int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
int inMode=MPI_MODE_RDONLY;
- char outFilename[filteredFasta.length()];
- strcpy(outFilename, filteredFasta.c_str());
-
- char inFileName[fastafileNames[s].length()];
- strcpy(inFileName, fastafileNames[s].c_str());
+ char* outFilename = new char[filteredFasta.length()];\r
+ memcpy(outFilename, filteredFasta.c_str(), filteredFasta.length());
+
+ char* inFileName = new char[fastafileNames[s].length()];\r
+ memcpy(inFileName, fastafileNames[s].c_str(), fastafileNames[s].length());
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 inFileName;
+ delete outFilename;
+
if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); 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 seq(iss); gobble(iss);
if(count % 10 == 0){ //output to file
//send results to parent
int length = outputString.length();
- char buf[length];
- strcpy(buf, outputString.c_str());
+ char* buf = new char[length];\r
+ memcpy(buf, outputString.c_str(), length);
MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
outputString = "";
+ delete buf;
}
}
if(outputString != ""){ //output to file
//send results to parent
int length = outputString.length();
- char buf[length];
- strcpy(buf, outputString.c_str());
+ char* buf = new char[length];\r
+ memcpy(buf, outputString.c_str(), length);
MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
outputString = "";
+ delete buf;
}
if((num) % 100 != 0){ cout << (num) << endl; m->mothurOutJustToLog(toString(num) + "\n"); }
MPI_Status status;
MPI_Comm_rank(MPI_COMM_WORLD, &pid);
- 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 = 0; i < ((processors-1)*5); i++) {
- MPI_Recv(&temp[0], (alignmentLength+1), MPI_INT, MPI_ANY_SOURCE, 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);
+ if(trump != '*' || 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 = 0; i < ((processors-1)*5); i++) {
+ MPI_Recv(&temp[0], (alignmentLength+1), MPI_INT, MPI_ANY_SOURCE, 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);
+ }
+
}
if (pid == 0) { //only one process should output the filter
MPI_Bcast(&filterString[0], alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
}else{
//recieve filterString
- char tempBuf[alignmentLength];
+ char* tempBuf = new char[alignmentLength];
MPI_Bcast(tempBuf, alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
filterString = tempBuf;
if (filterString.length() > alignmentLength) { filterString = filterString.substr(0, alignmentLength); }
+ delete tempBuf;
}
MPI_Barrier(MPI_COMM_WORLD);
//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 seq(iss);
if (seq.getAligned().length() != alignmentLength) { cout << "Alignment length is " << alignmentLength << " and sequence " << seq.getName() << " has length " << seq.getAligned().length() << ", please correct." << endl; exit(1); }
projects / mothur.git / blobdiff