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|
/*
* Copyright (C) by Argonne National Laboratory
* See COPYRIGHT in top-level directory
*/
#include "ad_nfs.h"
#include "adio_extern.h"
#ifdef HAVE_UNISTD_H
#include <unistd.h>
#endif
void ADIOI_NFS_ReadContig(ADIO_File fd, void *buf, int count,
MPI_Datatype datatype, int file_ptr_type,
ADIO_Offset offset, ADIO_Status * status, int *error_code)
{
ssize_t err = -1;
MPI_Count datatype_size, len;
ADIO_Offset bytes_xfered = 0;
size_t rd_count;
static char myname[] = "ADIOI_NFS_READCONTIG";
char *p;
if (count == 0) {
err = 0;
goto fn_exit;
}
MPI_Type_size_x(datatype, &datatype_size);
len = datatype_size * count;
if (file_ptr_type == ADIO_INDIVIDUAL) {
offset = fd->fp_ind;
}
p = buf;
while (bytes_xfered < len) {
rd_count = len - bytes_xfered;
/* FreeBSD and Darwin workaround: bigger than INT_MAX is an error */
if (rd_count > INT_MAX)
rd_count = INT_MAX;
if (fd->atomicity)
ADIOI_WRITE_LOCK(fd, offset + bytes_xfered, SEEK_SET, rd_count);
else
ADIOI_READ_LOCK(fd, offset + bytes_xfered, SEEK_SET, rd_count);
#ifdef ADIOI_MPE_LOGGING
MPE_Log_event(ADIOI_MPE_read_a, 0, NULL);
#endif
err = pread(fd->fd_sys, p, rd_count, offset + bytes_xfered);
/* --BEGIN ERROR HANDLING-- */
if (err == -1) {
*error_code = MPIO_Err_create_code(MPI_SUCCESS,
MPIR_ERR_RECOVERABLE, myname, __LINE__, MPI_ERR_IO,
"**io", "**io %s", strerror(errno));
}
/* --END ERROR HANDLING-- */
#ifdef ADIOI_MPE_LOGGING
MPE_Log_event(ADIOI_MPE_read_b, 0, NULL);
#endif
ADIOI_UNLOCK(fd, offset + bytes_xfered, SEEK_SET, rd_count);
if (err == 0) {
/* end of file */
break;
}
bytes_xfered += err;
p += err;
}
fd->fp_sys_posn = offset + bytes_xfered;
if (file_ptr_type == ADIO_INDIVIDUAL) {
fd->fp_ind += bytes_xfered;
}
fn_exit:
#ifdef HAVE_STATUS_SET_BYTES
if (status && err != -1)
MPIR_Status_set_bytes(status, datatype, bytes_xfered);
#endif
*error_code = MPI_SUCCESS;
}
#ifdef ADIOI_MPE_LOGGING
#define ADIOI_BUFFERED_READ \
{ \
if (req_off >= readbuf_off + readbuf_len) { \
readbuf_off = req_off; \
readbuf_len = (int) (MPL_MIN(max_bufsize, end_offset-readbuf_off+1)); \
MPE_Log_event(ADIOI_MPE_lseek_a, 0, NULL); \
lseek(fd->fd_sys, readbuf_off, SEEK_SET); \
MPE_Log_event(ADIOI_MPE_lseek_b, 0, NULL); \
if (!(fd->atomicity)) ADIOI_READ_LOCK(fd, readbuf_off, SEEK_SET, readbuf_len); \
MPE_Log_event(ADIOI_MPE_read_a, 0, NULL); \
err = read(fd->fd_sys, readbuf, readbuf_len); \
MPE_Log_event(ADIOI_MPE_read_b, 0, NULL); \
if (!(fd->atomicity)) ADIOI_UNLOCK(fd, readbuf_off, SEEK_SET, readbuf_len); \
if (err == -1) err_flag = 1; \
} \
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 + MPL_MIN(max_bufsize, \
end_offset-readbuf_off+1)); \
MPE_Log_event(ADIOI_MPE_lseek_a, 0, NULL); \
lseek(fd->fd_sys, readbuf_off+partial_read, SEEK_SET); \
MPE_Log_event(ADIOI_MPE_lseek_b, 0, NULL); \
if (!(fd->atomicity)) ADIOI_READ_LOCK(fd, readbuf_off+partial_read, SEEK_SET, readbuf_len-partial_read); \
MPE_Log_event(ADIOI_MPE_read_a, 0, NULL); \
err = read(fd->fd_sys, readbuf+partial_read, readbuf_len-partial_read); \
MPE_Log_event(ADIOI_MPE_read_b, 0, NULL); \
if (!(fd->atomicity)) ADIOI_UNLOCK(fd, readbuf_off+partial_read, SEEK_SET, readbuf_len-partial_read); \
if (err == -1) err_flag = 1; \
} \
memcpy((char *)buf + userbuf_off, readbuf+req_off-readbuf_off, req_len); \
}
#else
#define ADIOI_BUFFERED_READ \
{ \
if (req_off >= readbuf_off + readbuf_len) { \
readbuf_off = req_off; \
readbuf_len = (int) (MPL_MIN(max_bufsize, end_offset-readbuf_off+1)); \
lseek(fd->fd_sys, readbuf_off, SEEK_SET); \
if (!(fd->atomicity)) ADIOI_READ_LOCK(fd, readbuf_off, SEEK_SET, readbuf_len); \
err = read(fd->fd_sys, readbuf, readbuf_len); \
if (!(fd->atomicity)) ADIOI_UNLOCK(fd, readbuf_off, SEEK_SET, readbuf_len); \
if (err == -1) err_flag = 1; \
} \
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 + MPL_MIN(max_bufsize, \
end_offset-readbuf_off+1)); \
lseek(fd->fd_sys, readbuf_off+partial_read, SEEK_SET); \
if (!(fd->atomicity)) ADIOI_READ_LOCK(fd, readbuf_off+partial_read, SEEK_SET, readbuf_len-partial_read); \
err = read(fd->fd_sys, readbuf+partial_read, readbuf_len-partial_read); \
if (!(fd->atomicity)) ADIOI_UNLOCK(fd, readbuf_off+partial_read, SEEK_SET, readbuf_len-partial_read); \
if (err == -1) err_flag = 1; \
} \
memcpy((char *)buf + userbuf_off, readbuf+req_off-readbuf_off, req_len); \
}
#endif
void ADIOI_NFS_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;
ADIO_Offset i_offset, new_brd_size, brd_size, size;
int i, j, k, err, err_flag = 0, st_index = 0;
MPI_Count num, bufsize;
int n_etypes_in_filetype;
ADIO_Offset n_filetypes, etype_in_filetype, st_n_filetypes, size_in_filetype;
ADIO_Offset abs_off_in_filetype = 0, new_frd_size, frd_size = 0, st_frd_size;
MPI_Count filetype_size, etype_size, buftype_size, partial_read;
MPI_Aint lb, filetype_extent, buftype_extent;
int buf_count, buftype_is_contig, filetype_is_contig;
ADIO_Offset userbuf_off, req_len, sum;
ADIO_Offset off, req_off, disp, end_offset = 0, readbuf_off, start_off;
char *readbuf, *tmp_buf, *value;
int info_flag;
unsigned max_bufsize, readbuf_len;
static char myname[] = "ADIOI_NFS_READSTRIDED";
ADIOI_Datatype_iscontig(datatype, &buftype_is_contig);
ADIOI_Datatype_iscontig(fd->filetype, &filetype_is_contig);
MPI_Type_size_x(fd->filetype, &filetype_size);
if (!filetype_size) {
#ifdef HAVE_STATUS_SET_BYTES
MPIR_Status_set_bytes(status, datatype, 0);
#endif
*error_code = MPI_SUCCESS;
return;
}
MPI_Type_get_extent(fd->filetype, &lb, &filetype_extent);
MPI_Type_size_x(datatype, &buftype_size);
MPI_Type_get_extent(datatype, &lb, &buftype_extent);
etype_size = fd->etype_size;
ADIOI_Assert((buftype_size * count) ==
((ADIO_Offset) (MPI_Count) buftype_size * (ADIO_Offset) count));
bufsize = buftype_size * count;
/* get max_bufsize from the info object. */
value = (char *) ADIOI_Malloc((MPI_MAX_INFO_VAL + 1) * sizeof(char));
ADIOI_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. */
flat_buf = ADIOI_Flatten_and_find(datatype);
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 = (unsigned) (MPL_MIN(max_bufsize, end_offset - readbuf_off + 1));
/* if atomicity is true, lock (exclusive) the region to be accessed */
if (fd->atomicity)
ADIOI_WRITE_LOCK(fd, start_off, SEEK_SET, end_offset - start_off + 1);
#ifdef ADIOI_MPE_LOGGING
MPE_Log_event(ADIOI_MPE_lseek_a, 0, NULL);
#endif
lseek(fd->fd_sys, readbuf_off, SEEK_SET);
#ifdef ADIOI_MPE_LOGGING
MPE_Log_event(ADIOI_MPE_lseek_b, 0, NULL);
#endif
if (!(fd->atomicity))
ADIOI_READ_LOCK(fd, readbuf_off, SEEK_SET, readbuf_len);
#ifdef ADIOI_MPE_LOGGING
MPE_Log_event(ADIOI_MPE_read_a, 0, NULL);
#endif
err = read(fd->fd_sys, readbuf, readbuf_len);
#ifdef ADIOI_MPE_LOGGING
MPE_Log_event(ADIOI_MPE_read_b, 0, NULL);
#endif
if (!(fd->atomicity))
ADIOI_UNLOCK(fd, readbuf_off, SEEK_SET, readbuf_len);
if (err == -1)
err_flag = 1;
for (j = 0; j < count; j++)
for (i = 0; i < flat_buf->count; i++) {
userbuf_off = (ADIO_Offset) 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)
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 */
if (err_flag) {
*error_code = MPIO_Err_create_code(MPI_SUCCESS,
MPIR_ERR_RECOVERABLE, myname,
__LINE__, MPI_ERR_IO, "**io",
"**io %s", strerror(errno));
} else
*error_code = MPI_SUCCESS;
}
else { /* noncontiguous in file */
flat_file = ADIOI_Flatten_and_find(fd->filetype);
disp = fd->disp;
if (file_ptr_type == ADIO_INDIVIDUAL) {
/* Wei-keng reworked type processing to be a bit more efficient */
offset = fd->fp_ind - disp;
n_filetypes = (offset - flat_file->indices[0]) / filetype_extent;
offset -= (ADIO_Offset) n_filetypes *filetype_extent;
/* now offset is local to this extent */
/* find the block where offset is located, skip blocklens[i]==0 */
for (i = 0; i < flat_file->count; i++) {
ADIO_Offset dist;
if (flat_file->blocklens[i] == 0)
continue;
dist = flat_file->indices[i] + flat_file->blocklens[i] - offset;
/* frd_size is from offset to the end of block i */
if (dist == 0) {
i++;
offset = flat_file->indices[i];
frd_size = flat_file->blocklens[i];
break;
}
if (dist > 0) {
frd_size = dist;
break;
}
}
st_index = i; /* starting index in flat_file->indices[] */
offset += disp + (ADIO_Offset) n_filetypes *filetype_extent;
} else {
n_etypes_in_filetype = filetype_size / etype_size;
n_filetypes = offset / n_etypes_in_filetype;
etype_in_filetype = 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;
/* Wei-keng Liao: read request is within a single flat_file contig
* block e.g. with subarray types that actually describe the whole
* array */
if (buftype_is_contig && bufsize <= frd_size) {
/* a count of bytes can overflow. operate on original type instead */
ADIO_ReadContig(fd, buf, count, datatype, ADIO_EXPLICIT_OFFSET,
offset, status, error_code);
if (file_ptr_type == ADIO_INDIVIDUAL) {
/* update MPI-IO file pointer to point to the first byte that
* can be accessed in the fileview. */
fd->fp_ind = offset + bufsize;
if (bufsize == frd_size) {
do {
st_index++;
if (st_index == flat_file->count) {
st_index = 0;
n_filetypes++;
}
} while (flat_file->blocklens[st_index] == 0);
fd->fp_ind = disp + flat_file->indices[st_index]
+ n_filetypes * filetype_extent;
}
}
fd->fp_sys_posn = -1; /* set it to null. */
#ifdef HAVE_STATUS_SET_BYTES
MPIR_Status_set_bytes(status, datatype, bufsize);
#endif
return;
}
/* 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_offset = 0;
j = st_index;
off = offset;
frd_size = MPL_MIN(st_frd_size, bufsize);
while (i_offset < bufsize) {
i_offset += frd_size;
end_offset = off + frd_size - 1;
j = (j + 1) % flat_file->count;
n_filetypes += (j == 0) ? 1 : 0;
while (flat_file->blocklens[j] == 0) {
j = (j + 1) % flat_file->count;
n_filetypes += (j == 0) ? 1 : 0;
}
off = disp + flat_file->indices[j] + n_filetypes * (ADIO_Offset) filetype_extent;
frd_size = MPL_MIN(flat_file->blocklens[j], bufsize - i_offset);
}
/* if atomicity is true, lock (exclusive) the region to be accessed */
if (fd->atomicity)
ADIOI_WRITE_LOCK(fd, start_off, SEEK_SET, end_offset - start_off + 1);
/* initial read into readbuf */
readbuf_off = offset;
readbuf = (char *) ADIOI_Malloc(max_bufsize);
readbuf_len = (int) (MPL_MIN(max_bufsize, end_offset - readbuf_off + 1));
#ifdef ADIOI_MPE_LOGGING
MPE_Log_event(ADIOI_MPE_lseek_a, 0, NULL);
#endif
lseek(fd->fd_sys, offset, SEEK_SET);
#ifdef ADIOI_MPE_LOGGING
MPE_Log_event(ADIOI_MPE_lseek_b, 0, NULL);
#endif
if (!(fd->atomicity))
ADIOI_READ_LOCK(fd, offset, SEEK_SET, readbuf_len);
#ifdef ADIOI_MPE_LOGGING
MPE_Log_event(ADIOI_MPE_read_a, 0, NULL);
#endif
err = read(fd->fd_sys, readbuf, readbuf_len);
#ifdef ADIOI_MPE_LOGGING
MPE_Log_event(ADIOI_MPE_read_b, 0, NULL);
#endif
if (!(fd->atomicity))
ADIOI_UNLOCK(fd, offset, SEEK_SET, readbuf_len);
if (err == -1)
err_flag = 1;
if (buftype_is_contig && !filetype_is_contig) {
/* contiguous in memory, noncontiguous in file. should be the most
common case. */
i_offset = 0;
j = st_index;
off = offset;
n_filetypes = st_n_filetypes;
frd_size = MPL_MIN(st_frd_size, bufsize);
while (i_offset < 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_offset;
ADIOI_BUFFERED_READ}
i_offset += frd_size;
if (off + frd_size < disp + flat_file->indices[j] +
flat_file->blocklens[j] + n_filetypes * (ADIO_Offset) 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 {
j = (j + 1) % flat_file->count;
n_filetypes += (j == 0) ? 1 : 0;
while (flat_file->blocklens[j] == 0) {
j = (j + 1) % flat_file->count;
n_filetypes += (j == 0) ? 1 : 0;
}
off = disp + flat_file->indices[j] +
n_filetypes * (ADIO_Offset) filetype_extent;
frd_size = MPL_MIN(flat_file->blocklens[j], bufsize - i_offset);
}
}
} else {
/* noncontiguous in memory as well as in file */
flat_buf = ADIOI_Flatten_and_find(datatype);
k = num = buf_count = 0;
i_offset = 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 = MPL_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_offset;
ADIOI_BUFFERED_READ}
new_frd_size = frd_size;
new_brd_size = brd_size;
if (size == frd_size) {
/* reached end of contiguous block in file */
j = (j + 1) % flat_file->count;
n_filetypes += (j == 0) ? 1 : 0;
while (flat_file->blocklens[j] == 0) {
j = (j + 1) % flat_file->count;
n_filetypes += (j == 0) ? 1 : 0;
}
off = disp + flat_file->indices[j] +
n_filetypes * (ADIO_Offset) filetype_extent;
new_frd_size = flat_file->blocklens[j];
if (size != brd_size) {
i_offset += 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_offset = 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)
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 */
if (err_flag) {
*error_code = MPIO_Err_create_code(MPI_SUCCESS,
MPIR_ERR_RECOVERABLE, myname,
__LINE__, MPI_ERR_IO, "**io",
"**io %s", strerror(errno));
} else
*error_code = MPI_SUCCESS;
}
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
}
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