int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
int inMode=MPI_MODE_RDONLY;
-
- char outFilename[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[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()];
+ //memcpy(inFileName, fastafile.c_str(), fastafile.length());
- char inFileName[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;
+
if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); delete chimera; return 0; }
if (pid == 0) { //you are the root process
//print header
int length = outTemp.length();
- char buf2[length];
- strcpy(buf2, outTemp.c_str());
+ char* buf2 = new char[length];
+ memcpy(buf2, outTemp.c_str(), length);
+
MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status);
-
+ delete buf2;
+
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(&outMPI);
MPI_File_close(&outMPIAccnos);
+ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
+
//delete accnos file if blank
if (pid == 0) {
if (!MPIWroteAccnos) {
#else
ifstream inFASTA;
- openInputFile(candidateFileNames[s], inFASTA);
+ openInputFile(fastafile, inFASTA);
numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
inFASTA.close();
lines.push_back(new linePair(0, numSeqs));
//read next sequence
int length = MPIPos[start+i+1] - MPIPos[start+i];
- char buf4[length];
+ char* buf4 = new char[length];
+
MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
string tempBuf = buf4;
if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
istringstream iss (tempBuf,istringstream::in);
+ delete buf4;
Sequence* candidateSeq = new Sequence(iss); gobble(iss);