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Merge branch 'dev'

This commit is contained in:
Heng Li 2014-10-17 12:14:40 -04:00
parent 44a185f2c1 8af17b3478
commit 6deafdadca
2 changed files with 41 additions and 28 deletions
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67
bwashm.c
View File

@ -13,15 +13,15 @@ int bwa_shm_stage(bwaidx_t *idx, const char *hint, const char *_tmpfn)
{ {
const char *name; const char *name;
uint8_t *shm, *shm_idx; uint8_t *shm, *shm_idx;
uint16_t *cnt, i; uint16_t *cnt;
int shmid, to_init = 0, l; int shmid, to_init = 0, l;
char path[PATH_MAX + 1], *p, *tmpfn = (char*)_tmpfn; char path[PATH_MAX + 1], *tmpfn = (char*)_tmpfn;
if (hint == 0 || hint[0] == 0) return -1; if (hint == 0 || hint[0] == 0) return -1;
for (name = hint + strlen(hint) - 1; name >= hint && *name != '/'; --name); for (name = hint + strlen(hint) - 1; name >= hint && *name != '/'; --name);
++name; ++name;
if ((shmid = shm_open("/bwactl", O_RDWR, 0444)) < 0) { if ((shmid = shm_open("/bwactl", O_RDWR, 0)) < 0) {
shmid = shm_open("/bwactl", O_CREAT|O_RDWR|O_EXCL, 0644); shmid = shm_open("/bwactl", O_CREAT|O_RDWR|O_EXCL, 0644);
to_init = 1; to_init = 1;
} }
@ -32,15 +32,6 @@ int bwa_shm_stage(bwaidx_t *idx, const char *hint, const char *_tmpfn)
if (to_init) { if (to_init) {
memset(shm, 0, BWA_CTL_SIZE); memset(shm, 0, BWA_CTL_SIZE);
cnt[1] = 4; cnt[1] = 4;
} else {
for (i = 0, p = (char*)shm + 4; i < cnt[0]; ++i) {
if (strcmp(p + 8, name) == 0) break;
p += 9 + strlen(p + 8);
}
if (i < cnt[0]) {
fprintf(stderr, "[W::%s] index '%s' is already in shared memory\n", __func__, name);
return -1;
}
} }
if (idx->mem == 0) bwa_idx2mem(idx); if (idx->mem == 0) bwa_idx2mem(idx);
@ -62,15 +53,15 @@ int bwa_shm_stage(bwaidx_t *idx, const char *hint, const char *_tmpfn)
} }
strcat(strcpy(path, "/bwaidx-"), name); strcat(strcpy(path, "/bwaidx-"), name);
l = 8 + strlen(name) + 1;
if (cnt[1] + l > BWA_CTL_SIZE) return -1;
memcpy(shm + cnt[1], &idx->l_mem, 8);
memcpy(shm + cnt[1] + 8, name, l - 8);
if ((shmid = shm_open(path, O_CREAT|O_RDWR|O_EXCL, 0644)) < 0) { if ((shmid = shm_open(path, O_CREAT|O_RDWR|O_EXCL, 0644)) < 0) {
shm_unlink(path); shm_unlink(path);
perror("shm_open()"); perror("shm_open()");
return -1; return -1;
} }
l = 8 + strlen(name) + 1;
if (cnt[1] + l > BWA_CTL_SIZE) return -1;
memcpy(shm + cnt[1], &idx->l_mem, 8);
memcpy(shm + cnt[1] + 8, name, l - 8);
cnt[1] += l; ++cnt[0]; cnt[1] += l; ++cnt[0];
ftruncate(shmid, idx->l_mem); ftruncate(shmid, idx->l_mem);
shm_idx = mmap(0, idx->l_mem, PROT_READ|PROT_WRITE, MAP_SHARED, shmid, 0); shm_idx = mmap(0, idx->l_mem, PROT_READ|PROT_WRITE, MAP_SHARED, shmid, 0);
@ -106,7 +97,7 @@ bwaidx_t *bwa_idx_load_from_shm(const char *hint)
if (hint == 0 || hint[0] == 0) return 0; if (hint == 0 || hint[0] == 0) return 0;
for (name = hint + strlen(hint) - 1; name >= hint && *name != '/'; --name); for (name = hint + strlen(hint) - 1; name >= hint && *name != '/'; --name);
++name; ++name;
if ((shmid = shm_open("/bwactl", O_RDONLY, 0444)) < 0) return 0; if ((shmid = shm_open("/bwactl", O_RDONLY, 0)) < 0) return 0;
shm = mmap(0, BWA_CTL_SIZE, PROT_READ, MAP_SHARED, shmid, 0); shm = mmap(0, BWA_CTL_SIZE, PROT_READ, MAP_SHARED, shmid, 0);
cnt = (uint16_t*)shm; cnt = (uint16_t*)shm;
if (cnt[0] == 0) return 0; if (cnt[0] == 0) return 0;
@ -118,7 +109,7 @@ bwaidx_t *bwa_idx_load_from_shm(const char *hint)
if (i == cnt[0]) return 0; if (i == cnt[0]) return 0;
strcat(strcpy(path, "/bwaidx-"), name); strcat(strcpy(path, "/bwaidx-"), name);
if ((shmid = shm_open(path, O_RDONLY, 0444)) < 0) return 0; if ((shmid = shm_open(path, O_RDONLY, 0)) < 0) return 0;
shm_idx = mmap(0, l_mem, PROT_READ, MAP_SHARED, shmid, 0); shm_idx = mmap(0, l_mem, PROT_READ, MAP_SHARED, shmid, 0);
idx = calloc(1, sizeof(bwaidx_t)); idx = calloc(1, sizeof(bwaidx_t));
bwa_mem2idx(l_mem, shm_idx, idx); bwa_mem2idx(l_mem, shm_idx, idx);
@ -126,12 +117,32 @@ bwaidx_t *bwa_idx_load_from_shm(const char *hint)
return idx; return idx;
} }
int bwa_shm_test(const char *hint)
{
int shmid;
uint16_t *cnt, i;
char *p, *shm;
const char *name;
if (hint == 0 || hint[0] == 0) return 0;
for (name = hint + strlen(hint) - 1; name >= hint && *name != '/'; --name);
++name;
if ((shmid = shm_open("/bwactl", O_RDONLY, 0)) < 0) return 0;
shm = mmap(0, BWA_CTL_SIZE, PROT_READ, MAP_SHARED, shmid, 0);
cnt = (uint16_t*)shm;
for (i = 0, p = shm + 4; i < cnt[0]; ++i) {
if (strcmp(p + 8, name) == 0) return 1;
p += strlen(p) + 9;
}
return 0;
}
int bwa_shm_list(void) int bwa_shm_list(void)
{ {
int shmid; int shmid;
uint16_t *cnt, i; uint16_t *cnt, i;
char *p, *shm; char *p, *shm;
if ((shmid = shm_open("/bwactl", O_RDONLY, 0444)) < 0) return -1; if ((shmid = shm_open("/bwactl", O_RDONLY, 0)) < 0) return -1;
shm = mmap(0, BWA_CTL_SIZE, PROT_READ, MAP_SHARED, shmid, 0); shm = mmap(0, BWA_CTL_SIZE, PROT_READ, MAP_SHARED, shmid, 0);
cnt = (uint16_t*)shm; cnt = (uint16_t*)shm;
for (i = 0, p = shm + 4; i < cnt[0]; ++i) { for (i = 0, p = shm + 4; i < cnt[0]; ++i) {
@ -150,7 +161,7 @@ int bwa_shm_destroy(void)
char *p, *shm; char *p, *shm;
char path[PATH_MAX + 1]; char path[PATH_MAX + 1];
if ((shmid = shm_open("/bwactl", O_RDONLY, 0444)) < 0) return -1; if ((shmid = shm_open("/bwactl", O_RDONLY, 0)) < 0) return -1;
shm = mmap(0, BWA_CTL_SIZE, PROT_READ, MAP_SHARED, shmid, 0); shm = mmap(0, BWA_CTL_SIZE, PROT_READ, MAP_SHARED, shmid, 0);
cnt = (uint16_t*)shm; cnt = (uint16_t*)shm;
for (i = 0, p = shm + 4; i < cnt[0]; ++i) { for (i = 0, p = shm + 4; i < cnt[0]; ++i) {
@ -186,13 +197,15 @@ int main_shm(int argc, char *argv[])
return 1; return 1;
} }
if (optind < argc) { if (optind < argc) {
bwaidx_t *idx; if (bwa_shm_test(argv[optind]) == 0) {
idx = bwa_idx_load_from_disk(argv[optind], BWA_IDX_ALL); bwaidx_t *idx;
if (bwa_shm_stage(idx, argv[optind], tmpfn) < 0) { idx = bwa_idx_load_from_disk(argv[optind], BWA_IDX_ALL);
fprintf(stderr, "[E::%s] failed to stage the index in shared memory\n", __func__); if (bwa_shm_stage(idx, argv[optind], tmpfn) < 0) {
ret = 1; fprintf(stderr, "[E::%s] failed to stage the index in shared memory\n", __func__);
} ret = 1;
bwa_idx_destroy(idx); }
bwa_idx_destroy(idx);
} else fprintf(stderr, "[M::%s] index '%s' is already in shared memory\n", __func__, argv[optind]);
} }
if (to_list) bwa_shm_list(); if (to_list) bwa_shm_list();
if (to_drop) bwa_shm_destroy(); if (to_drop) bwa_shm_destroy();

2
main.c
View File

@ -4,7 +4,7 @@
#include "utils.h" #include "utils.h"
#ifndef PACKAGE_VERSION #ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.10-r907-dirty" #define PACKAGE_VERSION "0.7.10-r912-dirty"
#endif #endif
int bwa_fa2pac(int argc, char *argv[]); int bwa_fa2pac(int argc, char *argv[]);