Changing timing from TICTOC to gettimeofday

Code/Duality_Technologies/GWAS/build/CMakeCache.txt

@@ -32,7 +32,7 @@ CMAKE_AR:FILEPATH=/usr/bin/ar
 
 //Choose the type of build, options are: None Debug Release RelWithDebInfo
 // MinSizeRel ...
-CMAKE_BUILD_TYPE:STRING=
+CMAKE_BUILD_TYPE:STRING=RELEASE
 
 //Enable/Disable color output during build.
 CMAKE_COLOR_MAKEFILE:BOOL=ON

Code/Duality_Technologies/GWAS/build/CMakeFiles/demo-chi2.dir/flags.make

@@ -6,5 +6,5 @@ CXX_DEFINES = -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_
 
 CXX_INCLUDES = -I/home/noah/Documents/School/CS-6643-Bioinformatics/CS-6643-Bioinformatics-Research-Project/Code/Duality_Technologies/PALISADE/install/include/palisade -I/home/noah/Documents/School/CS-6643-Bioinformatics/CS-6643-Bioinformatics-Research-Project/Code/Duality_Technologies/PALISADE/install/include/palisade/core -I/home/noah/Documents/School/CS-6643-Bioinformatics/CS-6643-Bioinformatics-Research-Project/Code/Duality_Technologies/PALISADE/install/include/palisade/pke
 
-CXX_FLAGS =  -Wall -Werror -O3  -DPALISADE_VERSION=1.11.8 -Wno-parentheses -DMATHBACKEND=2 -fopenmp -fopenmp -std=c++20
+CXX_FLAGS =  -Wall -Werror -O3  -DPALISADE_VERSION=1.11.8 -Wno-parentheses -DMATHBACKEND=2 -fopenmp -fopenmp -O3 -DNDEBUG -O1 -fopenmp -std=c++20
 

Code/Duality_Technologies/GWAS/build/CMakeFiles/demo-chi2.dir/link.txt

@@ -1 +1 @@
-/usr/bin/c++  -Wall -Werror -O3  -DPALISADE_VERSION=1.11.8 -Wno-parentheses -DMATHBACKEND=2 -fopenmp -fopenmp -Wl,-rpath -Wl,/usr/lib -Wl,--enable-new-dtags "CMakeFiles/demo-chi2.dir/demo-chi2.cpp.o" "CMakeFiles/demo-chi2.dir/avail_mem.cpp.o" -o demo-chi2   -L/home/noah/Documents/School/CS-6643-Bioinformatics/CS-6643-Bioinformatics-Research-Project/Code/Duality_Technologies/PALISADE/install/lib  -Wl,-rpath,/home/noah/Documents/School/CS-6643-Bioinformatics/CS-6643-Bioinformatics-Research-Project/Code/Duality_Technologies/PALISADE/build/lib:/home/noah/Documents/School/CS-6643-Bioinformatics/CS-6643-Bioinformatics-Research-Project/Code/Duality_Technologies/PALISADE/install/lib /home/noah/Documents/School/CS-6643-Bioinformatics/CS-6643-Bioinformatics-Research-Project/Code/Duality_Technologies/PALISADE/build/lib/libPALISADEpke.so.1.11.8 /home/noah/Documents/School/CS-6643-Bioinformatics/CS-6643-Bioinformatics-Research-Project/Code/Duality_Technologies/PALISADE/build/lib/libPALISADEbinfhe.so.1.11.8 -fopenmp /usr/lib/libboost_mpi.so.1.80.0 /usr/lib/libmpi_cxx.so /usr/lib/libmpi.so /home/noah/Documents/School/CS-6643-Bioinformatics/CS-6643-Bioinformatics-Research-Project/Code/Duality_Technologies/PALISADE/build/lib/libPALISADEcore.so.1.11.8 -fopenmp /usr/lib/libboost_serialization.so.1.80.0 /usr/lib/libmpi_cxx.so /usr/lib/libmpi.so 
+/usr/bin/c++  -Wall -Werror -O3  -DPALISADE_VERSION=1.11.8 -Wno-parentheses -DMATHBACKEND=2 -fopenmp -fopenmp -O3 -DNDEBUG -O1 -fopenmp -Wl,-rpath -Wl,/usr/lib -Wl,--enable-new-dtags "CMakeFiles/demo-chi2.dir/demo-chi2.cpp.o" "CMakeFiles/demo-chi2.dir/avail_mem.cpp.o" -o demo-chi2   -L/home/noah/Documents/School/CS-6643-Bioinformatics/CS-6643-Bioinformatics-Research-Project/Code/Duality_Technologies/PALISADE/install/lib  -Wl,-rpath,/home/noah/Documents/School/CS-6643-Bioinformatics/CS-6643-Bioinformatics-Research-Project/Code/Duality_Technologies/PALISADE/build/lib:/home/noah/Documents/School/CS-6643-Bioinformatics/CS-6643-Bioinformatics-Research-Project/Code/Duality_Technologies/PALISADE/install/lib /home/noah/Documents/School/CS-6643-Bioinformatics/CS-6643-Bioinformatics-Research-Project/Code/Duality_Technologies/PALISADE/build/lib/libPALISADEpke.so.1.11.8 /home/noah/Documents/School/CS-6643-Bioinformatics/CS-6643-Bioinformatics-Research-Project/Code/Duality_Technologies/PALISADE/build/lib/libPALISADEbinfhe.so.1.11.8 -fopenmp /usr/lib/libboost_mpi.so.1.80.0 /usr/lib/libmpi_cxx.so /usr/lib/libmpi.so /home/noah/Documents/School/CS-6643-Bioinformatics/CS-6643-Bioinformatics-Research-Project/Code/Duality_Technologies/PALISADE/build/lib/libPALISADEcore.so.1.11.8 -fopenmp /usr/lib/libboost_serialization.so.1.80.0 /usr/lib/libmpi_cxx.so /usr/lib/libmpi.so 

Code/Duality_Technologies/GWAS/build/cmake_install.cmake

@@ -12,7 +12,7 @@ if(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)
     string(REGEX REPLACE "^[^A-Za-z0-9_]+" ""
            CMAKE_INSTALL_CONFIG_NAME "${BUILD_TYPE}")
   else()
-    set(CMAKE_INSTALL_CONFIG_NAME "")
+    set(CMAKE_INSTALL_CONFIG_NAME "RELEASE")
   endif()
   message(STATUS "Install configuration: \"${CMAKE_INSTALL_CONFIG_NAME}\"")
 endif()

Code/Duality_Technologies/GWAS/data/0_0result.txt

@@ -1,5 +1,5 @@
-Key Generation Time: 		0.023 s
+Key Generation Time: 		0.02361 s
-Encoding and Encryption Time: 	9.675 s
+Encoding and Encryption Time: 	9.65614 s
-Computation Time: 		1.814 s
+Computation Time: 		1.80108 s
-Decryption & Decoding Time: 	0.159 s
+Decryption & Decoding Time: 	0.159233 s
-End-to-end Runtime: 		11.974 s
+End-to-end Runtime: 		11.9779 s

Code/Duality_Technologies/GWAS/data/1_0result.txt

@@ -1,5 +0,0 @@
-Key Generation Time: 		0.029 s
-Encoding and Encryption Time: 	5.157 s
-Computation Time: 		1.37 s
-Decryption & Decoding Time: 	0.209 s
-End-to-end Runtime: 		6.988 s

Code/Duality_Technologies/GWAS/data/result.txt

@@ -1,5 +0,0 @@
-Key Generation Time: 		0.023 s
-Encoding and Encryption Time: 	9.686 s
-Computation Time: 		1.842 s
-Decryption & Decoding Time: 	0.159 s
-End-to-end Runtime: 		12.014 s

Code/Duality_Technologies/GWAS/demo-chi2.cpp

@@ -183,12 +183,13 @@ int main(int argc, char *argv[]) {
 	cc->Enable(SHE);
 	cc->Enable(LEVELEDSHE);
 
-	TimeVar t;
+ 	struct timeval t1,t2;
-	TIC(t);
+    gettimeofday(&t1,NULL);
-
 	auto keyPair = cc->KeyGen();
+    gettimeofday(&t2,NULL);
+
+	keyGenTime += (t2.tv_sec-t1.tv_sec)*1000.0+(t2.tv_usec-t1.tv_usec)/1000.0;
 
-	keyGenTime += TOC(t);
 
     for (int i = 0; i < std::ceil((double)node_samples/(double)batch_size); i++)
     {
@@ -213,8 +214,6 @@ int main(int argc, char *argv[]) {
     	world.isend(0, 3, decryptionTime);
     	world.isend(0, 4, endToEndTime);
     	world.isend(0, 5, ioTime);
-
-
     }
     
     world.barrier();
@@ -225,11 +224,11 @@ int main(int argc, char *argv[]) {
         	task_times.push_back(0);
    	 	}
     	task_times.at(0) += keyGenTime;
-		task_times.at(1) = encryptionTime;
+		task_times.at(1) += encryptionTime;
-		task_times.at(2)= computationTime;
+		task_times.at(2) += computationTime;
-		task_times.at(3) = decryptionTime;
+		task_times.at(3) += decryptionTime;
-		task_times.at(4) = endToEndTime;
+		task_times.at(4) += endToEndTime;
-		task_times.at(5) = ioTime;
+		task_times.at(5) += ioTime;
 
 
 
@@ -243,12 +242,12 @@ int main(int argc, char *argv[]) {
 			}
 		}
 
-		std::cout << "\nTotal Key Generation Time: \t\t" << task_times.at(0)/1000 << " s" << std::endl;
+		std::cout << "\nTotal Key Generation Time: \t\t" << task_times.at(0)/1000.0 << " s" << std::endl;
-		std::cout << "Total Encoding and Encryption Time: \t" << task_times.at(1)/1000 << " s" << std::endl;
+		std::cout << "Total Encoding and Encryption Time: \t" << task_times.at(1)/1000.0 << " s" << std::endl;
-		std::cout << "Total Computation Time: \t\t" << task_times.at(2)/1000 << " s" << std::endl;
+		std::cout << "Total Computation Time: \t\t" << task_times.at(2)/1000.0 << " s" << std::endl;
-		std::cout << "Total Decryption & Decoding Time: \t" << task_times.at(3)/1000 << " s" << std::endl;
+		std::cout << "Total Decryption & Decoding Time: \t" << task_times.at(3)/1000.0 << " s" << std::endl;
-		std::cout << "Total File IO Time: \t\t\t" << task_times.at(5)/1000 << " s" << std::endl;
+		std::cout << "Total File IO Time: \t\t\t" << task_times.at(5)/1000.0 << " s" << std::endl;
-		std::cout << "Total End-to-end Runtime: \t\t" << task_times.at(4)/1000 << " s" << std::endl;
+		std::cout << "Total End-to-end Runtime: \t\t" << task_times.at(4)/1000.0 << " s" << std::endl;
 
     }
 
@@ -261,10 +260,8 @@ void RunChi2(const string &SNPDir,
 		double &keyGenTime, double &encryptionTime, double &computationTime, double &decryptionTime, double &endToEndTime, double &ioTime,
 		CryptoContext<DCRTPoly> &cc, auto &keyPair, int batch_num, mpi::communicator &world) {
 
-	TimeVar t;
+	struct timeval t1,t2;
-	TimeVar tAll;
+    gettimeofday(&t1,NULL);
-
-	TIC(tAll);
 
 	//std::cout << "\n======CHI-SQUARE SOLUTION========\n" << std::endl;
 
@@ -279,12 +276,14 @@ void RunChi2(const string &SNPDir,
 	usint m = 65536;
 	double scalingFactor = 2.5e-6;
 
-	TIC(t);
+	struct timeval t3,t4;
+    gettimeofday(&t3,NULL);
 	ReadSNPFile(headersS,sData,yData,SNPDir + "/" + SNPFileName,N,M, file_start);
-	ioTime += TOC(t);
+	gettimeofday(&t4,NULL);
-
+	ioTime += (t4.tv_sec-t3.tv_sec)*1000.0+(t4.tv_usec-t3.tv_usec)/1000.0;
-	TIC(t);
 
+	struct timeval t5,t6;
+    gettimeofday(&t5,NULL);
 	size_t sizeS = (size_t)std::ceil((double)sData[0].size()/(m/4));
 
 	std::vector<std::vector<std::vector<std::complex<double>>>> sDataArray(sizeS);
@@ -325,10 +324,11 @@ void RunChi2(const string &SNPDir,
 		Y[i] = cc->Encrypt(keyPair.publicKey, sTemp2);
 	}
 
-	encryptionTime += TOC(t);
+	gettimeofday(&t6,NULL);
-
+	encryptionTime += (t6.tv_sec-t5.tv_sec)*1000.0+(t6.tv_usec-t5.tv_usec)/1000.0;
-	TIC(t);
 
+	struct timeval t7,t8;
+    gettimeofday(&t7,NULL);
 	Plaintext d = cc->MakeCKKSPackedPlaintext(std::vector<std::complex<double>>(m/4,2*N));
 	d->SetFormat(EVALUATION);
 
@@ -420,9 +420,11 @@ void RunChi2(const string &SNPDir,
 
 	}
 
-	computationTime += TOC(t);
+	gettimeofday(&t8,NULL);
+	computationTime += (t8.tv_sec-t7.tv_sec)*1000.0+(t8.tv_usec-t7.tv_usec)/1000.0;
 
-	TIC(t);
+	struct timeval t9,t10;
+    gettimeofday(&t9,NULL);
 
 	std::vector<Plaintext> pN(sizeS);
 	std::vector<Plaintext> pD(sizeS);
@@ -436,7 +438,8 @@ void RunChi2(const string &SNPDir,
 		cc->Decrypt(keyPair.secretKey, orD[s] , &(oddD[s]));
 	}
 
-	decryptionTime += TOC(t);
+	gettimeofday(&t10,NULL);
+	decryptionTime += (t10.tv_sec-t9.tv_sec)*1000.0+(t10.tv_usec-t9.tv_usec)/1000.0;
 
 	std::vector<double> chival(headersS.size());
 	std::vector<double> pval(headersS.size());
@@ -491,7 +494,8 @@ void RunChi2(const string &SNPDir,
 	//std::cout << "Computation Time: \t\t" << computationTime/1000 << " s" << std::endl;
 	//std::cout << "Decryption & Decoding Time: \t" << decryptionTime/1000 << " s" << std::endl;
 
-	endToEndTime += TOC(tAll);
+	gettimeofday(&t2,NULL);
+	endToEndTime += (t2.tv_sec-t1.tv_sec)*1000.0+(t2.tv_usec-t1.tv_usec)/1000.0;
 
     //std::cout << "\nEnd-to-end Runtime: \t\t" << endToEndTime/1000 << " s" << std::endl;