ad_read_str.c

mpi并行计算的c++代码 可用vc或gcc编译通过 可以用来搭建并行计算试验环境

/* -*- Mode: C; c-basic-offset:4 ; -*- */
/* 
 *
 *   Copyright (C) 1997 University of Chicago. 
 *   See COPYRIGHT notice in top-level directory.
 */

#include "adio.h"
#include "adio_extern.h"

#define ADIOI_BUFFERED_READ \
{ \
    if (req_off >= readbuf_off + readbuf_len) { \
	readbuf_off = req_off; \
	readbuf_len = (int) (ADIOI_MIN(max_bufsize, end_offset-readbuf_off+1));\
	ADIO_ReadContig(fd, readbuf, readbuf_len, MPI_BYTE, \
              ADIO_EXPLICIT_OFFSET, readbuf_off, &status1, error_code); \
        if (*error_code != MPI_SUCCESS) return; \
    } \
    while (req_len > readbuf_off + readbuf_len - req_off) { \
	partial_read = (int) (readbuf_off + readbuf_len - req_off); \
	tmp_buf = (char *) ADIOI_Malloc(partial_read); \
	memcpy(tmp_buf, readbuf+readbuf_len-partial_read, partial_read); \
	ADIOI_Free(readbuf); \
	readbuf = (char *) ADIOI_Malloc(partial_read + max_bufsize); \
	memcpy(readbuf, tmp_buf, partial_read); \
	ADIOI_Free(tmp_buf); \
	readbuf_off += readbuf_len-partial_read; \
	readbuf_len = (int) (partial_read + ADIOI_MIN(max_bufsize, \
				       end_offset-readbuf_off+1)); \
	ADIO_ReadContig(fd, readbuf+partial_read, readbuf_len-partial_read, \
             MPI_BYTE, ADIO_EXPLICIT_OFFSET, readbuf_off+partial_read, \
             &status1, error_code); \
        if (*error_code != MPI_SUCCESS) return; \
    } \
    memcpy((char *)buf + userbuf_off, readbuf+req_off-readbuf_off, req_len); \
}


void ADIOI_GEN_ReadStrided(ADIO_File fd, void *buf, int count,
                       MPI_Datatype datatype, int file_ptr_type,
                       ADIO_Offset offset, ADIO_Status *status, int
                       *error_code)
{
/* offset is in units of etype relative to the filetype. */

    ADIOI_Flatlist_node *flat_buf, *flat_file;
    int i, j, k, brd_size, frd_size=0, st_index=0;
    int bufsize, num, size, sum, n_etypes_in_filetype, size_in_filetype;
    int n_filetypes, etype_in_filetype;
    ADIO_Offset abs_off_in_filetype=0;
    int filetype_size, etype_size, buftype_size, req_len, partial_read;
    MPI_Aint filetype_extent, buftype_extent; 
    int buf_count, buftype_is_contig, filetype_is_contig;
    ADIO_Offset userbuf_off;
    ADIO_Offset off, req_off, disp, end_offset=0, readbuf_off, start_off;
    char *readbuf, *tmp_buf, *value;
    int flag, st_frd_size, st_n_filetypes, readbuf_len;
    int new_brd_size, new_frd_size, info_flag, max_bufsize;
    ADIO_Status status1;

    if (fd->hints->ds_read == ADIOI_HINT_DISABLE) {
    	/* if user has disabled data sieving on reads, use naive
	 * approach instead.
	 */
	ADIOI_GEN_ReadStrided_naive(fd, 
				    buf,
				    count,
				    datatype,
				    file_ptr_type,
				    offset,
				    status,
				    error_code);
    	return;
    }

    *error_code = MPI_SUCCESS;  /* changed below if error */

    ADIOI_Datatype_iscontig(datatype, &buftype_is_contig);
    ADIOI_Datatype_iscontig(fd->filetype, &filetype_is_contig);

    MPI_Type_size(fd->filetype, &filetype_size);
    if ( ! filetype_size ) {
	*error_code = MPI_SUCCESS; 
	return;
    }

    MPI_Type_extent(fd->filetype, &filetype_extent);
    MPI_Type_size(datatype, &buftype_size);
    MPI_Type_extent(datatype, &buftype_extent);
    etype_size = fd->etype_size;

    bufsize = buftype_size * count;

/* get max_bufsize from the info object. */

    value = (char *) ADIOI_Malloc((MPI_MAX_INFO_VAL+1)*sizeof(char));
    MPI_Info_get(fd->info, "ind_rd_buffer_size", MPI_MAX_INFO_VAL, value, 
                 &info_flag);
    max_bufsize = atoi(value);
    ADIOI_Free(value);


    if (!buftype_is_contig && filetype_is_contig) {

/* noncontiguous in memory, contiguous in file. */

	ADIOI_Flatten_datatype(datatype);
	flat_buf = ADIOI_Flatlist;
	while (flat_buf->type != datatype) flat_buf = flat_buf->next;

        off = (file_ptr_type == ADIO_INDIVIDUAL) ? fd->fp_ind : 
                 fd->disp + etype_size * offset;

	start_off = off;
	end_offset = off + bufsize - 1;
        readbuf_off = off;
        readbuf = (char *) ADIOI_Malloc(max_bufsize);
        readbuf_len = (int) (ADIOI_MIN(max_bufsize, end_offset-readbuf_off+1));

/* if atomicity is true, lock (exclusive) the region to be accessed */
        if ((fd->atomicity) && (fd->file_system != ADIO_PIOFS) && (fd->file_system != ADIO_PVFS))
            ADIOI_WRITE_LOCK(fd, start_off, SEEK_SET, end_offset-start_off+1);

        ADIO_ReadContig(fd, readbuf, readbuf_len, MPI_BYTE, 
            ADIO_EXPLICIT_OFFSET, readbuf_off, &status1, error_code);
	if (*error_code != MPI_SUCCESS) return;

        for (j=0; j<count; j++) 
            for (i=0; i<flat_buf->count; i++) {
                userbuf_off = j*buftype_extent + flat_buf->indices[i];
		req_off = off;
		req_len = flat_buf->blocklens[i];
		ADIOI_BUFFERED_READ
                off += flat_buf->blocklens[i];
            }

        if ((fd->atomicity) && (fd->file_system != ADIO_PIOFS) && (fd->file_system != ADIO_PVFS))
            ADIOI_UNLOCK(fd, start_off, SEEK_SET, end_offset-start_off+1);

        if (file_ptr_type == ADIO_INDIVIDUAL) fd->fp_ind = off;

	ADIOI_Free(readbuf); 
    }

    else {  /* noncontiguous in file */

/* filetype already flattened in ADIO_Open */
	flat_file = ADIOI_Flatlist;
	while (flat_file->type != fd->filetype) flat_file = flat_file->next;
	disp = fd->disp;

	if (file_ptr_type == ADIO_INDIVIDUAL) {
	    offset = fd->fp_ind; /* in bytes */
	    n_filetypes = -1;
	    flag = 0;
	    while (!flag) {
                n_filetypes++;
		for (i=0; i<flat_file->count; i++) {
		    if (disp + flat_file->indices[i] + 
                        (ADIO_Offset) n_filetypes*filetype_extent + flat_file->blocklens[i] 
                            >= offset) {
			st_index = i;
			frd_size = (int) (disp + flat_file->indices[i] + 
			        (ADIO_Offset) n_filetypes*filetype_extent
			         + flat_file->blocklens[i] - offset);
			flag = 1;
			break;
		    }
		}
	    }
	}
	else {
	    n_etypes_in_filetype = filetype_size/etype_size;
	    n_filetypes = (int) (offset / n_etypes_in_filetype);
	    etype_in_filetype = (int) (offset % n_etypes_in_filetype);
	    size_in_filetype = etype_in_filetype * etype_size;
 
	    sum = 0;
	    for (i=0; i<flat_file->count; i++) {
		sum += flat_file->blocklens[i];
		if (sum > size_in_filetype) {
		    st_index = i;
		    frd_size = sum - size_in_filetype;
		    abs_off_in_filetype = flat_file->indices[i] +
			size_in_filetype - (sum - flat_file->blocklens[i]);
		    break;
		}
	    }

	    /* abs. offset in bytes in the file */
	    offset = disp + (ADIO_Offset) n_filetypes*filetype_extent + abs_off_in_filetype;
	}

        start_off = offset;

       /* Calculate end_offset, the last byte-offset that will be accessed.
         e.g., if start_offset=0 and 100 bytes to be read, end_offset=99*/

	st_frd_size = frd_size;
	st_n_filetypes = n_filetypes;
	i = 0;
	j = st_index;
	off = offset;
	frd_size = ADIOI_MIN(st_frd_size, bufsize);
	while (i < bufsize) {
	    i += frd_size;
	    end_offset = off + frd_size - 1;

	    if (j < (flat_file->count - 1)) j++;
	    else {
		j = 0;
		n_filetypes++;
	    }

	    off = disp + flat_file->indices[j] + (ADIO_Offset) n_filetypes*filetype_extent;
	    frd_size = ADIOI_MIN(flat_file->blocklens[j], bufsize-i);
	}

/* if atomicity is true, lock (exclusive) the region to be accessed */
        if ((fd->atomicity) && (fd->file_system != ADIO_PIOFS) && (fd->file_system != ADIO_PVFS))
            ADIOI_WRITE_LOCK(fd, start_off, SEEK_SET, end_offset-start_off+1);

	readbuf_off = 0;
	readbuf_len = 0;
	readbuf = (char *) ADIOI_Malloc(max_bufsize);

	if (buftype_is_contig && !filetype_is_contig) {

/* contiguous in memory, noncontiguous in file. should be the most
   common case. */

	    i = 0;
	    j = st_index;
	    off = offset;
	    n_filetypes = st_n_filetypes;
	    frd_size = ADIOI_MIN(st_frd_size, bufsize);
	    while (i < bufsize) {
                if (frd_size) { 
                    /* TYPE_UB and TYPE_LB can result in 
                       frd_size = 0. save system call in such cases */ 
		    /* lseek(fd->fd_sys, off, SEEK_SET);
		    err = read(fd->fd_sys, ((char *) buf) + i, frd_size);*/

		    req_off = off;
		    req_len = frd_size;
		    userbuf_off = i;
		    ADIOI_BUFFERED_READ
		}
		i += frd_size;

                if (off + frd_size < disp + flat_file->indices[j] +
                   flat_file->blocklens[j] + (ADIO_Offset) n_filetypes*filetype_extent)
                       off += frd_size;
                /* did not reach end of contiguous block in filetype.
                   no more I/O needed. off is incremented by frd_size. */
                else {
		    if (j < (flat_file->count - 1)) j++;
		    else {
			j = 0;
			n_filetypes++;
		    }
		    off = disp + flat_file->indices[j] + 
                                        (ADIO_Offset) n_filetypes*filetype_extent;
		    frd_size = ADIOI_MIN(flat_file->blocklens[j], bufsize-i);
		}
	    }
	}
	else {
/* noncontiguous in memory as well as in file */

	    ADIOI_Flatten_datatype(datatype);
	    flat_buf = ADIOI_Flatlist;
	    while (flat_buf->type != datatype) flat_buf = flat_buf->next;

	    k = num = buf_count = 0;
	    i = (int) (flat_buf->indices[0]);
	    j = st_index;
	    off = offset;
	    n_filetypes = st_n_filetypes;
	    frd_size = st_frd_size;
	    brd_size = flat_buf->blocklens[0];

	    while (num < bufsize) {
		size = ADIOI_MIN(frd_size, brd_size);
		if (size) {
		    /* lseek(fd->fd_sys, off, SEEK_SET);
		    err = read(fd->fd_sys, ((char *) buf) + i, size); */

		    req_off = off;
		    req_len = size;
		    userbuf_off = i;
		    ADIOI_BUFFERED_READ
		}

		new_frd_size = frd_size;
		new_brd_size = brd_size;

		if (size == frd_size) {
/* reached end of contiguous block in file */
		    if (j < (flat_file->count - 1)) j++;
		    else {
			j = 0;
			n_filetypes++;
		    }

		    off = disp + flat_file->indices[j] + 
                                              (ADIO_Offset) n_filetypes*filetype_extent;

		    new_frd_size = flat_file->blocklens[j];
		    if (size != brd_size) {
			i += size;
			new_brd_size -= size;
		    }
		}

		if (size == brd_size) {
/* reached end of contiguous block in memory */

		    k = (k + 1)%flat_buf->count;
		    buf_count++;
		    i = (int) (buftype_extent*(buf_count/flat_buf->count) +
			flat_buf->indices[k]);
		    new_brd_size = flat_buf->blocklens[k];
		    if (size != frd_size) {
			off += size;
			new_frd_size -= size;
		    }
		}
		num += size;
		frd_size = new_frd_size;
                brd_size = new_brd_size;
	    }
	}
	
        if ((fd->atomicity) && (fd->file_system != ADIO_PIOFS) && (fd->file_system != ADIO_PVFS))
            ADIOI_UNLOCK(fd, start_off, SEEK_SET, end_offset-start_off+1);

	if (file_ptr_type == ADIO_INDIVIDUAL) fd->fp_ind = off;

	ADIOI_Free(readbuf); /* malloced in the buffered_read macro */
    }

    fd->fp_sys_posn = -1;   /* set it to null. */

#ifdef HAVE_STATUS_SET_BYTES
    MPIR_Status_set_bytes(status, datatype, bufsize);
/* This is a temporary way of filling in status. The right way is to 
   keep track of how much data was actually read and placed in buf 
   by ADIOI_BUFFERED_READ. */
#endif

    if (!buftype_is_contig) ADIOI_Delete_flattened(datatype);
}