/* 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;
}
/* flushes file named in src_file to dst_dir and fills in meta based on flush,
* returns success of flush */
static int scr_flush_a_file(const char* src_file, const char* dst_dir, scr_meta* meta)
{
int flushed = SCR_SUCCESS;
int tmp_rc;
/* build full name to destination file */
scr_path* dst_path = scr_path_from_str(src_file);
scr_path_basename(dst_path);
scr_path_prepend_str(dst_path, dst_dir);
scr_path_reduce(dst_path);
char* dst_file = scr_path_strdup(dst_path);
/* copy file */
int crc_valid = 0;
uLong crc;
uLong* crc_p = NULL;
if (scr_crc_on_flush) {
crc_valid = 1;
crc_p = &crc;
}
tmp_rc = scr_file_copy(src_file, dst_file, scr_file_buf_size, crc_p);
if (tmp_rc != SCR_SUCCESS) {
crc_valid = 0;
flushed = SCR_FAILURE;
}
scr_dbg(2, "scr_flush_a_file: Read and copied %s to %s with success code %d @ %s:%d",
src_file, dst_file, tmp_rc, __FILE__, __LINE__
);
/* if file has crc32, check it against the one computed during the copy,
* otherwise if scr_crc_on_flush is set, record crc32 */
if (crc_valid) {
uLong crc_meta;
if (scr_meta_get_crc32(meta, &crc_meta) == SCR_SUCCESS) {
if (crc != crc_meta) {
/* detected a crc mismatch during the copy */
/* TODO: unlink the copied file */
/* scr_file_unlink(dst_file); */
/* mark the file as invalid */
scr_meta_set_complete(meta, 0);
flushed = SCR_FAILURE;
scr_err("scr_flush_a_file: CRC32 mismatch detected when flushing file %s to %s @ %s:%d",
src_file, dst_file, __FILE__, __LINE__
);
/* TODO: would be good to log this, but right now only rank 0 can write log entries */
/*
if (scr_log_enable) {
time_t now = scr_log_seconds();
scr_log_event("CRC32 MISMATCH", dst_file, NULL, &now, NULL);
}
*/
}
} else {
/* the crc was not already in the metafile, but we just computed it, so set it */
scr_meta_set_crc32(meta, crc);
}
}
/* TODO: check that written filesize matches expected filesize */
/* fill out meta data, set complete field based on flush success */
/* (we don't update the meta file here, since perhaps the file in cache is ok and only the flush failed) */
int complete = (flushed == SCR_SUCCESS);
scr_meta_set_complete(meta, complete);
/* free destination file string and path */
scr_free(&dst_file);
scr_path_delete(&dst_path);
return flushed;
}
/* read contents of summary file */
static int scr_fetch_summary(
const char* summary_dir,
scr_hash* file_list)
{
/* assume that we won't succeed in our fetch attempt */
int rc = SCR_SUCCESS;
/* check whether summary file exists and is readable */
if (scr_my_rank_world == 0) {
/* check that we can access the directory */
if (scr_file_is_readable(summary_dir) != SCR_SUCCESS) {
scr_err("Failed to access summary directory %s @ %s:%d",
summary_dir, __FILE__, __LINE__
);
rc = SCR_FAILURE;
}
}
/* broadcast success code from rank 0 */
MPI_Bcast(&rc, 1, MPI_INT, 0, scr_comm_world);
if (rc != SCR_SUCCESS) {
return rc;
}
/* add path to file list */
scr_hash_util_set_str(file_list, SCR_KEY_PATH, summary_dir);
/* build path to summary file */
scr_path* dataset_path = scr_path_from_str(summary_dir);
scr_path* meta_path = scr_path_dup(dataset_path);
scr_path_append_str(meta_path, ".scr");
scr_path_reduce(meta_path);
/* rank 0 reads the summary file */
scr_hash* header = scr_hash_new();
if (scr_my_rank_world == 0) {
/* build path to summary file */
scr_path* summary_path = scr_path_dup(meta_path);
scr_path_append_str(summary_path, "summary.scr");
const char* summary_file = scr_path_strdup(summary_path);
/* open file for reading */
int fd = scr_open(summary_file, O_RDONLY);
if (fd >= 0) {
/* read summary hash */
ssize_t header_size = scr_hash_read_fd(summary_file, fd, header);
if (header_size < 0) {
rc = SCR_FAILURE;
}
/* TODO: check that the version is correct */
/* close the file */
scr_close(summary_file, fd);
} else {
scr_err("Failed to open summary file %s @ %s:%d",
summary_file, __FILE__, __LINE__
);
rc = SCR_FAILURE;
}
/* free summary path and string */
scr_free(&summary_file);
scr_path_delete(&summary_path);
}
/* broadcast success code from rank 0 */
MPI_Bcast(&rc, 1, MPI_INT, 0, scr_comm_world);
if (rc != SCR_SUCCESS) {
goto cleanup;
}
/* broadcast the summary hash */
scr_hash_bcast(header, 0, scr_comm_world);
/* extract and record the datast in file list */
scr_hash* dataset_hash = scr_hash_new();
scr_dataset* dataset = scr_hash_get(header, SCR_SUMMARY_6_KEY_DATASET);
scr_hash_merge(dataset_hash, dataset);
scr_hash_set(file_list, SCR_SUMMARY_6_KEY_DATASET, dataset_hash);
/* build path to rank2file map */
scr_path* rank2file_path = scr_path_dup(meta_path);
scr_path_append_str(rank2file_path, "rank2file.scr");
/* fetch file names and offsets containing file hash data */
int valid = 0;
char* file = NULL;
unsigned long offset = 0;
if (scr_my_rank_world == 0) {
/* rank 0 is only valid reader to start with */
valid = 1;
file = scr_path_strdup(rank2file_path);
offset = 0;
}
if (scr_fetch_rank2file_map(dataset_path, 1, &valid, &file, &offset)
!= SCR_SUCCESS)
{
rc = SCR_FAILURE;
}
/* create hashes to exchange data */
scr_hash* send = scr_hash_new();
scr_hash* recv = scr_hash_new();
/* read data from file */
if (valid) {
/* open file if necessary */
int fd = scr_open(file, O_RDONLY);
if (fd >= 0) {
/* create hash to hold file contents */
scr_hash* save = scr_hash_new();
/* read hash from file */
scr_lseek(file, fd, offset, SEEK_SET);
ssize_t readsize = scr_hash_read_fd(file, fd, save);
if (readsize < 0) {
scr_err("Failed to read rank2file map file %s @ %s:%d",
file, __FILE__, __LINE__
);
rc = SCR_FAILURE;
}
/* check that the number of ranks match */
int ranks = 0;
scr_hash_util_get_int(save, SCR_SUMMARY_6_KEY_RANKS, &ranks);
if (ranks != scr_ranks_world) {
scr_err("Invalid number of ranks in %s, got %d expected %d @ %s:%d",
file, ranks, scr_ranks_world, __FILE__, __LINE__
);
rc = SCR_FAILURE;
}
/* delete current send hash, set it to values from file,
* delete file hash */
scr_hash_delete(&send);
send = scr_hash_extract(save, SCR_SUMMARY_6_KEY_RANK);
scr_hash_delete(&save);
/* close the file */
scr_close(file, fd);
} else {
scr_err("Failed to open rank2file map %s @ %s:%d",
file, __FILE__, __LINE__
);
rc = SCR_FAILURE;
}
/* delete file name string */
scr_free(&file);
}
/* check that everyone read the data ok */
if (! scr_alltrue(rc == SCR_SUCCESS)) {
rc = SCR_FAILURE;
goto cleanup_hashes;
}
/* scatter to groups */
scr_hash_exchange_direction(send, recv, scr_comm_world, SCR_HASH_EXCHANGE_RIGHT);
/* iterate over the ranks that sent data to us, and set up our
* list of files */
scr_hash_elem* elem;
for (elem = scr_hash_elem_first(recv);
elem != NULL;
elem = scr_hash_elem_next(elem))
{
/* the key is the source rank, which we don't care about,
* the info we need is in the element hash */
scr_hash* elem_hash = scr_hash_elem_hash(elem);
/* get pointer to file hash */
scr_hash* file_hash = scr_hash_get(elem_hash, SCR_SUMMARY_6_KEY_FILE);
if (file_hash != NULL) {
/* TODO: parse summary file format */
scr_hash_merge(file_list, elem_hash);
} else {
rc = SCR_FAILURE;
}
}
/* fill in file list parameters */
if (rc == SCR_SUCCESS) {
/* if we're not using containers, add PATH entry for each of our
* files */
scr_hash* files = scr_hash_get(file_list, SCR_KEY_FILE);
for (elem = scr_hash_elem_first(files);
elem != NULL;
elem = scr_hash_elem_next(elem))
{
/* get the file name */
char* file = scr_hash_elem_key(elem);
/* combine the file name with the summary directory to build a
* full path to the file */
scr_path* path_full = scr_path_dup(dataset_path);
scr_path_append_str(path_full, file);
/* subtract off last component to get just the path */
scr_path_dirname(path_full);
char* path = scr_path_strdup(path_full);
/* record path in file list */
scr_hash* hash = scr_hash_elem_hash(elem);
scr_hash_util_set_str(hash, SCR_KEY_PATH, path);
/* free the path and string */
scr_free(&path);
scr_path_delete(&path_full);
}
}
/* check that everyone read the data ok */
if (! scr_alltrue(rc == SCR_SUCCESS)) {
rc = SCR_FAILURE;
goto cleanup_hashes;
}
cleanup_hashes:
/* delete send and receive hashes */
scr_hash_delete(&recv);
scr_hash_delete(&send);
/* free string and path for rank2file map */
scr_path_delete(&rank2file_path);
cleanup:
/* free the header hash */
scr_hash_delete(&header);
/* free path for dataset directory */
scr_path_delete(&meta_path);
scr_path_delete(&dataset_path);
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;
}
/* attempt to fetch most recent checkpoint from prefix directory into
* cache, fills in map if successful and sets fetch_attempted to 1 if
* any fetch is attempted, returns SCR_SUCCESS if successful */
int scr_fetch_sync(scr_filemap* map, int* fetch_attempted)
{
/* we only return success if we successfully fetch a checkpoint */
int rc = SCR_FAILURE;
double time_start, time_end, time_diff;
/* start timer */
if (scr_my_rank_world == 0) {
time_start = MPI_Wtime();
}
/* have rank 0 read the index file */
scr_hash* index_hash = NULL;
int read_index_file = 0;
if (scr_my_rank_world == 0) {
/* create an empty hash to store our index */
index_hash = scr_hash_new();
/* read the index file */
if (scr_index_read(scr_prefix_path, index_hash) == SCR_SUCCESS) {
read_index_file = 1;
}
}
/* don't enter while loop below if rank 0 failed to read index file */
int continue_fetching = 1;
MPI_Bcast(&read_index_file, 1, MPI_INT, 0, scr_comm_world);
if (! read_index_file) {
continue_fetching = 0;
}
/* now start fetching, we keep trying until we exhaust all valid
* checkpoints */
char target[SCR_MAX_FILENAME];
int current_checkpoint_id = -1;
while (continue_fetching) {
/* create a new path */
scr_path* fetch_path = scr_path_new();
/* initialize our target directory to empty string */
strcpy(target, "");
/* rank 0 determines the directory to fetch from */
if (scr_my_rank_world == 0) {
/* read the current directory if it's set */
char* current_str;
if (scr_index_get_current(index_hash, ¤t_str) == SCR_SUCCESS) {
size_t current_str_len = strlen(current_str) + 1;
if (current_str_len <= sizeof(target)) {
strcpy(target, current_str);
} else {
/* ERROR */
}
}
/* lookup the checkpoint id */
int next_checkpoint_id = -1;
if (strcmp(target, "") != 0) {
/* we have a subdirectory name, lookup the checkpoint id
* corresponding to this directory */
scr_index_get_id_by_dir(index_hash, target, &next_checkpoint_id);
} else {
/* otherwise, just get the most recent complete checkpoint
* (that's older than the current id) */
scr_index_get_most_recent_complete(index_hash, current_checkpoint_id, &next_checkpoint_id, target);
}
current_checkpoint_id = next_checkpoint_id;
/* TODODSET: need to verify that dataset is really a checkpoint
* and keep searching if not */
/* if we have a subdirectory (target) name, build the full fetch
* directory */
if (strcmp(target, "") != 0) {
/* record that we're attempting a fetch of this checkpoint in
* the index file */
*fetch_attempted = 1;
if (current_checkpoint_id != -1) {
scr_index_mark_fetched(index_hash, current_checkpoint_id, target);
scr_index_write(scr_prefix_path, index_hash);
}
/* we have a subdirectory, now build the full path */
scr_path_append(fetch_path, scr_prefix_path);
scr_path_append_str(fetch_path, target);
scr_path_reduce(fetch_path);
}
}
/* broadcast fetch path from rank 0 */
scr_path_bcast(fetch_path, 0, scr_comm_world);
/* check whether we've got a path */
if (! scr_path_is_null(fetch_path)) {
/* got something, attempt to fetch the checkpoint */
int dset_id, ckpt_id;
rc = scr_fetch_files(map, fetch_path, &dset_id, &ckpt_id);
if (rc == SCR_SUCCESS) {
/* set the dataset and checkpoint ids */
scr_dataset_id = dset_id;
scr_checkpoint_id = ckpt_id;
/* we succeeded in fetching this checkpoint, set current to
* point to it, and stop fetching */
if (scr_my_rank_world == 0) {
scr_index_set_current(index_hash, target);
scr_index_write(scr_prefix_path, index_hash);
}
continue_fetching = 0;
} else {
/* we tried to fetch, but we failed, mark it as failed in
* the index file so we don't try it again */
if (scr_my_rank_world == 0) {
/* unset the current pointer */
scr_index_unset_current(index_hash);
if (current_checkpoint_id != -1 && strcmp(target, "") != 0) {
scr_index_mark_failed(index_hash, current_checkpoint_id, target);
}
scr_index_write(scr_prefix_path, index_hash);
}
}
} else {
/* we ran out of valid checkpoints in the index file,
* bail out of the loop */
continue_fetching = 0;
}
/* free fetch path */
scr_path_delete(&fetch_path);
}
/* delete the index hash */
if (scr_my_rank_world == 0) {
scr_hash_delete(&index_hash);
}
/* broadcast whether we actually attempted to fetch anything
* (only rank 0 knows) */
MPI_Bcast(fetch_attempted, 1, MPI_INT, 0, scr_comm_world);
/* stop timer for fetch */
if (scr_my_rank_world == 0) {
time_end = MPI_Wtime();
time_diff = time_end - time_start;
scr_dbg(1, "scr_fetch_files: return code %d, %f secs", rc, time_diff);
}
return rc;
}