path: root/src/H5Farray.c

/*
 * Copyright (C) 1998-2001 NCSA
 *		           All rights reserved.
 *
 * Programmer:  Robb Matzke <matzke@llnl.gov>
 *              Thursday, January 15, 1998
 *
 * 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 int would
 *		translate to a 10x20x4 array of bytes at this level.
 */

#define H5F_PACKAGE		/*suppress error about including H5Fpkg	  */

#include "H5private.h"
#include "H5Dprivate.h"
#include "H5Eprivate.h"
#include "H5Fpkg.h"
#include "H5FDprivate.h"	/*file driver				  */
#include "H5Iprivate.h"
#include "H5MMprivate.h"	/*memory management			  */
#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
static int interface_initialize_g = 0;



/*-------------------------------------------------------------------------
 * Function:	H5F_arr_read
 *
 * 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.  External
 *		files are described according to the external file list, EFL.
 *		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:	Non-negative on success/Negative on failure
 *
 * Programmer:	Robb Matzke
 *              Friday, January 16, 1998
 *
 * Modifications:
 *		Albert Cheng, 1998-06-02
 *		Added xfer_mode argument
 *
 * 		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, hid_t dxpl_id, const H5O_layout_t *layout,
            H5P_genplist_t *dc_plist, 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	*/
    hssize_t	mem_stride[H5O_LAYOUT_NDIMS];	/*strides through memory*/
    hsize_t	hslab_size[H5O_LAYOUT_NDIMS];	/*hyperslab size	*/
    hsize_t	idx[H5O_LAYOUT_NDIMS];		/*multi-dim counter	*/
    size_t	mem_start;			/*byte offset to start	*/
    hsize_t	file_start;			/*byte offset to start	*/
    hsize_t	max_data = 0;			/*bytes in dataset	*/
    hsize_t	elmt_size = 1;			/*bytes per element	*/
    hsize_t	nelmts, z;			/*number of elements	*/
    unsigned	ndims;				/*stride dimensionality	*/
    haddr_t	addr;				/*address in file	*/
    int	j;				    /*counters		*/
    unsigned	u;				    /*counters		*/
    hbool_t	carray;				/*carry for subtraction	*/
    struct H5O_efl_t efl;                       /* External File List info */
#ifdef H5_HAVE_PARALLEL
    H5FD_mpio_xfer_t xfer_mode=H5FD_MPIO_INDEPENDENT;
#endif /* H5_HAVE_PARALLEL */
    herr_t      ret_value = SUCCEED;            /* Return value */
   
    FUNC_ENTER_NOAPI(H5F_arr_read, FAIL);

    /* Check args */
    assert(f);
    assert(layout);
    assert(_hslab_size);
    assert(file_offset);
    assert(mem_offset);
    assert(mem_size);
    assert(buf);
    /* Make certain we have the correct type of property list */
    assert(TRUE==H5P_isa_class(dxpl_id,H5P_DATASET_XFER));

    /* Make a local copy of size so we can modify it */
    H5V_vector_cpy(layout->ndims, hslab_size, _hslab_size);

#ifdef H5_HAVE_PARALLEL
    /* Get the transfer mode for MPIO transfers */
    if(IS_H5FD_MPIO(f)) {
        hid_t driver_id;                /* VFL driver ID */
        H5P_genplist_t *plist;          /* Property list */

        /* Get the plist structure */
        if(NULL == (plist = H5I_object(dxpl_id)))
            HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "can't find object for ID");

        /* Get the driver ID */
        if(H5P_get(plist, H5D_XFER_VFL_ID_NAME, &driver_id)<0)
            HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve VFL driver ID");

        /* Check if we are using the MPIO driver (for the DXPL) */
        if(H5FD_MPIO==driver_id) {
            /* Get the transfer mode */
            xfer_mode=H5P_peek_unsigned(plist, H5D_XFER_IO_XFER_MODE_NAME);
        } /* end if */
    } /* end if */
    
    /* Collective MPIO access is unsupported for non-contiguous datasets */
    if (H5D_CONTIGUOUS!=layout->type && H5FD_MPIO_COLLECTIVE==xfer_mode)
	HGOTO_ERROR (H5E_DATASET, H5E_READERROR, FAIL, "collective access on non-contiguous datasets not supported yet");
#endif /* H5_HAVE_PARALLEL */

    /* Get necessary properties from property list */
    if(H5P_get(dc_plist, H5D_CRT_EXT_FILE_LIST_NAME, &efl) < 0)
        HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get EFL value");

    switch (layout->type) {
        case H5D_CONTIGUOUS:
            ndims = layout->ndims;
            /*
             * Offsets must not be negative for this type of storage.
             */
            for (u=0; u<ndims; u++) {
                if (mem_offset[u]<0 || file_offset[u]<0)
                    HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "negative offsets are not valid");
            }

            /*
             * 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.
             */
            H5_ASSIGN_OVERFLOW(mem_start,H5V_hyper_stride(ndims, hslab_size, mem_size, mem_offset, mem_stride/*out*/),hsize_t,size_t);
            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);
            if (efl.nused>0) {
                addr = 0;
            } else {
                addr = layout->addr;

                /* Compute the size of the dataset in bytes */
                for(u=0, max_data=1; u<layout->ndims; u++)
                    max_data *= layout->dim[u];

                /* Adjust the maximum size of the data by the offset into it */
                max_data -= file_start;
            }
            addr += file_start;
            buf += mem_start;

            /*
             * Now begin to walk through the array, copying data from disk to
             * memory.
             */
#ifdef H5_HAVE_PARALLEL
            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;

                H5_ASSIGN_OVERFLOW(temp,nelmts,hsize_t,unsigned long);
                MPI_Allreduce(&temp, &max, 1, MPI_UNSIGNED_LONG, MPI_MAX,
                      H5FD_mpio_communicator(f->shared->lf));
                MPI_Allreduce(&temp, &min, 1, MPI_UNSIGNED_LONG, MPI_MIN,
                      H5FD_mpio_communicator(f->shared->lf));
#ifdef AKC
                printf("nelmts=%lu, min=%lu, max=%lu\n", temp, min, max);
#endif
                if (max != min)
                    HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "collective access with unequal number of blocks not supported yet");
            }
#endif /* H5_HAVE_PARALLEL */

            for (z=0; z<nelmts; z++) {
                /* Read directly from file if the dataset is in an external file */
                /* Note: We can't use data sieve buffers for datasets in external files
                 *  because the 'addr' of all external files is set to 0 (above) and
                 *  all datasets in external files would alias to the same set of
                 *  file offsets, totally mixing up the data sieve buffer information. -QAK
                 */
                if (efl.nused>0) {
                    H5_CHECK_OVERFLOW(elmt_size,hsize_t,size_t);
                    if (H5O_efl_read(f, &efl, addr, (size_t)elmt_size, buf)<0)
                        HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "external data read failed");
                } else {
                    H5_CHECK_OVERFLOW(elmt_size,hsize_t,size_t);
                    if (H5F_contig_read(f, max_data, H5FD_MEM_DRAW, addr, (size_t)elmt_size, dxpl_id, buf)<0)
                        HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "block read failed");
                } /* end else */

                /* Decrement indices and advance pointers */
                for (j=ndims-1, carray=TRUE; j>=0 && carray; --j) {
                    addr += file_stride[j];
                    buf += mem_stride[j];

                    /* Adjust the maximum size of the data by the offset into it */
                    max_data -= file_stride[j];

                    if (--idx[j])
                        carray = FALSE;
                    else
                        idx[j] = hslab_size[j];
                }
            }
            break;

        case H5D_CHUNKED:
            /*
             * This method is unable to access external raw data files
             */
            if (efl.nused>0)
                HGOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "chunking and external files are mutually exclusive");

            /* Go get the data from the chunks */
            if (H5F_istore_read(f, dxpl_id, layout, dc_plist, mem_size,
                    mem_offset, file_offset, hslab_size, buf)<0)
                HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "chunked read failed");
            break;

        default:
            assert("not implemented yet" && 0);
            HGOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout");
    }

done:
    FUNC_LEAVE_NOAPI(ret_value);
}


/*-------------------------------------------------------------------------
 * Function:	H5F_arr_write
 *
 * 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 data is stored in external files according to the
 *		external file list, EFL. 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:	Non-negative on success/Negative on failure
 *
 * Programmer:	Robb Matzke
 *              Friday, January 16, 1998
 *
 * Modifications:
 *		Albert Cheng, 1998-06-02
 *		Added xfer_mode argument
 *
 * 		Robb Matzke, 1998-09-28
 *		Added `xfer' argument, removed `xfer_mode' argument since it
 *		is a member of H5D_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, hid_t dxpl_id, H5O_layout_t *layout,
            H5P_genplist_t *dc_plist,
            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	*/
    hssize_t	mem_stride[H5O_LAYOUT_NDIMS];	/*strides through memory*/
    hsize_t	hslab_size[H5O_LAYOUT_NDIMS];	/*hyperslab size	*/
    hsize_t	idx[H5O_LAYOUT_NDIMS];		/*multi-dim counter	*/
    hsize_t	mem_start;			/*byte offset to start	*/
    hsize_t	file_start;			/*byte offset to start	*/
    hsize_t	max_data = 0;			/*bytes in dataset	*/
    hsize_t	elmt_size = 1;			/*bytes per element	*/
    hsize_t	nelmts, z;			/*number of elements	*/
    unsigned	ndims;				/*dimensionality	*/
    haddr_t	addr;				/*address in file	*/
    int	j;				    /*counters		*/
    unsigned	u;				    /*counters		*/
    hbool_t	carray;				/*carry for subtraction	*/
    struct H5O_efl_t efl;                       /* External File List info */
#ifdef H5_HAVE_PARALLEL
    H5FD_mpio_xfer_t xfer_mode=H5FD_MPIO_INDEPENDENT;
#endif /* H5_HAVE_PARALLEL */
    herr_t      ret_value = SUCCEED;            /* Return value */
   
    FUNC_ENTER_NOAPI(H5F_arr_write, FAIL);

    /* Check args */
    assert(f);
    assert(layout);
    assert(_hslab_size);
    assert(file_offset);
    assert(mem_offset);
    assert(mem_size);
    assert(buf);
    /* Make certain we have the correct type of property list */
    assert(TRUE==H5P_isa_class(dxpl_id,H5P_DATASET_XFER));

    /* Make a local copy of _size so we can modify it */
    H5V_vector_cpy(layout->ndims, hslab_size, _hslab_size);

#ifdef H5_HAVE_PARALLEL
    /* Get the transfer mode for MPIO transfers */
    if(IS_H5FD_MPIO(f)) {
        hid_t driver_id;            /* VFL driver ID */
        H5P_genplist_t *plist;      /* Property list */

        /* Get the plist structure */
        if(NULL == (plist = H5I_object(dxpl_id)))
            HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "can't find object for ID");

        /* Get the driver ID */
        if(H5P_get(plist, H5D_XFER_VFL_ID_NAME, &driver_id)<0)
            HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve VFL driver ID");

        /* Check if we are using the MPIO driver (for the DXPL) */
        if(H5FD_MPIO==driver_id) {
            /* Get the transfer mode */
            xfer_mode=H5P_peek_unsigned(plist, H5D_XFER_IO_XFER_MODE_NAME);
        } /* end if */
    } /* end if */
    
    if (H5D_CONTIGUOUS!=layout->type && H5FD_MPIO_COLLECTIVE==xfer_mode)
	HGOTO_ERROR (H5E_DATASET, H5E_WRITEERROR, FAIL, "collective access on non-contiguous datasets not supported yet");
#endif /* H5_HAVE_PARALLEL */
    
    /* Get necessary properties from property list */
    if(H5P_get(dc_plist, H5D_CRT_EXT_FILE_LIST_NAME, &efl) < 0)
        HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get EFL value");

    switch (layout->type) {
        case H5D_CONTIGUOUS:
            ndims = layout->ndims;
            /*
             * Offsets must not be negative for this type of storage.
             */
            for (u=0; u<ndims; u++) {
                if (mem_offset[u]<0 || file_offset[u]<0)
                    HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "negative offsets are not valid");
            }

            /*
             * Calculate the strides needed to walk through the array on disk.
             * 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);

            /*
             * 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);
            
            if (efl.nused>0) {
                addr = 0;
            } else {
                addr = layout->addr;

                /* Compute the size of the dataset in bytes */
                for(u=0, max_data=1; u<layout->ndims; u++)
                    max_data *= layout->dim[u];

                /* Adjust the maximum size of the data by the offset into it */
                max_data -= file_start;
            }
            addr += file_start;
            buf += mem_start;

            /*
             * Now begin to walk through the array, copying data from memory to
             * disk.
             */
#ifdef H5_HAVE_PARALLEL
            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;

                H5_ASSIGN_OVERFLOW(temp,nelmts,hsize_t,unsigned long);
                MPI_Allreduce(&temp, &max, 1, MPI_UNSIGNED_LONG, MPI_MAX,
                      H5FD_mpio_communicator(f->shared->lf));
                MPI_Allreduce(&temp, &min, 1, MPI_UNSIGNED_LONG, MPI_MIN,
                      H5FD_mpio_communicator(f->shared->lf));
#ifdef AKC
                printf("nelmts=%lu, min=%lu, max=%lu\n", temp, min, max);
#endif
                if (max != min)
                    HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "collective access with unequal number of blocks not supported yet");
            }
#endif /* H5_HAVE_PARALLEL */

            for (z=0; z<nelmts; z++) {

                /* Write to file */
                if (efl.nused>0) {
                    H5_CHECK_OVERFLOW(elmt_size,hsize_t,size_t);
                    if (H5O_efl_write(f, &efl, addr, (size_t)elmt_size, buf)<0)
                        HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "external data write failed");
                } else {
                    H5_CHECK_OVERFLOW(elmt_size,hsize_t,size_t);
                    if (H5F_contig_write(f, max_data, H5FD_MEM_DRAW, addr, (size_t)elmt_size, dxpl_id, buf)<0)
                        HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "block write failed");
                } /* end else */

                /* Decrement indices and advance pointers */
                for (j=ndims-1, carray=TRUE; j>=0 && carray; --j) {
                    addr += file_stride[j];
                    buf += mem_stride[j];
                    
                    /* Adjust the maximum size of the data by the offset into it */
                    max_data -= file_stride[j];

                    if (--idx[j])
                        carray = FALSE;
                    else
                        idx[j] = hslab_size[j];
                }

            }
            break;

        case H5D_CHUNKED:
            /*
             * This method is unable to access external raw data files
             */
            if (efl.nused>0)
                HGOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "chunking and external files are mutually exclusive");

            /* Write the read to the chunks */
            if (H5F_istore_write(f, dxpl_id, layout, dc_plist, mem_size,
                    mem_offset, file_offset, hslab_size, buf)<0)
                HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "chunked write failed");
            break;

        default:
            assert("not implemented yet" && 0);
            HGOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout");
    }

done:
    FUNC_LEAVE_NOAPI(ret_value);
}