@ -835,7 +835,9 @@ herr_t
 H5F_istore_create(H5F_t *f, H5O_layout_t *layout /*out */ )
 {
     H5F_istore_ud1_t        udata;
+#ifndef NDEBUG
     int                     i;
+#endif
 
     FUNC_ENTER(H5F_istore_create, FAIL);
 
diff --git a/src/H5Oefl.c b/src/H5Oefl.c
index 1b3fa6a..5f2db2a 100644
--- a/src/H5Oefl.c
+++ b/src/H5Oefl.c
@@ -373,7 +373,7 @@ H5O_efl_read (H5F_t *f, const H5O_efl_t *efl, haddr_t *addr, size_t size,
 	      uint8 *buf)
 {
     int		i, fd=-1;
-    size_t	to_read, cur, skip;
+    size_t	to_read, cur, skip=0;
     ssize_t	n;
     herr_t	ret_value = FAIL;
     
@@ -458,7 +458,7 @@ H5O_efl_write (H5F_t *f, const H5O_efl_t *efl, haddr_t *addr, size_t size,
 	       const uint8 *buf)
 {
     int		i, fd=-1;
-    size_t	to_write, cur, skip;
+    size_t	to_write, cur, skip=0;
     herr_t	ret_value = FAIL;
     
     FUNC_ENTER (H5O_efl_write, FAIL);
diff --git a/src/H5S.c b/src/H5S.c
index d3a1ff9..c371e4b 100644
--- a/src/H5S.c
+++ b/src/H5S.c
@@ -538,6 +538,7 @@ H5S_get_npoints_max(const H5S_t *ds)
 
     FUNC_LEAVE(ret_value);
 }
+
 
 /*-------------------------------------------------------------------------
  * Function:	H5Sget_ndims
@@ -1310,6 +1311,8 @@ H5S_find (const H5S_t *mem_space, const H5S_t *file_space)
 	_conv.mscat = H5S_simp_mscat;
 	_conv.mgath = H5S_simp_mgath;
 	_conv.fscat = H5S_simp_fscat;
+	_conv.read = H5S_simp_read;
+	_conv.write = H5S_simp_write;
 	conv = &_conv;
     }
     
diff --git a/src/H5Sprivate.h b/src/H5Sprivate.h
index c8a3aae..fbce725 100644
--- a/src/H5Sprivate.h
+++ b/src/H5Sprivate.h
@@ -88,6 +88,18 @@ typedef struct H5S_tconv_t {
 		    const struct H5O_efl_t *efl, size_t elmt_size,
 		    const H5S_t *file_space, const H5S_number_t *numbering,
 		    size_t start, size_t nelmts, const void *tconv_buf);
+
+    /* Read from file to application w/o intermediate scratch buffer */
+    herr_t (*read)(H5F_t *f, const struct H5O_layout_t *layout,
+		   const struct H5O_efl_t *efl, size_t elmt_size,
+		   const H5S_t *file_space, const H5S_t *mem_space,
+		   void *buf/*out*/);
+
+    /* Write directly from app buffer to file */
+    herr_t (*write)(H5F_t *f, const struct H5O_layout_t *layout,
+		    const struct H5O_efl_t *efl, size_t elmt_size,
+		    const H5S_t *file_space, const H5S_t *mem_space,
+		    const void *buf);
 } H5S_conv_t;
 
 H5S_t *H5S_copy (const H5S_t *src);
@@ -125,4 +137,12 @@ herr_t H5S_simp_fscat (H5F_t *f, const struct H5O_layout_t *layout,
 		       const struct H5O_efl_t *efl, size_t elmt_size,
 		       const H5S_t *file_space, const H5S_number_t *numbering,
 		       size_t start, size_t nelmts, const void *tconv_buf);
+herr_t H5S_simp_read (H5F_t *f, const struct H5O_layout_t *layout,
+		      const struct H5O_efl_t *efl, size_t elmt_size,
+		      const H5S_t *file_space, const H5S_t *mem_space,
+		      void *buf/*out*/);
+herr_t H5S_simp_write (H5F_t *f, const struct H5O_layout_t *layout,
+		       const struct H5O_efl_t *efl, size_t elmt_size,
+		       const H5S_t *file_space, const H5S_t *mem_space,
+		       const void *buf);
 #endif
diff --git a/src/H5Ssimp.c b/src/H5Ssimp.c
index ee2d680..6f1f498 100644
--- a/src/H5Ssimp.c
+++ b/src/H5Ssimp.c
@@ -471,3 +471,218 @@ H5S_simp_fscat (H5F_t *f, const struct H5O_layout_t *layout,
 
     FUNC_LEAVE (SUCCEED);
 }
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5S_simp_read
+ *
+ * Purpose:	Reads a dataset from file F directly into application memory
+ *		BUF performing data space conversion in a single step from
+ *		FILE_SPACE to MEM_SPACE. The dataset is stored in the file
+ *		according to the LAYOUT and EFL (external file list) and data
+ *		point in the file is ELMT_SIZE bytes.
+ *
+ * Return:	Success:	SUCCEED
+ *
+ *		Failure:	FAIL
+ *
+ * Programmer:	Robb Matzke
+ *              Thursday, March 12, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5S_simp_read (H5F_t *f, const struct H5O_layout_t *layout,
+	       const struct H5O_efl_t *efl, size_t elmt_size,
+	       const H5S_t *file_space, const H5S_t *mem_space,
+	       void *buf/*out*/)
+{
+    size_t	hslab_size[H5O_LAYOUT_NDIMS];
+    size_t	file_offset[H5O_LAYOUT_NDIMS];
+    size_t	mem_size[H5O_LAYOUT_NDIMS];
+    size_t	mem_offset[H5O_LAYOUT_NDIMS];
+    int		i;
+
+    FUNC_ENTER (H5S_simp_read, FAIL);
+
+#ifndef NDEBUG
+    assert (file_space->type==mem_space->type);
+    assert (file_space->u.simple.rank==mem_space->u.simple.rank);
+    for (i=0; i<file_space->u.simple.rank; i++) {
+	if (file_space->hslab_def && mem_space->hslab_def) {
+	    assert (1==file_space->h.stride[i]);
+	    assert (1==mem_space->h.stride[i]);
+	    assert (file_space->h.count[i]==mem_space->h.count[i]);
+	} else if (file_space->hslab_def) {
+	    assert (1==file_space->h.stride[i]);
+	    assert (file_space->h.count[i]==mem_space->u.simple.size[i]);
+	} else if (mem_space->hslab_def) {
+	    assert (1==mem_space->h.stride[i]);
+	    assert (file_space->u.simple.size[i]==mem_space->h.count[i]);
+	} else {
+	    assert (file_space->u.simple.size[i]==
+		    mem_space->u.simple.size[i]);
+	}
+    }
+#endif
+	
+
+    /*
+     * Calculate size of hyperslab and offset of hyperslab into file and
+     * memory.
+     */
+    if (file_space->hslab_def) {
+	for (i=0; i<file_space->u.simple.rank; i++) {
+	    hslab_size[i] = file_space->h.count[i];
+	}
+    } else {
+	for (i=0; i<file_space->u.simple.rank; i++) {
+	    hslab_size[i] = file_space->u.simple.size[i];
+	}
+    }
+    for (i=0; i<mem_space->u.simple.rank; i++) {
+	mem_size[i] = mem_space->u.simple.size[i];
+    }
+    if (file_space->hslab_def) {
+	for (i=0; i<file_space->u.simple.rank; i++) {
+	    file_offset[i] = file_space->h.start[i];
+	}
+    } else {
+	for (i=0; i<file_space->u.simple.rank; i++) {
+	    file_offset[i] = 0;
+	}
+    }
+    if (mem_space->hslab_def) {
+	for (i=0; i<mem_space->u.simple.rank; i++) {
+	    mem_offset[i] = mem_space->h.start[i];
+	}
+    } else {
+	for (i=0; i<mem_space->u.simple.rank; i++) {
+	    mem_offset[i] = 0;
+	}
+    }
+    hslab_size[file_space->u.simple.rank] = elmt_size;
+    mem_size[file_space->u.simple.rank] = elmt_size;
+    file_offset[file_space->u.simple.rank] = 0;
+    mem_offset[file_space->u.simple.rank] = 0;
+    
+    /* Read the hyperslab */
+    if (H5F_arr_read (f, layout, efl, hslab_size,
+		      mem_size, mem_offset, file_offset, buf)<0) {
+	HRETURN_ERROR (H5E_IO, H5E_READERROR, FAIL, "unable to read dataset");
+    }
+
+    FUNC_LEAVE (SUCCEED);
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5S_simp_write
+ *
+ * Purpose:	Write a dataset from application memory BUF directly into
+ *		file F performing data space conversion in a single step from
+ *		MEM_SPACE to FILE_SPACE. The dataset is stored in the file
+ *		according to the LAYOUT and EFL (external file list) and data
+ *		point in the file is ELMT_SIZE bytes.
+ *
+ * Return:	Success:	SUCCEED
+ *
+ *		Failure:	FAIL
+ *
+ * Programmer:	Robb Matzke
+ *              Thursday, March 12, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5S_simp_write (H5F_t *f, const struct H5O_layout_t *layout,
+		const struct H5O_efl_t *efl, size_t elmt_size,
+		const H5S_t *file_space, const H5S_t *mem_space,
+		const void *buf)
+{
+    size_t	hslab_size[H5O_LAYOUT_NDIMS];
+    size_t	file_offset[H5O_LAYOUT_NDIMS];
+    size_t	mem_size[H5O_LAYOUT_NDIMS];
+    size_t	mem_offset[H5O_LAYOUT_NDIMS];
+    int		i;
+
+    FUNC_ENTER (H5S_simp_write, FAIL);
+
+#ifndef NDEBUG
+    assert (file_space->type==mem_space->type);
+    assert (file_space->u.simple.rank==mem_space->u.simple.rank);
+    for (i=0; i<file_space->u.simple.rank; i++) {
+	if (file_space->hslab_def && mem_space->hslab_def) {
+	    assert (1==file_space->h.stride[i]);
+	    assert (1==mem_space->h.stride[i]);
+	    assert (file_space->h.count[i]==mem_space->h.count[i]);
+	} else if (file_space->hslab_def) {
+	    assert (1==file_space->h.stride[i]);
+	    assert (file_space->h.count[i]==mem_space->u.simple.size[i]);
+	} else if (mem_space->hslab_def) {
+	    assert (1==mem_space->h.stride[i]);
+	    assert (file_space->u.simple.size[i]==mem_space->h.count[i]);
+	} else {
+	    assert (file_space->u.simple.size[i]==
+		    mem_space->u.simple.size[i]);
+	}
+    }
+#endif
+	
+
+    /*
+     * Calculate size of hyperslab and offset of hyperslab into file and
+     * memory.
+     */
+    if (file_space->hslab_def) {
+	for (i=0; i<file_space->u.simple.rank; i++) {
+	    hslab_size[i] = file_space->h.count[i];
+	}
+    } else {
+	for (i=0; i<file_space->u.simple.rank; i++) {
+	    hslab_size[i] = file_space->u.simple.size[i];
+	}
+    }
+    for (i=0; i<mem_space->u.simple.rank; i++) {
+	mem_size[i] = mem_space->u.simple.size[i];
+    }
+    if (file_space->hslab_def) {
+	for (i=0; i<file_space->u.simple.rank; i++) {
+	    file_offset[i] = file_space->h.start[i];
+	}
+    } else {
+	for (i=0; i<file_space->u.simple.rank; i++) {
+	    file_offset[i] = 0;
+	}
+    }
+    if (mem_space->hslab_def) {
+	for (i=0; i<mem_space->u.simple.rank; i++) {
+	    mem_offset[i] = mem_space->h.start[i];
+	}
+    } else {
+	for (i=0; i<mem_space->u.simple.rank; i++) {
+	    mem_offset[i] = 0;
+	}
+    }
+    hslab_size[file_space->u.simple.rank] = elmt_size;
+    mem_size[file_space->u.simple.rank] = elmt_size;
+    file_offset[file_space->u.simple.rank] = 0;
+    mem_offset[file_space->u.simple.rank] = 0;
+    
+    /* Write the hyperslab */
+    if (H5F_arr_write (f, layout, efl, hslab_size,
+		       mem_size, mem_offset, file_offset, buf)<0) {
+	HRETURN_ERROR (H5E_IO, H5E_WRITEERROR, FAIL,
+		       "unable to write dataset");
+    }
+
+    FUNC_LEAVE (SUCCEED);
+}
+
+
+	
+    
diff --git a/src/H5Tpkg.h b/src/H5Tpkg.h
index a934b23..be52256 100644
--- a/src/H5Tpkg.h
+++ b/src/H5Tpkg.h
@@ -100,8 +100,6 @@ H5T_path_t *H5T_path_find (const H5T_t *src, const H5T_t *dst,
                            hbool_t create, H5T_conv_t func);
 
 /* Conversion functions */
-herr_t H5T_conv_noop (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
-		      size_t nelmts, void *buf, void *bkg);
 herr_t H5T_conv_order (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
 		       size_t nelmts, void *_buf, void *bkg);
 herr_t H5T_conv_struct (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
diff --git a/src/H5Tprivate.h b/src/H5Tprivate.h
index d67c38d..6af43b8 100644
--- a/src/H5Tprivate.h
+++ b/src/H5Tprivate.h
@@ -41,4 +41,11 @@ herr_t H5T_sort_by_offset (H5T_t *dt);
 herr_t H5T_pack (H5T_t *dt);
 herr_t H5T_debug (H5T_t *dt, FILE * stream);
 H5T_conv_t H5T_find (const H5T_t *src, const H5T_t *dst, H5T_cdata_t **pcdata);
+
+/*
+ * This conversion function is here so we can determine whether a conversion
+ * is a no-op or not.  The other conversion functions can go in H5Tpkg.h
+ */
+herr_t H5T_conv_noop (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
+		      size_t nelmts, void *buf, void *bkg);
 #endif
diff --git a/src/H5V.c b/src/H5V.c
index 85d8752..c9f3de2 100644
--- a/src/H5V.c
+++ b/src/H5V.c
@@ -502,23 +502,30 @@ H5V_stride_copy(intn n, size_t elmt_size, const size_t *size,
 
     FUNC_ENTER(H5V_stride_copy, FAIL);
 
-    H5V_vector_cpy(n, idx, size);
-    nelmts = H5V_vector_reduce_product(n, size);
-    for (i = 0; i < nelmts; i++) {
 
-	/* Copy an element */
-	HDmemcpy(dst, src, elmt_size);
+    if (n) {
+	H5V_vector_cpy(n, idx, size);
+	nelmts = H5V_vector_reduce_product(n, size);
+	for (i = 0; i < nelmts; i++) {
 
-	/* Decrement indices and advance pointers */
-	for (j = n - 1, carry = TRUE; j >= 0 && carry; --j) {
-	    src += src_stride[j];
-	    dst += dst_stride[j];
+	    /* Copy an element */
+	    HDmemcpy(dst, src, elmt_size);
 
-	    if (--idx[j]) carry = FALSE;
-	    else idx[j] = size[j];
+	    /* Decrement indices and advance pointers */
+	    for (j = n - 1, carry = TRUE; j >= 0 && carry; --j) {
+		src += src_stride[j];
+		dst += dst_stride[j];
+
+		if (--idx[j]) carry = FALSE;
+		else idx[j] = size[j];
+	    }
 	}
+    } else {
+	HDmemcpy (dst, src, elmt_size);
+	HRETURN (SUCCEED);
     }
 
+
     FUNC_LEAVE(SUCCEED);
 }