From: westcott Date: Tue, 24 May 2011 19:39:22 +0000 (+0000) Subject: paralellized seq.error and dist.shared added some error checks to libshuff and dist... X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=ec1b5bc7460ac8ad40f54f0729900d9ed98e7292 paralellized seq.error and dist.shared added some error checks to libshuff and dist.seqs --- diff --git a/matrixoutputcommand.cpp b/matrixoutputcommand.cpp index 7fbd830..9c7a836 100644 --- a/matrixoutputcommand.cpp +++ b/matrixoutputcommand.cpp @@ -58,6 +58,7 @@ vector MatrixOutputCommand::setParameters(){ CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups); CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson", "jclass-thetayc", "", "", "",true,false); parameters.push_back(pcalc); CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "",false,false); parameters.push_back(poutput); + CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors); CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); @@ -75,7 +76,7 @@ string MatrixOutputCommand::getHelpString(){ try { string helpString = ""; ValidCalculators validCalculator; - helpString += "The dist.shared command parameters are shared, groups, calc, output and label. shared is a required, unless you have a valid current file.\n"; + helpString += "The dist.shared command parameters are shared, groups, calc, output, processors and label. shared is a required, unless you have a valid current file.\n"; helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n"; helpString += "The group names are separated by dashes. The label parameter allows you to select what distance levels you would like distance matrices created for, and is also separated by dashes.\n"; helpString += "The dist.shared command should be in the following format: dist.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n"; @@ -181,6 +182,10 @@ MatrixOutputCommand::MatrixOutputCommand(string option) { m->splitAtDash(groups, Groups); m->Groups = Groups; } + + string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); } + m->setProcessors(temp); + convert(temp, processors); calc = validParameter.validFile(parameters, "calc", false); if (calc == "not found") { calc = "jclass-thetayc"; } @@ -318,6 +323,12 @@ int MatrixOutputCommand::execute(){ if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups. I cannot run the command."); m->mothurOutEndLine(); delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0;} numGroups = lookup.size(); + lines.resize(processors); + for (int i = 0; i < processors; i++) { + lines[i].start = int (sqrt(float(i)/float(processors)) * numGroups); + lines[i].end = int (sqrt(float(i+1)/float(processors)) * numGroups); + cout << i << '\t' << lines[i].start << '\t' << lines[i].end << endl; + } if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->Groups.clear(); return 0; } @@ -410,7 +421,7 @@ int MatrixOutputCommand::execute(){ } } /***********************************************************/ -void MatrixOutputCommand::printSims(ostream& out) { +void MatrixOutputCommand::printSims(ostream& out, vector< vector >& simMatrix) { try { out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint); @@ -444,63 +455,160 @@ void MatrixOutputCommand::printSims(ostream& out) { /***********************************************************/ int MatrixOutputCommand::process(vector thisLookup){ try { - - EstOutput data; - vector subset; - - //for each calculator - for(int i = 0 ; i < matrixCalculators.size(); i++) { + EstOutput data; + vector subset; + vector< vector > calcDists; calcDists.resize(matrixCalculators.size()); //one for each calc, this will be used to make .dist files + + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + if(processors == 1){ + driver(thisLookup, 0, numGroups, calcDists); + }else{ + int process = 1; + vector processIDS; + + //loop through and create all the processes you want + while (process != processors) { + int pid = fork(); + + if (pid > 0) { + processIDS.push_back(pid); + process++; + }else if (pid == 0){ + driver(thisLookup, lines[process].start, lines[process].end, calcDists); - //initialize simMatrix - simMatrix.clear(); - simMatrix.resize(numGroups); - for (int p = 0; p < simMatrix.size(); p++) { - for (int j = 0; j < simMatrix.size(); j++) { - simMatrix[p].push_back(0.0); + string tempdistFileName = m->getRootName(m->getSimpleName(sharedfile)) + toString(getpid()) + ".dist"; + ofstream outtemp; + m->openOutputFile(tempdistFileName, outtemp); + + for (int i = 0; i < calcDists.size(); i++) { + outtemp << calcDists[i].size() << endl; + + for (int j = 0; j < calcDists[i].size(); j++) { + outtemp << calcDists[i][j].seq1 << '\t' << calcDists[i][j].seq2 << '\t' << calcDists[i][j].dist << endl; } } + outtemp.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); + } + } + + //parent do your part + driver(thisLookup, lines[0].start, lines[0].end, calcDists); + + //force parent to wait until all the processes are done + for (int i = 0; i < processIDS.size(); i++) { + int temp = processIDS[i]; + wait(&temp); + } + + for (int i = 0; i < processIDS.size(); i++) { + string tempdistFileName = m->getRootName(m->getSimpleName(sharedfile)) + toString(processIDS[i]) + ".dist"; + ifstream intemp; + m->openInputFile(tempdistFileName, intemp); + + for (int k = 0; k < calcDists.size(); k++) { + int size = 0; + intemp >> size; m->gobble(intemp); + + for (int j = 0; j < size; j++) { + int seq1 = 0; + int seq2 = 0; + float dist = 1.0; + + intemp >> seq1 >> seq2 >> dist; m->gobble(intemp); + + seqDist tempDist(seq1, seq2, dist); + calcDists[k].push_back(tempDist); + } + } + intemp.close(); + remove(tempdistFileName.c_str()); + } + + } +#else + driver(thisLookup, 0, numGroups, calcDists); +#endif + + for (int i = 0; i < calcDists.size(); i++) { + if (m->control_pressed) { break; } + + //initialize matrix + vector< vector > matrix; //square matrix to represent the distance + matrix.resize(thisLookup.size()); + for (int k = 0; k < thisLookup.size(); k++) { matrix[k].resize(thisLookup.size(), 0.0); } + + for (int j = 0; j < calcDists[i].size(); j++) { + int row = calcDists[i][j].seq1; + int column = calcDists[i][j].seq2; + float dist = calcDists[i][j].dist; + + matrix[row][column] = dist; + matrix[column][row] = dist; + } + + string distFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + output + ".dist"; + outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName); + ofstream outDist; + m->openOutputFile(distFileName, outDist); + outDist.setf(ios::fixed, ios::floatfield); outDist.setf(ios::showpoint); + + printSims(outDist, matrix); + + outDist.close(); + } + + return 0; + } + catch(exception& e) { + m->errorOut(e, "MatrixOutputCommand", "process"); + exit(1); + } +} +/**************************************************************************************************/ +int MatrixOutputCommand::driver(vector thisLookup, int start, int end, vector< vector >& calcDists) { + try { + + vector subset; + for (int k = start; k < end; k++) { // pass cdd each set of groups to compare + + for (int l = 0; l < k; l++) { - for (int k = 0; k < thisLookup.size(); k++) { - for (int l = k; l < thisLookup.size(); l++) { - if (k != l) { //we dont need to similiarity of a groups to itself - //get estimated similarity between 2 groups - - if (m->control_pressed) { return 0; } - - subset.clear(); //clear out old pair of sharedrabunds - //add new pair of sharedrabunds - subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]); - - //if this calc needs all groups to calculate the pair load all groups - if (matrixCalculators[i]->getNeedsAll()) { - //load subset with rest of lookup for those calcs that need everyone to calc for a pair - for (int w = 0; w < thisLookup.size(); w++) { - if ((w != k) && (w != l)) { subset.push_back(thisLookup[w]); } - } - } - - data = matrixCalculators[i]->getValues(subset); //saves the calculator outputs - //save values in similarity matrix - simMatrix[k][l] = 1.0 - data[0]; //convert similiarity to distance - simMatrix[l][k] = 1.0 - data[0]; //convert similiarity to distance + if (k != l) { //we dont need to similiarity of a groups to itself + subset.clear(); //clear out old pair of sharedrabunds + //add new pair of sharedrabunds + subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]); + + for(int i=0;igetNeedsAll()) { + //load subset with rest of lookup for those calcs that need everyone to calc for a pair + for (int w = 0; w < thisLookup.size(); w++) { + if ((w != k) && (w != l)) { subset.push_back(thisLookup[w]); } } } + + vector tempdata = matrixCalculators[i]->getValues(subset); //saves the calculator outputs + + if (m->control_pressed) { return 1; } + + seqDist temp(l, k, (1.0 - tempdata[0])); + calcDists[i].push_back(temp); } - - exportFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + output + ".dist"; - m->openOutputFile(exportFileName, out); - outputNames.push_back(exportFileName); outputTypes["phylip"].push_back(exportFileName); - - printSims(out); - out.close(); - } - - return 0; + } + } + return 0; } catch(exception& e) { - m->errorOut(e, "MatrixOutputCommand", "process"); + m->errorOut(e, "MatrixOutputCommand", "driver"); exit(1); } }