/* given a filename, its meta data, its list of segments, and list of destination containers,
* copy file to container files */
static int scr_flush_file_to_containers(
const char* file,
scr_meta* meta,
scr_hash* segments,
const char* dst_dir)
{
/* check that we got something for a source file */
if (file == NULL || strcmp(file, "") == 0) {
scr_err("Invalid source file @ %s:%d",
__FILE__, __LINE__
);
return SCR_FAILURE;
}
/* check that our other arguments are valid */
if (meta == NULL || segments == NULL) {
scr_err("Invalid metadata or segments @ %s:%d",
__FILE__, __LINE__
);
return SCR_FAILURE;
}
/* open the file for reading */
int fd_src = scr_open(file, O_RDONLY);
if (fd_src < 0) {
scr_err("Opening file to copy: scr_open(%s) errno=%d %s @ %s:%d",
file, errno, strerror(errno), __FILE__, __LINE__
);
return SCR_FAILURE;
}
#if !defined(__APPLE__)
/* TODO:
posix_fadvise(fd, 0, 0, POSIX_FADV_DONTNEED | POSIX_FADV_SEQUENTIAL)
that tells the kernel that you don't ever need the pages
from the file again, and it won't bother keeping them in the page cache.
*/
posix_fadvise(fd_src, 0, 0, POSIX_FADV_DONTNEED | POSIX_FADV_SEQUENTIAL);
#endif
/* get the buffer size we'll use to write to the file */
unsigned long buf_size = scr_file_buf_size;
/* allocate buffer to read in file chunks */
char* buf = (char*) SCR_MALLOC(buf_size);
/* initialize crc value */
uLong crc;
if (scr_crc_on_flush) {
crc = crc32(0L, Z_NULL, 0);
}
int rc = SCR_SUCCESS;
/* write out each segment */
scr_hash_sort_int(segments, SCR_HASH_SORT_ASCENDING);
scr_hash_elem* elem;
for (elem = scr_hash_elem_first(segments);
elem != NULL;
elem = scr_hash_elem_next(elem))
{
/* get the container info for this segment */
scr_hash* hash = scr_hash_elem_hash(elem);
/* get the offset into the container and the length of the segment (both in bytes) */
char* container_name;
unsigned long container_offset, segment_length;
if (scr_container_get_name_offset_length(hash,
&container_name, &container_offset, &segment_length) != SCR_SUCCESS)
{
scr_err("Failed to get segment offset and length @ %s:%d",
__FILE__, __LINE__
);
rc = SCR_FAILURE;
break;
}
/* build full name to destination file */
scr_path* dst_path = scr_path_from_str(dst_dir);
scr_path_append_str(dst_path, container_name);
scr_path_reduce(dst_path);
char* dst_file = scr_path_strdup(dst_path);
/* open container file for writing -- we don't truncate here because more than one
* process may be writing to the same file */
int fd_container = scr_open(dst_file, O_WRONLY);
if (fd_container < 0) {
scr_err("Opening file for writing: scr_open(%s) errno=%d %s @ %s:%d",
dst_file, errno, strerror(errno), __FILE__, __LINE__
);
rc = SCR_FAILURE;
break;
}
#if !defined(__APPLE__)
/* TODO:
posix_fadvise(fd, 0, 0, POSIX_FADV_DONTNEED | POSIX_FADV_SEQUENTIAL)
that tells the kernel that you don't ever need the pages
from the file again, and it won't bother keeping them in the page cache.
*/
posix_fadvise(fd_container, 0, 0, POSIX_FADV_DONTNEED | POSIX_FADV_SEQUENTIAL);
#endif
/* seek to offset within container */
off_t pos = (off_t) container_offset;
if (lseek(fd_container, pos, SEEK_SET) == (off_t)-1) {
/* our seek failed, return an error */
scr_err("Failed to seek to byte %lu in %s @ %s:%d",
pos, dst_file, __FILE__, __LINE__
);
rc = SCR_FAILURE;
break;
}
/* copy data from file into container in chunks */
unsigned long remaining = segment_length;
while (remaining > 0) {
/* read / write up to buf_size bytes at a time from file */
unsigned long count = remaining;
if (count > buf_size) {
count = buf_size;
}
/* attempt to read buf_size bytes from file */
int nread = scr_read_attempt(file, fd_src, buf, count);
/* if we read some bytes, write them out */
if (nread > 0) {
/* optionally compute crc value as we go */
if (scr_crc_on_flush) {
crc = crc32(crc, (const Bytef*) buf, (uInt) nread);
}
/* write our nread bytes out */
int nwrite = scr_write_attempt(dst_file, fd_container, buf, nread);
/* check for a write error or a short write */
if (nwrite != nread) {
/* write had a problem, stop copying and return an error */
rc = SCR_FAILURE;
break;
}
/* subtract the bytes we've processed from the number remaining */
remaining -= (unsigned long) nread;
}
/* assume a short read is an error */
if (nread < count) {
/* read had a problem, stop copying and return an error */
rc = SCR_FAILURE;
break;
}
/* check for a read error, stop copying and return an error */
if (nread < 0) {
/* read had a problem, stop copying and return an error */
rc = SCR_FAILURE;
break;
}
}
/* close container */
if (scr_close(dst_file, fd_container) != SCR_SUCCESS) {
rc = SCR_FAILURE;
}
/* free the container file name and path */
scr_free(&dst_file);
scr_path_delete(&dst_path);
}
/* close the source file */
if (scr_close(file, fd_src) != SCR_SUCCESS) {
rc = SCR_FAILURE;
}
/* free buffer */
scr_free(&buf);
/* verify / set crc value */
if (rc == SCR_SUCCESS) {
uLong crc2;
if (scr_crc_on_flush) {
if (scr_meta_get_crc32(meta, &crc2) == SCR_SUCCESS) {
/* if a crc is already set in the meta data, check that we computed the same value */
if (crc != crc2) {
scr_err("CRC32 mismatch detected when flushing file %s @ %s:%d",
file, __FILE__, __LINE__
);
rc = SCR_FAILURE;
}
} else {
/* if there is no crc set, let's set it now */
scr_meta_set_crc32(meta, crc);
}
}
}
return rc;
}
/* copy src_file (full path) to dest_path and return new full path in dest_file */
int scr_file_copy(
const char* src_file,
const char* dst_file,
unsigned long buf_size,
uLong* crc)
{
/* check that we got something for a source file */
if (src_file == NULL || strcmp(src_file, "") == 0) {
scr_err("Invalid source file @ %s:%d",
__FILE__, __LINE__
);
return SCR_FAILURE;
}
/* check that we got something for a destination file */
if (dst_file == NULL || strcmp(dst_file, "") == 0) {
scr_err("Invalid destination file @ %s:%d",
__FILE__, __LINE__
);
return SCR_FAILURE;
}
/* open src_file for reading */
int src_fd = scr_open(src_file, O_RDONLY);
if (src_fd < 0) {
scr_err("Opening file to copy: scr_open(%s) errno=%d %s @ %s:%d",
src_file, errno, strerror(errno), __FILE__, __LINE__
);
return SCR_FAILURE;
}
/* open dest_file for writing */
mode_t mode_file = scr_getmode(1, 1, 0);
int dst_fd = scr_open(dst_file, O_WRONLY | O_CREAT | O_TRUNC, mode_file);
if (dst_fd < 0) {
scr_err("Opening file for writing: scr_open(%s) errno=%d %s @ %s:%d",
dst_file, errno, strerror(errno), __FILE__, __LINE__
);
scr_close(src_file, src_fd);
return SCR_FAILURE;
}
/* TODO:
posix_fadvise(fd, 0, 0, POSIX_FADV_DONTNEED | POSIX_FADV_SEQUENTIAL)
that tells the kernel that you don't ever need the pages
from the file again, and it won't bother keeping them in the page cache.
*/
posix_fadvise(src_fd, 0, 0, POSIX_FADV_DONTNEED | POSIX_FADV_SEQUENTIAL);
posix_fadvise(dst_fd, 0, 0, POSIX_FADV_DONTNEED | POSIX_FADV_SEQUENTIAL);
/* allocate buffer to read in file chunks */
char* buf = (char*) malloc(buf_size);
if (buf == NULL) {
scr_err("Allocating memory: malloc(%llu) errno=%d %s @ %s:%d",
buf_size, errno, strerror(errno), __FILE__, __LINE__
);
scr_close(dst_file, dst_fd);
scr_close(src_file, src_fd);
return SCR_FAILURE;
}
/* initialize crc values */
if (crc != NULL) {
*crc = crc32(0L, Z_NULL, 0);
}
int rc = SCR_SUCCESS;
/* write chunks */
int copying = 1;
while (copying) {
/* attempt to read buf_size bytes from file */
int nread = scr_read_attempt(src_file, src_fd, buf, buf_size);
/* if we read some bytes, write them out */
if (nread > 0) {
/* optionally compute crc value as we go */
if (crc != NULL) {
*crc = crc32(*crc, (const Bytef*) buf, (uInt) nread);
}
/* write our nread bytes out */
int nwrite = scr_write_attempt(dst_file, dst_fd, buf, nread);
/* check for a write error or a short write */
if (nwrite != nread) {
/* write had a problem, stop copying and return an error */
copying = 0;
rc = SCR_FAILURE;
}
}
/* assume a short read means we hit the end of the file */
if (nread < buf_size) {
copying = 0;
}
/* check for a read error, stop copying and return an error */
if (nread < 0) {
/* read had a problem, stop copying and return an error */
copying = 0;
rc = SCR_FAILURE;
}
}
/* free buffer */
scr_free(&buf);
/* close source and destination files */
if (scr_close(dst_file, dst_fd) != SCR_SUCCESS) {
rc = SCR_FAILURE;
}
if (scr_close(src_file, src_fd) != SCR_SUCCESS) {
rc = SCR_FAILURE;
}
/* unlink the file if the copy failed */
if (rc != SCR_SUCCESS) {
unlink(dst_file);
}
return rc;
}
int main(int argc, char* argv[])
{
int i, j;
int index = 1;
/* print usage if not enough arguments were given */
if (argc < 2) {
printf("Usage: scr_rebuild_xor <size> <root> <missing_xor_filename> <ordered_remaining_xor_filenames>\n");
return 1;
}
/* TODO: want to pass this on command line? */
/* get current working directory */
char dsetdir[SCR_MAX_FILENAME];
scr_getcwd(dsetdir, sizeof(dsetdir));
/* create and reduce path for dataset */
scr_path* path_dset = scr_path_from_str(dsetdir);
scr_path_reduce(path_dset);
/* allocate buffers */
char* buffer_A = malloc(buffer_size * sizeof(char));
char* buffer_B = malloc(buffer_size * sizeof(char));
if (buffer_A == NULL || buffer_B == NULL) {
scr_err("Failed to allocate buffer memory @ %s:%d",
__FILE__, __LINE__
);
return 1;
}
/* read in the size of the XOR set */
int xor_set_size = (int) strtol(argv[index++], (char **)NULL, 10);
if (xor_set_size <= 0) {
scr_err("Invalid XOR set size argument %s @ %s:%d",
argv[index-1], __FILE__, __LINE__
);
return 1;
}
/* allocate memory for data structures based on the XOR set size */
int* num_files = malloc(xor_set_size * sizeof(int));
int* offsets = malloc(xor_set_size * sizeof(int));
char** xor_files = malloc(xor_set_size * sizeof(char*));
int* xor_fds = malloc(xor_set_size * sizeof(int));
scr_hash** xor_headers = malloc(xor_set_size * sizeof(scr_hash*));
if (num_files == NULL || offsets == NULL || xor_files == NULL || xor_fds == NULL || xor_headers == NULL) {
scr_err("Failed to allocate buffer memory @ %s:%d",
__FILE__, __LINE__
);
return 1;
}
/* read in the rank of the missing process (the root) */
int root = (int) strtol(argv[index++], (char **)NULL, 10);
if (root < 0 || root >= xor_set_size) {
scr_err("Invalid root argument %s @ %s:%d",
argv[index-1], __FILE__, __LINE__
);
return 1;
}
/* read in the missing xor filename */
xor_files[0] = strdup(argv[index++]);
if (xor_files[0] == NULL) {
scr_err("Failed to dup XOR filename @ %s:%d",
__FILE__, __LINE__
);
return 1;
}
/* read in the xor filenames (expected to be in order of XOR segment number) */
/* we order ranks so that root is index 0, the rank to the right of root is index 1, and so on */
for (i=0; i < xor_set_size; i++) {
xor_headers[i] = scr_hash_new();
/* we'll get the XOR file name for root from the header stored in the XOR file of the partner */
if (i == root) {
continue;
}
/* adjust the index relative to root */
j = i - root;
if (j < 0) {
j += xor_set_size;
}
/* copy the XOR file name */
xor_files[j] = strdup(argv[index++]);
if (xor_files[j] == NULL) {
scr_err("Failed to dup XOR filename @ %s:%d",
__FILE__, __LINE__
);
return 1;
}
}
/* open each of the xor files and read in the headers */
for (i=1; i < xor_set_size; i++) {
/* open each xor file for reading */
xor_fds[i] = scr_open(xor_files[i], O_RDONLY);
if (xor_fds[i] < 0) {
scr_err("Opening xor segment file: scr_open(%s) errno=%d %s @ %s:%d",
xor_files[i], errno, strerror(errno), __FILE__, __LINE__
);
return 1;
}
/* read the header from this xor file */
if (scr_hash_read_fd(xor_files[i], xor_fds[i], xor_headers[i]) < 0) {
scr_err("Failed to read XOR header from %s @ %s:%d",
xor_files[i], __FILE__, __LINE__
);
return 1;
}
}
/* build header for missing XOR file */
int partner_rank = -1;
if (xor_set_size >= 2) {
scr_hash_merge(xor_headers[0], xor_headers[1]);
/* fetch our own file list from rank to our right */
scr_hash* rhs_hash = scr_hash_get(xor_headers[1], SCR_KEY_COPY_XOR_PARTNER);
scr_hash* current_hash = scr_hash_new();
scr_hash_merge(current_hash, rhs_hash);
scr_hash_set(xor_headers[0], SCR_KEY_COPY_XOR_CURRENT, current_hash);
/* we are the partner to the rank to our left */
scr_hash* lhs_hash = scr_hash_get(xor_headers[xor_set_size-1], SCR_KEY_COPY_XOR_CURRENT);
scr_hash* partner_hash = scr_hash_new();
scr_hash_merge(partner_hash, lhs_hash);
scr_hash_set(xor_headers[0], SCR_KEY_COPY_XOR_PARTNER, partner_hash);
/* get global rank of partner */
if (scr_hash_util_get_int(lhs_hash, SCR_KEY_COPY_XOR_RANK, &partner_rank) != SCR_SUCCESS) {
scr_err("Failed to read partner rank from XOR file header in %s @ %s:%d",
xor_files[xor_set_size-1], __FILE__, __LINE__
);
return 1;
}
}
/* get a pointer to the current hash for the missing rank */
scr_hash* missing_current_hash = scr_hash_get(xor_headers[0], SCR_KEY_COPY_XOR_CURRENT);
/* read the rank */
int my_rank = -1;
if (scr_hash_util_get_int(missing_current_hash, SCR_KEY_COPY_XOR_RANK, &my_rank) != SCR_SUCCESS) {
scr_err("Failed to read rank from XOR file header in %s @ %s:%d",
xor_files[0], __FILE__, __LINE__
);
return 1;
}
/* get the dataset */
scr_dataset* dataset = scr_hash_get(xor_headers[0], SCR_KEY_COPY_XOR_DATASET);
/* read the dataset id */
int dset_id = -1;
if (scr_dataset_get_id(dataset, &dset_id) != SCR_SUCCESS) {
scr_err("Failed to read dataset id from XOR file header in %s @ %s:%d",
xor_files[0], __FILE__, __LINE__
);
return 1;
}
/* read the ranks */
int num_ranks = -1;
if (scr_hash_util_get_int(xor_headers[0], SCR_KEY_COPY_XOR_RANKS, &num_ranks) != SCR_SUCCESS) {
scr_err("Failed to read ranks from XOR file header in %s @ %s:%d",
xor_files[0], __FILE__, __LINE__
);
return 1;
}
/* get name of partner's fmap */
scr_path* path_partner_map = scr_path_from_str(".scr");
scr_path_append_strf(path_partner_map, "fmap.%d.scr", partner_rank);
/* extract partner's flush descriptor */
scr_hash* flushdesc = scr_hash_new();
scr_filemap* partner_map = scr_filemap_new();
scr_filemap_read(path_partner_map, partner_map);
scr_filemap_get_flushdesc(partner_map, dset_id, partner_rank, flushdesc);
scr_filemap_delete(&partner_map);
/* delete partner map path */
scr_path_delete(&path_partner_map);
/* determine whether we should preserve user directories */
int preserve_dirs = 0;
scr_hash_util_get_int(flushdesc, SCR_SCAVENGE_KEY_PRESERVE, &preserve_dirs);
/* read the chunk size */
unsigned long chunk_size = 0;
if (scr_hash_util_get_unsigned_long(xor_headers[0], SCR_KEY_COPY_XOR_CHUNK, &chunk_size) != SCR_SUCCESS) {
scr_err("Failed to read chunk size from XOR file header in %s @ %s:%d",
xor_files[0], __FILE__, __LINE__
);
return 1;
}
/* determine number of files each member wrote in XOR set */
for (i=0; i < xor_set_size; i++) {
/* record the number of files for this rank */
scr_hash* current_hash = scr_hash_get(xor_headers[i], SCR_KEY_COPY_XOR_CURRENT);
if (scr_hash_util_get_int(current_hash, SCR_KEY_COPY_XOR_FILES, &num_files[i]) != SCR_SUCCESS) {
scr_err("Failed to read number of files from %s @ %s:%d",
xor_files[i], __FILE__, __LINE__
);
return 1;
}
}
/* count the total number of files and set the offsets array */
int total_num_files = 0;
for (i=0; i < xor_set_size; i++) {
offsets[i] = total_num_files;
total_num_files += num_files[i];
}
/* allocate space for a file descriptor, file name pointer, and filesize for each user file */
int* user_fds = (int*) malloc(total_num_files * sizeof(int));
char** user_files = (char**) malloc(total_num_files * sizeof(char*));
char** user_rel_files = (char**) malloc(total_num_files * sizeof(char*));
unsigned long* user_filesizes = (unsigned long*) malloc(total_num_files * sizeof(unsigned long));
if (user_fds == NULL || user_files == NULL || user_rel_files == NULL || user_filesizes == NULL) {
scr_err("Failed to allocate buffer memory @ %s:%d",
__FILE__, __LINE__
);
return 1;
}
/* get file name, file size, and open each of the user files that we have */
for (i=0; i < xor_set_size; i++) {
scr_hash* current_hash = scr_hash_get(xor_headers[i], SCR_KEY_COPY_XOR_CURRENT);
/* for each file belonging to this rank, get filename, filesize, and open file */
for (j=0; j < num_files[i]; j++) {
int offset = offsets[i] + j;
/* get the meta data for this file */
scr_meta* meta = scr_hash_get_kv_int(current_hash, SCR_KEY_COPY_XOR_FILE, j);
if (meta == NULL) {
scr_err("Failed to read meta data for file %d in %s @ %s:%d",
j, xor_files[i], __FILE__, __LINE__
);
return 1;
}
/* record the filesize of this file */
if (scr_meta_get_filesize(meta, &user_filesizes[offset]) != SCR_SUCCESS) {
scr_err("Failed to read filesize field for file %d in %s @ %s:%d",
j, xor_files[i], __FILE__, __LINE__
);
return 1;
}
/* get filename */
char* origname;
if (scr_meta_get_origname(meta, &origname) != SCR_SUCCESS) {
scr_err("Failed to read original name for file %d in %s @ %s:%d",
j, xor_files[i], __FILE__, __LINE__
);
return 1;
}
/* construct full path to user file */
scr_path* path_user_full = scr_path_from_str(origname);
if (preserve_dirs) {
/* get original path of file */
char* origpath;
if (scr_meta_get_origpath(meta, &origpath) != SCR_SUCCESS) {
scr_err("Failed to read original path for file %d in %s @ %s:%d",
j, xor_files[i], __FILE__, __LINE__
);
return 1;
}
/* construct full path to file */
scr_path_prepend_str(path_user_full, origpath);
} else {
/* construct full path to file */
scr_path_prepend(path_user_full, path_dset);
}
/* reduce path to user file */
scr_path_reduce(path_user_full);
/* make a copy of the full path */
user_files[offset] = scr_path_strdup(path_user_full);
/* make a copy of relative path */
scr_path* path_user_rel = scr_path_relative(path_dset, path_user_full);
user_rel_files[offset] = scr_path_strdup(path_user_rel);
scr_path_delete(&path_user_rel);
/* free the full path */
scr_path_delete(&path_user_full);
/* open the file */
if (i == 0) {
/* create directory for file */
scr_path* user_dir_path = scr_path_from_str(user_files[offset]);
scr_path_reduce(user_dir_path);
scr_path_dirname(user_dir_path);
if (! scr_path_is_null(user_dir_path)) {
char* user_dir = scr_path_strdup(user_dir_path);
mode_t mode_dir = scr_getmode(1, 1, 1);
if (scr_mkdir(user_dir, mode_dir) != SCR_SUCCESS) {
scr_err("Failed to create directory for user file %s @ %s:%d",
user_dir, __FILE__, __LINE__
);
return 1;
}
scr_free(&user_dir);
}
scr_path_delete(&user_dir_path);
/* open missing file for writing */
mode_t mode_file = scr_getmode(1, 1, 0);
user_fds[offset] = scr_open(user_files[offset], O_WRONLY | O_CREAT | O_TRUNC, mode_file);
if (user_fds[offset] < 0) {
scr_err("Opening user file for writing: scr_open(%s) errno=%d %s @ %s:%d",
user_files[offset], errno, strerror(errno), __FILE__, __LINE__
);
return 1;
}
} else {
/* open existing file for reading */
user_fds[offset] = scr_open(user_files[offset], O_RDONLY);
if (user_fds[offset] < 0) {
scr_err("Opening user file for reading: scr_open(%s) errno=%d %s @ %s:%d",
user_files[offset], errno, strerror(errno), __FILE__, __LINE__
);
return 1;
}
}
}
}
/* finally, open the xor file for the missing rank */
mode_t mode_file = scr_getmode(1, 1, 0);
xor_fds[0] = scr_open(xor_files[0], O_WRONLY | O_CREAT | O_TRUNC, mode_file);
if (xor_fds[0] < 0) {
scr_err("Opening xor file to be reconstructed: scr_open(%s) errno=%d %s @ %s:%d",
xor_files[0], errno, strerror(errno), __FILE__, __LINE__
);
return 1;
}
int rc = 0;
/* write the header to the XOR file of the missing rank */
if (scr_hash_write_fd(xor_files[0], xor_fds[0], xor_headers[0]) < 0) {
rc = 1;
}
/* this offset array records the current position we are in the logical file for each rank */
unsigned long* offset = malloc(xor_set_size * sizeof(unsigned long));
if (offset == NULL) {
scr_err("Failed to allocate buffer memory @ %s:%d",
__FILE__, __LINE__
);
return 1;
}
for (i=0; i < xor_set_size; i++) {
offset[i] = 0;
}
unsigned long write_pos = 0;
int chunk_id;
for (chunk_id = 0; chunk_id < xor_set_size && rc == 0; chunk_id++) {
size_t nread = 0;
while (nread < chunk_size && rc == 0) {
/* read upto buffer_size bytes at a time */
size_t count = chunk_size - nread;
if (count > buffer_size) {
count = buffer_size;
}
/* clear our buffer */
memset(buffer_A, 0, count);
/* read a segment from each rank and XOR it into our buffer */
for (i=1; i < xor_set_size; i++) {
/* read the next set of bytes for this chunk from my file into send_buf */
if (chunk_id != ((i + root) % xor_set_size)) {
/* read chunk from the logical file for this rank */
if (scr_read_pad_n(num_files[i], &user_files[offsets[i]], &user_fds[offsets[i]],
buffer_B, count, offset[i], &user_filesizes[offsets[i]]) != SCR_SUCCESS)
{
/* our read failed, set the return code to an error */
rc = 1;
count = 0;
}
offset[i] += count;
} else {
/* read chunk from the XOR file for this rank */
if (scr_read_attempt(xor_files[i], xor_fds[i], buffer_B, count) != count) {
/* our read failed, set the return code to an error */
rc = 1;
count = 0;
}
}
/* TODO: XORing with unsigned long would be faster here (if chunk size is multiple of this size) */
/* merge the blocks via xor operation */
for (j = 0; j < count; j++) {
buffer_A[j] ^= buffer_B[j];
}
}
/* at this point, we have the data from the missing rank, write it out */
if (chunk_id != root) {
/* write chunk to logical file for the missing rank */
if (scr_write_pad_n(num_files[0], &user_files[0], &user_fds[0],
buffer_A, count, write_pos, &user_filesizes[0]) != SCR_SUCCESS)
{
/* our write failed, set the return code to an error */
rc = 1;
}
write_pos += count;
} else {
/* write chunk to xor file for the missing rank */
if (scr_write_attempt(xor_files[0], xor_fds[0], buffer_A, count) != count) {
/* our write failed, set the return code to an error */
rc = 1;
}
}
nread += count;
}
}
/* close each of the user files */
for (i=0; i < total_num_files; i++) {
if (scr_close(user_files[i], user_fds[i]) != SCR_SUCCESS) {
rc = 1;
}
}
/* close each of the XOR files */
for (i=0; i < xor_set_size; i++) {
if (scr_close(xor_files[i], xor_fds[i]) != SCR_SUCCESS) {
rc = 1;
}
}
/* if the write failed, delete the files we just wrote, and return an error */
if (rc != 0) {
for (j=0; j < num_files[0]; j++) {
scr_file_unlink(user_files[j]);
}
scr_file_unlink(xor_files[0]);
return 1;
}
/* check that filesizes are correct */
unsigned long filesize;
for (j=0; j < num_files[0]; j++) {
filesize = scr_file_size(user_files[j]);
if (filesize != user_filesizes[j]) {
/* the filesize check failed, so delete the file */
scr_file_unlink(user_files[j]);
/* mark the file as incomplete */
scr_meta* meta = scr_hash_get_kv_int(missing_current_hash, SCR_KEY_COPY_XOR_FILE, j);
scr_meta_set_complete(meta, 0);
rc = 1;
}
}
/* TODO: we didn't record the filesize of the XOR file for the missing rank anywhere */
/* create a filemap for this rank */
scr_filemap* map = scr_filemap_new();
if (map == NULL) {
scr_err("Failed to allocate filemap @ %s:%d",
__FILE__, __LINE__
);
return 1;
}
/* record the dataset information in the filemap */
scr_filemap_set_dataset(map, dset_id, my_rank, dataset);
/* write meta data for each of the user files and add each one to the filemap */
for (j=0; j < num_files[0]; j++) {
/* add user file to filemap and record meta data */
char* user_file_relative = user_rel_files[j];
scr_filemap_add_file(map, dset_id, my_rank, user_file_relative);
scr_meta* meta = scr_hash_get_kv_int(missing_current_hash, SCR_KEY_COPY_XOR_FILE, j);
scr_filemap_set_meta(map, dset_id, my_rank, user_file_relative, meta);
}
/* write meta data for xor file and add it to the filemap */
scr_filemap_add_file(map, dset_id, my_rank, xor_files[0]);
unsigned long full_chunk_filesize = scr_file_size(xor_files[0]);
int missing_complete = 1;
scr_meta* meta_chunk = scr_meta_new();
scr_meta_set_filename(meta_chunk, xor_files[0]);
scr_meta_set_filetype(meta_chunk, SCR_META_FILE_XOR);
scr_meta_set_filesize(meta_chunk, full_chunk_filesize);
/* TODO: remove this from meta file, for now it's needed in scr_index.c */
scr_meta_set_ranks(meta_chunk, num_ranks);
scr_meta_set_complete(meta_chunk, missing_complete);
scr_filemap_set_meta(map, dset_id, my_rank, xor_files[0], meta_chunk);
/* set expected number of files for the missing rank */
int expected_num_files = scr_filemap_num_files(map, dset_id, my_rank);
scr_filemap_set_expected_files(map, dset_id, my_rank, expected_num_files);
/* compute, check, and store crc values with files */
for (j=0; j < num_files[0]; j++) {
/* compute crc on user file */
char* user_file_relative = user_rel_files[j];
if (scr_compute_crc(map, dset_id, my_rank, user_file_relative) != SCR_SUCCESS) {
/* the crc check failed, so delete the file */
scr_file_unlink(user_files[j]);
rc = 1;
}
}
if (scr_compute_crc(map, dset_id, my_rank, xor_files[0]) != SCR_SUCCESS) {
/* the crc check failed, so delete the file */
scr_file_unlink(xor_files[0]);
rc = 1;
}
/* store flush descriptor */
scr_filemap_set_flushdesc(map, dset_id, my_rank, flushdesc);
/* write filemap for this rank */
scr_path* path_map = scr_path_from_str(".scr");
scr_path_append_strf(path_map, "fmap.%d.scr", my_rank);
if (scr_filemap_write(path_map, map) != SCR_SUCCESS) {
rc = 1;
}
scr_path_delete(&path_map);
/* delete the map */
scr_filemap_delete(&map);
scr_meta_delete(&meta_chunk);
/* delete the flush/scavenge descriptor */
scr_hash_delete(&flushdesc);
scr_free(&offset);
for (i=0; i < total_num_files; i++) {
scr_free(&user_rel_files[i]);
scr_free(&user_files[i]);
}
scr_free(&user_filesizes);
scr_free(&user_rel_files);
scr_free(&user_files);
scr_free(&user_fds);
for (i=0; i < xor_set_size; i++) {
scr_hash_delete(&xor_headers[i]);
}
for (i=0; i < xor_set_size; i++) {
scr_free(&xor_files[i]);
}
scr_free(&xor_headers);
scr_free(&xor_fds);
scr_free(&xor_files);
scr_free(&offsets);
scr_free(&num_files);
scr_free(&buffer_B);
scr_free(&buffer_A);
scr_path_delete(&path_dset);
return rc;
}
/* logically concatenate n opened files and read count bytes from this logical file into buf starting
* from offset, pad with zero on end if missing data */
int scr_read_pad_n(int n, char** files, int* fds,
char* buf, unsigned long count, unsigned long offset, unsigned long* filesizes)
{
int i = 0;
size_t pos = 0;
off_t nseek = 0;
off_t nread = 0;
/* pass through files until we find the one containing our offset */
while (i < n && (nseek + filesizes[i]) <= offset) {
nseek += filesizes[i];
i++;
}
/* seek to the proper position in the current file */
if (i < n) {
pos = offset - nseek;
nseek += pos;
if (lseek(fds[i], pos, SEEK_SET) == (off_t)-1) {
/* our seek failed, return an error */
scr_err("Failed to seek to byte %lu in %s @ %s:%d",
pos, files[i], __FILE__, __LINE__
);
return SCR_FAILURE;
}
}
/* read data from files */
while (nread < count && i < n) {
/* assume we'll read the remainder of the current file */
size_t num_to_read = filesizes[i] - pos;
/* if we don't need to read the whole remainder of the file, adjust to the smaller amount */
if (num_to_read > count - nread) {
num_to_read = count - nread;
}
/* read data from file and add to the total read count */
if (scr_read_attempt(files[i], fds[i], buf + nread, num_to_read) != num_to_read) {
/* our read failed, return an error */
return SCR_FAILURE;
}
nread += num_to_read;
/* advance to next file and seek to byte 0 */
i++;
if (i < n) {
pos = 0;
if (lseek(fds[i], pos, SEEK_SET) == (off_t)-1) {
/* our seek failed, return an error */
scr_err("Failed to seek to byte %lu in %s @ %s:%d",
pos, files[i], __FILE__, __LINE__
);
return SCR_FAILURE;
}
}
}
/* if count is bigger than all of our file data, pad with zeros on the end */
if (nread < count) {
memset(buf + nread, 0, count - nread);
}
return SCR_SUCCESS;
}
