noah/CS-6643-Bioinformatics-Research-Project
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Adding file IO timing param

Browse Source
This commit is contained in:
Noah L. Schrick 2022-12-04 19:16:32 -06:00
parent fc184f4679
commit dfe2f7b3cf
8 changed files with 49168 additions and 49158 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

BIN
Code/Duality_Technologies/GWAS/build/CMakeFiles/demo-chi2.dir/demo-chi2.cpp.o
View File

Binary file not shown.

BIN
Code/Duality_Technologies/GWAS/build/demo-chi2
View File

Binary file not shown.

32764
Code/Duality_Technologies/GWAS/data/0_0chi2.txt
View File

File diff suppressed because it is too large Load Diff

32768
Code/Duality_Technologies/GWAS/data/0_0odds.txt
View File

File diff suppressed because it is too large Load Diff

32764
Code/Duality_Technologies/GWAS/data/0_0pvalue.txt
View File

File diff suppressed because it is too large Load Diff

10
Code/Duality_Technologies/GWAS/data/0_0result.txt
View File

@ -1,5 +1,5 @@
Key Generation Time: 0.024 s
Encoding and Encryption Time: 5.123 s
Computation Time: 1.372 s
Decryption & Decoding Time: 0.169 s
End-to-end Runtime: 6.994 s
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

18
Code/Duality_Technologies/GWAS/demo-chi2.cpp
View File

@ -156,6 +156,7 @@ int main(int argc, char *argv[]) {
double computationTime(0.0);
double decryptionTime(0.0);
double endToEndTime(0.0);
double ioTime(0.0);
//usint m = 16384;
usint m = 65536;
@ -200,7 +201,7 @@ int main(int argc, char *argv[]) {
int file_start = node_start + (batch_size*i);
std::cout << "Node " << world.rank() << " running batch " << i << " with batch size " << batch_gen << std::endl;
RunChi2(SNPDir, SNPFileName, pValue, Runtime, std::to_string(batch_gen), SNPs, file_start, keyGenTime, encryptionTime, computationTime, decryptionTime, endToEndTime, cc, keyPair, i, world);
RunChi2(SNPDir, SNPFileName, pValue, Runtime, std::to_string(batch_gen), SNPs, file_start, keyGenTime, encryptionTime, computationTime, decryptionTime, endToEndTime, ioTime, cc, keyPair, i, world);
}
std::cout << "Node " << world.rank() << " completed all batches." << std::endl;
@ -211,6 +212,8 @@ int main(int argc, char *argv[]) {
world.isend(0, 2, computationTime);
world.isend(0, 3, decryptionTime);
world.isend(0, 4, endToEndTime);
world.isend(0, 5, ioTime);
}
@ -218,7 +221,7 @@ int main(int argc, char *argv[]) {
if (world.rank() == 0){
std::vector<double> task_times;
for (int task = 0; task < 5; task++){
for (int task = 0; task < 6; task++){
task_times.push_back(0);
}
task_times.at(0) += keyGenTime;
@ -226,9 +229,12 @@ int main(int argc, char *argv[]) {
task_times.at(2)= computationTime;
task_times.at(3) = decryptionTime;
task_times.at(4) = endToEndTime;
task_times.at(5) = ioTime;
if (world.size() > 1){
for (int j = 0; j < 5; j++){
for (int j = 0; j < 6; j++){
while (world.iprobe(mpi::any_source, j)){
double tmp;
world.recv(mpi::any_source, j, tmp);
@ -241,6 +247,7 @@ int main(int argc, char *argv[]) {
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;
}
@ -250,7 +257,8 @@ int main(int argc, char *argv[]) {
void RunChi2(const string &SNPDir,
const string &SNPFileName, const string &pValue, const string &Runtime, const string &SampleSize, const string &SNPs,
size_t file_start, double &keyGenTime, double &encryptionTime, double &computationTime, double &decryptionTime, double &endToEndTime,
size_t file_start,
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;
@ -271,7 +279,9 @@ void RunChi2(const string &SNPDir,
usint m = 65536;
double scalingFactor = 2.5e-6;
TIC(t);
ReadSNPFile(headersS,sData,yData,SNPDir + "/" + SNPFileName,N,M, file_start);
ioTime += TOC(t);
TIC(t);

2
Code/Duality_Technologies/GWAS/demo_chi2.h
View File

@ -13,7 +13,7 @@ const double EPSILON = 1.0E-08;
void RunChi2(const string &SNPDir,
const string &SNPFileName, const string &pValue, const string &Runtime, const string &SampleSize, const string &SNPs,
size_t file_start,
double &keyGenTime, double &encryptionTime, double &computationTime, double &decryptionTime, double &endToEndTime,
double &keyGenTime, double &encryptionTime, double &computationTime, double &decryptionTime, double &endToEndTime, double &ioTime,
CryptoContext<DCRTPoly> &cc, auto &keyPair, int batch_num, mpi::communicator &world);