我一直在努力改善我的程序的执行时间。下面的函数是类KAT的一个方法，它也有references、samples和pointerMatrix作为变量。有 3 个参考文献和 3 个样本。我开始使用智能指针是因为 refAligner.align(sample) 的结果很大。
当我单独测量每个部分的执行时间时，总计在 400-500 秒之间。但是，整个函数的执行时间是它的两倍。我注意到在“Add to matrix:”的最后一个 std::cout 和“Entire alignment:”的 std::cout 之间有相当长的等待，所以在那段时间里可能发生了什么，但我不知道是什么.在这段额外的执行时间内发生了什么？我很乐意提供更多代码/信息！谢谢！
class KAT {
private:
std::string REFERENCES_FOLDER = "/References";
std::string SAMPLES_FOLDER = "/Samples";
Input input;
References references;
Filenames referenceFilenames;
Samples samples;
Filenames sampleFilenames;
std::vector<std::vector<std::unique_ptr<Alignment>>> pointerMatrix;
Results result;
void readReferences();
void calculateReferencesTextIndex();
void readSamples();
void createKmers();
void alignAllSamplesToAllReferences();
Results createResult();
void copyAlignmentsToResult();
public:
KAT(Input input_): input(input_) { }
Results align();
};
这是有问题的方法。
void KAT::alignAllSamplesToAllReferences() {
auto start1 = std::chrono::high_resolution_clock::now();
for (Reference reference : references) {
auto start2 = std::chrono::high_resolution_clock::now();
ReferenceAligner refAligner(reference);
std::vector<std::unique_ptr<Alignment>> alignPointers;
auto stop2 = std::chrono::high_resolution_clock::now();
auto duration2 = std::chrono::duration_cast<std::chrono::seconds>(stop2 - start2);
std::cout << "RefAligner Class: " << duration2.count() << std::endl;
for (Sample sample: samples) {
auto start3 = std::chrono::high_resolution_clock::now();
std::unique_ptr<Alignment> aligmentPointer = refAligner.align(sample);
alignPointers.push_back(std::move(aligmentPointer));
auto stop3 = std::chrono::high_resolution_clock::now();
auto duration3 = std::chrono::duration_cast<std::chrono::seconds>(stop3 - start3);
std::cout << "Align and pushback: " << duration3.count() << std::endl;
}
auto start4 = std::chrono::high_resolution_clock::now();
pointerMatrix.push_back(std::move(alignPointers));
auto stop4 = std::chrono::high_resolution_clock::now();
auto duration4 = std::chrono::duration_cast<std::chrono::seconds>(stop4 - start4);
std::cout << "Add to matrix: " << duration4.count() << std::endl;
}
auto stop1 = std::chrono::high_resolution_clock::now();
auto duration1 = std::chrono::duration_cast<std::chrono::seconds>(stop1 - start1);
std::cout << "Entire alignment: " << duration1.count() << std::endl;
}
这些是我得到的执行时间，它们非常一致。如果我将个人时间加起来，我会得到 414 秒。
Aligning...
RefAligner Class: 0
Align and pushback: 12
Align and pushback: 44
Align and pushback: 21
Add to matrix: 0
RefAligner Class: 0
Align and pushback: 18
Align and pushback: 70
Align and pushback: 35
Add to matrix: 0
RefAligner Class: 0
Align and pushback: 46
Align and pushback: 115
Align and pushback: 53
Add to matrix: 0
Entire alignment: 999
Align all samples: 999
Create Results: 0
Writing results...
Main: 1171