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-rw-r--r--src/H5Farray.c395
1 files changed, 267 insertions, 128 deletions
diff --git a/src/H5Farray.c b/src/H5Farray.c
index 9b2d194..8f5e3b4 100644
--- a/src/H5Farray.c
+++ b/src/H5Farray.c
@@ -5,8 +5,11 @@
* Programmer: Robb Matzke <robb@arborea.spizella.com>
* Thursday, January 15, 1998
*
- * Purpose: Provides I/O facilities for multi-dimensional arrays of bytes
- * stored with various layout policies.
+ * Purpose: Provides I/O facilities for multi-dimensional arrays of bytes
+ * stored with various layout policies. If the caller is
+ * interested in arrays of elements >1 byte then add an extra
+ * dimension. For example, a 10x20 array of int32 would
+ * translate to a 10x20x4 array of bytes at this level.
*/
#include <H5private.h>
#include <H5Dprivate.h>
@@ -14,25 +17,25 @@
#include <H5Fprivate.h>
#include <H5MFprivate.h>
#include <H5Oprivate.h>
+#include <H5Vprivate.h>
/* Interface initialization */
-#define PABLO_MASK H5F_arr_mask
-#define INTERFACE_INIT NULL
-static intn interface_initialize_g = FALSE;
+#define PABLO_MASK H5F_arr_mask
+#define INTERFACE_INIT NULL
+static intn interface_initialize_g = FALSE;
+
+
/*-------------------------------------------------------------------------
- * Function: H5F_arr_create
+ * Function: H5F_arr_create
*
- * Purpose: Creates an array of bytes. When called to create an array of
- * some type, the fastest varying dimension corresponds to an
- * instance of that type. That is, a 10x20 array of int32 is
- * really a 10x20x4 array of bytes.
+ * Purpose: Creates an array of bytes.
*
- * Return: Success: SUCCEED
+ * Return: Success: SUCCEED
*
- * Failure: FAIL
+ * Failure: FAIL
*
- * Programmer: Robb Matzke
+ * Programmer: Robb Matzke
* Friday, January 16, 1998
*
* Modifications:
@@ -40,180 +43,316 @@ static intn interface_initialize_g = FALSE;
*-------------------------------------------------------------------------
*/
herr_t
-H5F_arr_create(H5F_t *f, struct H5O_layout_t *layout /*in,out */ )
+H5F_arr_create (H5F_t *f, struct H5O_layout_t *layout/*in,out*/)
{
- intn i;
- size_t nbytes;
-
- FUNC_ENTER(H5F_arr_create, FAIL);
+ intn i;
+ size_t nbytes;
+
+ FUNC_ENTER (H5F_arr_create, FAIL);
/* check args */
- assert(f);
- assert(layout);
- H5F_addr_undef(&(layout->addr)); /*just in case we fail */
-
+ assert (f);
+ assert (layout);
+ H5F_addr_undef (&(layout->addr)); /*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) {
- HRETURN_ERROR(H5E_IO, H5E_NOSPACE, FAIL,
- "unable to reserve file space");
- }
- break;
+ /* 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) {
+ HRETURN_ERROR (H5E_IO, H5E_NOSPACE, FAIL,
+ "unable to reserve file space");
+ }
+ break;
case H5D_CHUNKED:
- /* Create the root of the B-tree that describes chunked storage */
- if (H5F_istore_create(f, layout /*out */ ) < 0) {
- HRETURN_ERROR(H5E_IO, H5E_CANTINIT, FAIL,
- "unable to initialize chunked storage");
- }
- break;
+ /* Create the root of the B-tree that describes chunked storage */
+ if (H5F_istore_create (f, layout/*out*/)<0) {
+ HRETURN_ERROR (H5E_IO, H5E_CANTINIT, FAIL,
+ "unable to initialize chunked storage");
+ }
+ break;
default:
- assert("not implemented yet" && 0);
- HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL,
- "unsupported storage layout");
- break;
+ assert ("not implemented yet" && 0);
+ HRETURN_ERROR (H5E_IO, H5E_UNSUPPORTED, FAIL,
+ "unsupported storage layout");
+ break;
}
- FUNC_LEAVE(SUCCEED);
+ FUNC_LEAVE (SUCCEED);
}
+
/*-------------------------------------------------------------------------
- * Function: H5F_arr_read
+ * Function: H5F_arr_read
*
- * Purpose: Reads a hyperslab of a file byte array into a byte array in
- * memory which has the same dimensions as the hyperslab.
+ * Purpose: Reads a hyperslab of a file byte array into a hyperslab of
+ * a byte array in memory. The data is read from file F and the
+ * array's size and storage information is in LAYOUT. The
+ * hyperslab offset is FILE_OFFSET[] in the file and
+ * MEM_OFFSET[] in memory (offsets are relative to the origin of
+ * the array) and the size of the hyperslab is HSLAB_SIZE[]. The
+ * total size of the file array is implied in the LAYOUT
+ * argument and the total size of the memory array is
+ * MEM_SIZE[]. The dimensionality of these vectors is implied by
+ * the LAYOUT argument.
*
- * Return: Success: SUCCEED
+ * Return: Success: SUCCEED
*
- * Failure: FAIL
+ * Failure: FAIL
*
- * Programmer: Robb Matzke
+ * Programmer: Robb Matzke
* Friday, January 16, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
-herr_t
-H5F_arr_read(H5F_t *f, const struct H5O_layout_t *layout,
- const size_t offset[], const size_t size[],
- void *buf /*out */ )
+herr_t
+H5F_arr_read (H5F_t *f, const struct H5O_layout_t *layout,
+ const size_t _hslab_size[], const size_t file_offset[],
+ const size_t mem_offset[], const size_t mem_size[],
+ void *_buf/*out*/)
{
- intn i;
- size_t nbytes;
- size_t zero_offset[H5O_LAYOUT_NDIMS];
-
- FUNC_ENTER(H5F_arr_read, FAIL);
+ uint8 *buf = (uint8 *)_buf; /*cast for arithmetic */
+ size_t file_stride[H5O_LAYOUT_NDIMS]; /*strides through file */
+ size_t mem_stride[H5O_LAYOUT_NDIMS]; /*strides through memory*/
+ size_t hslab_size[H5O_LAYOUT_NDIMS]; /*hyperslab size */
+ size_t idx[H5O_LAYOUT_NDIMS]; /*multi-dim counter */
+ size_t mem_start, file_start; /*byte offsets to start */
+ size_t elmt_size = 1; /*bytes per element */
+ intn nelmts; /*number of elements */
+ intn ndims; /*stride dimensionality */
+ haddr_t addr; /*address in file */
+ intn i, j; /*counters */
+ hbool_t carray; /*carry for subtraction */
+
+ FUNC_ENTER (H5F_arr_read, FAIL);
/* Check args */
- assert(f);
- assert(layout);
- if (!offset) {
- HDmemset(zero_offset, 0, sizeof zero_offset);
- offset = zero_offset;
- }
- assert(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);
switch (layout->type) {
case H5D_CONTIGUOUS:
- /*
- * We currently only support complete I/O.
- */
- for (i = 0; i < layout->ndims; i++) {
- assert(0 == offset[i]);
- assert(size[i] == layout->dim[i]);
- }
- for (i = 0, nbytes = 1; i < layout->ndims; i++)
- nbytes *= layout->dim[i];
- if (H5F_block_read(f, &(layout->addr), nbytes, buf) < 0) {
- HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, "block read failed");
- }
- break;
+ /*
+ * Calculate the strides needed to walk through the array on disk
+ * and memory. Optimize the strides to result in the fewest number of
+ * I/O requests.
+ */
+ ndims = layout->ndims;
+ 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
+ * that counts from SIZE down to zero and IDX is the counter. Each
+ * 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);
+ addr = layout->addr;
+ H5F_addr_inc (&addr, file_start);
+ buf += mem_start;
+
+ /*
+ * Now begin to walk through the array, copying data from disk to
+ * memory.
+ */
+ for (i=0; i<nelmts; i++) {
+
+ /* Read from file */
+ if (H5F_block_read (f, &addr, elmt_size, 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) {
+
+ H5F_addr_inc (&addr, file_stride[j]);
+ buf += mem_stride[j];
+
+ if (--idx[j]) carray = FALSE;
+ else idx[j] = hslab_size[j];
+ }
+ }
+ break;
case H5D_CHUNKED:
- if (H5F_istore_read(f, layout, offset, size, buf) < 0) {
- HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, "chunked read failed");
- }
- break;
+ /*
+ * This method is unable to copy into a proper hyperslab.
+ */
+ 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");
+ }
+ }
+ if (H5F_istore_read (f, layout, file_offset, hslab_size, buf)<0) {
+ 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");
- break;
+ assert ("not implemented yet" && 0);
+ HRETURN_ERROR (H5E_IO, H5E_UNSUPPORTED, FAIL,
+ "unsupported storage layout");
+ break;
}
- FUNC_LEAVE(SUCCEED);
+ FUNC_LEAVE (SUCCEED);
}
+
/*-------------------------------------------------------------------------
- * Function: H5F_arr_write
+ * Function: H5F_arr_write
*
- * Purpose: Writes an array to a hyperslab of a file byte array. The
- * memory array and the hyperslab are the same size.
+ * Purpose: Copies a hyperslab of a memory array to a hyperslab of a
+ * file array. The data is written to file F and the file
+ * array's size and storage information is implied by LAYOUT.
+ * The hyperslab offset is FILE_OFFSET[] in the file and
+ * MEM_OFFSET[] in memory (offsets are relative to the origin of
+ * the array) and the size of the hyperslab is HSLAB_SIZE[].
+ * The total size of the file array is implied by the LAYOUT
+ * argument and the total size of the memory array is
+ * MEM_SIZE[]. The dimensionality of these vectors is implied
+ * by the LAYOUT argument.
*
- * Return: Success: SUCCEED
+ * Return: Success: SUCCEED
*
- * Failure: FAIL
+ * Failure: FAIL
*
- * Programmer: Robb Matzke
+ * Programmer: Robb Matzke
* Friday, January 16, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
-herr_t
-H5F_arr_write(H5F_t *f, const struct H5O_layout_t *layout,
- const size_t offset[], const size_t size[],
- const void *buf)
+herr_t
+H5F_arr_write (H5F_t *f, const struct H5O_layout_t *layout,
+ const size_t _hslab_size[], const size_t file_offset[],
+ const size_t mem_offset[], const size_t mem_size[],
+ const void *_buf)
{
- intn i;
- size_t nbytes;
-
- FUNC_ENTER(H5F_arr_write, FAIL);
+ const uint8 *buf = (const uint8 *)_buf; /*cast for arithmetic */
+ size_t file_stride[H5O_LAYOUT_NDIMS]; /*strides through file */
+ size_t mem_stride[H5O_LAYOUT_NDIMS]; /*strides through memory*/
+ size_t hslab_size[H5O_LAYOUT_NDIMS]; /*hyperslab size */
+ size_t idx[H5O_LAYOUT_NDIMS]; /*multi-dim counter */
+ size_t mem_start, file_start; /*byte offsets to start */
+ size_t elmt_size = 1; /*bytes per element */
+ intn nelmts; /*number of elements */
+ intn ndims; /*dimensionality */
+ haddr_t addr; /*address in file */
+ intn i, j; /*counters */
+ hbool_t carray; /*carry for subtraction */
+
+ FUNC_ENTER (H5F_arr_write, FAIL);
/* Check args */
- assert(f);
- assert(layout);
- assert(offset);
- assert(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);
+
switch (layout->type) {
case H5D_CONTIGUOUS:
- /*
- * We currently only support complete I/O.
- */
- for (i = 0; i < layout->ndims; i++) {
- assert(0 == offset[i]);
- assert(size[i] == layout->dim[i]);
- }
- for (i = 0, nbytes = 1; i < layout->ndims; i++)
- nbytes *= layout->dim[i];
- if (H5F_block_write(f, &(layout->addr), nbytes, buf) < 0) {
- HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "block write failed");
- }
- break;
+ /*
+ * Calculate the strides needed to walk through the array on disk.
+ * Optimize the strides to result in the fewest number of I/O
+ * requests.
+ */
+ ndims = layout->ndims;
+ 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
+ * that counts from SIZE down to zero and IDX is the counter. Each
+ * 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);
+ addr = layout->addr;
+ H5F_addr_inc (&addr, file_start);
+ buf += mem_start;
+
+ /*
+ * Now begin to walk through the array, copying data from memory to
+ * disk.
+ */
+ for (i=0; i<nelmts; i++) {
+
+ /* Write to file */
+ if (H5F_block_write (f, &addr, elmt_size, 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) {
+
+ H5F_addr_inc (&addr, file_stride[j]);
+ buf += mem_stride[j];
+
+ if (--idx[j]) carray = FALSE;
+ else idx[j] = hslab_size[j];
+ }
+
+ }
+ break;
case H5D_CHUNKED:
- if (H5F_istore_write(f, layout, offset, size, buf) < 0) {
- HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "chunked write failed");
- }
- break;
+ /*
+ * This method is unable to copy from a proper hyperslab.
+ */
+ 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");
+ }
+ }
+ if (H5F_istore_write (f, layout, 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");
- break;
+ assert ("not implemented yet" && 0);
+ HRETURN_ERROR (H5E_IO, H5E_UNSUPPORTED, FAIL,
+ "unsupported storage layout");
+ break;
}
- FUNC_LEAVE(SUCCEED);
+ FUNC_LEAVE (SUCCEED);
}