添加了一些统计时间的代码

Co-authored-by: Copilot <copilot@github.com>

src/sort/phase_2_merge.cpp

@@ -186,6 +186,8 @@ static void mtCopyBams(void* data, long idx, int tid) {
     Phase2PipelineArg& p = *(Phase2PipelineArg*)data;
     MergeCompressData& mergeData = p.mergeData[p.mergeOrder % p.MERGE_BUF_NUM];
 
+    idx += mergeData.lastRoundIdx;
+
     auto& bams = mergeData.blockDataArr[idx].bamPtrArr;
     auto& blockData = mergeData.blockDataArr[idx].blockBuf;
 
@@ -262,20 +264,22 @@ static bool doPhase2Merge(Phase2PipelineArg& p, Phase2BamHeap<BamGreaterThan>& h
         }
     }
     // 并行拷贝bam数据
-    if (p.mergeOrder == 43) {
+    //if (p.mergeOrder == 43) {
-        spdlog::info("curIdx: {}, bytes: {}", mergeData.curIdx, mergeData.curBytes);
+    //    spdlog::info("curIdx: {}, bytes: {}", mergeData.curIdx, mergeData.curBytes);
-    }
+    //}
-    spdlog::info("curIdx: {}", mergeData.curIdx);
+    spdlog::info("curIdx: {}, lastIdx: {}, diff: {}", mergeData.curIdx, mergeData.lastRoundIdx, mergeData.curIdx - mergeData.lastRoundIdx);
-    if (mergeData.lastRoundIdx != p.compressBlocksThreshold) { // 回头再想想
-
-    }
 
+    PROF_G_BEG(phase2_copyBam);
     if (mergeData.curIdx < p.compressBlocksThreshold) {
-        kt_for(p.numThread, mtCopyBams, &p, mergeData.curIdx + 1);
+        kt_for(p.numThread, mtCopyBams, &p, mergeData.curIdx + 1 - mergeData.lastRoundIdx);
         // kt_for(p.numThread, mtCopyBams, &p, mergeData.curIdx);
+        mergeData.lastRoundIdx = mergeData.curIdx;
     } else {
-        kt_for(p.numThread, mtCopyBams, &p, mergeData.curIdx);
+        kt_for(p.numThread, mtCopyBams, &p, mergeData.curIdx - mergeData.lastRoundIdx);
+        mergeData.lastRoundIdx = 0;
     }
+    PROF_G_END(phase2_copyBam);
+
     // if (mergeFull != nullptr && * mergeFull) {
     // if (mergeData.curIdx == 2) {
     //     for (int n = 0; n < mergeData.curIdx; ++n) {
@@ -310,10 +314,9 @@ static bool doPhase2Merge(Phase2PipelineArg& p, Phase2BamHeap<BamGreaterThan>& h
          for (int i = 0; i <= mergeData.curIdx; ++i) {
              all_bams += mergeData.blockDataArr[i].bamNum;
          }
-         spdlog::info("phase2 merge sort order: {}, write bam id: {}, all bams: {}", p.mergeOrder, write_bam_id, all_bams);
+         //spdlog::info("phase2 merge sort order: {}, write bam id: {}, all bams: {}", p.mergeOrder, write_bam_id, all_bams);
      }
     // spdlog::info("curIdx: {}", mergeData.curIdx);
-
      return finish;
 }
 

src/sort/phase_2_read.cpp

@@ -48,7 +48,7 @@ bool doReadMidFiles(Phase2PipelineArg& p) {
         finishNum += f.finish;
         //spdlog::info("fid: {}, readyNum: {}", i, f.readyReadBufNum);
     }
-    spdlog::info("phase2 read order: {}, finishNum: {}, files: {}", p.readOrder, finishNum, p.midFiles.size());
+    // spdlog::info("phase2 read order: {}, finishNum: {}, files: {}", p.readOrder, finishNum, p.midFiles.size());
     finish = finishNum == p.midFiles.size();
     PROF_G_END(phase2_read);
     return finish;
@@ -283,7 +283,7 @@ bool doPhase2Uncompress(Phase2PipelineArg& p) {
     }
     PROF_G_END(phase2_uncompress);
 
-    spdlog::info("phase2 uncompress order: {}, read bams: {}, blocks: {}", p.uncompressOrder, read_bam_id, block_id);
+    // spdlog::info("phase2 uncompress order: {}, read bams: {}, blocks: {}", p.uncompressOrder, read_bam_id, block_id);
 
     return hasUncompress;
 

src/sort/phase_2_write.cpp

@@ -66,7 +66,7 @@ static void mtCompressBlock(void* data, long idx, int tid) {
 }
 
 static void doCompress(Phase2PipelineArg& p) {
-    PROF_G_BEG(compress);
+    PROF_G_BEG(phase2_compress);
     auto& compressBuf = p.compressBuf[p.compressOrder % p.COMPRESS_BUF_NUM];
     auto& mergeData = p.mergeData[p.compressOrder % p.MERGE_BUF_NUM];
     compressBuf.Clear();
@@ -78,8 +78,8 @@ static void doCompress(Phase2PipelineArg& p) {
         all_bams += mergeData.blockDataArr[i].bamNum;
     }
     mergeData.Clear();
-    spdlog::info("compress order: {}, bytes: {}, bams: {}", p.compressOrder, compressBuf.curLen, all_bams);
+    // spdlog::info("compress order: {}, bytes: {}, bams: {}", p.compressOrder, compressBuf.curLen, all_bams);
-    PROF_G_END(compress);
+    PROF_G_END(phase2_compress);
 
     // 调试用
 #if 0

src/util/profiling.cpp

@@ -63,13 +63,15 @@ int displayProfiling(int nthread) {
     PRINT_GP(merge);
     PRINT_GP(compress);
     PRINT_GP(write_mid);
-    PRINT_GP(phase2_compress);
     PRINT_GP(read_mid);
-    PRINT_GP(write_final);
     PRINT_GP(mid_all);
     PRINT_GP(phase2_read);
     PRINT_GP(phase2_uncompress);
     PRINT_GP(phase2_copyToMerge);
+    PRINT_GP(phase2_copyBam);
+    PRINT_GP(phase2_merge);
+    PRINT_GP(phase2_compress);
+    PRINT_GP(write_final);
     PRINT_GP(phase2);
 
     PRINT_TP(sort, nthread);

src/util/profiling.h

@@ -79,6 +79,7 @@ enum {
     GP_phase2_read,
     GP_phase2_uncompress,
     GP_phase2_copyToMerge,
+    GP_phase2_copyBam,
     GP_phase2_merge,
     GP_phase2_compress,
     GP_read_mid,