if (abort == true) { return 0; }
+ int startTime = time(NULL);
+
int numSeqs = alignDB.getNumSeqs();
cutoff += 0.005;
string outputFile;
-
+
if (output == "lt") { //does the user want lower triangle phylip formatted file
outputFile = outputDir + getRootName(getSimpleName(fastafile)) + "phylip.dist";
remove(outputFile.c_str());
outputFile = outputDir + getRootName(getSimpleName(fastafile)) + "square.dist";
remove(outputFile.c_str());
}
+
+
+#ifdef USE_MPI
+
+ int pid, start, end;
+ int tag = 2001;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ MPI_Status status;
+ MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+
+ //each process gets where it should start and stop in the file
+ start = int (sqrt(float(pid)/float(processors)) * numSeqs);
+ end = int (sqrt(float(pid+1)/float(processors)) * numSeqs);
+
+ if (output != "lt") {
+ MPI_File outMPI;
+ int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
+
+ //char* filename = new char[outputFile.length()];
+ //memcpy(filename, outputFile.c_str(), outputFile.length());
+
+ char filename[1024];
+ strcpy(filename, outputFile.c_str());
+
+ MPI_File_open(MPI_COMM_WORLD, filename, amode, MPI_INFO_NULL, &outMPI);
+ //delete filename;
+
+ if (pid == 0) { //you are the root process
+
+ //do your part
+ string outputMyPart;
+ driverMPI(start, end, outMPI, cutoff);
+
+ if (m->control_pressed) { MPI_File_close(&outMPI); delete distCalculator; return 0; }
+
+ //wait on chidren
+ for(int i = 1; i < processors; i++) {
+ if (m->control_pressed) { MPI_File_close(&outMPI); delete distCalculator; return 0; }
+
+ char buf[4];
+ MPI_Recv(buf, 4, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
+ }
+ }else { //you are a child process
+ //do your part
+ driverMPI(start, end, outMPI, cutoff);
+
+ if (m->control_pressed) { MPI_File_close(&outMPI); delete distCalculator; return 0; }
+
+ char buf[4];
+ strcpy(buf, "done");
+ //tell parent you are done.
+ MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
+ }
+
+ MPI_File_close(&outMPI);
+
+ }else { //lower triangle format
+ if (pid == 0) { //you are the root process
+
+ //do your part
+ string outputMyPart;
+ long mySize;
+ driverMPI(start, end, outputFile, mySize);
+
+ if (m->control_pressed) { delete distCalculator; return 0; }
+
+ int amode=MPI_MODE_APPEND|MPI_MODE_WRONLY|MPI_MODE_CREATE; //
+ MPI_File outMPI;
+ MPI_File inMPI;
+
+ //char* filename = new char[outputFile.length()];
+ //memcpy(filename, outputFile.c_str(), outputFile.length());
+
+ char filename[1024];
+ strcpy(filename, outputFile.c_str());
+
+ MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
+ //delete filename;
+
+ //wait on chidren
+ for(int b = 1; b < processors; b++) {
+ long fileSize;
+
+ if (m->control_pressed) { MPI_File_close(&outMPI); delete distCalculator; return 0; }
+
+ MPI_Recv(&fileSize, 1, MPI_LONG, b, tag, MPI_COMM_WORLD, &status);
+
+ string outTemp = outputFile + toString(b) + ".temp";
+
+ char* buf = new char[outTemp.length()];
+ memcpy(buf, outTemp.c_str(), outTemp.length());
+
+ MPI_File_open(MPI_COMM_SELF, buf, MPI_MODE_DELETE_ON_CLOSE|MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
+ delete buf;
+
+ int count = 0;
+ while (count < fileSize) {
+ char buf2[1];
+ MPI_File_read(inMPI, buf2, 1, MPI_CHAR, &status);
+ MPI_File_write(outMPI, buf2, 1, MPI_CHAR, &status);
+ count += 1;
+ }
+
+ MPI_File_close(&inMPI); //deleted on close
+ }
+
+ MPI_File_close(&outMPI);
+ }else { //you are a child process
+ //do your part
+ long size;
+ driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size);
+
+ if (m->control_pressed) { delete distCalculator; return 0; }
+
+ //tell parent you are done.
+ MPI_Send(&size, 1, MPI_LONG, 0, tag, MPI_COMM_WORLD);
+ }
+ }
+#else
+
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
//if you don't need to fork anything
if(processors == 1){
driver(0, numSeqs, outputFile, cutoff);
remove((outputFile + toString(it->second) + ".temp").c_str());
}
}
-#else
+ #else
ifstream inFASTA;
driver(0, numSeqs, outputFile, cutoff);
+ #endif
+
#endif
+ if (m->control_pressed) { delete distCalculator; remove(outputFile.c_str()); return 0; }
+
+ #ifdef USE_MPI
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+
+ if (pid == 0) { //only one process should output to screen
+ #endif
if (output == "square") { convertMatrix(outputFile); }
+ ifstream fileHandle;
+ fileHandle.open(outputFile.c_str());
+ if(fileHandle) {
+ gobble(fileHandle);
+ if (fileHandle.eof()) { m->mothurOut(outputFile + " is blank. This can result if there are no distances below your cutoff."); m->mothurOutEndLine(); }
+ }
+
+
+ #ifdef USE_MPI
+ }
+ #endif
+
+ if (m->control_pressed) { delete distCalculator; remove(outputFile.c_str()); return 0; }
+
delete distCalculator;
m->mothurOutEndLine();
m->mothurOut("Output File Name: "); m->mothurOutEndLine();
m->mothurOut(outputFile); m->mothurOutEndLine();
m->mothurOutEndLine();
-
+ m->mothurOut("It took " + toString(time(NULL) - startTime) + " to calculate the distances for " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
return 0;
}
outFile << name << '\t';
}
for(int j=0;j<i;j++){
+
+ if (m->control_pressed) { outFile.close(); return 0; }
+
distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
double dist = distCalculator->getDist();
exit(1);
}
}
+#ifdef USE_MPI
+/**************************************************************************************************/
+/////// need to fix to work with calcs and sequencedb
+int DistanceCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, float cutoff){
+ try {
+ MPI_Status status;
+ int startTime = time(NULL);
+
+ string outputString = "";
+
+ for(int i=startLine;i<endLine;i++){
+
+ for(int j=0;j<i;j++){
+
+ if (m->control_pressed) { return 0; }
+
+ distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
+ double dist = distCalculator->getDist();
+
+ if(dist <= cutoff){
+ if (output == "column") { outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n'); }
+ }
+
+ if (output == "square") { //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(i % 100 == 0){
+ //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
+ cout << i << '\t' << (time(NULL) - startTime) << endl;
+ }
+
+
+ //send results to parent
+ int length = outputString.length();
+
+ char* buf = new char[length];
+ memcpy(buf, outputString.c_str(), length);
+
+ MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
+ outputString = "";
+ delete buf;
+
+ }
+
+ //m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
+ cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
+ return 1;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DistanceCommand", "driverMPI");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+/////// need to fix to work with calcs and sequencedb
+int DistanceCommand::driverMPI(int startLine, int endLine, string file, long& size){
+ try {
+ MPI_Status status;
+
+ MPI_File outMPI;
+ int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
+
+ //char* filename = new char[file.length()];
+ //memcpy(filename, file.c_str(), file.length());
+
+ char filename[1024];
+ strcpy(filename, file.c_str());
+
+ MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
+ //delete filename;
+
+ int startTime = time(NULL);
+
+ string outputString = "";
+ size = 0;
+
+ if((output == "lt") && startLine == 0){ outputString += toString(alignDB.getNumSeqs()) + "\n"; }
+
+ for(int i=startLine;i<endLine;i++){
+ if(output == "lt") {
+ string name = alignDB.get(i).getName();
+ if (name.length() < 10) { //pad with spaces to make compatible
+ while (name.length() < 10) { name += " "; }
+ }
+ outputString += name + "\t";
+ }
+ for(int j=0;j<i;j++){
+
+ if (m->control_pressed) { return 0; }
+
+ distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
+ double dist = distCalculator->getDist();
+
+ if (output == "lt") { outputString += toString(dist) + "\t"; }
+ }
+
+ if (output == "lt") { outputString += "\n"; }
+
+
+ if(i % 100 == 0){
+ //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
+ cout << i << '\t' << (time(NULL) - startTime) << endl;
+ }
+
+
+ //send results to parent
+ int length = outputString.length();
+ char* buf = new char[length];
+ memcpy(buf, outputString.c_str(), length);
+
+ MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
+ size += outputString.length();
+ outputString = "";
+ delete buf;
+ }
+
+ //m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
+ cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
+ MPI_File_close(&outMPI);
+
+ return 1;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DistanceCommand", "driverMPI");
+ exit(1);
+ }
+}
+#endif
/**************************************************************************************************/
-void DistanceCommand::convertMatrix(string outputFile) {
+int DistanceCommand::convertMatrix(string outputFile) {
try{
//sort file by first column so the distances for each row are together
//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) {
remove(outfile.c_str());
+ return 1;
+
}
catch(exception& e) {
m->errorOut(e, "DistanceCommand", "convertMatrix");
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<string, float> rowDists; //take advantage of the fact that maps are already sorted by key
+ map<string, float>::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{
projects / mothur.git / blobdiff