+ MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
+
+ if (m->control_pressed) { MPI_File_close(&inMPI); return 0; }
+
+ if (pid == 0) { //you are the root process
+ MPIPos = m->setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
+ numSeqs += num;
+
+ //send file positions to all processes
+ for(int i = 1; i < processors; i++) {
+ MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
+ MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
+ }
+
+ //figure out how many sequences you have to do
+ numSeqsPerProcessor = num / processors;
+ int startIndex = pid * numSeqsPerProcessor;
+ if(pid == (processors - 1)){ numSeqsPerProcessor = num - pid * numSeqsPerProcessor; }
+
+
+ //do your part
+ MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI, MPIPos);
+
+ if (m->control_pressed) { MPI_File_close(&inMPI); return 0; }
+
+ }else { //i am the child process
+ MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
+ MPIPos.resize(num+1);
+ numSeqs += num;
+ MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
+
+ //figure out how many sequences you have to align
+ numSeqsPerProcessor = num / processors;
+ int startIndex = pid * numSeqsPerProcessor;
+ if(pid == (processors - 1)){ numSeqsPerProcessor = num - pid * numSeqsPerProcessor; }
+
+
+ //do your part
+ MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI, MPIPos);
+
+ if (m->control_pressed) { MPI_File_close(&inMPI); return 0; }
+ }
+
+ MPI_File_close(&inMPI);
+ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
+
+#else
+
+ vector<unsigned long long> positions;
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ positions = m->divideFile(fastafileNames[s], processors);
+ for (int i = 0; i < (positions.size()-1); i++) {
+ lines.push_back(new linePair(positions[i], positions[(i+1)]));
+ }
+
+ if(processors == 1){
+ int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
+ numSeqs += numFastaSeqs;
+ }else{
+ int numFastaSeqs = createProcessesCreateFilter(F, fastafileNames[s]);
+ numSeqs += numFastaSeqs;
+ }
+ #else
+ if(processors == 1){
+ lines.push_back(new linePair(0, 1000));
+ int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
+ numSeqs += numFastaSeqs;
+ }else {
+ int numFastaSeqs = 0;
+ positions = m->setFilePosFasta(fastafileNames[s], numFastaSeqs);
+ if (positions.size() < processors) { processors = positions.size(); }
+
+ //figure out how many sequences you have to process
+ int numSeqsPerProcessor = numFastaSeqs / processors;
+ for (int i = 0; i < processors; i++) {
+ int startIndex = i * numSeqsPerProcessor;
+ if(i == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor; }
+ lines.push_back(new linePair(positions[startIndex], numSeqsPerProcessor));
+ }
+
+ numFastaSeqs = createProcessesCreateFilter(F, fastafileNames[s]);
+ numSeqs += numFastaSeqs;
+ }
+ #endif
+ //save the file positions so we can reuse them in the runFilter function
+ savedPositions[s] = positions;
+
+ if (m->control_pressed) { return filterString; }
+#endif
+
+ }
+ }
+
+
+#ifdef USE_MPI
+ int pid;
+ int Atag = 1; int Ttag = 2; int Ctag = 3; int Gtag = 4; int Gaptag = 5;
+ MPI_Status status;
+
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+
+ if(trump != '*' || m->isTrue(vertical) || soft != 0){
+
+ if (pid == 0) { //only one process should output the filter
+
+ vector<int> temp; temp.resize(alignmentLength+1);
+
+ //get the frequencies from the child processes
+ for(int i = 1; i < processors; i++) {
+
+ for (int j = 0; j < 5; j++) {
+
+ MPI_Recv(&temp[0], (alignmentLength+1), MPI_INT, i, 2001, MPI_COMM_WORLD, &status);
+ int receiveTag = temp[temp.size()-1]; //child process added a int to the end to indicate what letter count this is for
+
+ if (receiveTag == Atag) { //you are recieveing the A frequencies
+ for (int k = 0; k < alignmentLength; k++) { F.a[k] += temp[k]; }
+ }else if (receiveTag == Ttag) { //you are recieveing the T frequencies
+ for (int k = 0; k < alignmentLength; k++) { F.t[k] += temp[k]; }
+ }else if (receiveTag == Ctag) { //you are recieveing the C frequencies
+ for (int k = 0; k < alignmentLength; k++) { F.c[k] += temp[k]; }
+ }else if (receiveTag == Gtag) { //you are recieveing the G frequencies
+ for (int k = 0; k < alignmentLength; k++) { F.g[k] += temp[k]; }
+ }else if (receiveTag == Gaptag) { //you are recieveing the gap frequencies
+ for (int k = 0; k < alignmentLength; k++) { F.gap[k] += temp[k]; }
+ }
+ }
+ }
+ }else{
+
+ //send my fequency counts
+ F.a.push_back(Atag);
+ int ierr = MPI_Send(&(F.a[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
+ F.t.push_back(Ttag);
+ ierr = MPI_Send (&(F.t[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
+ F.c.push_back(Ctag);
+ ierr = MPI_Send(&(F.c[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
+ F.g.push_back(Gtag);
+ ierr = MPI_Send(&(F.g[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
+ F.gap.push_back(Gaptag);
+ ierr = MPI_Send(&(F.gap[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
+ }
+
+ }
+
+ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case