//
#include "getmetacommunitycommand.h"
-#include "qFinderDMM.h"
+
//**********************************************************************************************************************
vector<string> GetMetaCommunityCommand::setParameters(){
CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
CommandParameter pminpartitions("minpartitions", "Number", "", "5", "", "", "","",false,false,true); parameters.push_back(pminpartitions);
- CommandParameter pmaxpartitions("maxpartitions", "Number", "", "10", "", "", "","",false,false,true); parameters.push_back(pmaxpartitions);
+ CommandParameter pmaxpartitions("maxpartitions", "Number", "", "100", "", "", "","",false,false,true); parameters.push_back(pmaxpartitions);
CommandParameter poptimizegap("optimizegap", "Number", "", "3", "", "", "","",false,false,true); parameters.push_back(poptimizegap);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
string GetMetaCommunityCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The get.metacommunity command parameters are shared, label, groups, minpartitions, maxpartitions and optimizegap. The shared file is required. \n";
+ helpString += "The get.communitytype command parameters are shared, label, groups, minpartitions, maxpartitions, optimizegap and processors. The shared file is required. \n";
helpString += "The label parameter is used to analyze specific labels in your input. labels are separated by dashes.\n";
helpString += "The groups parameter allows you to specify which of the groups in your shared file you would like analyzed. Group names are separated by dashes.\n";
helpString += "The minpartitions parameter is used to .... Default=5.\n";
helpString += "The maxpartitions parameter is used to .... Default=10.\n";
helpString += "The optimizegap parameter is used to .... Default=3.\n";
- helpString += "The get.metacommunity command should be in the following format: get.metacommunity(shared=yourSharedFile).\n";
+ helpString += "The processors parameter allows you to specify number of processors to use. The default is 1.\n";
+ helpString += "The get.communitytype command should be in the following format: get.communitytype(shared=yourSharedFile).\n";
return helpString;
}
catch(exception& e) {
if (type == "fit") { pattern = "[filename],[distance],mix.fit"; }
else if (type == "relabund") { pattern = "[filename],[distance],[tag],mix.relabund"; }
- else if (type == "design") { pattern = "[filename],mix.design"; }
+ else if (type == "design") { pattern = "[filename],[distance],mix.design"; }
else if (type == "matrix") { pattern = "[filename],[distance],[tag],mix.posterior"; }
else if (type == "parameters") { pattern = "[filename],[distance],mix.parameters"; }
else if (type == "summary") { pattern = "[filename],[distance],mix.summary"; }
temp = validParameter.validFile(parameters, "optimizegap", false); if (temp == "not found"){ temp = "3"; }
m->mothurConvert(temp, optimizegap);
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
+ m->mothurConvert(temp, processors);
+
string groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; }
else { m->splitAtDash(groups, Groups); }
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
- process(lookup);
+ createProcesses(lookup);
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
lookup = input.getSharedRAbundVectors(lastLabel);
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
- process(lookup);
+ createProcesses(lookup);
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
- process(lookup);
+ createProcesses(lookup);
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
}
}
//**********************************************************************************************************************
-int GetMetaCommunityCommand::process(vector<SharedRAbundVector*>& thislookup){
+int GetMetaCommunityCommand::createProcesses(vector<SharedRAbundVector*>& thislookup){
try {
- double minLaplace = 1e10;
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ #else
+ processors=1; //qFinderDMM not thread safe
+ #endif
+
+ vector<int> processIDS;
+ int process = 1;
+ int num = 0;
int minPartition = 0;
+
+ //sanity check
+ if (maxpartitions < processors) { processors = maxpartitions; }
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
variables["[distance]"] = thislookup[0]->getLabel();
string outputFileName = getOutputFileName("fit", variables);
outputNames.push_back(outputFileName); outputTypes["fit"].push_back(outputFileName);
+
+ //divide the partitions between the processors
+ vector< vector<int> > dividedPartitions;
+ vector< vector<string> > rels, matrix;
+ vector<string> doneFlags;
+ dividedPartitions.resize(processors);
+ rels.resize(processors);
+ matrix.resize(processors);
+
+ //for each file group figure out which process will complete it
+ //want to divide the load intelligently so the big files are spread between processes
+ for (int i=1; i<=maxpartitions; i++) {
+ //cout << i << endl;
+ int processToAssign = (i+1) % processors;
+ if (processToAssign == 0) { processToAssign = processors; }
+
+ if (m->debug) { m->mothurOut("[DEBUG]: assigning " + toString(i) + " to process " + toString(processToAssign-1) + "\n"); }
+ dividedPartitions[(processToAssign-1)].push_back(i);
+
+ variables["[tag]"] = toString(i);
+ string relName = getOutputFileName("relabund", variables);
+ string mName = getOutputFileName("matrix", variables);
+ rels[(processToAssign-1)].push_back(relName);
+ matrix[(processToAssign-1)].push_back(mName);
+ }
+
+ for (int i = 0; i < processors; i++) { //read from everyone elses, just write to yours
+ string tempDoneFile = m->getRootName(m->getSimpleName(sharedfile)) + toString(i) + ".done.temp";
+ doneFlags.push_back(tempDoneFile);
+ ofstream out;
+ m->openOutputFile(tempDoneFile, out); //clear out
+ out.close();
+ }
+
+
+#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){
+ outputNames.clear();
+ num = processDriver(thislookup, dividedPartitions[process], (outputFileName + toString(getpid())), rels[process], matrix[process], doneFlags, process);
+
+ //pass numSeqs to parent
+ ofstream out;
+ string tempFile = toString(getpid()) + ".outputNames.temp";
+ m->openOutputFile(tempFile, out);
+ out << num << endl;
+ out << outputNames.size() << endl;
+ for (int i = 0; i < outputNames.size(); i++) { out << outputNames[i] << 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);
+ }
+ }
+
+ //do my part
+ m->mothurOut("K\tNLE\t\tlogDet\tBIC\t\tAIC\t\tLaplace\n");
+ minPartition = processDriver(thislookup, dividedPartitions[0], outputFileName, rels[0], matrix[0], doneFlags, 0);
+
+ //force parent to wait until all the processes are done
+ for (int i=0;i<processIDS.size();i++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
+
+ vector<string> tempOutputNames = outputNames;
+ for (int i=0;i<processIDS.size();i++) {
+ ifstream in;
+ string tempFile = toString(processIDS[i]) + ".outputNames.temp";
+ m->openInputFile(tempFile, in);
+ if (!in.eof()) {
+ int tempNum = 0;
+ in >> tempNum; m->gobble(in);
+ if (tempNum < minPartition) { minPartition = tempNum; }
+ in >> tempNum; m->gobble(in);
+ for (int i = 0; i < tempNum; i++) {
+ string tempName = "";
+ in >> tempName; m->gobble(in);
+ tempOutputNames.push_back(tempName);
+ }
+ }
+ in.close(); m->mothurRemove(tempFile);
+
+ m->appendFilesWithoutHeaders(outputFileName + toString(processIDS[i]), outputFileName);
+ m->mothurRemove(outputFileName + toString(processIDS[i]));
+ }
+
+ if (processors > 1) {
+ outputNames.clear();
+ for (int i = 0; i < tempOutputNames.size(); i++) { //remove files if needed
+ string name = tempOutputNames[i];
+ vector<string> parts;
+ m->splitAtChar(name, parts, '.');
+ bool keep = true;
+ if (((parts[parts.size()-1] == "relabund") || (parts[parts.size()-1] == "posterior")) && (parts[parts.size()-2] == "mix")) {
+ string tempNum = parts[parts.size()-3];
+ int num; m->mothurConvert(tempNum, num);
+ //if (num > minPartition) {
+ // m->mothurRemove(tempOutputNames[i]);
+ // keep = false; if (m->debug) { m->mothurOut("[DEBUG]: removing " + tempOutputNames[i] + ".\n"); }
+ //}
+ }
+ if (keep) { outputNames.push_back(tempOutputNames[i]); }
+ }
+
+ //reorder fit file
+ ifstream in;
+ m->openInputFile(outputFileName, in);
+ string headers = m->getline(in); m->gobble(in);
+
+ map<int, string> file;
+ while (!in.eof()) {
+ string numString, line;
+ int num;
+ in >> numString; line = m->getline(in); m->gobble(in);
+ m->mothurConvert(numString, num);
+ file[num] = line;
+ }
+ in.close();
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+ out << headers << endl;
+ for (map<int, string>::iterator it = file.begin(); it != file.end(); it++) {
+ out << it->first << '\t' << it->second << endl;
+ if (m->debug) { m->mothurOut("[DEBUG]: printing: " + toString(it->first) + '\t' + it->second + ".\n"); }
+ }
+ out.close();
+ }
+
+#else
+ /*
+ vector<metaCommunityData*> pDataArray;
+ DWORD dwThreadIdArray[processors-1];
+ HANDLE hThreadArray[processors-1];
+
+ //Create processor worker threads.
+ for( int i=1; i<processors; i++ ){
+ //copy lookup
+ //make copy of lookup so we don't get access violations
+ vector<SharedRAbundVector*> newLookup;
+ for (int k = 0; k < thislookup.size(); k++) {
+ SharedRAbundVector* temp = new SharedRAbundVector();
+ temp->setLabel(thislookup[k]->getLabel());
+ temp->setGroup(thislookup[k]->getGroup());
+ newLookup.push_back(temp);
+ }
+
+ //for each bin
+ for (int k = 0; k < thislookup[0]->getNumBins(); k++) {
+ if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; }
+ for (int j = 0; j < thislookup.size(); j++) { newLookup[j]->push_back(thislookup[j]->getAbundance(k), thislookup[j]->getGroup()); }
+ }
+
+ processIDS.push_back(i);
+
+ // Allocate memory for thread data.
+ metaCommunityData* tempMeta = new metaCommunityData(newLookup, m, dividedPartitions[i], outputFileName + toString(i), rels[i], matrix[i], minpartitions, maxpartitions, optimizegap);
+ pDataArray.push_back(tempMeta);
+
+ hThreadArray[i] = CreateThread(NULL, 0, MyMetaCommunityThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
+ }
+
+ //do my part
+ minPartition = processDriver(thislookup, dividedPartitions[0], outputFileName, rels[0], matrix[0]);
+
+ //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++){
+ if (pDataArray[i]->minPartition < minPartition) { minPartition = pDataArray[i]->minPartition; }
+ for (int j = 0; j < pDataArray[i]->outputNames.size(); j++) {
+ outputNames.push_back(pDataArray[i]->outputNames[j]);
+ }
+ m->appendFilesWithoutHeaders(outputFileName + toString(processIDS[i]), outputFileName);
+ m->mothurRemove(outputFileName + toString(processIDS[i]));
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
+ } */
+ //do my part
+ m->mothurOut("K\tNLE\t\tlogDet\tBIC\t\tAIC\t\tLaplace\n");
+ minPartition = processDriver(thislookup, dividedPartitions[0], outputFileName, rels[0], matrix[0], doneFlags, 0);
+#endif
+ for (int i = 0; i < processors; i++) { //read from everyone elses, just write to yours
+ string tempDoneFile = m->getRootName(m->getSimpleName(sharedfile)) + toString(i) + ".done.temp";
+ m->mothurRemove(tempDoneFile);
+ }
+
+ if (m->control_pressed) { return 0; }
+
+ if (m->debug) { m->mothurOut("[DEBUG]: minPartition = " + toString(minPartition) + "\n"); }
+
+ //run generate Summary function for smallest minPartition
+ variables["[tag]"] = toString(minPartition);
+ generateSummaryFile(minPartition, variables);
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetMetaCommunityCommand", "createProcesses");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int GetMetaCommunityCommand::processDriver(vector<SharedRAbundVector*>& thislookup, vector<int>& parts, string outputFileName, vector<string> relabunds, vector<string> matrix, vector<string> doneFlags, int processID){
+ try {
+
+ double minLaplace = 1e10;
+ int minPartition = 0;
ofstream fitData;
m->openOutputFile(outputFileName, fitData);
cout.setf(ios::showpoint);
vector< vector<int> > sharedMatrix;
- for (int i = 0; i < thislookup.size(); i++) { sharedMatrix.push_back(thislookup[i]->getAbundances()); }
+ vector<string> thisGroups;
+ for (int i = 0; i < thislookup.size(); i++) { sharedMatrix.push_back(thislookup[i]->getAbundances()); thisGroups.push_back(thislookup[i]->getGroup()); }
- m->mothurOut("K\tNLE\t\tlogDet\tBIC\t\tAIC\t\tLaplace\n");
fitData << "K\tNLE\tlogDet\tBIC\tAIC\tLaplace" << endl;
- for(int numPartitions=1;numPartitions<=maxpartitions;numPartitions++){
+ for(int i=0;i<parts.size();i++){
+
+ int numPartitions = parts[i];
+
+ if (m->debug) { m->mothurOut("[DEBUG]: running partition " + toString(numPartitions) + "\n"); }
if (m->control_pressed) { break; }
+ //check to see if anyone else is done
+ for (int j = 0; j < doneFlags.size(); j++) {
+ if (!m->isBlank(doneFlags[j])) { //another process has finished
+ //are they done at a lower partition?
+ ifstream in;
+ m->openInputFile(doneFlags[j], in);
+ int tempNum;
+ in >> tempNum; in.close();
+ if (tempNum < numPartitions) { break; } //quit, because someone else has finished
+ }
+ }
+
qFinderDMM findQ(sharedMatrix, numPartitions);
double laplace = findQ.getLaplace();
}
m->mothurOutEndLine();
- variables["[tag]"] = toString(numPartitions);
- string relabund = getOutputFileName("relabund", variables);
+ string relabund = relabunds[i];
outputNames.push_back(relabund); outputTypes["relabund"].push_back(relabund);
- string matrix = getOutputFileName("matrix", variables);
- outputNames.push_back(matrix); outputTypes["matrix"].push_back(matrix);
+ string matrixName = matrix[i];
+ outputNames.push_back(matrixName); outputTypes["matrix"].push_back(matrixName);
- findQ.printZMatrix(matrix, m->getGroups());
+ findQ.printZMatrix(matrixName, thisGroups);
findQ.printRelAbund(relabund, m->currentBinLabels);
- if(optimizegap != -1 && (numPartitions - minPartition) >= optimizegap && numPartitions >= minpartitions){ break; }
+ if(optimizegap != -1 && (numPartitions - minPartition) >= optimizegap && numPartitions >= minpartitions){
+ string tempDoneFile = m->getRootName(m->getSimpleName(sharedfile)) + toString(processID) + ".done.temp";
+ ofstream outDone;
+ m->openOutputFile(tempDoneFile, outDone);
+ outDone << minPartition << endl;
+ outDone.close();
+ break;
+ }
}
fitData.close();
//minPartition = 4;
if (m->control_pressed) { return 0; }
-
- generateSummaryFile(minpartitions, outputTypes["relabund"][0], outputTypes["relabund"][outputTypes["relabund"].size()-1], outputTypes["matrix"][outputTypes["matrix"].size()-1], thislookup[0]->getLabel());
-
- return 0;
+ return minPartition;
}
catch(exception& e) {
- m->errorOut(e, "GetMetaCommunityCommand", "process");
+ m->errorOut(e, "GetMetaCommunityCommand", "processDriver");
exit(1);
}
}
/**************************************************************************************************/
-vector<double> GetMetaCommunityCommand::generateDesignFile(int numPartitions, string input){
+vector<double> GetMetaCommunityCommand::generateDesignFile(int numPartitions, map<string,string> variables){
try {
vector<double> piValues(numPartitions, 0);
ifstream postFile;
+ variables["[tag]"] = toString(numPartitions);
+ string input = getOutputFileName("matrix", variables);
m->openInputFile(input, postFile);//((fileRoot + toString(numPartitions) + "mix.posterior").c_str()); //matrix file
- map<string, string> variables;
- variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(input));
+ variables.erase("[tag]");
string outputFileName = getOutputFileName("design", variables);
ofstream designFile;
m->openOutputFile(outputFileName, designFile);
inline bool summaryFunction(summaryData i, summaryData j){ return i.difference > j.difference; }
/**************************************************************************************************/
-int GetMetaCommunityCommand::generateSummaryFile(int numPartitions, string reference, string partFile, string designInput, string label){
+int GetMetaCommunityCommand::generateSummaryFile(int numPartitions, map<string,string> v){
try {
vector<summaryData> summary;
double mean, lci, uci;
- vector<double> piValues = generateDesignFile(numPartitions, designInput);
+ vector<double> piValues = generateDesignFile(numPartitions, v);
ifstream referenceFile;
+ map<string, string> variables;
+ variables["[filename]"] = v["[filename]"];
+ variables["[distance]"] = v["[distance]"];
+ variables["[tag]"] = "1";
+ string reference = getOutputFileName("relabund", variables);
m->openInputFile(reference, referenceFile); //((fileRoot + label + ".1mix.relabund").c_str());
+ variables["[tag]"] = toString(numPartitions);
+ string partFile = getOutputFileName("relabund", variables);
ifstream partitionFile;
m->openInputFile(partFile, partitionFile); //((fileRoot + toString(numPartitions) + "mix.relabund").c_str());
sort(summary.begin(), summary.end(), summaryFunction);
- map<string, string> variables;
- variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
- variables["[distance]"] = label;
+ variables.erase("[tag]");
string outputFileName = getOutputFileName("parameters", variables);
outputNames.push_back(outputFileName); outputTypes["parameters"].push_back(outputFileName);
if (m->control_pressed) { return 0; }
string summaryFileName = getOutputFileName("summary", variables);
- outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
+ outputNames.push_back(summaryFileName); outputTypes["summary"].push_back(summaryFileName);
ofstream summaryFile;
m->openOutputFile(summaryFileName, summaryFile); //((fileRoot + "mix.summary").c_str());
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