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Changing timing from TICTOC to gettimeofday

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This commit is contained in:
Noah L. Schrick 2022-12-04 20:05:27 -06:00
parent dfe2f7b3cf
commit 7e2e283529
20 changed files with 49129 additions and 147439 deletions
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2
Code/Duality_Technologies/GWAS/build/CMakeCache.txt
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@ -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

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

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

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Code/Duality_Technologies/GWAS/build/cmake_install.cmake
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@ -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()

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Code/Duality_Technologies/GWAS/data/0_0chi2.txt
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Code/Duality_Technologies/GWAS/data/0_0odds.txt
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Code/Duality_Technologies/GWAS/data/0_0result.txt
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@ -1,5 +1,5 @@
Key Generation Time: 0.023 s
Encoding and Encryption Time: 9.675 s
Computation Time: 1.814 s
Decryption & Decoding Time: 0.159 s
End-to-end Runtime: 11.974 s
Key Generation Time: 0.02361 s
Encoding and Encryption Time: 9.65614 s
Computation Time: 1.80108 s
Decryption & Decoding Time: 0.159233 s
End-to-end Runtime: 11.9779 s

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

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Code/Duality_Technologies/GWAS/data/odds.txt
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Code/Duality_Technologies/GWAS/data/result.txt
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@ -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

68
Code/Duality_Technologies/GWAS/demo-chi2.cpp
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@ -183,12 +183,13 @@ int main(int argc, char *argv[]) {
cc->Enable(SHE);
cc->Enable(LEVELEDSHE);
TimeVar t;
TIC(t);
struct timeval t1,t2;
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(2)= computationTime;
task_times.at(3) = decryptionTime;
task_times.at(4) = endToEndTime;
task_times.at(5) = ioTime;
task_times.at(1) += encryptionTime;
task_times.at(2) += computationTime;
task_times.at(3) += decryptionTime;
task_times.at(4) += endToEndTime;
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 << "Total Encoding and Encryption Time: \t" << task_times.at(1)/1000 << " s" << std::endl;
std::cout << "Total Computation Time: \t\t" << task_times.at(2)/1000 << " s" << std::endl;
std::cout << "Total Decryption & Decoding Time: \t" << task_times.at(3)/1000 << " s" << std::endl;
std::cout << "Total File IO Time: \t\t\t" << task_times.at(5)/1000 << " s" << std::endl;
std::cout << "Total End-to-end Runtime: \t\t" << task_times.at(4)/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)/1000.0 << " 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)/1000.0 << " 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)/1000.0 << " 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;
TimeVar tAll;
TIC(tAll);
struct timeval t1,t2;
gettimeofday(&t1,NULL);
//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);
TIC(t);
gettimeofday(&t4,NULL);
ioTime += (t4.tv_sec-t3.tv_sec)*1000.0+(t4.tv_usec-t3.tv_usec)/1000.0;
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);
TIC(t);
gettimeofday(&t6,NULL);
encryptionTime += (t6.tv_sec-t5.tv_sec)*1000.0+(t6.tv_usec-t5.tv_usec)/1000.0;
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;