/*
* Modified from the Infomap implementation.
* Reading the given network data in Pajek format.
*/
void load_pajek_format_network(string fName, Network &network) {
string line;
string buf;
string nameBuf;
/* Read network in Pajek format with nodes ordered 1, 2, 3, ..., N, */
/* each directed link occurring only once, and link weights > 0. */
/* For more information, see http://vlado.fmf.uni-lj.si/pub/networks/pajek/. */
/* Node weights are optional and sets the relative proportion to which */
/* each node receives teleporting random walkers. Default value is 1. */
/* Example network with three nodes and four directed and weighted links: */
/* *Vertices 3 */
/* 1 "Name of first node" 1.0 */
/* 2 "Name of second node" 2.0 */
/* 3 "Name of third node" 1.0 */
/* *Arcs 4 */
/* 1 2 1.0 */
/* 1 3 1.7 */
/* 2 3 2.0 */
/* 3 2 1.2 */
cout << "Reading network " << fName << " file\n" << flush;
ifstream net(fName.c_str());
network.setNNode(0);
istringstream ss;
while(network.NNode() == 0){
if(getline(net,line) == NULL){
cout << "the network file is not in Pajek format...exiting" << endl;
exit(-1);
}
else{
ss.clear();
ss.str(line);
ss >> buf;
if(buf == "*Vertices" || buf == "*vertices" || buf == "*VERTICES"){
ss >> buf;
network.setNNode(atoi(buf.c_str()));
}
else{
cout << "the network file is not in Pajek format...exiting" << endl;
exit(-1);
}
}
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();
}
void generate_sub_modules(Network &network, int numTh, double threshold, int maxIter) {
int numNodes = network.NNode();
struct timeval t1, t2;
gettimeofday(&t1, NULL);
vector<SubModule*>().swap(network.subModules); // swap network.subModules vector with the empty vector.
network.subModules.reserve(numNodes);
vector<int>(numNodes).swap(network.ndToSubMod);
omp_set_num_threads(numTh);
vector<vector<SubModule> > tmpSubModList(numTh); // generate 'numTh' of vector<SubModule>.
for(int i = 0; i < numTh; i++) {
tmpSubModList[i].reserve(numNodes);
}
gettimeofday(&t2, NULL);
cout << "initialization time for generate_sub_modules(): " << elapsedTimeInSec(t1, t2) << endl;
struct timeval tPar1, tPar2;
gettimeofday(&tPar1, NULL);
MTRand *Rand = new MTRand();
int numSmallMods = network.smActiveMods.size();
cout << "number of small modules: " << numSmallMods << endl;
#pragma omp parallel for schedule(dynamic, 100)
for (int i = 0; i < numSmallMods; i++) {
int myID = omp_get_thread_num(); // get my thread ID.
Module* mod = &(network.modules[network.smActiveMods[i]]);
// check whether the current module has more than one node or not.
if (mod->NumMembers() > 1) {
int modIdx = mod->Index();
map<int, int> origNodeID; //map from newNodeID to original Node ID. a.k.a. <newNodeID, origNodeID>
Network newNetwork;
generate_network_from_module(newNetwork, mod, origNodeID);
newNetwork.R = Rand;
partition_module_network(newNetwork, 1, threshold, maxIter, true); // fast = true..
int nActiveMods = newNetwork.smActiveMods.size();
// Adding sub-modules from a new network of the corresponding module to the list of subModules...
for (int j = 0; j < nActiveMods; j++) {
SubModule subMod(newNetwork.modules[newNetwork.smActiveMods[j]], origNodeID, modIdx);
tmpSubModList[myID].push_back(subMod);
}
}
else {
// This is the special case that the module has ONLY ONE member.
SubModule subMod(*mod);
tmpSubModList[myID].push_back(subMod);
}
} // End of for
//} // End of parallel.
gettimeofday(&tPar2, NULL);
cout << "Time for parallel for loop for SMALL-MODULES:\t" << elapsedTimeInSec(tPar1, tPar2) << " (sec)" << endl;
///////////////////////////////
// Larger-Modules
gettimeofday(&tPar1, NULL);
int numLargeMods = network.lgActiveMods.size();
cout << "number of large modules: " << numLargeMods << endl;
for (int i = 0; i < numLargeMods; i++) {
Module* mod = &(network.modules[network.lgActiveMods[i]]);
// NO-NEED to check the size of the current module.
int modIdx = mod->Index();
map<int, int> origNodeID; //map from newNodeID to original Node ID. a.k.a. <newNodeID, origNodeID>
Network newNetwork;
generate_network_from_module(newNetwork, mod, origNodeID, numTh);
newNetwork.R = Rand;
partition_module_network(newNetwork, numTh, threshold, maxIter, true); // fast = true..
// Adding sub-modules from a new network of the corresponding module to the list of subModules...
int nActiveMods = newNetwork.smActiveMods.size();
#pragma omp parallel for //schedule(dynamic)
for (int j = 0; j < nActiveMods; j++) {
SubModule subMod(newNetwork.modules[newNetwork.smActiveMods[j]], origNodeID, modIdx);
tmpSubModList[omp_get_thread_num()].push_back(subMod);
}
nActiveMods = newNetwork.lgActiveMods.size();
#pragma omp parallel for schedule(dynamic)
for (int j = 0; j < nActiveMods; j++) {
SubModule subMod(newNetwork.modules[newNetwork.lgActiveMods[j]], origNodeID, modIdx);
tmpSubModList[omp_get_thread_num()].push_back(subMod);
}
} // End of parallel for.
gettimeofday(&tPar2, NULL);
cout << "Time for parallel for loop for LARGE-MODULES:\t" << elapsedTimeInSec(tPar1, tPar2) << " (sec)" << endl;
gettimeofday(&t1, NULL);
int numSubMods = 0;
for (int i = 0; i < numTh; i++) {
for (vector<SubModule>::iterator it = tmpSubModList[i].begin(); it != tmpSubModList[i].end(); it++) {
network.subModules.push_back(&(*it));
for (vector<int>::iterator ndIt = it->members.begin(); ndIt != it->members.end(); ndIt++)
network.ndToSubMod[*ndIt] = numSubMods;
numSubMods++;
}
}
gettimeofday(&t2, NULL);
cout << "sequential subModules push_back() time:\t" << elapsedTimeInSec(t1, t2) << " (sec)" << endl;
gettimeofday(&t1, NULL);
network.generateSuperNodesFromSubModules(numTh);
gettimeofday(&t2, NULL);
cout << "generateSuperNodesFromSubModules() time:\t" << elapsedTimeInSec(t1, t2) << " (sec)" << endl;
}
/*
* 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;
}