diff options
Diffstat (limited to 'src/H5Farray.c')
| -rw-r--r-- | src/H5Farray.c | 395 |
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); } |