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r904: optionally create tmp files for shm staging

This commit is contained in:
Heng Li 2014-10-16 10:52:59 -04:00
parent 97a3102c89
commit ad0da1418f
2 changed files with 42 additions and 11 deletions
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51
bwashm.c
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@ -9,13 +9,13 @@
#include <stdio.h>
#include "bwa.h"
int bwa_shm_stage(bwaidx_t *idx, const char *hint)
int bwa_shm_stage(bwaidx_t *idx, const char *hint, const char *_tmpfn)
{
const char *name;
uint8_t *shm, *shm_idx;
uint16_t *cnt, i;
int shmid, to_init = 0, l;
char path[PATH_MAX + 1], *p;
char path[PATH_MAX + 1], *p, *tmpfn = (char*)_tmpfn;
if (hint == 0 || hint[0] == 0) return -1;
for (name = hint + strlen(hint) - 1; name >= hint && *name != '/'; --name);
@ -45,6 +45,22 @@ int bwa_shm_stage(bwaidx_t *idx, const char *hint)
if (idx->mem == 0) bwa_idx2mem(idx);
if (tmpfn) {
FILE *fp;
if ((fp = fopen(tmpfn, "wb")) != 0) {
int64_t rest = idx->l_mem;
while (rest > 0) {
int64_t l = rest < 0x1000000? rest : 0x1000000;
rest -= fwrite(&idx->mem[idx->l_mem - rest], 1, l, fp);
}
fclose(fp);
free(idx->mem); idx->mem = 0;
} else {
fprintf(stderr, "[W::%s] fail to create the temporary file. Option '-f' is ignored.\n", __func__);
tmpfn = 0;
}
}
strcat(strcpy(path, "/bwaidx-"), name);
l = 8 + strlen(name) + 1;
if (cnt[1] + l > BWA_CTL_SIZE) return -1;
@ -58,9 +74,21 @@ int bwa_shm_stage(bwaidx_t *idx, const char *hint)
cnt[1] += l; ++cnt[0];
ftruncate(shmid, idx->l_mem);
shm_idx = mmap(0, idx->l_mem, PROT_READ|PROT_WRITE, MAP_SHARED, shmid, 0);
memcpy(shm_idx, idx->mem, idx->l_mem);
free(idx->mem);
idx->mem = shm_idx;
if (tmpfn) {
FILE *fp;
fp = fopen(tmpfn, "rb");
int64_t rest = idx->l_mem;
while (rest > 0) {
int64_t l = rest < 0x1000000? rest : 0x1000000;
rest -= fread(&shm_idx[idx->l_mem - rest], 1, l, fp);
}
fclose(fp);
unlink(tmpfn);
} else {
memcpy(shm_idx, idx->mem, idx->l_mem);
free(idx->mem);
}
bwa_mem2idx(idx->l_mem, shm_idx, idx);
idx->is_shm = 1;
return 0;
}
@ -140,14 +168,17 @@ int bwa_shm_destroy(void)
int main_shm(int argc, char *argv[])
{
int c, to_list = 0, to_drop = 0, ret = 0;
while ((c = getopt(argc, argv, "ld")) >= 0) {
char *tmpfn = 0;
while ((c = getopt(argc, argv, "ldf:")) >= 0) {
if (c == 'l') to_list = 1;
else if (c == 'd') to_drop = 1;
else if (c == 'f') tmpfn = optarg;
}
if (optind == argc && !to_list && !to_drop) {
fprintf(stderr, "\nUsage: bwa shm [-d|-l] [idxbase]\n\n");
fprintf(stderr, "Options: -d destroy all indices in shared memory\n");
fprintf(stderr, " -l list names of indices in shared memory\n\n");
fprintf(stderr, "\nUsage: bwa shm [-d|-l] [-f tmpFile] [idxbase]\n\n");
fprintf(stderr, "Options: -d destroy all indices in shared memory\n");
fprintf(stderr, " -l list names of indices in shared memory\n");
fprintf(stderr, " -f FILE temporary file to reduce peak memory\n\n");
return 1;
}
if (optind < argc && (to_list || to_drop)) {
@ -157,7 +188,7 @@ int main_shm(int argc, char *argv[])
if (optind < argc) {
bwaidx_t *idx;
idx = bwa_idx_load_from_disk(argv[optind], BWA_IDX_ALL);
if (bwa_shm_stage(idx, argv[optind]) < 0) {
if (bwa_shm_stage(idx, argv[optind], tmpfn) < 0) {
fprintf(stderr, "[E::%s] failed to stage the index in shared memory\n", __func__);
ret = 1;
}

2
main.c
View File

@ -4,7 +4,7 @@
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.10-r903-dirty"
#define PACKAGE_VERSION "0.7.10-r904-dirty"
#endif
int bwa_fa2pac(int argc, char *argv[]);