EstOutput Parsimony::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, CountTable* ct) { try { int process = 1; vector<int> processIDS; EstOutput results; #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) //loop through and create all the processes you want while (process != processors) { int pid = fork(); if (pid > 0) { processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later process++; }else if (pid == 0){ EstOutput myresults; myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, ct); if (m->control_pressed) { exit(0); } //pass numSeqs to parent ofstream out; string tempFile = outputDir + toString(getpid()) + ".pars.results.temp"; m->openOutputFile(tempFile, out); out << myresults.size() << endl; for (int i = 0; i < myresults.size(); i++) { out << myresults[i] << '\t'; } out << endl; out.close(); exit(0); }else { m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); } exit(0); } } results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, ct); //force parent to wait until all the processes are done for (int i=0;i<processIDS.size();i++) { int temp = processIDS[i]; wait(&temp); } if (m->control_pressed) { return results; } //get data created by processes for (int i=0;i<processIDS.size();i++) { ifstream in; string s = outputDir + toString(processIDS[i]) + ".pars.results.temp"; m->openInputFile(s, in); //get scores if (!in.eof()) { int num; in >> num; m->gobble(in); if (m->control_pressed) { break; } double w; for (int j = 0; j < num; j++) { in >> w; results.push_back(w); } m->gobble(in); } in.close(); m->mothurRemove(s); } #else //fill in functions vector<parsData*> pDataArray; DWORD dwThreadIdArray[processors-1]; HANDLE hThreadArray[processors-1]; vector<CountTable*> cts; vector<Tree*> trees; //Create processor worker threads. for( int i=1; i<processors; i++ ){ CountTable* copyCount = new CountTable(); copyCount->copy(ct); Tree* copyTree = new Tree(copyCount); copyTree->getCopy(t); cts.push_back(copyCount); trees.push_back(copyTree); parsData* temppars = new parsData(m, lines[i].start, lines[i].num, namesOfGroupCombos, copyTree, copyCount); pDataArray.push_back(temppars); processIDS.push_back(i); hThreadArray[i-1] = CreateThread(NULL, 0, MyParsimonyThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]); } results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, ct); //Wait until all threads have terminated. WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE); //Close all thread handles and free memory allocations. for(int i=0; i < pDataArray.size(); i++){ for (int j = 0; j < pDataArray[i]->results.size(); j++) { results.push_back(pDataArray[i]->results[j]); } delete cts[i]; delete trees[i]; CloseHandle(hThreadArray[i]); delete pDataArray[i]; } #endif return results; }
EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, CountTable* ct) { try { int process = 1; vector<int> processIDS; bool recalc = false; EstOutput results; #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) //loop through and create all the processes you want while (process != processors) { pid_t pid = fork(); if (pid > 0) { processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later process++; }else if (pid == 0){ EstOutput myresults; myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, ct); if (m->control_pressed) { exit(0); } //pass numSeqs to parent ofstream out; string tempFile = outputDir + m->mothurGetpid(process) + ".unweighted.results.temp"; m->openOutputFile(tempFile, out); out << myresults.size() << endl; for (int i = 0; i < myresults.size(); i++) { out << myresults[i] << '\t'; } out << endl; out.close(); exit(0); }else { m->mothurOut("[ERROR]: unable to spawn the number of processes you requested, reducing number to " + toString(process) + "\n"); processors = process; for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); } //wait to die for (int i=0;i<processIDS.size();i++) { int temp = processIDS[i]; wait(&temp); } m->control_pressed = false; for (int i=0;i<processIDS.size();i++) { m->mothurRemove(outputDir + (toString(processIDS[i]) + ".unweighted.results.temp")); } recalc = true; break; } } if (recalc) { //test line, also set recalc to true. //for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); } for (int i=0;i<processIDS.size();i++) { int temp = processIDS[i]; wait(&temp); } m->control_pressed = false; for (int i=0;i<processIDS.size();i++) {m->mothurRemove(outputDir + (toString(processIDS[i]) + ".unweighted.results.temp"));}processors=3; m->mothurOut("[ERROR]: unable to spawn the number of processes you requested, reducing number to " + toString(processors) + "\n"); //if the users enters no groups then give them the score of all groups int numGroups = m->getNumGroups(); //calculate number of comparsions int numComp = 0; vector< vector<string> > namesOfGroupCombos; for (int r=0; r<numGroups; r++) { for (int l = 0; l < r; l++) { numComp++; vector<string> groups; groups.push_back((m->getGroups())[r]); groups.push_back((m->getGroups())[l]); namesOfGroupCombos.push_back(groups); } } if (numComp != 1) { vector<string> groups; if (numGroups == 0) { //get score for all users groups for (int i = 0; i < (ct->getNamesOfGroups()).size(); i++) { if ((ct->getNamesOfGroups())[i] != "xxx") { groups.push_back((ct->getNamesOfGroups())[i]); } } namesOfGroupCombos.push_back(groups); }else { for (int i = 0; i < m->getNumGroups(); i++) { groups.push_back((m->getGroups())[i]); } namesOfGroupCombos.push_back(groups); } } lines.clear(); int remainingPairs = namesOfGroupCombos.size(); int startIndex = 0; for (int remainingProcessors = processors; remainingProcessors > 0; remainingProcessors--) { int numPairs = remainingPairs; //case for last processor if (remainingProcessors != 1) { numPairs = ceil(remainingPairs / remainingProcessors); } lines.push_back(linePair(startIndex, numPairs)); //startIndex, numPairs startIndex = startIndex + numPairs; remainingPairs = remainingPairs - numPairs; } results.clear(); processIDS.resize(0); process = 1; //loop through and create all the processes you want while (process != processors) { pid_t pid = fork(); if (pid > 0) { processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later process++; }else if (pid == 0){ EstOutput myresults; myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, ct); if (m->control_pressed) { exit(0); } //pass numSeqs to parent ofstream out; string tempFile = outputDir + m->mothurGetpid(process) + ".unweighted.results.temp"; m->openOutputFile(tempFile, out); out << myresults.size() << endl; for (int i = 0; i < myresults.size(); i++) { out << myresults[i] << '\t'; } out << endl; out.close(); exit(0); }else { m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); } exit(0); } } } results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, ct); //force parent to wait until all the processes are done for (int i=0;i<(processors-1);i++) { int temp = processIDS[i]; wait(&temp); } if (m->control_pressed) { return results; } //get data created by processes for (int i=0;i<(processors-1);i++) { ifstream in; string s = outputDir + toString(processIDS[i]) + ".unweighted.results.temp"; m->openInputFile(s, in); //get quantiles if (!in.eof()) { int num; in >> num; m->gobble(in); if (m->control_pressed) { break; } double w; for (int j = 0; j < num; j++) { in >> w; results.push_back(w); } m->gobble(in); } in.close(); m->mothurRemove(s); } #else //fill in functions vector<unweightedData*> pDataArray; DWORD dwThreadIdArray[processors-1]; HANDLE hThreadArray[processors-1]; vector<CountTable*> cts; vector<Tree*> trees; //Create processor worker threads. for( int i=1; i<processors; i++ ){ CountTable* copyCount = new CountTable(); copyCount->copy(ct); Tree* copyTree = new Tree(copyCount); copyTree->getCopy(t); cts.push_back(copyCount); trees.push_back(copyTree); unweightedData* tempweighted = new unweightedData(m, lines[i].start, lines[i].num, namesOfGroupCombos, copyTree, copyCount, includeRoot); pDataArray.push_back(tempweighted); processIDS.push_back(i); hThreadArray[i-1] = CreateThread(NULL, 0, MyUnWeightedThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]); } results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, ct); //Wait until all threads have terminated. WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE); //Close all thread handles and free memory allocations. for(int i=0; i < pDataArray.size(); i++){ for (int j = 0; j < pDataArray[i]->results.size(); j++) { results.push_back(pDataArray[i]->results[j]); } delete cts[i]; delete trees[i]; CloseHandle(hThreadArray[i]); delete pDataArray[i]; } #endif return results; }