#ifdef USE_MPI
m->mothurOut("When using MPI, the processors parameter is set to the number of MPI processes running. \n");
#endif
- m->mothurOut("The window parameter allows you to specify the window size for searching for chimeras, default=1/4 sequence length. \n");
+ m->mothurOut("The window parameter allows you to specify the window size for searching for chimeras, default=300. \n");
m->mothurOut("The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default=25.\n");
m->mothurOut("The conservation parameter allows you to enter a frequency file containing the highest bases frequency at each place in the alignment.\n");
m->mothurOut("The quantile parameter allows you to enter a file containing quantiles for a template files sequences, if you use the filter the quantile file generated becomes unique to the fasta file you used.\n");
int start = time(NULL);
- chimera = new Pintail(fastafile, templatefile, filter, processors, maskfile, consfile, quanfile, window, increment, outputDir);
-
//set user options
if (maskfile == "default") { m->mothurOut("I am using the default 236627 EU009184.1 Shigella dysenteriae str. FBD013."); m->mothurOutEndLine(); }
-
+ chimera = new Pintail(fastafile, templatefile, filter, processors, maskfile, consfile, quanfile, window, increment, outputDir);
+
string outputFileName, accnosFileName;
if (maskfile != "") {
outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + maskfile + ".pintail.chimeras";
int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
int inMode=MPI_MODE_RDONLY;
- char* outFilename = new char[outputFileName.length()];\r
- memcpy(outFilename, outputFileName.c_str(), outputFileName.length());
+ //char* outFilename = new char[outputFileName.length()];
+ //memcpy(outFilename, outputFileName.c_str(), outputFileName.length());
+
+ char outFilename[1024];
+ strcpy(outFilename, outputFileName.c_str());
- char* outAccnosFilename = new char[accnosFileName.length()];\r
- memcpy(outAccnosFilename, accnosFileName.c_str(), accnosFileName.length());
+ //char* outAccnosFilename = new char[accnosFileName.length()];
+ //memcpy(outAccnosFilename, accnosFileName.c_str(), accnosFileName.length());
+
+ char outAccnosFilename[1024];
+ strcpy(outAccnosFilename, accnosFileName.c_str());
- char* inFileName = new char[fastafile.length()];\r
- memcpy(inFileName, fastafile.c_str(), fastafile.length());
+ //char* inFileName = new char[fastafile.length()];
+ //memcpy(inFileName, fastafile.c_str(), fastafile.length());
+
+ char inFileName[1024];
+ strcpy(inFileName, fastafile.c_str());
MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
- delete inFileName;
- delete outFilename;
- delete outAccnosFilename;
+ //delete inFileName;
+ //delete outFilename;
+ //delete outAccnosFilename;
if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); delete chimera; return 0; }
MPIPos = setFilePosFasta(fastafile, numSeqs); //fills MPIPos, returns numSeqs
//send file positions to all processes
- MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //send numSeqs
- MPI_Bcast(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos
+ for(int i = 1; i < processors; i++) {
+ MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
+ MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
+ }
//figure out how many sequences you have to align
numSeqsPerProcessor = numSeqs / processors;
- if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; }
int startIndex = pid * numSeqsPerProcessor;
+ if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; }
+
//align your part
driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
if (tempResult != 0) { MPIWroteAccnos = true; }
}
}else{ //you are a child process
- MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs
+ MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
MPIPos.resize(numSeqs+1);
- MPI_Bcast(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
+ MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
//figure out how many sequences you have to align
numSeqsPerProcessor = numSeqs / processors;
- if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; }
int startIndex = pid * numSeqsPerProcessor;
+ if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; }
+
//align your part
driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
MPI_File_close(&inMPI);
MPI_File_close(&outMPI);
MPI_File_close(&outMPIAccnos);
+ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
//delete accnos file if blank
if (pid == 0) {