From 56c687d23dbebec2ba33fb72311ea438d03c6e2e Mon Sep 17 00:00:00 2001 From: zzh Date: Sun, 18 Jan 2026 00:40:44 +0800 Subject: [PATCH] =?UTF-8?q?=E6=94=B9=E5=8F=98=E4=BA=86seq=E4=B8=8Etask?= =?UTF-8?q?=E5=85=B3=E8=81=94=E7=9A=84=E6=96=B9=E5=BC=8F=EF=BC=8C=E5=9C=A8?= =?UTF-8?q?=E7=BA=BF=E7=A8=8B=E4=B8=AD=E5=B0=86task=E4=BF=A1=E6=81=AF?= =?UTF-8?q?=E4=B8=8E=E5=AF=B9=E5=BA=94=E7=9A=84seq=E5=85=B3=E8=81=94?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- Makefile | 2 +- bwa.h | 5 +++-- mate_sw.h | 9 +++++++++ paired_sam.c | 34 +++++++++++++++++++++++----------- run.sh | 14 +++++++------- 5 files changed, 43 insertions(+), 21 deletions(-) diff --git a/Makefile b/Makefile index bbb27a2..d2e64f4 100644 --- a/Makefile +++ b/Makefile @@ -2,7 +2,7 @@ CC= gcc CFLAGS= -g -Wall -Wno-unused-function -mavx2 -mavx512bw -O3 WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS -SAM_EXACT= -DSAM_EXACT +SAM_EXACT= #-DSAM_EXACT SHOW_PERF= -DSHOW_PERF SHOW_DATA_PERF= -DSHOW_DATA_PERF FILTER_FULL_MATCH= #-DFILTER_FULL_MATCH diff --git a/bwa.h b/bwa.h index 9f7b7a3..66ddfa5 100644 --- a/bwa.h +++ b/bwa.h @@ -86,8 +86,9 @@ typedef struct { int m_name, m_comment, m_seq, m_qual; char *name, *comment, *seq, *qual; msw_task_ptr_v msw; - //int_v msw; - // kstring_t sam; + msw_seq_task_v msw_task; + // int_v msw; + // kstring_t sam; } bseq1_t; typedef struct { diff --git a/mate_sw.h b/mate_sw.h index 4f6b483..30a4a42 100644 --- a/mate_sw.h +++ b/mate_sw.h @@ -32,6 +32,15 @@ typedef kvec_t(msw_task_t) msw_task_v; // mate sw task的指针数组 typedef kvec_t(msw_task_t*) msw_task_ptr_v; +// 每个seq保留task所在的线程，和数组idx +typedef struct { + int arr_idx; // 是u8还是i16 + int thread_idx; // 在哪个线程 + int task_idx; // 数组内的索引 +} msw_seq_task_t; + +typedef kvec_t(msw_seq_task_t) msw_seq_task_v; + ////////////////////////////////////////////// // 用来存放获取的mate sw阶段的ref序列 diff --git a/paired_sam.c b/paired_sam.c index 9d03e4e..9464733 100644 --- a/paired_sam.c +++ b/paired_sam.c @@ -130,7 +130,10 @@ static void get_matesw_tasks(const mem_opt_t* opt, const bntseq_t* bns, const ui p->re = re; p->seq_id = sid; p->aj = a_j; - p->to = task_order++; + p->to = task_order++; // 有啥用？ 应该是用来合并u8和i16的时候排序用 + + msw_seq_task_t seq_task = {0, tid, msw8->n - 1}; + kv_push(msw_seq_task_t, seq->msw_task, seq_task); // kv_push(msw_task_t*, seq->msw, p); // 将matesw任务和对应的seq关联起来，这里放指针是不行的，因为指针位置会变，要保存offset才行 // kv_push(int, seq->msw, msw8->n - 1); // 这里需要考虑i16, 本线程的msw的offset } @@ -556,8 +559,11 @@ no_pairing: free(h[1].cigar); end_clear: - _destory_clear_vec(s[0].msw); - _destory_clear_vec(s[1].msw); + //_destory_clear_vec(s[0].msw); + //_destory_clear_vec(s[1].msw); + + _destory_clear_vec(s[0].msw_task); + _destory_clear_vec(s[1].msw_task); free(a[0].a); free(a[1].a); @@ -607,8 +613,11 @@ static void workder_gen_sam(void* data, int idx, int tid) { _clear_vec(bb[0]); _clear_vec(bb[1]); for (i = 0; i < 2; ++i) - for (j = 0; j < s[!i].msw.n; ++j) { - msw_task_t* t = s[!i].msw.a[j]; + //for (j = 0; j < s[!i].msw.n; ++j) { + // msw_task_t* t = s[!i].msw.a[j]; + for (k = 0; k < s[!i].msw_task.n; ++k) { + msw_seq_task_t st = s[!i].msw_task.a[k]; + msw_task_t* t = &w->msw->t_msw_tasks_u8[st.thread_idx].a[st.task_idx]; kv_push(mem_alnreg_t, bb[i], a[i].a[t->aj]); } #endif @@ -619,8 +628,11 @@ static void workder_gen_sam(void* data, int idx, int tid) { int origin_n = a[si].n; #endif // 这里应该先给task排序，因为u8和i16是分开排序的，需要合在一起 - for (k = 0; k < s[si].msw.n; ++k) { - msw_task_t* t = s[si].msw.a[k]; + //for (k = 0; k < s[si].msw.n; ++k) { + // msw_task_t* t = s[si].msw.a[k]; + for (k = 0; k < s[si].msw_task.n; ++k) { + msw_seq_task_t st = s[si].msw_task.a[k]; + msw_task_t* t = &w->msw->t_msw_tasks_u8[st.thread_idx].a[st.task_idx]; #ifdef SAM_EXACT mem_alnreg_t* b = &bb[i].a[k]; #else @@ -686,7 +698,7 @@ static void gather_matesw_task(mem_worker_t* w, msw_task_v* thread_tasks, msw_ta for (j = 0; j < thread_tasks[i].n; ++j) { msw_task_t* tp = &thread_tasks[i].a[j]; kv_push(msw_task_t*, *tasks, tp); - kv_push(msw_task_t*, w->seqs[tp->seq_id].msw, tp); + // kv_push(msw_task_t*, w->seqs[tp->seq_id].msw, tp); } } } @@ -755,7 +767,6 @@ void gen_paired_sam(mem_worker_t* w) { // 更新stats PROF_START(update_stats_cache); update_msw_stats(w); - // 开辟缓冲区 alloc_update_cache_avx512(w); PROF_END(gprof[G_update_stats_cache], update_stats_cache); @@ -765,10 +776,9 @@ void gen_paired_sam(mem_worker_t* w) { gather_matesw_task(w, w->msw->t_msw_tasks_u8, &w->msw->p_msw_tasks_u8); gather_matesw_task(w, w->msw->t_msw_tasks_i16, &w->msw->p_msw_tasks_i16); PROF_END(gprof[G_gather_matesw_task], gather_matesw_task); + PROF_START(calc_matesw); - int msw_batch_n = (w->msw->p_msw_tasks_u8.n + w->opt->msw_batch_size - 1) / w->opt->msw_batch_size; - // 3. 处理msw任务 if (w->msw->p_msw_tasks_u8.n > 0) kt_for(w->opt->n_threads, worker_calc_matesw_avx512_u8, w, msw_batch_n); @@ -777,7 +787,9 @@ void gen_paired_sam(mem_worker_t* w) { PROF_END(gprof[G_calc_matesw], calc_matesw); // 4. 生成sam + PROF_START(gen_sam); kt_for(w->opt->n_threads, workder_gen_sam, w, batch_n); + PROF_END(gprof[G_gen_sam], gen_sam); } fprintf(stderr, "zzh %d : 8: %ld 16: %ld\n", i, w->msw->p_msw_tasks_u8.n, w->msw->p_msw_tasks_i16.n); } \ No newline at end of file diff --git a/run.sh b/run.sh index eba86de..fd7d398 100755 --- a/run.sh +++ b/run.sh @@ -1,11 +1,11 @@ -thread=1 +thread=64 make clean; make -j 32 -#n1=~/data/dataset/D2/n1.fq.gz -#n2=~/data/dataset/D2/n2.fq.gz -n1=~/data/dataset/D2/d1.fq -n2=~/data/dataset/D2/d2.fq +n1=~/data/dataset/D2/n1.fq.gz +n2=~/data/dataset/D2/n2.fq.gz +#n1=~/data/dataset/D2/d1.fq +#n2=~/data/dataset/D2/d2.fq #n1=~/data/SRR25735656_1.fastq.gz #n2=~/data/SRR25735656_2.fastq.gz @@ -17,8 +17,8 @@ reference=~/data/reference/fmt/human_g1k_v37_decoy.fasta #out=/dev/null #out=./oldsam-D2-out.sam -#out=./D2-1.sam -out=./d.sam +out=./D2-1.sam +#out=./d.sam prog=./fastalign #prog=/home/zzh/fastbwa