inFASTA.close();
////////////create filter/////////////////
+ m->mothurOut("Creating Filter... "); m->mothurOutEndLine();
filter = createFilter();
+ m->mothurOutEndLine(); m->mothurOutEndLine();
+
if (m->control_pressed) { return 0; }
#ifdef USE_MPI
////////////run filter/////////////////
+ m->mothurOut("Running Filter... "); m->mothurOutEndLine();
+
filterSequences();
-
+
+ m->mothurOutEndLine(); m->mothurOutEndLine();
+
int filteredLength = 0;
for(int i=0;i<alignmentLength;i++){
if(filter[i] == '1'){ filteredLength++; }
string filteredFasta = outputDir + getRootName(getSimpleName(fastafileNames[s])) + "filter.fasta";
#ifdef USE_MPI
- int pid, start, end;
+ int pid, start, end, numSeqsPerProcessor, num;
int tag = 2001;
+ vector<long>MPIPos;
MPI_Status status;
MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
MPI_File outMPI;
+ MPI_File tempMPI;
MPI_File inMPI;
int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
int inMode=MPI_MODE_RDONLY;
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);
+ if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); return 0; }
+
if (pid == 0) { //you are the root process
- setLines(fastafileNames[s]);
-
- char bufF[alignmentLength];
- strcpy(bufF, filter.c_str());
-
- for (int j = 0; j < lines.size(); j++) { //each process
- if (j != 0) { //don't send to yourself
- MPI_Send(&lines[j]->start, 1, MPI_INT, j, tag, MPI_COMM_WORLD); //start position in file
- MPI_Send(&bufferSizes[j], 1, MPI_INT, j, tag, MPI_COMM_WORLD); //how bytes for the read
- MPI_Send(bufF, alignmentLength, MPI_CHAR, j, tag, MPI_COMM_WORLD);
- }
- }
+ MPIPos = setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
+ numSeqs += num;
- //read your peice of file
- char buf[bufferSizes[0]];
- MPI_File_read_at(inMPI, lines[0]->start, buf, bufferSizes[0], MPI_CHAR, &status);
- istringstream iss (buf,istringstream::in);
+ //send file positions to all processes
+ MPI_Bcast(&num, 1, MPI_INT, 0, MPI_COMM_WORLD); //send numSeqs
+ MPI_Bcast(&MPIPos[0], (num+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos
+ //figure out how many sequences you have to do
+ numSeqsPerProcessor = num / processors;
+ if(pid == (processors - 1)){ numSeqsPerProcessor = num - pid * numSeqsPerProcessor; }
+ int startIndex = pid * numSeqsPerProcessor;
+
//do your part
- driverMPIRun(iss, outMPI);
+ driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
+
+ if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); return 0; }
//wait on chidren
for(int i = 1; i < processors; i++) {
}
}else { //you are a child process
- //receive your section of file
- int startPos, bufferSize;
- char bufF[alignmentLength];
- MPI_Recv(&startPos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
- MPI_Recv(&bufferSize, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
- MPI_Recv(bufF, alignmentLength, MPI_CHAR, 0, tag, MPI_COMM_WORLD, &status);
+ MPI_Bcast(&num, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs
+ numSeqs += num;
+ MPIPos.resize(num+1);
+ MPI_Bcast(&MPIPos[0], (num+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
- filter = bufF; //filter was made by process 0 so other processes need to get it
-
- //read your peice of file
- char buf2[bufferSize];
- MPI_File_read_at(inMPI, startPos, buf2, bufferSize, MPI_CHAR, &status);
- istringstream iss (buf2,istringstream::in);
+ //figure out how many sequences you have to align
+ numSeqsPerProcessor = num / processors;
+ if(pid == (processors - 1)){ numSeqsPerProcessor = num - pid * numSeqsPerProcessor; }
+ int startIndex = pid * numSeqsPerProcessor;
+
+ //align your part
+ driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
+
+ if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); return 0; }
- //do your part
- driverMPIRun(iss, outMPI);
-
char buf[4];
strcpy(buf, "done");
exit(1);
}
}
+#ifdef USE_MPI
/**************************************************************************************/
-int FilterSeqsCommand::driverMPIRun(istringstream& in, MPI_File& outMPI) {
+int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<long>& MPIPos) {
try {
string outputString = "";
int count = 0;
MPI_Status status;
- while (!in.eof()) {
+ for(int i=0;i<num;i++){
+
+ if (m->control_pressed) { return 0; }
+
+ //read next sequence
+ int length = MPIPos[start+i+1] - MPIPos[start+i];
+ char buf4[length];
+ MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
- Sequence seq(in); gobble(in);
+ string tempBuf = buf4;
+ if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
+ istringstream iss (tempBuf,istringstream::in);
+
+ Sequence seq(iss); gobble(iss);
if (seq.getName() != "") {
string align = seq.getAligned();
}
}
+
+ if((i+1) % 100 == 0){ cout << (i+1) << endl; m->mothurOutJustToLog(toString(i+1) + "\n"); }
}
if(outputString != ""){ //output to file
MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
outputString = "";
}
-
+
+ if((num) % 100 != 0){ cout << (num) << endl; m->mothurOutJustToLog(toString(num) + "\n"); }
return 0;
}
exit(1);
}
}
+#endif
/**************************************************************************************/
int FilterSeqsCommand::driverRunFilter(string F, string outputFilename, string inputFilename, linePair* line) {
try {
for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
#ifdef USE_MPI
- int pid;
- int Atag = 1; int Ttag = 2; int Ctag = 3; int Gtag = 4; int Gaptag = 5;
+ int pid, numSeqsPerProcessor, num;
int tag = 2001;
+ vector<long> MPIPos;
MPI_Status status;
MPI_File inMPI;
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
- setLines(fastafileNames[s]);
-
- for (int j = 0; j < lines.size(); j++) { //each process
- if (j != 0) { //don't send to yourself
- MPI_Send(&lines[j]->start, 1, MPI_INT, j, tag, MPI_COMM_WORLD); //start position in file
- MPI_Send(&numSeqs, 1, MPI_INT, j, tag, MPI_COMM_WORLD);
- MPI_Send(&bufferSizes[j], 1, MPI_INT, j, tag, MPI_COMM_WORLD); //how bytes for the read
- }
- }
-
- char buf[bufferSizes[0]];
- MPI_File_read_at(inMPI, 0, buf, bufferSizes[0], MPI_CHAR, &status);
-
- string tempBuf = buf;
- if (tempBuf.length() > bufferSizes[0]) { tempBuf = tempBuf.substr(0, bufferSizes[0]); }
-
- MPICreateFilter(F, tempBuf);
-
- if (m->control_pressed) { MPI_File_close(&inMPI); return filterString; }
-
- vector<int> temp; temp.resize(alignmentLength+1);
+ MPIPos = setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
+ numSeqs += num;
- //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, tag, 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]; }
- }
- }
-
+ //send file positions to all processes
+ MPI_Bcast(&num, 1, MPI_INT, 0, MPI_COMM_WORLD); //send numSeqs
+ MPI_Bcast(&MPIPos[0], (num+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos
+
+ //figure out how many sequences you have to do
+ numSeqsPerProcessor = num / processors;
+ if(pid == (processors - 1)){ numSeqsPerProcessor = num - pid * numSeqsPerProcessor; }
+ int startIndex = 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
- int startPos, bufferSize;
- MPI_Recv(&startPos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
- MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
- MPI_Recv(&bufferSize, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
-
- //send freqs
- char buf2[bufferSize];
- MPI_File_read_at(inMPI, startPos, buf2, bufferSize, MPI_CHAR, &status);
-
- string tempBuf = buf2;
- if (tempBuf.length() > bufferSize) { tempBuf = tempBuf.substr(0, bufferSize); }
-
- MPICreateFilter(F, tempBuf);
-
- if (m->control_pressed) { MPI_File_close(&inMPI); return filterString; }
+ MPI_Bcast(&num, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs
+ MPIPos.resize(num+1);
+ numSeqs += num;
+ MPI_Bcast(&MPIPos[0], (num+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
+
+ //figure out how many sequences you have to align
+ numSeqsPerProcessor = num / processors;
+ if(pid == (processors - 1)){ numSeqsPerProcessor = num - pid * numSeqsPerProcessor; }
+ int startIndex = pid * numSeqsPerProcessor;
+
+ //do your part
+ MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI, MPIPos);
- //send my fequency counts
- F.a.push_back(Atag);
- 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+1), MPI_INT, 0, tag, MPI_COMM_WORLD);
- F.c.push_back(Ctag);
- 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+1), MPI_INT, 0, tag, MPI_COMM_WORLD);
- F.gap.push_back(Gaptag);
- ierr = MPI_Send(&(F.gap[0]), (alignmentLength+1), MPI_INT, 0, tag, MPI_COMM_WORLD);
+ if (m->control_pressed) { MPI_File_close(&inMPI); return 0; }
}
- MPI_Barrier(MPI_COMM_WORLD);
MPI_File_close(&inMPI);
#else
}
}
+
+#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 (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
+#endif
F.setNumSeqs(numSeqs);
if(isTrue(vertical) == 1) { F.doVertical(); }
if(soft != 0) { F.doSoft(); }
filterString = F.getFilter();
-
+
+#ifdef USE_MPI
+ //send filter string to kids
+ MPI_Bcast(&filterString[0], alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
+ }else{
+ //recieve filterString
+ char tempBuf[alignmentLength];
+ MPI_Bcast(tempBuf, alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
+
+ filterString = tempBuf;
+ if (filterString.length() > alignmentLength) { filterString = filterString.substr(0, alignmentLength); }
+ }
+
+ MPI_Barrier(MPI_COMM_WORLD);
+#endif
+
+
return filterString;
}
catch(exception& e) {
exit(1);
}
}
+#ifdef USE_MPI
/**************************************************************************************/
-int FilterSeqsCommand::MPICreateFilter(Filters& F, string input) {
+int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File& inMPI, vector<long>& MPIPos) {
try {
- vector<string> seqStrings;
- parseBuffer(input, seqStrings);
+ MPI_Status status;
+ int pid;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
- for(int i=0;i<seqStrings.size();i++){
+ for(int i=0;i<num;i++){
- if (seqStrings[i].length() != alignmentLength) { cout << i << '\t' << seqStrings[i].length() << "Sequences are not all the same length, please correct." << endl; m->control_pressed = true; }
-
- if (m->control_pressed) { return 1; }
+ if (m->control_pressed) { return 0; }
+
+ //read next sequence
+ int length = MPIPos[start+i+1] - MPIPos[start+i];
+
+ char buf4[length];
+ MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
- Sequence seq("", seqStrings[i]);
+ string tempBuf = buf4;
+ if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
+ istringstream iss (tempBuf,istringstream::in);
+
+ 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); }
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(); }
+ if((i+1) % 100 == 0){ cout << (i+1) << endl; m->mothurOutJustToLog(toString(i+1) + "\n"); }
}
//report progress
- if((seqStrings.size()) % 100 != 0){ m->mothurOut(toString(seqStrings.size())); m->mothurOutEndLine(); }
+ if((num) % 100 != 0){ cout << num << endl; m->mothurOutJustToLog(toString(num) + "\n"); }
return 0;
}
exit(1);
}
}
-
+#endif
/**************************************************************************************************/
int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) {
exit(1);
}
}
-/**************************************************************************************************/
-int FilterSeqsCommand::parseBuffer(string file, vector<string>& seqs) {
- try {
- istringstream iss (file); //,istringstream::in
- string name, seqstring;
-
- while (!iss.eof()) {
-
- if (m->control_pressed) { return 0; }
-
- Sequence seq(iss); gobble(iss);
-
- if (seq.getName() != "") {
- seqs.push_back(seq.getAligned());
- }
- }
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "FilterSeqsCommand", "parseBuffer");
- exit(1);
- }
-}
/**************************************************************************************/
projects / mothur.git / blobdiff