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#include <sys/types.h>
#include <sys/mman.h>
#include <string.h>
#include <stdlib.h>
#include <limits.h>
#include <unistd.h>
#include <fcntl.h>
#include <errno.h>
#include <stdio.h>
#include "bwa.h"
#ifndef PATH_MAX
# define PATH_MAX 1024
#endif
int bwa_shm_stage(bwaidx_t *idx, const char *hint, const char *_tmpfn)
{
const char *name;
uint8_t *shm, *shm_idx;
uint16_t *cnt;
int shmid, to_init = 0, l;
char path[PATH_MAX + 1], *tmpfn = (char*)_tmpfn;
if (hint == 0 || hint[0] == 0) return -1;
for (name = hint + strlen(hint) - 1; name >= hint && *name != '/'; --name);
++name;
if ((shmid = shm_open("/bwactl", O_RDWR, 0)) < 0) {
shmid = shm_open("/bwactl", O_CREAT|O_RDWR|O_EXCL, 0644);
to_init = 1;
}
if (shmid < 0) return -1;
ftruncate(shmid, BWA_CTL_SIZE);
shm = mmap(0, BWA_CTL_SIZE, PROT_READ|PROT_WRITE, MAP_SHARED, shmid, 0);
cnt = (uint16_t*)shm;
if (to_init) {
memset(shm, 0, BWA_CTL_SIZE);
cnt[1] = 4;
}
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);
if ((shmid = shm_open(path, O_CREAT|O_RDWR|O_EXCL, 0644)) < 0) {
shm_unlink(path);
perror("shm_open()");
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];
ftruncate(shmid, idx->l_mem);
shm_idx = mmap(0, idx->l_mem, PROT_READ|PROT_WRITE, MAP_SHARED, shmid, 0);
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;
}
bwaidx_t *bwa_idx_load_from_shm(const char *hint)
{
const char *name;
uint8_t *shm, *shm_idx;
uint16_t *cnt, i;
char *p, path[PATH_MAX + 1];
int shmid;
int64_t l_mem;
bwaidx_t *idx;
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;
if (cnt[0] == 0) return 0;
for (i = 0, p = (char*)(shm + 4); i < cnt[0]; ++i) {
memcpy(&l_mem, p, 8); p += 8;
if (strcmp(p, name) == 0) break;
p += strlen(p) + 1;
}
if (i == cnt[0]) return 0;
strcat(strcpy(path, "/bwaidx-"), name);
if ((shmid = shm_open(path, O_RDONLY, 0)) < 0) return 0;
shm_idx = mmap(0, l_mem, PROT_READ, MAP_SHARED, shmid, 0);
idx = calloc(1, sizeof(bwaidx_t));
bwa_mem2idx(l_mem, shm_idx, idx);
idx->is_shm = 1;
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 shmid;
uint16_t *cnt, i;
char *p, *shm;
if ((shmid = shm_open("/bwactl", O_RDONLY, 0)) < 0) return -1;
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) {
int64_t l_mem;
memcpy(&l_mem, p, 8); p += 8;
printf("%s\t%ld\n", p, (long)l_mem);
p += strlen(p) + 1;
}
return 0;
}
int bwa_shm_destroy(void)
{
int shmid;
uint16_t *cnt, i;
char *p, *shm;
char path[PATH_MAX + 1];
if ((shmid = shm_open("/bwactl", O_RDONLY, 0)) < 0) return -1;
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) {
int64_t l_mem;
memcpy(&l_mem, p, 8); p += 8;
strcat(strcpy(path, "/bwaidx-"), p);
shm_unlink(path);
p += strlen(p) + 1;
}
munmap(shm, BWA_CTL_SIZE);
shm_unlink("/bwactl");
return 0;
}
int main_shm(int argc, char *argv[])
{
int c, to_list = 0, to_drop = 0, ret = 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] [-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)) {
fprintf(stderr, "[E::%s] open -l or -d cannot be used when 'idxbase' is present\n", __func__);
return 1;
}
if (optind < argc) {
if (bwa_shm_test(argv[optind]) == 0) {
bwaidx_t *idx;
idx = bwa_idx_load_from_disk(argv[optind], BWA_IDX_ALL);
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;
}
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_drop) bwa_shm_destroy();
return ret;
}
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