X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=distancecommand.cpp;h=e18defe2603a8781c0e928192582cab0120e4eae;hb=30f2d98fffb579b870c8969ddcc1dfc61ccbb70a;hp=23f2834648bb905ff2139c4bc05de59760e4729b;hpb=30c1fd8c45b6f0d66c17f2714dbb58b8ddccdce2;p=mothur.git diff --git a/distancecommand.cpp b/distancecommand.cpp index 23f2834..e18defe 100644 --- a/distancecommand.cpp +++ b/distancecommand.cpp @@ -194,46 +194,42 @@ int DistanceCommand::execute(){ start = int (sqrt(float(pid)/float(processors)) * numSeqs); end = int (sqrt(float(pid+1)/float(processors)) * numSeqs); + MPI_File outMPI; + int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY; + + char filename[outputFile.length()]; + strcpy(filename, outputFile.c_str()); + + MPI_File_open(MPI_COMM_WORLD, filename, amode, MPI_INFO_NULL, &outMPI); + if (pid == 0) { //you are the root process + //do your part string outputMyPart; - driverMPI(start, end, outputMyPart, cutoff); + driverMPI(start, end, outMPI, cutoff); - ofstream out; - openOutputFile(outputFile, out); - - out << outputMyPart; - - //get the childrens parts + //wait on chidren for(int i = 1; i < processors; i++) { - int length; - MPI_Recv(&length, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status); - - char buf[length]; - - MPI_Recv(buf, length, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status); - - outputMyPart = buf; - out << outputMyPart; + char buf[4]; + MPI_Recv(buf, 4, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status); } - out.close(); + if (output == "lt") { + convertToLowerTriangle(outputFile); + } }else { //you are a child process //do your part - string outputMyPart; - driverMPI(start, end, outputMyPart, cutoff); + driverMPI(start, end, outMPI, cutoff); - //send results to parent - int length = outputMyPart.length(); - char buf[length]; - strcpy(buf, outputMyPart.c_str()); + char buf[4]; + strcpy(buf, "done"); - MPI_Send( &length, 1, MPI_INT, 0, tag, MPI_COMM_WORLD); - MPI_Send(buf, length, MPI_CHAR, 0, tag, MPI_COMM_WORLD); + //tell parent you are done. + MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD); } - + MPI_File_close(&outMPI); #else #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) @@ -391,24 +387,15 @@ int DistanceCommand::driver(int startLine, int endLine, string dFileName, float } /**************************************************************************************************/ /////// need to fix to work with calcs and sequencedb -int DistanceCommand::driverMPI(int startLine, int endLine, string& outputString, float cutoff){ +int DistanceCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, float cutoff){ try { - + MPI_Status status; int startTime = time(NULL); - outputString = ""; - - if((output == "lt") && startLine == 0){ outputString += (toString(alignDB.getNumSeqs()) + '\n'); } + string outputString = ""; for(int i=startLine;icontrol_pressed) { return 0; } @@ -419,23 +406,40 @@ int DistanceCommand::driverMPI(int startLine, int endLine, string& outputString, if(dist <= cutoff){ if (output == "column") { outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n'); } } - if (output == "lt") { outputString += (toString(dist) + '\t'); } - if (output == "square") { //make a square column you can convert to square phylip + if ((output == "square") || (output == "lt")){ //make a square column you can convert to square phylip outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n'); outputString += (alignDB.get(j).getName() + ' ' + alignDB.get(i).getName() + ' ' + toString(dist) + '\n'); } } - if (output == "lt") { outputString += '\n'; } - if(i % 100 == 0){ m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine(); } + if(i % 10 == 0){ //output to file + //send results to parent + int length = outputString.length(); + char buf[length]; + strcpy(buf, outputString.c_str()); + + MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status); + outputString = ""; + } + } + m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine(); + if(outputString != ""){ //output to file + //send results to parent + int length = outputString.length(); + char buf[length]; + strcpy(buf, outputString.c_str()); + + MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status); + outputString = ""; + } return 1; } @@ -533,6 +537,100 @@ int DistanceCommand::convertMatrix(string outputFile) { exit(1); } } +/**************************************************************************************************/ +int DistanceCommand::convertToLowerTriangle(string outputFile) { + try{ + + //sort file by first column so the distances for each row are together + string outfile = getRootName(outputFile) + "sorted.dist.temp"; + + //use the unix sort + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + string command = "sort -n " + outputFile + " -o " + outfile; + system(command.c_str()); + #else //sort using windows sort + string command = "sort " + outputFile + " /O " + outfile; + system(command.c_str()); + #endif + + + //output to new file distance for each row and save positions in file where new row begins + ifstream in; + openInputFile(outfile, in); + + ofstream out; + openOutputFile(outputFile, out); + + out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint); + + out << alignDB.getNumSeqs() << endl; + + //get first currentRow + string first, currentRow, second; + float dist; + int i, j; + i = 0; j = 0; + map rowDists; //take advantage of the fact that maps are already sorted by key + map::iterator it; + + in >> first; + currentRow = first; + + rowDists[first] = 0.00; //distance to yourself is 0.0 + + in.seekg(0); + //openInputFile(outfile, in); + + while(!in.eof()) { + if (m->control_pressed) { in.close(); remove(outfile.c_str()); out.close(); return 0; } + + in >> first >> second >> dist; gobble(in); + + if (first != currentRow) { + //print out last row + out << currentRow << '\t'; //print name + + //print dists + for (it = rowDists.begin(); it != rowDists.end(); it++) { + if (j >= i) { break; } + out << it->second << '\t'; + j++; + } + out << endl; + + //start new row + currentRow = first; + rowDists.clear(); + rowDists[first] = 0.00; + rowDists[second] = dist; + j = 0; + i++; + }else{ + rowDists[second] = dist; + } + } + //print out last row + out << currentRow << '\t'; //print name + + //print dists + for (it = rowDists.begin(); it != rowDists.end(); it++) { + out << it->second << '\t'; + } + out << endl; + + in.close(); + out.close(); + + remove(outfile.c_str()); + + return 1; + + } + catch(exception& e) { + m->errorOut(e, "DistanceCommand", "convertToLowerTriangle"); + exit(1); + } +} /************************************************************************************************** void DistanceCommand::appendFiles(string temp, string filename) { try{