MPI_Send(&bufferSizes[j], 1, MPI_INT, j, tag, MPI_COMM_WORLD); //how bytes for the read
}
}
- //cout << "done sending" << endl;
- //cout << "parent = " << pid << " lines = " << lines[pid]->start << '\t' << lines[pid]->numSeqs << " size = " << lines.size() << endl;
-
- cout << "parent = " << pid << " address of Filter " << &F << " address of FilterString " << &filterString << " address of numSeqs = " << &numSeqs << " address of soft = " << &soft << endl;
- char* buf = new char(bufferSizes[0]);
- //cout << pid << '\t' << bufferSizes[0] << " line 1 start pos = " << lines[1]->start << " buffer size 0 " << bufferSizes[0] << " buffer size 1 " << bufferSizes[1] << endl;
+ char buf[bufferSizes[0]];
MPI_File_read_at(in, 0, buf, bufferSizes[0], MPI_CHAR, &status);
-
- cout << pid << " done reading " << &buf << endl;
- string tempBuf = buf;
- delete buf;
- //cout << pid << '\t' << (tempBuf.substr(0, 10)) << endl;
-
- //parse buffer
- istringstream iss (tempBuf,istringstream::in);
- string name, seqstring;
- vector<string> seqs;
-
- while (iss) {
- if (m->control_pressed) { return filterString; }
- cout << "here" << endl;
- Sequence seq(iss);
- cout << "here1" << endl;
- gobble(iss);
- cout << seq.getName() << endl;
- if (seq.getName() != "") {
- seqs.push_back(seq.getAligned());
- }
-
- }
-
- for(int i=0;i<seqs.size();i++){
-
- if (m->control_pressed) { return filterString; }
-
- Sequence seq("", seqs[i]);
-
- if(trump != '*'){ F.doTrump(seq); }
- if(isTrue(vertical) || soft != 0){ F.getFreqs(seq); }
- cout.flush();
-
- //report progress
- if((i+1) % 100 == 0){ m->mothurOut(toString(i+1)); m->mothurOutEndLine(); }
- }
-
- //report progress
- if((seqs.size()) % 100 != 0){ m->mothurOut(toString(seqs.size())); m->mothurOutEndLine(); }
-
- //do your part
- //MPICreateFilter(F, seqs);
-
- vector<int> temp; temp.resize(alignmentLength);
+ MPICreateFilter(F, buf);
+
+ vector<int> temp; temp.resize(alignmentLength+1);
//get the frequencies from the child processes
for(int i = 0; i < ((processors-1)*5); i++) {
cout << "i = " << i << endl;
- int ierr = MPI_Recv(&temp, alignmentLength, MPI_INT, MPI_ANY_SOURCE, tag, MPI_COMM_WORLD, &status);
-
+ //vector<int> trial; trial.resize(10);
+ //cout << "trials size = " << trial.size() << endl;
+ //int ierr = MPI_Recv(&trial[0], 10, MPI_INT, MPI_ANY_SOURCE, tag, MPI_COMM_WORLD, &status);
+ int ierr = MPI_Recv(&temp[0], (alignmentLength+1), MPI_INT, MPI_ANY_SOURCE, tag, MPI_COMM_WORLD, &status);
+ cout << "recieved something" << endl;
+ //for (int g = 0; g < trial.size(); g++) { cout << trial[g] << '\t'; } cout << endl;
int receiveTag = temp[temp.size()-1]; //child process added a int to the end to indicate what letter count this is for
+ cout << "reciveve tag = " << receiveTag << endl;
+ for (int k = 0; k < alignmentLength; k++) { cout << k << '\t' << temp[k] << endl; }
+ cout << "done " << endl << endl;
int sender = status.MPI_SOURCE;
}else { //i am the child process
int startPos, numLines, bufferSize;
- cout << "child = " << pid << " address of Filter " << &F << " address of FilterString " << &filterString << " address of numSeqs = " << &numSeqs << " address of soft = " << &soft<< endl;
ierr = MPI_Recv(&startPos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
ierr = MPI_Recv(&numLines, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
ierr = MPI_Recv(&bufferSize, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
- //cout << "child = " << pid << " done recv messages startpos = " << startPos << " numLines = " << numLines << " buffersize = " << bufferSize << endl;
-
-
+
//send freqs
- char* buf2 = new char(bufferSize);
+ char buf2[bufferSize];
MPI_File_read_at( in, startPos, buf2, bufferSize, MPI_CHAR, &status);
- cout << pid << " done reading " << &buf2 << endl;
-
- string tempBuf = buf2;
- delete buf2;
- // cout << pid << '\t' << (tempBuf.substr(0, 10)) << endl;
- istringstream iss (tempBuf,istringstream::in);
-
- string name, seqstring;
- vector<string> seqs;
-
- while (iss) {
-
- if (m->control_pressed) { return filterString; }
- cout << "here" << endl;
- Sequence seq(iss);
- cout << "here1" << endl;
- gobble(iss);
- cout << seq.getName() << endl;
-
- if (seq.getName() != "") {
- seqs.push_back(seq.getAligned());
- }
- }
-
- for(int i=0;i<seqs.size();i++){
-
- if (m->control_pressed) { return filterString; }
-
- Sequence seq("", seqs[i]);
-
- if(trump != '*'){ F.doTrump(seq); }
- if(isTrue(vertical) || soft != 0){ F.getFreqs(seq); }
- cout.flush();
- //report progress
- if((i+1) % 100 == 0){ m->mothurOut(toString(i+1)); m->mothurOutEndLine(); }
- }
-
- //report progress
- if((seqs.size()) % 100 != 0){ m->mothurOut(toString(seqs.size())); m->mothurOutEndLine(); }
-
- //MPICreateFilter(F, seqs);
-
+ MPICreateFilter(F, buf2);
+
//send my fequency counts
F.a.push_back(Atag);
- int ierr = MPI_Send( &F.a[0], alignmentLength, MPI_INT, 0, tag, MPI_COMM_WORLD);
+ int ierr = MPI_Send(&(F.a[0]), (alignmentLength+1), MPI_INT, 0, tag, MPI_COMM_WORLD);
F.t.push_back(Ttag);
- ierr = MPI_Send( &F.t[0], alignmentLength, MPI_INT, 0, tag, MPI_COMM_WORLD);
+ ierr = MPI_Send (&(F.t[0]), (alignmentLength+1), MPI_INT, 0, tag, MPI_COMM_WORLD);
F.c.push_back(Ctag);
- ierr = MPI_Send( &F.c[0], alignmentLength, MPI_INT, 0, tag, MPI_COMM_WORLD);
+ ierr = MPI_Send(&(F.c[0]), (alignmentLength+1), MPI_INT, 0, tag, MPI_COMM_WORLD);
F.g.push_back(Gtag);
- ierr = MPI_Send( &F.g[0], alignmentLength, MPI_INT, 0, tag, MPI_COMM_WORLD);
+ ierr = MPI_Send(&(F.g[0]), (alignmentLength+1), MPI_INT, 0, tag, MPI_COMM_WORLD);
F.gap.push_back(Gaptag);
- ierr = MPI_Send( &F.gap[0], alignmentLength, MPI_INT, 0, tag, MPI_COMM_WORLD);
-
- cout << "child " << pid << " done sending counts" << endl;
+ ierr = MPI_Send(&(F.gap[0]), (alignmentLength+1), MPI_INT, 0, tag, MPI_COMM_WORLD);
}
MPI_Barrier(MPI_COMM_WORLD);
}
}
-#ifdef USE_MPI
-
-//merge all frequency data and create filter string
- //int pid;
- //MPI_Comm_rank(MPI_COMM_WORLD, &pid);
-
- //if (pid == 0) { //only one process should output to screen
-#endif
- cout << "made it here" << endl;
+ cout << "made it here, numSeqs = " << numSeqs << endl;
F.setNumSeqs(numSeqs);
if(isTrue(vertical) == 1) { F.doVertical(); }
}
}
/**************************************************************************************/
-int FilterSeqsCommand::MPICreateFilter(Filters& F, vector<string>& seqStrings) {
+int FilterSeqsCommand::MPICreateFilter(Filters& F, string input) {
try {
+ vector<string> seqStrings;
+ parseBuffer(input, seqStrings);
+
for(int i=0;i<seqStrings.size();i++){
if (m->control_pressed) { return 1; }
- Sequence seq("", seqStrings[0]);
+ Sequence seq("", seqStrings[i]);
if(trump != '*'){ F.doTrump(seq); }
if(isTrue(vertical) || soft != 0){ F.getFreqs(seq); }
istringstream iss (file,istringstream::in);
string name, seqstring;
-int pid;
-MPI_Comm_rank(MPI_COMM_WORLD, &pid);
- Sequence* seq34 = new Sequence();
-cout << "address of new sequence " << pid << '\t' << seq34 << endl;
-cout << "address of seqStrings " << pid << '\t' << &seqs << endl;
while (iss) {
if (m->control_pressed) { return 0; }
- cout << "here" << endl;
- Sequence* seq = new Sequence(iss);
- cout << "here1" << endl;
- gobble(iss);
- cout << seq->getName() << endl;
- if (seq->getName() != "") {
- seqs.push_back(seq->getAligned());
+
+ Sequence seq(iss); gobble(iss);
+
+ if (seq.getName() != "") {
+ seqs.push_back(seq.getAligned());
}
- delete seq;
}
return 0;
projects / mothur.git / blobdiff