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Merge pull request #3488 from ggouaillardet/topic/romio314_ad_nfs

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romio314: ad_nfs fixes for large files from upstream mpich
Этот коммит содержится в:
Gilles Gouaillardet 2017-05-09 16:58:02 +09:00 коммит произвёл GitHub
родитель 26f44da429 eaf050cfe1
Коммит a66909b8b4
2 изменённых файлов: 100 добавлений и 117 удалений
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116
ompi/mca/io/romio314/romio/adio/ad_nfs/ad_nfs_read.c
Просмотреть файл

@ -7,79 +7,68 @@
#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)
{
int err=-1;
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;
MPI_Type_size_x(datatype, &datatype_size);
len = datatype_size * count;
if (file_ptr_type == ADIO_EXPLICIT_OFFSET) {
if (fd->fp_sys_posn != offset) {
#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_WRITE_LOCK(fd, offset, SEEK_SET, len);
else ADIOI_READ_LOCK(fd, offset, SEEK_SET, len);
#ifdef ADIOI_MPE_LOGGING
MPE_Log_event( ADIOI_MPE_read_a, 0, NULL );
#endif
err = read(fd->fd_sys, buf, len);
#ifdef ADIOI_MPE_LOGGING
MPE_Log_event( ADIOI_MPE_read_b, 0, NULL );
#endif
ADIOI_UNLOCK(fd, offset, SEEK_SET, len);
fd->fp_sys_posn = offset + err;
/* individual file pointer not updated */
}
else { /* read from curr. location of ind. file pointer */
if (file_ptr_type == ADIO_INDIVIDUAL) {
offset = fd->fp_ind;
if (fd->fp_sys_posn != fd->fp_ind) {
#ifdef ADIOI_MPE_LOGGING
MPE_Log_event( ADIOI_MPE_lseek_a, 0, NULL );
#endif
lseek(fd->fd_sys, fd->fp_ind, SEEK_SET);
#ifdef ADIOI_MPE_LOGGING
MPE_Log_event( ADIOI_MPE_lseek_b, 0, NULL );
#endif
}
if (fd->atomicity)
ADIOI_WRITE_LOCK(fd, offset, SEEK_SET, len);
else ADIOI_READ_LOCK(fd, offset, SEEK_SET, len);
#ifdef ADIOI_MPE_LOGGING
MPE_Log_event( ADIOI_MPE_read_a, 0, NULL );
#endif
err = read(fd->fd_sys, buf, len);
#ifdef ADIOI_MPE_LOGGING
MPE_Log_event( ADIOI_MPE_read_b, 0, NULL );
#endif
ADIOI_UNLOCK(fd, offset, SEEK_SET, len);
fd->fp_ind += err;
fd->fp_sys_posn = fd->fp_ind;
}
/* --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));
return;
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;
}
/* --END ERROR HANDLING-- */
#ifdef HAVE_STATUS_SET_BYTES
MPIR_Status_set_bytes(status, datatype, err);
if (err != -1) MPIR_Status_set_bytes(status, datatype, bytes_xfered);
#endif
*error_code = MPI_SUCCESS;
@ -168,8 +157,9 @@ void ADIOI_NFS_ReadStrided(ADIO_File fd, void *buf, int count,
/* offset is in units of etype relative to the filetype. */
ADIOI_Flatlist_node *flat_buf, *flat_file;
int i, j, k, err=-1, brd_size, frd_size=0, st_index=0;
int bufsize, num, size, sum, n_etypes_in_filetype, size_in_filetype;
int i, j, k, err=-1, brd_size, st_index=0;
int num, size, sum, n_etypes_in_filetype, size_in_filetype;
MPI_Count bufsize;
int n_filetypes, etype_in_filetype;
ADIO_Offset abs_off_in_filetype=0;
int req_len, partial_read;
@ -179,8 +169,9 @@ void ADIOI_NFS_ReadStrided(ADIO_File fd, void *buf, int count,
ADIO_Offset userbuf_off;
ADIO_Offset off, req_off, disp, end_offset=0, readbuf_off, start_off;
char *readbuf, *tmp_buf, *value;
int st_frd_size, st_n_filetypes, readbuf_len;
int new_brd_size, new_frd_size, err_flag=0, info_flag, max_bufsize;
int st_n_filetypes, readbuf_len;
ADIO_Offset frd_size=0, new_frd_size, st_frd_size;
int new_brd_size, err_flag=0, info_flag, max_bufsize;
static char myname[] = "ADIOI_NFS_READSTRIDED";
@ -460,12 +451,13 @@ void ADIOI_NFS_ReadStrided(ADIO_File fd, void *buf, int count,
else {
/* noncontiguous in memory as well as in file */
ADIO_Offset i;
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]);
i = flat_buf->indices[0];
j = st_index;
off = offset;
n_filetypes = st_n_filetypes;
@ -510,8 +502,8 @@ void ADIOI_NFS_ReadStrided(ADIO_File fd, void *buf, int count,
k = (k + 1)%flat_buf->count;
buf_count++;
i = (int) (buftype_extent*(buf_count/flat_buf->count) +
flat_buf->indices[k]);
i = buftype_extent*(buf_count/flat_buf->count) +
flat_buf->indices[k];
new_brd_size = flat_buf->blocklens[k];
if (size != frd_size) {
off += size;

101
ompi/mca/io/romio314/romio/adio/ad_nfs/ad_nfs_write.c
Просмотреть файл

@ -7,76 +7,64 @@
#include "ad_nfs.h"
#include "adio_extern.h"
#ifdef HAVE_UNISTD_H
#include <unistd.h>
#endif
void ADIOI_NFS_WriteContig(ADIO_File fd, const void *buf, int count,
MPI_Datatype datatype, int file_ptr_type,
ADIO_Offset offset, ADIO_Status *status, int *error_code)
{
int err=-1;
ssize_t err=-1;
MPI_Count datatype_size, len;
ADIO_Offset bytes_xfered=0;
size_t wr_count;
static char myname[] = "ADIOI_NFS_WRITECONTIG";
char *p;
MPI_Type_size_x(datatype, &datatype_size);
len = datatype_size * count;
len = datatype_size * (ADIO_Offset)count;
if (file_ptr_type == ADIO_EXPLICIT_OFFSET) {
if (fd->fp_sys_posn != offset) {
#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
}
ADIOI_WRITE_LOCK(fd, offset, SEEK_SET, len);
#ifdef ADIOI_MPE_LOGGING
MPE_Log_event( ADIOI_MPE_write_a, 0, NULL );
#endif
err = write(fd->fd_sys, buf, len);
#ifdef ADIOI_MPE_LOGGING
MPE_Log_event( ADIOI_MPE_write_b, 0, NULL );
#endif
ADIOI_UNLOCK(fd, offset, SEEK_SET, len);
fd->fp_sys_posn = offset + err;
/* individual file pointer not updated */
}
else { /* write from curr. location of ind. file pointer */
if (file_ptr_type == ADIO_INDIVIDUAL) {
offset = fd->fp_ind;
if (fd->fp_sys_posn != fd->fp_ind) {
#ifdef ADIOI_MPE_LOGGING
MPE_Log_event( ADIOI_MPE_lseek_a, 0, NULL );
#endif
lseek(fd->fd_sys, fd->fp_ind, SEEK_SET);
#ifdef ADIOI_MPE_LOGGING
MPE_Log_event( ADIOI_MPE_lseek_b, 0, NULL );
#endif
}
ADIOI_WRITE_LOCK(fd, offset, SEEK_SET, len);
}
p = (char *)buf;
while (bytes_xfered < len) {
#ifdef ADIOI_MPE_LOGGING
MPE_Log_event( ADIOI_MPE_write_a, 0, NULL );
#endif
err = write(fd->fd_sys, buf, len);
wr_count = len - bytes_xfered;
/* work around FreeBSD and OS X defects*/
if (wr_count > INT_MAX)
wr_count = INT_MAX;
ADIOI_WRITE_LOCK(fd, offset+bytes_xfered, SEEK_SET, wr_count);
err = pwrite(fd->fd_sys, p, wr_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));
fd->fp_sys_posn = -1;
return;
}
/* --END ERROR HANDLING-- */
#ifdef ADIOI_MPE_LOGGING
MPE_Log_event( ADIOI_MPE_write_b, 0, NULL );
#endif
ADIOI_UNLOCK(fd, offset, SEEK_SET, len);
fd->fp_ind += err;
fd->fp_sys_posn = fd->fp_ind;
ADIOI_UNLOCK(fd, offset+bytes_xfered, SEEK_SET, wr_count);
bytes_xfered += err;
p += err;
}
/* --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));
return;
if (file_ptr_type == ADIO_INDIVIDUAL) {
fd->fp_ind += bytes_xfered;
}
/* --END ERROR HANDLING-- */
#ifdef HAVE_STATUS_SET_BYTES
MPIR_Status_set_bytes(status, datatype, err);
MPIR_Status_set_bytes(status, datatype, bytes_xfered);
#endif
*error_code = MPI_SUCCESS;
@ -272,8 +260,9 @@ void ADIOI_NFS_WriteStrided(ADIO_File fd, const void *buf, int count,
/* offset is in units of etype relative to the filetype. */
ADIOI_Flatlist_node *flat_buf, *flat_file;
int i, j, k, err=-1, bwr_size, fwr_size=0, st_index=0;
int bufsize, num, size, sum, n_etypes_in_filetype, size_in_filetype;
int i, j, k, err=-1, bwr_size, st_index=0;
int num, size, sum, n_etypes_in_filetype, size_in_filetype;
MPI_Count bufsize;
int n_filetypes, etype_in_filetype;
ADIO_Offset abs_off_in_filetype=0;
int req_len;
@ -283,8 +272,9 @@ void ADIOI_NFS_WriteStrided(ADIO_File fd, const void *buf, int count,
ADIO_Offset userbuf_off;
ADIO_Offset off, req_off, disp, end_offset=0, writebuf_off, start_off;
char *writebuf=NULL, *value;
int st_fwr_size, st_n_filetypes, writebuf_len, write_sz;
int new_bwr_size, new_fwr_size, err_flag=0, info_flag, max_bufsize;
int st_n_filetypes, writebuf_len, write_sz;
ADIO_Offset fwr_size = 0, new_fwr_size, st_fwr_size;
int new_bwr_size, err_flag=0, info_flag, max_bufsize;
static char myname[] = "ADIOI_NFS_WRITESTRIDED";
ADIOI_Datatype_iscontig(datatype, &buftype_is_contig);
@ -565,12 +555,13 @@ void ADIOI_NFS_WriteStrided(ADIO_File fd, const void *buf, int count,
else {
/* noncontiguous in memory as well as in file */
ADIO_Offset i;
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]);
i = flat_buf->indices[0];
j = st_index;
off = offset;
n_filetypes = st_n_filetypes;
@ -616,8 +607,8 @@ void ADIOI_NFS_WriteStrided(ADIO_File fd, const void *buf, int count,
k = (k + 1)%flat_buf->count;
buf_count++;
i = (int) (buftype_extent*(buf_count/flat_buf->count) +
flat_buf->indices[k]);
i = buftype_extent*(buf_count/flat_buf->count) +
flat_buf->indices[k];
new_bwr_size = flat_buf->blocklens[k];
if (size != fwr_size) {
off += size;