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Merge pull request #1279 from edgargabriel/pr/plfs-fixes-2

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fixes for the PLFS file system
Этот коммит содержится в:
Edgar Gabriel 2016-01-05 12:57:24 -06:00
родитель 6d073a8da4 1b0b849994
Коммит d827da5736
6 изменённых файлов: 25 добавлений и 185 удалений
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86
ompi/mca/fbtl/plfs/fbtl_plfs_preadv.c
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@ -28,74 +28,19 @@
ssize_t mca_fbtl_plfs_preadv (mca_io_ompio_file_t *fh ) ssize_t mca_fbtl_plfs_preadv (mca_io_ompio_file_t *fh )
{ {
Plfs_fd *pfd = NULL; Plfs_fd *pfd = fh->f_fs_ptr;
plfs_error_t plfs_ret; plfs_error_t plfs_ret;
pfd = fh->f_fs_ptr;
ssize_t total_bytes_read=0; ssize_t total_bytes_read=0;
int i;
int i, block=1; ssize_t bytes_read;
struct iovec *iov = NULL;
int iov_count = 0;
OMPI_MPI_OFFSET_TYPE iov_offset = 0;
if (NULL == fh->f_io_array) { if (NULL == fh->f_io_array) {
return OMPI_ERROR; return OMPI_ERROR;
} }
iov = (struct iovec *) malloc
(OMPIO_IOVEC_INITIAL_SIZE * sizeof (struct iovec));
if (NULL == iov) {
opal_output(1, "OUT OF MEMORY\n");
return OMPI_ERR_OUT_OF_RESOURCE;
}
for (i=0 ; i<fh->f_num_of_io_entries ; i++) { for (i=0 ; i<fh->f_num_of_io_entries ; i++) {
if (0 == iov_count) { plfs_ret = plfs_read( pfd, fh->f_io_array[i].memory_address, fh->f_io_array[i].length,
iov[iov_count].iov_base = fh->f_io_array[i].memory_address; (off_t )fh->f_io_array[i].offset, &bytes_read );
iov[iov_count].iov_len = fh->f_io_array[i].length;
iov_offset = (OMPI_MPI_OFFSET_TYPE)(intptr_t)fh->f_io_array[i].offset;
iov_count ++;
}
if (OMPIO_IOVEC_INITIAL_SIZE*block <= iov_count) {
block ++;
iov = (struct iovec *)realloc
(iov, OMPIO_IOVEC_INITIAL_SIZE * block *
sizeof(struct iovec));
if (NULL == iov) {
opal_output(1, "OUT OF MEMORY\n");
return OMPI_ERR_OUT_OF_RESOURCE;
}
}
if (fh->f_num_of_io_entries != i+1) {
if (((OMPI_MPI_OFFSET_TYPE)(intptr_t)fh->f_io_array[i].offset +
(OPAL_PTRDIFF_TYPE)fh->f_io_array[i].length) ==
(OMPI_MPI_OFFSET_TYPE)(intptr_t)fh->f_io_array[i+1].offset) {
iov[iov_count].iov_base =
fh->f_io_array[i+1].memory_address;
iov[iov_count].iov_len = fh->f_io_array[i+1].length;
iov_count ++;
continue;
}
}
// Find the total number of bytes to be read.
size_t bytes = 0;
for (int i = 0; i < iov_count; ++i) {
bytes += iov[i].iov_len;
}
// Allocate a temporary buffer to hold the data
char *buffer;
buffer = (char *) malloc (bytes);
if (buffer == NULL) {
return OMPI_ERROR;
}
// Read the data
ssize_t bytes_read;
plfs_ret = plfs_read( pfd, buffer, bytes, iov_offset, &bytes_read );
if (PLFS_SUCCESS != plfs_ret) { if (PLFS_SUCCESS != plfs_ret) {
opal_output(0, "fbtl_plfs_preadv: Error in plfs_read:\n%s\n", strplfserr(plfs_ret)); opal_output(0, "fbtl_plfs_preadv: Error in plfs_read:\n%s\n", strplfserr(plfs_ret));
return OMPI_ERROR; return OMPI_ERROR;
@ -104,27 +49,6 @@ ssize_t mca_fbtl_plfs_preadv (mca_io_ompio_file_t *fh )
if (bytes_read < 0) if (bytes_read < 0)
return OMPI_ERROR; return OMPI_ERROR;
total_bytes_read += bytes_read; total_bytes_read += bytes_read;
// Copy the data from BUFFER into the memory specified by IOV
bytes = bytes_read;
for (int i = 0; i < iov_count; ++i) {
size_t copy = MIN (iov[i].iov_len, bytes);
(void) memcpy ((void *) iov[i].iov_base, (void *) buffer, copy);
buffer += copy;
bytes -= copy;
if (bytes == 0) {
break;
}
}
iov_count = 0;
if ( NULL != buffer ) {
free (buffer);
buffer=NULL;
}
}
if (NULL != iov) {
free (iov);
iov = NULL;
} }
return total_bytes_read; return total_bytes_read;

90
ompi/mca/fbtl/plfs/fbtl_plfs_pwritev.c
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@ -28,102 +28,26 @@
ssize_t mca_fbtl_plfs_pwritev (mca_io_ompio_file_t *fh ) ssize_t mca_fbtl_plfs_pwritev (mca_io_ompio_file_t *fh )
{ {
Plfs_fd *pfd = NULL; Plfs_fd *pfd = fh->f_fs_ptr;
plfs_error_t plfs_ret; plfs_error_t plfs_ret;
pfd = fh->f_fs_ptr;
ssize_t total_bytes_written=0; ssize_t total_bytes_written=0;
ssize_t bytes_written;
int i, block = 1; int i;
struct iovec *iov = NULL;
int iov_count = 0;
OMPI_MPI_OFFSET_TYPE iov_offset = 0;
if (NULL == fh->f_io_array) { if (NULL == fh->f_io_array) {
return OMPI_ERROR; return OMPI_ERROR;
} }
iov = (struct iovec *) malloc
(OMPIO_IOVEC_INITIAL_SIZE * sizeof (struct iovec));
if (NULL == iov) {
opal_output(1, "OUT OF MEMORY\n");
return OMPI_ERR_OUT_OF_RESOURCE;
}
for (i=0 ; i<fh->f_num_of_io_entries ; i++) { for (i=0 ; i<fh->f_num_of_io_entries ; i++) {
if (0 == iov_count) { plfs_ret = plfs_write( pfd, fh->f_io_array[i].memory_address,
iov[iov_count].iov_base = fh->f_io_array[i].memory_address; fh->f_io_array[i].length,
iov[iov_count].iov_len = fh->f_io_array[i].length; (off_t) fh->f_io_array[i].offset,
iov_offset = (OMPI_MPI_OFFSET_TYPE)(intptr_t)fh->f_io_array[i].offset; fh->f_rank, &bytes_written );
iov_count ++;
}
if (OMPIO_IOVEC_INITIAL_SIZE*block <= iov_count) {
block ++;
iov = (struct iovec *)realloc
(iov, OMPIO_IOVEC_INITIAL_SIZE * block *
sizeof(struct iovec));
if (NULL == iov) {
opal_output(1, "OUT OF MEMORY\n");
return OMPI_ERR_OUT_OF_RESOURCE;
}
}
if (fh->f_num_of_io_entries != i+1) {
if (((OMPI_MPI_OFFSET_TYPE)(intptr_t)fh->f_io_array[i].offset +
(OPAL_PTRDIFF_TYPE)fh->f_io_array[i].length) ==
(OMPI_MPI_OFFSET_TYPE)(intptr_t)fh->f_io_array[i+1].offset) {
iov[iov_count].iov_base =
fh->f_io_array[i+1].memory_address;
iov[iov_count].iov_len = fh->f_io_array[i+1].length;
iov_count ++;
continue;
}
}
// Find the total number of bytes to be written.
size_t bytes = 0;
for (int i = 0; i < iov_count; ++i) {
bytes += iov[i].iov_len;
}
// Allocate a temporary buffer to hold the data
char *buffer=NULL;
buffer = (char *) malloc (bytes);
if (buffer == NULL) {
return OMPI_ERROR;
}
// Copy the data into BUFFER.
size_t to_copy = bytes;
char *bp = buffer;
for (int i = 0; i < iov_count; ++i) {
size_t copy = MIN (iov[i].iov_len, to_copy);
bp = mempcpy ((void *) bp, (void *) iov[i].iov_base, copy);
to_copy -= copy;
if (to_copy == 0) {
break;
}
}
// Write the data
ssize_t bytes_written;
plfs_ret = plfs_write( pfd, buffer, bytes, iov_offset, 0, &bytes_written );
if (PLFS_SUCCESS != plfs_ret) { if (PLFS_SUCCESS != plfs_ret) {
opal_output(0, "fbtl_plfs_pwritev: Error in plfs_write:\n%s\n", strplfserr(plfs_ret)); opal_output(0, "fbtl_plfs_pwritev: Error in plfs_write:\n%s\n", strplfserr(plfs_ret));
return OMPI_ERROR; return OMPI_ERROR;
} }
total_bytes_written += bytes_written; total_bytes_written += bytes_written;
iov_count = 0;
if ( NULL != buffer ) {
free ( buffer );
buffer=NULL;
}
}
if (NULL != iov) {
free (iov);
iov = NULL;
} }
return total_bytes_written; return total_bytes_written;

1
ompi/mca/fs/plfs/fs_plfs.h
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@ -30,7 +30,6 @@
#include <plfs.h> #include <plfs.h>
extern int mca_fs_plfs_priority; extern int mca_fs_plfs_priority;
extern int mca_fs_plfs_num_hostdir;
BEGIN_C_DECLS BEGIN_C_DECLS

7
ompi/mca/fs/plfs/fs_plfs_component.c
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@ -39,7 +39,6 @@ const char *mca_fs_plfs_component_version_string =
static int plfs_register(void); static int plfs_register(void);
int mca_fs_plfs_priority = 20; int mca_fs_plfs_priority = 20;
int mca_fs_plfs_num_hostdir = -1;
/* /*
* Instantiate the public struct with all of our public information * Instantiate the public struct with all of our public information
@ -77,12 +76,6 @@ plfs_register(void)
MCA_BASE_VAR_TYPE_INT, NULL, 0, 0, MCA_BASE_VAR_TYPE_INT, NULL, 0, 0,
OPAL_INFO_LVL_9, OPAL_INFO_LVL_9,
MCA_BASE_VAR_SCOPE_READONLY, &mca_fs_plfs_priority); MCA_BASE_VAR_SCOPE_READONLY, &mca_fs_plfs_priority);
mca_fs_plfs_num_hostdir = -1;
(void) mca_base_component_var_register(&mca_fs_plfs_component.fsm_version,
"num_hostdir", "number of host directories of a file over plfs",
MCA_BASE_VAR_TYPE_INT, NULL, 0, 0,
OPAL_INFO_LVL_9,
MCA_BASE_VAR_SCOPE_READONLY, &mca_fs_plfs_num_hostdir);
return OMPI_SUCCESS; return OMPI_SUCCESS;
} }

13
ompi/mca/fs/plfs/fs_plfs_file_close.c
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@ -49,7 +49,9 @@ mca_fs_plfs_file_close (mca_io_ompio_file_t *fh)
getcwd( wpath, sizeof(wpath) ); getcwd( wpath, sizeof(wpath) );
sprintf( wpath,"%s/%s",wpath,fh->f_filename ); sprintf( wpath,"%s/%s",wpath,fh->f_filename );
if(-1 == access(fh->f_filename, F_OK)) { plfs_ret = plfs_access(wpath, F_OK);
if ( PLFS_SUCCESS != plfs_ret ) {
opal_output(0, "fs_plfs_file_close: Error in plfs_access:\n%s\n", strplfserr(plfs_ret));
return OMPI_ERROR; // file doesn't exist return OMPI_ERROR; // file doesn't exist
} }
@ -66,7 +68,14 @@ mca_fs_plfs_file_close (mca_io_ompio_file_t *fh)
return OMPI_ERROR; return OMPI_ERROR;
} }
plfs_ret = plfs_close(fh->f_fs_ptr, 0, 0, amode ,NULL, &flags); plfs_ret = plfs_sync(fh->f_fs_ptr);
if (PLFS_SUCCESS != plfs_ret) {
opal_output(0, "fs_plfs_file_close: Error in plfs_sync:\n%s\n", strplfserr(plfs_ret));
return OMPI_ERROR;
}
plfs_ret = plfs_close(fh->f_fs_ptr, fh->f_rank, 0, amode ,NULL, &flags);
if (PLFS_SUCCESS != plfs_ret) { if (PLFS_SUCCESS != plfs_ret) {
opal_output(0, "fs_plfs_file_close: Error in plfs_close:\n%s\n", strplfserr(plfs_ret)); opal_output(0, "fs_plfs_file_close: Error in plfs_close:\n%s\n", strplfserr(plfs_ret));
return OMPI_ERROR; return OMPI_ERROR;

13
ompi/mca/fs/plfs/fs_plfs_file_open.c
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@ -53,8 +53,6 @@ mca_fs_plfs_file_open (struct ompi_communicator_t *comm,
plfs_error_t plfs_ret; plfs_error_t plfs_ret;
Plfs_fd *pfd = NULL; Plfs_fd *pfd = NULL;
char wpath[1024]; char wpath[1024];
size_t len = sizeof(int);
char key[] = "num_hostdirs";
rank = ompi_comm_rank ( comm ); rank = ompi_comm_rank ( comm );
@ -89,7 +87,7 @@ mca_fs_plfs_file_open (struct ompi_communicator_t *comm,
if (access_mode & MPI_MODE_CREATE) if (access_mode & MPI_MODE_CREATE)
amode = amode | O_CREAT; amode = amode | O_CREAT;
plfs_ret = plfs_open( &pfd, wpath, amode, 0, perm, NULL ); plfs_ret = plfs_open( &pfd, wpath, amode, fh->f_rank, perm, NULL );
fh->f_fs_ptr = pfd; fh->f_fs_ptr = pfd;
} }
@ -99,7 +97,7 @@ mca_fs_plfs_file_open (struct ompi_communicator_t *comm,
} }
if (0 != rank) { if (0 != rank) {
plfs_ret = plfs_open( &pfd, wpath, amode, 0, perm, NULL ); plfs_ret = plfs_open( &pfd, wpath, amode, fh->f_rank, perm, NULL );
if (PLFS_SUCCESS != plfs_ret) { if (PLFS_SUCCESS != plfs_ret) {
opal_output(0, "fs_plfs_file_open: Error in plfs_open:\n%s\n", strplfserr(plfs_ret)); opal_output(0, "fs_plfs_file_open: Error in plfs_open:\n%s\n", strplfserr(plfs_ret));
return OMPI_ERROR; return OMPI_ERROR;
@ -109,12 +107,5 @@ mca_fs_plfs_file_open (struct ompi_communicator_t *comm,
} }
} }
if (mca_fs_plfs_num_hostdir > 0) {
plfs_ret = plfs_setxattr( pfd, &mca_fs_plfs_num_hostdir, key, len );
if (PLFS_SUCCESS != plfs_ret) {
opal_output(0, "fs_plfs_file_open: Error in plfs_setxattr:\n%s\n", strplfserr(plfs_ret));
return OMPI_ERROR;
}
}
return OMPI_SUCCESS; return OMPI_SUCCESS;
} }