void print_twoLevel_Cluster(Network network, string networkName, string outDir) {
ofstream outFile;
ostringstream oss;
oss << outDir << "/" << networkName << ".tree";
outFile.open(oss.str().c_str());
outFile << "# Code length " << network.CodeLength()/log(2.0) << " in " << network.NModule() << " modules." << endl;
int nModules = network.modules.size();
int modIdx = 0;
for (int i = 0; i < nModules; i++) {
int nMembers = network.modules[i].NumMembers();
if (nMembers > 0)
modIdx++;
for (int j = 0; j < nMembers; j++) {
outFile << modIdx << ":" << j+1 << " " << network.modules[i].members[j]->Size() << " \"" << network.modules[i].members[j]->Name() << "\"" << endl;
}
}
outFile.close();
}
int main(int argc, char *argv[]) {
if( argc < 10){
cout << "Call: ./ompRelaxmap <seed> <network.net> <# threads> <# attempts> <threshold> <vThresh> <maxIter> <outDir> <prior/normal> [selflinks]" << endl;
exit(-1);
}
string outDir = string(argv[8]);
int maxIter = atoi(argv[7]); // Set the maximum number of iteration..
int Ntrials = atoi(argv[4]); // Set number of partition attempts
int numThreads = atoi(argv[3]); // Set number of threads...
string line;
string buf;
MTRand *R = new MTRand(stou(argv[1]));
string infile = string(argv[2]);
string networkFile = string(argv[2]);
string networkName(networkFile.begin() + networkFile.find_last_of("/"), networkFile.begin() + networkFile.find_last_of("."));
string networkType(infile.begin() + infile.find_last_of("."), infile.end());
double threshold = atof(argv[5]);
double vThresh = atof(argv[6]); // vertex-threshold: threshold for each vertex-movement.
cout << "Threshold = " << threshold << ", Vertex-Threshold = " << vThresh << endl;
vThresh *= -1; // change the threshold value for negative.
string priorFlag = string(argv[9]);
bool prior = false;
if (priorFlag == "prior")
prior = true;
bool includeSelfLinks = false;
if(argc == 11) {
string selfLinks(argv[10]);
if(selfLinks == "selflinks")
includeSelfLinks = true;
}
Network origNetwork; // default constructor is called.
origNetwork.R = R;
// time values for measuring elapsed times for each step...
struct timeval allStart, allEnd;
struct timeval noIOstart, noIOend;
struct timeval start, end;
gettimeofday(&allStart, NULL);
gettimeofday(&start, NULL);
if(networkType == ".net"){
load_pajek_format_network(networkFile, origNetwork);
}
else{
load_linkList_format_network(networkFile, origNetwork);
}
gettimeofday(&end, NULL);
cout << "Time for reading input data : " << elapsedTimeInSec(start, end) << " (sec)" << endl;
gettimeofday(&noIOstart, NULL);
int nNode = origNetwork.NNode();
double totNodeWeights = origNetwork.TotNodeWeights();
cout << "total Node weights = " << totNodeWeights << endl;
gettimeofday(&start, NULL);
for (int i = 0; i < nNode; i++) {
origNetwork.nodes[i].setTeleportWeight(origNetwork.nodes[i].NodeWeight()/totNodeWeights);
}
int NselfLinks = 0;
for(map<pair<int,int>,double>::iterator it = origNetwork.Edges.begin(); it != origNetwork.Edges.end(); it++){
int from = it->first.first;
int to = it->first.second;
double weight = it->second;
if(weight > 0.0){
if(from == to){
NselfLinks++;
//if(includeSelfLinks)
// origNetwork.nodes[from]->selfLink += weight;
}
else{
origNetwork.nodes[from].outLinks.push_back(make_pair(to,weight));
// we will going to update inLinks, after we got final flow of the network.
//origNetwork.nodes[to].inLinks.push_back(make_pair(from,weight));
}
}
}
if(includeSelfLinks)
//cout << "including " << NselfLinks << " self link(s)." << endl;
cout << "current version always excludes self links.\nignoring " << NselfLinks << " self link(s)." << endl;
else
cout << "ignoring " << NselfLinks << " self link(s)." << endl;
//Swap vector to free memory
map<pair<int,int>,double>().swap(origNetwork.Edges);
cout << "DONE: Parsing the given network ..." << endl;
gettimeofday(&end, NULL);
cout << "Time for parsing the given network : " << elapsedTimeInSec(start, end) << " (sec)" << endl;
gettimeofday(&start, NULL);
// Initialization.
origNetwork.initiate(numThreads);
// Now update inLinks..
for (int i = 0; i < nNode; i++) {
int nOutLinks = origNetwork.nodes[i].outLinks.size();
for (int j = 0; j < nOutLinks; j++)
origNetwork.nodes[origNetwork.nodes[i].outLinks[j].first].inLinks.push_back(make_pair(i,origNetwork.nodes[i].outLinks[j].second));
}
gettimeofday(&end, NULL);
cout << "DONE: Initiate() ... in " << elapsedTimeInSec(start, end) << " (sec)" << endl;
cout << "Initial Code Length: " << origNetwork.CodeLength()/log(2.0) << " in " << origNetwork.NModule() << " modules.\n";
// copy size of each node for print in order.
vector<double> nodeSize(nNode);
for (int i = 0; i < nNode; i++)
nodeSize[i] = origNetwork.nodes[i].Size();
cout << "Now partition the network starts...\n";
gettimeofday(&start, NULL);
bool fineTune = true;
bool fast = false; // This will be true only for sub-module partitioning...
int step = 1;
// Initial SuperStep running ...
double oldCodeLength = origNetwork.CodeLength();
stochastic_greedy_partition(origNetwork, numThreads, threshold, vThresh, maxIter, prior, fineTune, fast);
cout << "SuperStep [" << step << "] - codeLength = " << origNetwork.CodeLength()/log(2.0) << " in " << origNetwork.NModule() << " modules." << endl;
bool nextIter = true;
if ((oldCodeLength - origNetwork.CodeLength())/log(2.0) < threshold)
nextIter = false;
struct timeval subStart, subEnd;
while (nextIter) {
oldCodeLength = origNetwork.CodeLength();
stochastic_greedy_partition(origNetwork, numThreads, threshold, vThresh, maxIter, prior, fineTune, fast);
step++;
cout << "SuperStep [" << step << "] - codeLength = " << origNetwork.CodeLength()/log(2.0) << " in " << origNetwork.NModule() << " modules." << endl;
if ((oldCodeLength - origNetwork.CodeLength())/log(2.0) < threshold)
nextIter = false;
fineTune = !fineTune; // fine-tune and coarse-tune will be done alternatively.
if (nextIter && !fineTune) {
// Next iteration will be Coarse Tune.
gettimeofday(&subStart, NULL);
generate_sub_modules(origNetwork, numThreads, threshold, maxIter);
gettimeofday(&subEnd, NULL);
cout << "Time for finding sub-modules: " << elapsedTimeInSec(subStart, subEnd) << " (sec)" << endl;
}
}
gettimeofday(&end, NULL);
cout << "Time for partitioning : " << elapsedTimeInSec(start, end) << " (sec)" << endl;
cout << "DONE: Code Length = " << origNetwork.CodeLength()/log(2.0) << " in ";
cout << origNetwork.NModule() << " modules, with " << nNode << " nodes.\n" << endl;
gettimeofday(&noIOend, NULL);
gettimeofday(&allEnd, NULL);
cout << "Overall Elapsed Time for Module Detection (w/o file IO): " << elapsedTimeInSec(noIOstart, noIOend) << " (sec)" << endl;
cout << "Overall Elapsed Time for Module Detection (w/ file Reading): " << elapsedTimeInSec(allStart, allEnd) << " (sec)" << endl;
cout << "\nComputed Code Length = " << origNetwork.calculateCodeLength()/log(2.0) << endl;
//Print two-level clustering result in .tree file
print_twoLevel_Cluster(origNetwork, networkName, outDir);
// Print partition in Pajek's .clu format
ofstream outFile;
ostringstream oss;
oss.str("");
oss << outDir << "/" << networkName << ".clu";
outFile.open(oss.str().c_str());
outFile << "*Vertices " << nNode << "\x0D\x0A";
for(int i=0;i<nNode;i++)
outFile << origNetwork.nodes[i].ModIdx() + 1 << "\x0D\x0A";
outFile.close();
}
/**
* This function will be called for partitioning sub-Module of each module of the original graph.
* Thus, we would like to reduce printing from this function for providing high-level log.
*/
void partition_module_network(Network &network, int numTh, double threshold, int maxIter, bool fast) {
double oldCodeLength = network.CodeLength();
int iter = 0;
bool stop = false;
double tSequential;
int numMoved = 0;
while (!stop && iter < maxIter) {
oldCodeLength = network.CodeLength();
if (numTh == 1) {
numMoved = network.move();
}
else {
numMoved = network.parallelMove(numTh, tSequential);
}
iter++;
if ((oldCodeLength - network.CodeLength())/log(2.0) < threshold)
stop = true;
}
int outerLoop = 1;
network.updateMembersInModule();
if (fast)
return;
do {
oldCodeLength = network.CodeLength();
stop = false;
network.convertModulesToSuperNodes(numTh);
int spIter = 0;
while (!stop && spIter < maxIter) {
double innerOldCodeLength = network.CodeLength();
if (numTh == 1) {
numMoved = network.moveSuperNodes();
}
else {
numMoved = network.parallelMoveSuperNodes(numTh, tSequential);
}
spIter++;
if ((innerOldCodeLength - network.CodeLength())/log(2.0) < threshold)
stop = true;
}
network.updateMembersInModule();
outerLoop++;
} while ((oldCodeLength - network.CodeLength())/log(2.0) > threshold);
}
/*
* Procedure will be following:
* 1) in random sequential order, each node is moved to its neighbor module that results in the largest gain of the map eq.
* If no move results in a gain of the map equation, the node stays in its original module.
* 2) repeated 1) procedure, each time in a new random sequential order, until no move generates a gain of the map EQ.
*
* The 1) procedure is implemented in Network::move() function.
*/
void stochastic_greedy_partition(Network &network, int numTh, double threshold, double vThresh, int maxIter, bool prior, bool fineTune, bool fast) {
double oldCodeLength = network.CodeLength();
int iter = 0;
bool stop = false;
struct timeval outer_T1, outer_T2;
struct timeval inner_T1, inner_T2;
struct timeval seq_T1, seq_T2;
struct timeval convert_T1, convert_T2;
double tSequential = 0.0;
gettimeofday(&outer_T1, NULL);
int nActiveUnits = (fineTune) ? network.NNode() : network.superNodes.size();
cout << nActiveUnits << ", ";
// set initial active nodes list ...
vector<char>(nActiveUnits).swap(network.isActives);
vector<int>(nActiveUnits).swap(network.activeNodes);
for (int i = 0; i < nActiveUnits; i++) {
network.activeNodes[i] = i;
network.isActives[i] = 0; // initially set inactive nodes.
}
int numMoved = 0;
while (!stop && iter < maxIter) {
gettimeofday(&inner_T1, NULL);
oldCodeLength = network.CodeLength();
if (fineTune) {
if (numTh == 1) {
if (prior)
numMoved = network.prioritize_move(vThresh);
else
numMoved = network.move();
}
else {
if (prior)
numMoved = network.prioritize_parallelMove(numTh, tSequential, vThresh);
else
numMoved = network.parallelMove(numTh, tSequential);
}
}
else {
if (numTh == 1) {
if (prior)
numMoved = network.prioritize_moveSPnodes(vThresh);
else
numMoved = network.moveSuperNodes(); // If at least one node is moved, return true. Otherwise, return false.
}
else {
if (prior)
numMoved = network.prioritize_parallelMoveSPnodes(numTh, tSequential, vThresh);
else
numMoved = network.parallelMoveSuperNodes(numTh, tSequential);
}
}
iter++;
if (oldCodeLength - network.CodeLength() >= 0 && (oldCodeLength - network.CodeLength())/log(2.0) < threshold)
stop = true; //moved = false;
gettimeofday(&inner_T2, NULL);
// Print code length per iteration for DEBUG purpose.
cout << "Iteration " << iter << ": code length =\t" << network.CodeLength()/log(2.0) << "\t, ";
cout << "elapsed time:\t" << elapsedTimeInSec(inner_T1, inner_T2) << "\t(sec), ";
cout << "accumulated time:\t" << elapsedTimeInSec(outer_T1, inner_T2) << "\t(sec)\t";
cout << "sumExitPr = " << network.SumAllExitPr() << "\t";
cout << "numMoved:\t" << numMoved << endl;
}
gettimeofday(&seq_T1, NULL);
int outerLoop = 1;
network.updateMembersInModule();
gettimeofday(&seq_T2, NULL);
tSequential += elapsedTimeInSec(seq_T1, seq_T2);
if (fast)
return;
double tConvert = 0.0;
do {
oldCodeLength = network.CodeLength();
stop = false;
gettimeofday(&convert_T1, NULL);
network.convertModulesToSuperNodes(numTh);
gettimeofday(&convert_T2, NULL);
tConvert += elapsedTimeInSec(convert_T1, convert_T2);
nActiveUnits = network.superNodes.size();
cout << nActiveUnits << ", ";
// set initial active nodes list ...
vector<char>(nActiveUnits).swap(network.isActives);
vector<int>(nActiveUnits).swap(network.activeNodes);
for (int i = 0; i < nActiveUnits; i++) {
network.activeNodes[i] = i; // initially all active units are active.
network.isActives[i] = 0; // initially set inactive nodes.
}
int spIter = 0;
while (!stop && spIter < maxIter) {
gettimeofday(&inner_T1, NULL);
double innerOldCodeLength = network.CodeLength();
if (numTh == 1) {
if (prior)
numMoved = network.prioritize_moveSPnodes(vThresh);
else
numMoved = network.moveSuperNodes();
}
else {
if (prior)
numMoved = network.prioritize_parallelMoveSPnodes(numTh, tSequential, vThresh);
else
numMoved = network.parallelMoveSuperNodes(numTh, tSequential);
}
spIter++;
if (innerOldCodeLength - network.CodeLength() >= 0.0 && (innerOldCodeLength - network.CodeLength())/log(2.0) < threshold)
stop = true; //moved = false;
gettimeofday(&inner_T2, NULL);
// Print code length per spIter for DEBUG purpose.
cout << "SuperIteration " << outerLoop << "-" << spIter << ": code length =\t" << network.CodeLength()/log(2.0) << "\t, ";
cout << "elapsed time:\t" << elapsedTimeInSec(inner_T1, inner_T2) << "\t(sec), ";
cout << "accumulated time:\t" << elapsedTimeInSec(outer_T1, inner_T2) << "\t(sec)\t";
cout << "sumExitPr = " << network.SumAllExitPr() << "\t";
cout << "numMoved:\t" << numMoved << endl;
}
gettimeofday(&seq_T1, NULL);
network.updateMembersInModule();
outerLoop++;
gettimeofday(&seq_T2, NULL);
tSequential += elapsedTimeInSec(seq_T1, seq_T2);
} while ((oldCodeLength - network.CodeLength())/log(2.0) > threshold);
gettimeofday(&outer_T2, NULL);
cout << "Sequential running time for partition: " << tSequential << " (sec)" << endl;
cout << "Time for converting Module to SuperNode: " << tConvert << " (sec)" << endl;
cout << "Overall time for partition: " << elapsedTimeInSec(outer_T1, outer_T2) << "\t(sec)" << endl;
}