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)
}
/**************************************************************************************************/
/////// 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;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; }
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;
}
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