update .gitignore

[mothur.git] / shhhseqscommand.cpp

diff --git a/shhhseqscommand.cpp b/shhhseqscommand.cpp
index 3e3e5863c59abc69e4175eba7cb5b7d6f0e173c8..f6fd90da276951724132140828d27c9de3a0d47a 100644 (file)
--- a/shhhseqscommand.cpp
+++ b/shhhseqscommand.cpp
@@ -377,29 +377,32 @@ vector<string> ShhhSeqsCommand::createProcessesGroups(SequenceParser& parser, st
                
                //divide the groups between the processors
                vector<linePair> lines;
-               int numGroupsPerProcessor = groups.size() / processors;
-               for (int i = 0; i < processors; i++) {
-                       int startIndex =  i * numGroupsPerProcessor;
-                       int endIndex = (i+1) * numGroupsPerProcessor;
-                       if(i == (processors - 1)){      endIndex = groups.size();       }
-                       lines.push_back(linePair(startIndex, endIndex));
-               }
+               int remainingPairs = groups.size();
+        int startIndex = 0;
+        for (int remainingProcessors = processors; remainingProcessors > 0; remainingProcessors--) {
+            int numPairs = remainingPairs; //case for last processor
+            if (remainingProcessors != 1) { numPairs = ceil(remainingPairs / remainingProcessors); }
+            lines.push_back(linePair(startIndex, (startIndex+numPairs))); //startIndex, endIndex
+            startIndex = startIndex + numPairs;
+            remainingPairs = remainingPairs - numPairs;
+        }
+
                
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)         
                
                //loop through and create all the processes you want
                while (process != processors) {
-                       int pid = fork();
+                       pid_t pid = fork();
                        
                        if (pid > 0) {
                                processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
                                process++;
                        }else if (pid == 0){
-                               mapfileNames = driverGroups(parser, newFName + toString(getpid()) + ".temp", newNName + toString(getpid()) + ".temp", newMName, lines[process].start, lines[process].end, groups);
+                               mapfileNames = driverGroups(parser, newFName + m->mothurGetpid(process) + ".temp", newNName + m->mothurGetpid(process) + ".temp", newMName, lines[process].start, lines[process].end, groups);
                                
                                //pass filenames to parent
                                ofstream out;
-                               string tempFile = newMName + toString(getpid()) + ".temp";
+                               string tempFile = newMName + m->mothurGetpid(process) + ".temp";
                                m->openOutputFile(tempFile, out);
                                out << mapfileNames.size() << endl;
                                for (int i = 0; i < mapfileNames.size(); i++) {
@@ -474,6 +477,9 @@ vector<string> ShhhSeqsCommand::createProcessesGroups(SequenceParser& parser, st
                
                //Close all thread handles and free memory allocations.
                for(int i=0; i < pDataArray.size(); i++){
+            if (pDataArray[i]->count != (pDataArray[i]->end-pDataArray[i]->start)) {
+                m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end-pDataArray[i]->start) + " groups assigned to it, quitting. \n"); m->control_pressed = true; 
+            }
                        for (int j = 0; j < pDataArray[i]->mapfileNames.size(); j++) {
                                mapfileNames.push_back(pDataArray[i]->mapfileNames[j]);
                        }