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* 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);
+ //delete outFilename;
+ //delete inFileName;
+
if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); delete chimera; return 0; }
if (pid == 0) { //you are the root process
//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);