if (m->control_pressed) { return filterString; }
string seqAligned = seqs[i]->getAligned();
+
+ if (seqAligned.length() != filterString.length()) { m->mothurOut(seqs[i]->getName() + " is not the same length as the template sequences. Aborting!\n"); exit(1); }
for (int j = 0; j < seqAligned.length(); j++) {
//if this spot is a gap
m->mothurOut("Reading sequences from " + file + "..."); cout.flush();
#ifdef USE_MPI
- int pid;
- vector<long> positions;
+ int pid, processors;
+ vector<unsigned long int> positions;
int numSeqs;
+ int tag = 2001;
MPI_Status status;
MPI_File inMPI;
MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
-
- char inFileName[file.length()];
+ MPI_Comm_size(MPI_COMM_WORLD, &processors);
+
+ //char* inFileName = new char[file.length()];
+ //memcpy(inFileName, file.c_str(), file.length());
+
+ char inFileName[1024];
strcpy(inFileName, file.c_str());
MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
-
+ //delete inFileName;
+
if (pid == 0) {
positions = setFilePosFasta(file, 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(&positions[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(&positions[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
+ }
}else{
- MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs
+ MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
positions.resize(numSeqs+1);
- MPI_Bcast(&positions[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
+ MPI_Recv(&positions[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
}
//read file
//read next sequence
int seqlength = positions[i+1] - positions[i];
- char buf4[seqlength];
+ char* buf4 = new char[seqlength];
+
MPI_File_read_at(inMPI, positions[i], buf4, seqlength, MPI_CHAR, &status);
string tempBuf = buf4;
if (tempBuf.length() > seqlength) { tempBuf = tempBuf.substr(0, seqlength); }
-
+ delete buf4;
+
istringstream iss (tempBuf,istringstream::in);
Sequence* current = new Sequence(iss);
}
MPI_File_close(&inMPI);
+ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
#else
ifstream in;
MPI_Offset size;
MPI_Status status;
- char inFileName[filename.length()];
+ //char* inFileName = new char[filename.length()];
+ //memcpy(inFileName, filename.c_str(), filename.length());
+
+ char inFileName[1024];
strcpy(inFileName, filename.c_str());
MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
MPI_File_get_size(inMPI, &size);
+
+ //delete inFileName;
- char buffer[size];
+ char* buffer = new char[size];
MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status);
string tempBuf = buffer;
if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size); }
istringstream iss (tempBuf,istringstream::in);
+
+ delete buffer;
if (!iss.eof()) {
Sequence temp(iss);