/* this moves all files of the specified dataset in the cache to
* make them accessible to new rank mapping */
static int scr_distribute_files(scr_filemap* map, const scr_reddesc* red, int id)
{
int i, round;
int rc = SCR_SUCCESS;
/* TODO: mark dataset as being distributed in filemap,
* because if we fail in the middle of a distribute,
* we can't trust the contents of the files anymore,
* at which point it should be deleted */
/* clean out any incomplete files before we start */
scr_cache_clean(map);
/* for this dataset, get list of ranks we have data for */
int nranks = 0;
int* ranks = NULL;
scr_filemap_list_ranks_by_dataset(map, id, &nranks, &ranks);
/* walk backwards through the list of ranks, and set our start index
* to the rank which is the first rank that is equal to or higher
* than our own rank -- when we assign round ids below, this offsetting
* helps distribute the load */
int start_index = 0;
int invalid_rank_found = 0;
for (i = nranks-1; i >= 0; i--) {
int rank = ranks[i];
/* pick the first rank whose rank id is equal to or higher than our own */
if (rank >= scr_my_rank_world) {
start_index = i;
}
/* while we're at it, check that the rank is within range */
if (rank < 0 || rank >= scr_ranks_world) {
scr_err("Invalid rank id %d in world of %d @ %s:%d",
rank, scr_ranks_world, __FILE__, __LINE__
);
invalid_rank_found = 1;
}
}
/* check that we didn't find an invalid rank on any process */
if (! scr_alltrue(invalid_rank_found == 0)) {
scr_free(&ranks);
return SCR_FAILURE;
}
/* allocate array to record the rank we can send to in each round */
int* have_rank_by_round = (int*) SCR_MALLOC(sizeof(int) * nranks);
int* send_flag_by_round = (int*) SCR_MALLOC(sizeof(int) * nranks);
/* check that we have all of the files for each rank,
* and determine the round we can send them */
scr_hash* send_hash = scr_hash_new();
scr_hash* recv_hash = scr_hash_new();
for (round = 0; round < nranks; round++) {
/* get the rank id */
int index = (start_index + round) % nranks;
int rank = ranks[index];
/* record the rank indexed by the round number */
have_rank_by_round[round] = rank;
/* assume we won't be sending to this rank in this round */
send_flag_by_round[round] = 0;
/* if we have files for this rank, specify the round we can
* send those files in */
if (scr_bool_have_files(map, id, rank)) {
scr_hash_setf(send_hash, NULL, "%d %d", rank, round);
}
}
scr_hash_exchange(send_hash, recv_hash, scr_comm_world);
/* search for the minimum round we can get our files */
int retrieve_rank = -1;
int retrieve_round = -1;
scr_hash_elem* elem = NULL;
for (elem = scr_hash_elem_first(recv_hash);
elem != NULL;
elem = scr_hash_elem_next(elem))
{
/* get the rank id */
int rank = scr_hash_elem_key_int(elem);
/* get the round id */
scr_hash* round_hash = scr_hash_elem_hash(elem);
scr_hash_elem* round_elem = scr_hash_elem_first(round_hash);
char* round_str = scr_hash_elem_key(round_elem);
int round = atoi(round_str);
/* record this round and rank number if it's less than the current round */
if (round < retrieve_round || retrieve_round == -1) {
retrieve_round = round;
retrieve_rank = rank;
}
}
/* done with the round hashes, free them off */
scr_hash_delete(&recv_hash);
scr_hash_delete(&send_hash);
/* free off our list of ranks */
scr_free(&ranks);
/* for some redundancy schemes, we know at this point whether we
* can recover all files */
int can_get_files = (retrieve_rank != -1);
if (red->copy_type != SCR_COPY_XOR && !scr_alltrue(can_get_files)) {
/* print a debug message indicating which rank is missing files */
if (! can_get_files) {
scr_dbg(2, "Cannot find process that has my checkpoint files @ %s:%d",
__FILE__, __LINE__
);
}
return SCR_FAILURE;
}
/* get the maximum retrieve round */
int max_rounds = 0;
MPI_Allreduce(
&retrieve_round, &max_rounds, 1, MPI_INT, MPI_MAX, scr_comm_world
);
/* tell destination which round we'll take our files in */
send_hash = scr_hash_new();
recv_hash = scr_hash_new();
if (retrieve_rank != -1) {
scr_hash_setf(send_hash, NULL, "%d %d", retrieve_rank, retrieve_round);
}
scr_hash_exchange(send_hash, recv_hash, scr_comm_world);
/* determine which ranks want to fetch their files from us */
for(elem = scr_hash_elem_first(recv_hash);
elem != NULL;
elem = scr_hash_elem_next(elem))
{
/* get the round id */
scr_hash* round_hash = scr_hash_elem_hash(elem);
scr_hash_elem* round_elem = scr_hash_elem_first(round_hash);
char* round_str = scr_hash_elem_key(round_elem);
int round = atoi(round_str);
/* record whether this rank wants its files from us */
if (round >= 0 && round < nranks) {
send_flag_by_round[round] = 1;
}
}
/* done with the round hashes, free them off */
scr_hash_delete(&recv_hash);
scr_hash_delete(&send_hash);
int tmp_rc = 0;
/* run through rounds and exchange files */
for (round = 0; round <= max_rounds; round++) {
/* assume we don't need to send or receive any files this round */
int send_rank = MPI_PROC_NULL;
int recv_rank = MPI_PROC_NULL;
int send_num = 0;
int recv_num = 0;
/* check whether I can potentially send to anyone in this round */
if (round < nranks) {
/* have someone's files, check whether they are asking
* for them this round */
if (send_flag_by_round[round]) {
/* need to send files this round, remember to whom and how many */
int dst_rank = have_rank_by_round[round];
send_rank = dst_rank;
send_num = scr_filemap_num_files(map, id, dst_rank);
}
}
/* if I'm supposed to get my files this round, set the recv_rank */
if (retrieve_round == round) {
recv_rank = retrieve_rank;
}
/* TODO: another special case is to just move files if the
* processes are on the same node */
/* if i'm sending to myself, just move (rename) each file */
if (send_rank == scr_my_rank_world) {
/* get our file list */
int numfiles = 0;
char** files = NULL;
scr_filemap_list_files(map, id, send_rank, &numfiles, &files);
/* TODO: sort files in reverse order by size */
/* iterate over and rename each file */
for (i=0; i < numfiles; i++) {
/* get the current file name */
char* file = files[i];
/* lookup meta data for this file */
scr_meta* meta = scr_meta_new();
scr_filemap_get_meta(map, id, send_rank, file, meta);
/* get the path for this file based on its type
* and dataset id */
char* dir = NULL;
if (scr_meta_check_filetype(meta, SCR_META_FILE_USER) == SCR_SUCCESS) {
dir = scr_cache_dir_get(red, id);
} else {
dir = scr_cache_dir_hidden_get(red, id);
}
/* build the new file name */
scr_path* path_newfile = scr_path_from_str(file);
scr_path_basename(path_newfile);
scr_path_prepend_str(path_newfile, dir);
char* newfile = scr_path_strdup(path_newfile);
/* if the new file name is different from the old name, rename it */
if (strcmp(file, newfile) != 0) {
/* record the new filename to our map and write it to disk */
scr_filemap_add_file(map, id, send_rank, newfile);
scr_filemap_set_meta(map, id, send_rank, newfile, meta);
scr_filemap_write(scr_map_file, map);
/* rename the file */
scr_dbg(2, "Round %d: rename(%s, %s)", round, file, newfile);
tmp_rc = rename(file, newfile);
if (tmp_rc != 0) {
/* TODO: to cross mount points, if tmp_rc == EXDEV,
* open new file, copy, and delete orig */
scr_err("Moving checkpoint file: rename(%s, %s) %s errno=%d @ %s:%d",
file, newfile, strerror(errno), errno, __FILE__, __LINE__
);
rc = SCR_FAILURE;
}
/* remove the old name from the filemap and write it to disk */
scr_filemap_remove_file(map, id, send_rank, file);
scr_filemap_write(scr_map_file, map);
}
/* free the path and string */
scr_free(&newfile);
scr_path_delete(&path_newfile);
/* free directory string */
scr_free(&dir);
/* free meta data */
scr_meta_delete(&meta);
}
/* free the list of filename pointers */
scr_free(&files);
} else {
/* if we have files for this round, but the correspdonding
* rank doesn't need them, delete the files */
if (round < nranks && send_rank == MPI_PROC_NULL) {
int dst_rank = have_rank_by_round[round];
scr_unlink_rank(map, id, dst_rank);
}
/* sending to and/or recieving from another node */
if (send_rank != MPI_PROC_NULL || recv_rank != MPI_PROC_NULL) {
/* have someone to send to or receive from */
int have_outgoing = 0;
int have_incoming = 0;
if (send_rank != MPI_PROC_NULL) {
have_outgoing = 1;
}
if (recv_rank != MPI_PROC_NULL) {
have_incoming = 1;
}
/* first, determine how many files I will be receiving and
* tell how many I will be sending */
MPI_Request request[2];
MPI_Status status[2];
int num_req = 0;
if (have_incoming) {
MPI_Irecv(
&recv_num, 1, MPI_INT, recv_rank, 0,
scr_comm_world, &request[num_req]
);
num_req++;
}
if (have_outgoing) {
MPI_Isend(
&send_num, 1, MPI_INT, send_rank, 0,
scr_comm_world, &request[num_req]
);
num_req++;
}
if (num_req > 0) {
MPI_Waitall(num_req, request, status);
}
/* record how many files I will receive (need to distinguish
* between 0 files and not knowing) */
if (have_incoming) {
scr_filemap_set_expected_files(map, id, scr_my_rank_world, recv_num);
}
/* turn off send or receive flags if the file count is 0,
* nothing else to do */
if (send_num == 0) {
have_outgoing = 0;
send_rank = MPI_PROC_NULL;
}
if (recv_num == 0) {
have_incoming = 0;
recv_rank = MPI_PROC_NULL;
}
/* TODO: since we overwrite files in place in order to avoid
* running out of storage space, we should sort files in order
* of descending size for the next step */
/* get our file list for the destination */
int numfiles = 0;
char** files = NULL;
if (have_outgoing) {
scr_filemap_list_files(map, id, send_rank, &numfiles, &files);
}
/* while we have a file to send or receive ... */
while (have_incoming || have_outgoing) {
/* get the filename */
char* file = NULL;
scr_meta* send_meta = NULL;
if (have_outgoing) {
file = files[numfiles - send_num];
send_meta = scr_meta_new();
scr_filemap_get_meta(map, id, send_rank, file, send_meta);
}
/* exchange meta data so we can determine type of incoming file */
scr_meta* recv_meta = scr_meta_new();
scr_hash_sendrecv(send_meta, send_rank, recv_meta, recv_rank, scr_comm_world);
/* get the path for this file based on its type and dataset id */
char* dir = NULL;
if (have_incoming) {
if (scr_meta_check_filetype(recv_meta, SCR_META_FILE_USER) == SCR_SUCCESS) {
dir = scr_cache_dir_get(red, id);
} else {
dir = scr_cache_dir_hidden_get(red, id);
}
}
/* exhange file names with partners,
* building full path of incoming file */
char file_partner[SCR_MAX_FILENAME];
scr_swap_file_names(
file, send_rank, file_partner, sizeof(file_partner), recv_rank,
dir, scr_comm_world
);
/* free directory string */
scr_free(&dir);
/* free incoming meta data (we'll get this again later) */
scr_meta_delete(&recv_meta);
/* if we'll receive a file, record the name of our file
* in the filemap and write it to disk */
recv_meta = NULL;
if (recv_rank != MPI_PROC_NULL) {
recv_meta = scr_meta_new();
scr_filemap_add_file(map, id, scr_my_rank_world, file_partner);
scr_filemap_write(scr_map_file, map);
}
/* either sending or receiving a file this round, since we move files,
* it will be deleted or overwritten */
if (scr_swap_files(MOVE_FILES, file, send_meta, send_rank,
file_partner, recv_meta, recv_rank, scr_comm_world) != SCR_SUCCESS)
{
scr_err("Swapping files: %s to %d, %s from %d @ %s:%d",
file, send_rank, file_partner, recv_rank, __FILE__, __LINE__
);
rc = SCR_FAILURE;
}
/* if we received a file, record its meta data and decrement
* our receive count */
if (have_incoming) {
/* record meta data for the file we received */
scr_filemap_set_meta(map, id, scr_my_rank_world, file_partner, recv_meta);
scr_meta_delete(&recv_meta);
/* decrement receive count */
recv_num--;
if (recv_num == 0) {
have_incoming = 0;
recv_rank = MPI_PROC_NULL;
}
}
/* if we sent a file, remove it from the filemap and decrement
* our send count */
if (have_outgoing) {
/* remove file from the filemap */
scr_filemap_remove_file(map, id, send_rank, file);
scr_meta_delete(&send_meta);
/* decrement our send count */
send_num--;
if (send_num == 0) {
have_outgoing = 0;
send_rank = MPI_PROC_NULL;
}
}
/* update filemap on disk */
scr_filemap_write(scr_map_file, map);
}
/* free our file list */
scr_free(&files);
}
}
}
/* if we have more rounds than max rounds, delete the remainder of our files */
for (round = max_rounds+1; round < nranks; round++) {
/* have someone's files for this round, so delete them */
int dst_rank = have_rank_by_round[round];
scr_unlink_rank(map, id, dst_rank);
}
scr_free(&send_flag_by_round);
scr_free(&have_rank_by_round);
/* write out new filemap and free the memory resources */
scr_filemap_write(scr_map_file, map);
/* clean out any incomplete files */
scr_cache_clean(map);
/* TODO: if the exchange or redundancy rebuild failed,
* we should also delete any *good* files we received */
/* return whether distribute succeeded, it does not ensure we have
* all of our files, only that the transfer completed without failure */
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;
}
/* apply redundancy scheme to file and return number of bytes copied
* in bytes parameter */
int scr_reddesc_apply(
scr_filemap* map,
const scr_reddesc* c,
int id,
double* bytes)
{
/* initialize to 0 */
*bytes = 0.0;
/* step through each of my files for the specified dataset
* to scan for any incomplete files */
int valid = 1;
double my_bytes = 0.0;
scr_hash_elem* file_elem;
for (file_elem = scr_filemap_first_file(map, id, scr_my_rank_world);
file_elem != NULL;
file_elem = scr_hash_elem_next(file_elem))
{
/* get the filename */
char* file = scr_hash_elem_key(file_elem);
/* check the file */
if (! scr_bool_have_file(map, id, scr_my_rank_world, file, scr_ranks_world)) {
scr_dbg(2, "File determined to be invalid: %s", file);
valid = 0;
}
/* add up the number of bytes on our way through */
my_bytes += (double) scr_file_size(file);
/* if crc_on_copy is set, compute crc and update meta file
* (PARTNER does this during the copy) */
if (scr_crc_on_copy && c->copy_type != SCR_COPY_PARTNER) {
scr_compute_crc(map, id, scr_my_rank_world, file);
}
}
/* determine whether everyone's files are good */
int all_valid = scr_alltrue(valid);
if (! all_valid) {
if (scr_my_rank_world == 0) {
scr_dbg(1, "Exiting copy since one or more checkpoint files is invalid");
}
return SCR_FAILURE;
}
/* start timer */
time_t timestamp_start;
double time_start;
if (scr_my_rank_world == 0) {
timestamp_start = scr_log_seconds();
time_start = MPI_Wtime();
}
/* apply the redundancy scheme */
int rc = SCR_FAILURE;
switch (c->copy_type) {
case SCR_COPY_SINGLE:
rc = SCR_SUCCESS;
break;
case SCR_COPY_PARTNER:
rc = scr_reddesc_apply_partner(map, c, id);
break;
case SCR_COPY_XOR:
rc = scr_reddesc_apply_xor(map, c, id);
break;
}
/* record the number of files this task wrote during this dataset
* (need to remember when a task writes 0 files) */
int num_files = scr_filemap_num_files(map, id, scr_my_rank_world);
scr_filemap_set_expected_files(map, id, scr_my_rank_world, num_files);
scr_filemap_write(scr_map_file, map);
/* determine whether everyone succeeded in their copy */
int valid_copy = (rc == SCR_SUCCESS);
if (! valid_copy) {
scr_err("scr_copy_files failed with return code %d @ %s:%d",
rc, __FILE__, __LINE__
);
}
int all_valid_copy = scr_alltrue(valid_copy);
rc = all_valid_copy ? SCR_SUCCESS : SCR_FAILURE;
/* add up total number of bytes */
MPI_Allreduce(&my_bytes, bytes, 1, MPI_DOUBLE, MPI_SUM, scr_comm_world);
/* stop timer and report performance info */
if (scr_my_rank_world == 0) {
double time_end = MPI_Wtime();
double time_diff = time_end - time_start;
double bw = *bytes / (1024.0 * 1024.0 * time_diff);
scr_dbg(1, "scr_reddesc_apply: %f secs, %e bytes, %f MB/s, %f MB/s per proc",
time_diff, *bytes, bw, bw/scr_ranks_world
);
/* log data on the copy in the database */
if (scr_log_enable) {
char* dir = scr_cache_dir_get(c, id);
scr_log_transfer("COPY", c->base, dir, &id, ×tamp_start, &time_diff, bytes);
scr_free(&dir);
}
}
return rc;
}
/* fetch files listed in hash into specified cache directory,
* update filemap and fill in total number of bytes fetched,
* returns SCR_SUCCESS if successful */
static int scr_fetch_files_list(
const scr_hash* file_list,
const char* dir,
scr_filemap* map)
{
/* assume we'll succeed in fetching our files */
int rc = SCR_SUCCESS;
/* assume we don't have any files to fetch */
int my_num_files = 0;
/* get dataset id */
int id;
scr_dataset* dataset = scr_hash_get(file_list, SCR_KEY_DATASET);
scr_dataset_get_id(dataset, &id);
/* now iterate through the file list and fetch each file */
scr_hash_elem* file_elem = NULL;
scr_hash* files = scr_hash_get(file_list, SCR_KEY_FILE);
for (file_elem = scr_hash_elem_first(files);
file_elem != NULL;
file_elem = scr_hash_elem_next(file_elem))
{
/* get the filename */
char* file = scr_hash_elem_key(file_elem);
/* get a pointer to the hash for this file */
scr_hash* hash = scr_hash_elem_hash(file_elem);
/* check whether we are supposed to fetch this file */
/* TODO: this is a hacky way to avoid reading a redundancy file
* back in under the assumption that it's an original file, which
* breaks our redundancy computation due to a name conflict on
* the file names */
scr_hash_elem* no_fetch_hash = scr_hash_elem_get(hash, SCR_SUMMARY_6_KEY_NOFETCH);
if (no_fetch_hash != NULL) {
continue;
}
/* increment our file count */
my_num_files++;
/* build the destination file name */
scr_path* path_newfile = scr_path_from_str(file);
scr_path_basename(path_newfile);
scr_path_prepend_str(path_newfile, dir);
char* newfile = scr_path_strdup(path_newfile);
/* add the file to our filemap and write it to disk before creating
* the file, this way we have a record that it may exist before we
* actually start to fetch it */
scr_filemap_add_file(map, id, scr_my_rank_world, newfile);
scr_filemap_write(scr_map_file, map);
/* get the file size */
unsigned long filesize = 0;
if (scr_hash_util_get_unsigned_long(hash, SCR_KEY_SIZE, &filesize) != SCR_SUCCESS) {
scr_err("Failed to read file size from summary data @ %s:%d",
__FILE__, __LINE__
);
rc = SCR_FAILURE;
/* free path and string */
scr_free(&newfile);
scr_path_delete(&path_newfile);
break;
}
/* check for a complete flag */
int complete = 1;
if (scr_hash_util_get_int(hash, SCR_KEY_COMPLETE, &complete) != SCR_SUCCESS) {
/* in summary file, the absence of a complete flag on a file
* implies the file is complete */
complete = 1;
}
/* create a new meta data object for this file */
scr_meta* meta = scr_meta_new();
/* set the meta data */
scr_meta_set_filename(meta, newfile);
scr_meta_set_filetype(meta, SCR_META_FILE_USER);
scr_meta_set_filesize(meta, filesize);
scr_meta_set_complete(meta, 1);
/* TODODSET: move the ranks field elsewhere, for now it's needed
* by scr_index.c */
scr_meta_set_ranks(meta, scr_ranks_world);
/* get the crc, if set, and add it to the meta data */
uLong crc;
if (scr_hash_util_get_crc32(hash, SCR_KEY_CRC, &crc) == SCR_SUCCESS) {
scr_meta_set_crc32(meta, crc);
}
/* fetch file from containers if they are defined, otherwise fetch
* the native file */
scr_hash* segments = scr_hash_get(hash, SCR_SUMMARY_6_KEY_SEGMENT);
if (segments != NULL) {
/* get source path */
char* from_dir;
if (scr_hash_util_get_str(file_list, SCR_KEY_PATH, &from_dir) == SCR_SUCCESS) {
/* fetch file from containers */
if (scr_fetch_file_from_containers(newfile, meta, segments, from_dir) != SCR_SUCCESS) {
/* failed to fetch file, mark it as incomplete */
scr_meta_set_complete(meta, 0);
rc = SCR_FAILURE;
}
} else {
/* failed to find base dataset directory in file list */
rc = SCR_FAILURE;
}
} else {
/* fetch native file, lookup directory for this file */
char* from_dir;
if (scr_hash_util_get_str(hash, SCR_KEY_PATH, &from_dir) == SCR_SUCCESS) {
if (scr_fetch_file(newfile, from_dir, meta) != SCR_SUCCESS) {
/* failed to fetch file, mark it as incomplete */
scr_meta_set_complete(meta, 0);
rc = SCR_FAILURE;
}
} else {
/* failed to read source directory, mark file as incomplete */
scr_meta_set_complete(meta, 0);
rc = SCR_FAILURE;
}
}
/* TODODSET: want to write out filemap before we start to fetch
* each file? */
/* mark the file as complete */
scr_filemap_set_meta(map, id, scr_my_rank_world, newfile, meta);
/* free the meta data object */
scr_meta_delete(&meta);
/* free path and string */
scr_free(&newfile);
scr_path_delete(&path_newfile);
}
/* set the expected number of files for this dataset */
scr_filemap_set_expected_files(map, id, scr_my_rank_world, my_num_files);
scr_filemap_write(scr_map_file, map);
return rc;
}
/* copy files to a partner node */
static int scr_reddesc_apply_partner(
scr_filemap* map,
const scr_reddesc* c,
int id)
{
int rc = SCR_SUCCESS;
/* get pointer to partner state structure */
scr_reddesc_partner* state = (scr_reddesc_partner*) c->copy_state;
/* get a list of our files */
int numfiles = 0;
char** files = NULL;
scr_filemap_list_files(map, id, scr_my_rank_world, &numfiles, &files);
/* first, determine how many files we'll be sending and receiving
* with our partners */
MPI_Status status;
int send_num = numfiles;
int recv_num = 0;
MPI_Sendrecv(
&send_num, 1, MPI_INT, state->rhs_rank, 0,
&recv_num, 1, MPI_INT, state->lhs_rank, 0,
c->comm, &status
);
/* record how many files our partner will send */
scr_filemap_set_expected_files(map, id, state->lhs_rank_world, recv_num);
/* remember which node our partner is on (needed for scavenge) */
scr_hash* flushdesc = scr_hash_new();
scr_filemap_get_flushdesc(map, id, state->lhs_rank_world, flushdesc);
scr_hash_util_set_int(flushdesc, SCR_SCAVENGE_KEY_PRESERVE, scr_preserve_directories);
scr_hash_util_set_int(flushdesc, SCR_SCAVENGE_KEY_CONTAINER, scr_use_containers);
scr_hash_util_set_str(flushdesc, SCR_SCAVENGE_KEY_PARTNER, state->lhs_hostname);
scr_filemap_set_flushdesc(map, id, state->lhs_rank_world, flushdesc);
scr_hash_delete(&flushdesc);
/* record partner's redundancy descriptor hash */
scr_hash* lhs_desc_hash = scr_hash_new();
scr_hash* my_desc_hash = scr_hash_new();
scr_reddesc_store_to_hash(c, my_desc_hash);
scr_hash_sendrecv(my_desc_hash, state->rhs_rank, lhs_desc_hash, state->lhs_rank, c->comm);
scr_filemap_set_desc(map, id, state->lhs_rank_world, lhs_desc_hash);
scr_hash_delete(&my_desc_hash);
scr_hash_delete(&lhs_desc_hash);
/* store this info in our filemap before we receive any files */
scr_filemap_write(scr_map_file, map);
/* define directory to receive partner file in */
char* dir = scr_cache_dir_get(c, id);
/* for each potential file, step through a call to swap */
while (send_num > 0 || recv_num > 0) {
/* assume we won't send or receive in this step */
int send_rank = MPI_PROC_NULL;
int recv_rank = MPI_PROC_NULL;
/* if we have a file left to send,
* get the filename and destination rank */
char* file = NULL;
if (send_num > 0) {
int i = numfiles - send_num;
file = files[i];
send_rank = state->rhs_rank;
send_num--;
}
/* if we have a file left to receive, get the rank */
if (recv_num > 0) {
recv_rank = state->lhs_rank;
recv_num--;
}
/* exhange file names with partners */
char file_partner[SCR_MAX_FILENAME];
scr_swap_file_names(file, send_rank, file_partner, sizeof(file_partner), recv_rank, dir, c->comm);
/* if we'll receive a file, record the name of our partner's
* file in the filemap */
if (recv_rank != MPI_PROC_NULL) {
scr_filemap_add_file(map, id, state->lhs_rank_world, file_partner);
scr_filemap_write(scr_map_file, map);
}
/* get meta data of file we're sending */
scr_meta* send_meta = scr_meta_new();
scr_filemap_get_meta(map, id, scr_my_rank_world, file, send_meta);
/* exhange files with partners */
scr_meta* recv_meta = scr_meta_new();
if (scr_swap_files(COPY_FILES, file, send_meta, send_rank, file_partner, recv_meta, recv_rank, c->comm) != SCR_SUCCESS) {
rc = SCR_FAILURE;
}
scr_filemap_set_meta(map, id, state->lhs_rank_world, file_partner, recv_meta);
/* free meta data for these files */
scr_meta_delete(&recv_meta);
scr_meta_delete(&send_meta);
}
/* free cache directory string */
scr_free(&dir);
/* write out the updated filemap */
scr_filemap_write(scr_map_file, map);
/* free our list of files */
scr_free(&files);
return rc;
}