if (chimealns) { m->openOutputFile(alnsFileName, out2); out2.close(); }
int totalSeqs = 0;
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
if(processors == 1) { totalSeqs = driverGroups(parser, outputFileName, newFasta, accnosFileName, alnsFileName, 0, groups.size(), groups); }
else { totalSeqs = createProcessesGroups(parser, outputFileName, newFasta, accnosFileName, alnsFileName, groups); }
- #else
- totalSeqs = driverGroups(parser, outputFileName, newFasta, accnosFileName, alnsFileName, 0, groups.size(), groups);
- #endif
+
if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
int totalChimeras = deconvoluteResults(parser, outputFileName, accnosFileName, alnsFileName);
int numSeqs = 0;
int numChimeras = 0;
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ //#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
if(processors == 1){ numSeqs = driver(outputFileName, fastaFileNames[s], accnosFileName, alnsFileName, numChimeras); }
else{ numSeqs = createProcesses(outputFileName, fastaFileNames[s], accnosFileName, alnsFileName, numChimeras); }
- #else
- numSeqs = driver(outputFileName, fastaFileNames[s], accnosFileName, alnsFileName, numChimeras);
- #endif
+ //#else
+ // numSeqs = driver(outputFileName, fastaFileNames[s], accnosFileName, alnsFileName, numChimeras);
+ //#endif
if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
//remove file made for uchime
processIDS.clear();
int process = 1;
int num = 0;
+ vector<string> files;
+
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
//break up file into multiple files
- vector<string> files;
m->divideFile(filename, processors, files);
if (m->control_pressed) { return 0; }
}
in.close(); m->mothurRemove(tempFile);
}
+#else
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+ //Windows version shared memory, so be careful when passing variables through the preClusterData struct.
+ //Above fork() will clone, so memory is separate, but that's not the case with windows,
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+
+ //divide file
+ int count = 0;
+ int spot = 0;
+ map<int, ofstream*> filehandles;
+ map<int, ofstream*>::iterator it3;
+
+ ofstream* temp;
+ for (int i = 0; i < processors; i++) {
+ temp = new ofstream;
+ filehandles[i] = temp;
+ m->openOutputFile(filename+toString(i)+".temp", *(temp));
+ files.push_back(filename+toString(i)+".temp");
+ }
+
+ ifstream in;
+ m->openInputFile(filename, in);
+
+ while(!in.eof()) {
+
+ if (m->control_pressed) { in.close(); for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { (*(it3->second)).close(); delete it3->second; } return 0; }
+
+ Sequence tempSeq(in); m->gobble(in);
+
+ if (tempSeq.getName() != "") {
+ tempSeq.printSequence(*(filehandles[spot]));
+ spot++; count++;
+ if (spot == processors) { spot = 0; }
+ }
+ }
+ in.close();
+
+ //delete memory
+ for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
+ (*(it3->second)).close();
+ delete it3->second;
+ }
+
+ //sanity check for number of processors
+ if (count < processors) { processors = count; }
+
+ vector<uchimeData*> pDataArray;
+ DWORD dwThreadIdArray[processors-1];
+ HANDLE hThreadArray[processors-1];
+ vector<string> dummy; //used so that we can use the same struct for MyUchimeSeqsThreadFunction and MyUchimeThreadFunction
+
+ //Create processor worker threads.
+ for( int i=1; i<processors; i++ ){
+ // Allocate memory for thread data.
+ string extension = toString(i) + ".temp";
+
+ uchimeData* tempUchime = new uchimeData(outputFileName+extension, templatefile, files[i], "", "", "", accnos+extension, alns+extension, dummy, m, 0, 0, i);
+ tempUchime->setBooleans(useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, useChunks, useMinchunk, useIdsmoothwindow, useMinsmoothid, useMaxp, skipgaps, skipgaps2, useMinlen, useMaxlen, ucl, useQueryfract);
+ tempUchime->setVariables(abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract);
+
+ pDataArray.push_back(tempUchime);
+ processIDS.push_back(i);
+
+ //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
+ //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
+ hThreadArray[i-1] = CreateThread(NULL, 0, MyUchimeSeqsThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
+ }
+
+
+ //using the main process as a worker saves time and memory
+ num = driver(outputFileName, files[0], accnos, alns, numChimeras);
+ //Wait until all threads have terminated.
+ WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
+
+ //Close all thread handles and free memory allocations.
+ for(int i=0; i < pDataArray.size(); i++){
+ num += pDataArray[i]->count;
+ numChimeras += pDataArray[i]->numChimeras;
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
+ }
+#endif
//append output files
for(int i=0;i<processIDS.size();i++){
//get rid of the file pieces.
for (int i = 0; i < files.size(); i++) { m->mothurRemove(files[i]); }
-#endif
return num;
}
catch(exception& e) {
int temp = processIDS[i];
wait(&temp);
}
-#endif
for (int i = 0; i < processIDS.size(); i++) {
ifstream in;
if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
in.close(); m->mothurRemove(tempFile);
}
+
+#else
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+ //Windows version shared memory, so be careful when passing variables through the preClusterData struct.
+ //Above fork() will clone, so memory is separate, but that's not the case with windows,
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+
+ vector<uchimeData*> pDataArray;
+ DWORD dwThreadIdArray[processors-1];
+ HANDLE hThreadArray[processors-1];
+
+ //Create processor worker threads.
+ for( int i=1; i<processors; i++ ){
+ // Allocate memory for thread data.
+ string extension = toString(i) + ".temp";
+
+ uchimeData* tempUchime = new uchimeData(outputFName+extension, templatefile, filename+extension, fastafile, namefile, groupfile, accnos+extension, alns+extension, groups, m, lines[i].start, lines[i].end, i);
+ tempUchime->setBooleans(useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, useChunks, useMinchunk, useIdsmoothwindow, useMinsmoothid, useMaxp, skipgaps, skipgaps2, useMinlen, useMaxlen, ucl, useQueryfract);
+ tempUchime->setVariables(abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract);
+
+ pDataArray.push_back(tempUchime);
+ processIDS.push_back(i);
+
+ //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
+ //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
+ hThreadArray[i-1] = CreateThread(NULL, 0, MyUchimeThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
+ }
+
+ //using the main process as a worker saves time and memory
+ num = driverGroups(parser, outputFName, filename, accnos, alns, lines[0].start, lines[0].end, groups);
+
+ //Wait until all threads have terminated.
+ WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
+
+ //Close all thread handles and free memory allocations.
+ for(int i=0; i < pDataArray.size(); i++){
+ num += pDataArray[i]->count;
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
+ }
+#endif
+
//append output files
for(int i=0;i<processIDS.size();i++){
m->appendFiles((outputFName + toString(processIDS[i]) + ".temp"), outputFName);
projects / mothur.git / blobdiff