Added benchmark timing

CMakeLists.txt

@@ -11,7 +11,7 @@ set(CMAKE_CXX_STANDARD_REQUIRED ON)
 # Optimisation flags
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
 set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -g")
-set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -O3 /O2")
+set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -O3")
 
 # Add library subdirectory
 add_subdirectory (${CMAKE_SOURCE_DIR}/lib)

ISSLScoreOfftargets/ISSLScoreOfftargets.cpp

@@ -32,6 +32,8 @@ string signatureToSequence(uint64_t sig, uint64_t seqLen)
 
 int main(int argc, char** argv)
 {
+ auto startLoading = std::chrono::high_resolution_clock::now();
+
  if (argc < 4) {
  fprintf(stderr, "Usage: %s [issltable] [query file] [max distance] [score-threshold] [score-method]\n", argv[0]);
  exit(1);
@@ -221,6 +223,9 @@ int main(int argc, char** argv)
  sliceLimitOffset += sliceLimit;
  }
 
+ auto endLoading = std::chrono::high_resolution_clock::now();
+ auto startProcessing = std::chrono::high_resolution_clock::now();
+
  //TODO: rewrite
  /** Load query file (candidate guides)
  * and prepare memory for calculated global scores
@@ -259,7 +264,6 @@ int main(int argc, char** argv)
  }
 
  /** Begin scoring */
- omp_set_num_threads(32);
  #pragma omp parallel
  {
  vector<uint64_t> offtargetToggles(numOfftargetToggles);
@@ -459,6 +463,20 @@ int main(int argc, char** argv)
  }
  }
 
+ auto endProcessing = std::chrono::high_resolution_clock::now();
+ vector<std::chrono::nanoseconds> durations;
+ durations.push_back(endProcessing - startLoading);
+ durations.push_back(endProcessing - startProcessing);
+ durations.push_back(endLoading - startLoading);
+
+ for (const auto& duration : durations)
+ {
+ std::chrono::minutes minutes = std::chrono::duration_cast<std::chrono::minutes>(duration);
+ std::chrono::seconds seconds = std::chrono::duration_cast<std::chrono::seconds>(duration - minutes);
+ printf("%02ld:%02ld\t", minutes.count(), seconds.count());
+ }
+ printf("\n");
+
  /** Print global scores to stdout */
  for (size_t searchIdx = 0; searchIdx < querySignatures.size(); searchIdx++) {
  auto querySequence = signatureToSequence(querySignatures[searchIdx], 20);

ISSLScoreOfftargets/ISSLScoreOfftargets.hpp

@@ -7,6 +7,7 @@
 #include <vector>
 #include <boost/iostreams/device/mapped_file.hpp>
 #include <omp.h>
+#include <chrono>
 #include "../include/phmap/phmap.h"
 #include "../include/libpopcnt/libpopcnt.h"
 #include "../include/otScorePenalties.hpp"

ISSLScoreOfftargetsMMF/ISSLScoreOfftargetsMMF.cpp

@@ -33,6 +33,8 @@ string signatureToSequence(uint64_t sig, uint64_t seqLen)
 
 int main(int argc, char** argv)
 {
+ auto startLoading = std::chrono::high_resolution_clock::now();
+
  if (argc < 4) {
  fprintf(stderr, "Usage: %s [issltable] [query file] [max distance] [score-threshold] [score-method]\n", argv[0]);
  exit(1);
@@ -196,6 +198,9 @@ int main(int argc, char** argv)
  }
  }
 
+ auto endLoading = std::chrono::high_resolution_clock::now();
+ auto startProcessing = std::chrono::high_resolution_clock::now();
+
  //TODO: rewrite
  /** Load query file (candidate guides)
  * and prepare memory for calculated global scores
@@ -223,9 +228,9 @@ int main(int argc, char** argv)
  fclose(fp);
 
  /** Binary encode query sequences */
-#pragma omp parallel
+ #pragma omp parallel
  {
-#pragma omp for
+ #pragma omp for
  for (int i = 0; i < queryCount; i++) {
  char* ptr = &queryDataSet[i * seqLineLength];
  uint64_t signature = sequenceToSignature(ptr, 20);
@@ -234,7 +239,6 @@ int main(int argc, char** argv)
  }
 
  /** Begin scoring */
- omp_set_num_threads(32);
  #pragma omp parallel
  {
  vector<uint64_t> offtargetToggles(numOfftargetToggles);
@@ -434,6 +438,20 @@ int main(int argc, char** argv)
  }
  }
 
+ auto endProcessing = std::chrono::high_resolution_clock::now();
+ vector<std::chrono::nanoseconds> durations;
+ durations.push_back(endProcessing - startLoading);
+ durations.push_back(endProcessing - startProcessing);
+ durations.push_back(endLoading - startLoading);
+
+ for (const auto& duration : durations)
+ {
+ std::chrono::minutes minutes = std::chrono::duration_cast<std::chrono::minutes>(duration);
+ std::chrono::seconds seconds = std::chrono::duration_cast<std::chrono::seconds>(duration - minutes);
+ printf("%02ld:%02ld\t", minutes.count(), seconds.count());
+ }
+ printf("\n");
+
  /** Print global scores to stdout */
  for (size_t searchIdx = 0; searchIdx < querySignatures.size(); searchIdx++) {
  auto querySequence = signatureToSequence(querySignatures[searchIdx], 20);

ISSLScoreOfftargetsMMF/ISSLScoreOfftargetsMMF.hpp

@@ -7,6 +7,7 @@
 #include <vector>
 #include <boost/iostreams/device/mapped_file.hpp>
 #include <omp.h>
+#include <chrono>
 #include "../include/phmap/phmap.h"
 #include "../include/libpopcnt/libpopcnt.h"
 #include "../include/otScorePenalties.hpp"