namesOfGroupCombos.push_back(groups);
}
}
+
+ lines.clear();
+ int numPairs = namesOfGroupCombos.size();
+ int numPairsPerProcessor = numPairs / processors;
+
+ for (int i = 0; i < processors; i++) {
+ int startPos = i * numPairsPerProcessor;
+ if(i == processors - 1){ numPairsPerProcessor = numPairs - i * numPairsPerProcessor; }
+ lines.push_back(linePair(startPos, numPairsPerProcessor));
+ }
+
+ data = createProcesses(t, namesOfGroupCombos, ct);
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
- if(processors == 1){
- data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), ct);
- }else{
- int numPairs = namesOfGroupCombos.size();
-
- int numPairsPerProcessor = numPairs / processors;
-
- for (int i = 0; i < processors; i++) {
- int startPos = i * numPairsPerProcessor;
-
- if(i == processors - 1){
- numPairsPerProcessor = numPairs - i * numPairsPerProcessor;
- }
-
- lines.push_back(linePair(startPos, numPairsPerProcessor));
- }
- data = createProcesses(t, namesOfGroupCombos, ct);
- lines.clear();
- }
- #else
- data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), ct);
- #endif
-
+ lines.clear();
+
return data;
}
catch(exception& e) {
EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, CountTable* ct) {
try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
- int process = 1;
+ int process = 1;
vector<int> processIDS;
EstOutput results;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+
//loop through and create all the processes you want
while (process != processors) {
if (m->control_pressed) { exit(0); }
- m->mothurOut("Merging results."); m->mothurOutEndLine();
+ //m->mothurOut("Merging results."); m->mothurOutEndLine();
//pass numSeqs to parent
ofstream out;
in.close();
m->mothurRemove(s);
}
+#else
+ //fill in functions
+ vector<unweightedData*> pDataArray;
+ DWORD dwThreadIdArray[processors-1];
+ HANDLE hThreadArray[processors-1];
+ vector<CountTable*> cts;
+ vector<Tree*> trees;
+
+ //Create processor worker threads.
+ for( int i=1; i<processors; i++ ){
+ CountTable* copyCount = new CountTable();
+ copyCount->copy(ct);
+ Tree* copyTree = new Tree(copyCount);
+ copyTree->getCopy(t);
+
+ cts.push_back(copyCount);
+ trees.push_back(copyTree);
+
+ unweightedData* tempweighted = new unweightedData(m, lines[i].start, lines[i].num, namesOfGroupCombos, copyTree, copyCount, includeRoot);
+ pDataArray.push_back(tempweighted);
+ processIDS.push_back(i);
+
+ hThreadArray[i-1] = CreateThread(NULL, 0, MyUnWeightedThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
+ }
+
+ results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, ct);
- m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine();
+ //Wait until all threads have terminated.
+ WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
- return results;
-#endif
+ //Close all thread handles and free memory allocations.
+ for(int i=0; i < pDataArray.size(); i++){
+ for (int j = 0; j < pDataArray[i]->results.size(); j++) { results.push_back(pDataArray[i]->results[j]); }
+ delete cts[i];
+ delete trees[i];
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
+ }
+
+#endif
+ return results;
}
catch(exception& e) {
m->errorOut(e, "Unweighted", "createProcesses");
int count = 0;
int total = num;
- int twentyPercent = (total * 0.20);
- if (twentyPercent == 0) { twentyPercent = 1; }
-
-
+
for (int h = start; h < (start+num); h++) {
if (m->control_pressed) { return results; }
}
count++;
- //report progress
- //if((count % twentyPercent) == 0) { float tempOut = (count / (float)total); if (isnan(tempOut) || isinf(tempOut)) { tempOut = 0.0; } m->mothurOut("Percentage complete: " + toString((int(tempOut) * 100.0))); m->mothurOutEndLine(); }
- }
-
- //report progress
- //if((count % twentyPercent) != 0) { float tempOut = (count / (float)total); if (isnan(tempOut) || isinf(tempOut)) { tempOut = 0.0; } m->mothurOut("Percentage complete: " + toString((int(tempOut) * 100.0))); m->mothurOutEndLine(); }
+ }
return results;
}
namesOfGroupCombos.push_back(groups);
}
}
+
+ lines.clear();
+ int numPairs = namesOfGroupCombos.size();
+ int numPairsPerProcessor = numPairs / processors;
+
+ for (int i = 0; i < processors; i++) {
+ int startPos = i * numPairsPerProcessor;
+ if(i == processors - 1){ numPairsPerProcessor = numPairs - i * numPairsPerProcessor; }
+ lines.push_back(linePair(startPos, numPairsPerProcessor));
+ }
+
+ data = createProcesses(t, namesOfGroupCombos, true, ct);
+ lines.clear();
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
- if(processors == 1){
- data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), true, ct);
- }else{
- int numPairs = namesOfGroupCombos.size();
-
- int numPairsPerProcessor = numPairs / processors;
-
- for (int i = 0; i < processors; i++) {
- int startPos = i * numPairsPerProcessor;
- if(i == processors - 1){
- numPairsPerProcessor = numPairs - i * numPairsPerProcessor;
- }
- lines.push_back(linePair(startPos, numPairsPerProcessor));
- }
-
- data = createProcesses(t, namesOfGroupCombos, true, ct);
-
- lines.clear();
- }
- #else
- data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), true, ct);
- #endif
-
return data;
}
catch(exception& e) {
EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, bool usingGroups, CountTable* ct) {
try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
- int process = 1;
+ int process = 1;
vector<int> processIDS;
EstOutput results;
-
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+
//loop through and create all the processes you want
while (process != processors) {
int pid = fork();
in.close();
m->mothurRemove(s);
}
+#else
+ //for some reason it doesn't seem to be calculating hte random trees scores. all scores are the same even though copytree appears to be randomized.
+
+ /*
+ //fill in functions
+ vector<unweightedData*> pDataArray;
+ DWORD dwThreadIdArray[processors-1];
+ HANDLE hThreadArray[processors-1];
+ vector<CountTable*> cts;
+ vector<Tree*> trees;
+
+ //Create processor worker threads.
+ for( int i=1; i<processors; i++ ){
+ CountTable* copyCount = new CountTable();
+ copyCount->copy(ct);
+ Tree* copyTree = new Tree(copyCount);
+ copyTree->getCopy(t);
+
+ cts.push_back(copyCount);
+ trees.push_back(copyTree);
+
+ unweightedData* tempweighted = new unweightedData(m, lines[i].start, lines[i].num, namesOfGroupCombos, copyTree, copyCount, includeRoot);
+ pDataArray.push_back(tempweighted);
+ processIDS.push_back(i);
+
+ hThreadArray[i-1] = CreateThread(NULL, 0, MyUnWeightedRandomThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
+ }
+
+ results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, usingGroups, ct);
- return results;
-#endif
+ //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++){
+ for (int j = 0; j < pDataArray[i]->results.size(); j++) { results.push_back(pDataArray[i]->results[j]); }
+ delete cts[i];
+ delete trees[i];
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
+ } */
+
+ results = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), usingGroups, ct);
+#endif
+ return results;
}
catch(exception& e) {
m->errorOut(e, "Unweighted", "createProcesses");
if (isnan(UW) || isinf(UW)) { UW = 0; }
results[count] = UW;
- }
+ }
count++;
}
projects / mothur.git / blobdiff