if (abort == true) { return 0; }
+ int startTime = time(NULL);
+
int numSeqs = alignDB.getNumSeqs();
cutoff += 0.005;
//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);
-
- 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, outMPI, cutoff);
+ if (output != "lt") {
+ 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 (m->control_pressed) { MPI_File_close(&outMPI); delete distCalculator; return 0; }
+
+ 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; }
- //wait on chidren
- for(int i = 1; i < processors; i++) {
char buf[4];
- MPI_Recv(buf, 4, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
+ strcpy(buf, "done");
+ //tell parent you are done.
+ MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
}
- if (output == "lt") {
- convertToLowerTriangle(outputFile);
- }
+ MPI_File_close(&outMPI);
- }else { //you are a child process
- //do your part
- driverMPI(start, end, outMPI, cutoff);
-
- char buf[4];
- strcpy(buf, "done");
+ }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[outputFile.length()];
+ strcpy(filename, outputFile.c_str());
- //tell parent you are done.
- MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
+ MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
+
+ //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[outTemp.length()];
+ strcpy(buf, outTemp.c_str());
+
+ MPI_File_open(MPI_COMM_SELF, buf, MPI_MODE_DELETE_ON_CLOSE|MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
+
+ int count = 0;
+ while (count < fileSize) { //read 1000 characters at a time
+ //send freqs
+ 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);
+ }
}
-
- MPI_File_close(&outMPI);
#else
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
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;
}
if (output == "column") { outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n'); }
}
- if ((output == "square") || (output == "lt")){ //make a square column you can convert to square phylip
+ 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();
+ //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
+ cout << i << '\t' << (time(NULL) - startTime) << endl;
}
- 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 = "";
- }
+
+ //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());
+ //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[file.length()];
+ strcpy(filename, file.c_str());
+
+ MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
+
+ 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();
- MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
- outputString = "";
+ 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[length];
+ strcpy(buf, outputString.c_str());
+
+ MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
+ size += outputString.length();
+ outputString = "";
+
+
}
+ //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) {
projects / mothur.git / blobdiff