pre.cluster unable to spawn necessary processes adjustment.

[mothur.git] / chimeraperseuscommand.cpp

diff --git a/chimeraperseuscommand.cpp b/chimeraperseuscommand.cpp
index 0547802198960198d9d2a063bc498e79f04bfe33..ef3058d8cda30d8781e9a0057c9e93d77feeb1b9 100644 (file)
--- a/chimeraperseuscommand.cpp
+++ b/chimeraperseuscommand.cpp
@@ -1077,29 +1077,32 @@ int ChimeraPerseusCommand::createProcessesGroups(string outputFName, string accn
                
                //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){
-                               num = driverGroups(outputFName + toString(getpid()) + ".temp", accnos + toString(getpid()) + ".temp", accnos + ".byCount." + toString(getpid()) + ".temp", lines[process].start, lines[process].end, groups);
+                               num = driverGroups(outputFName + toString(m->mothurGetpid(process)) + ".temp", accnos + toString(m->mothurGetpid(process)) + ".temp", accnos + ".byCount." + toString(m->mothurGetpid(process)) + ".temp", lines[process].start, lines[process].end, groups);
                                
                                //pass numSeqs to parent
                                ofstream out;
-                               string tempFile = outputFName + toString(getpid()) + ".num.temp";
+                               string tempFile = outputFName + toString(m->mothurGetpid(process)) + ".num.temp";
                                m->openOutputFile(tempFile, out);
                                out << num << endl;
                                out.close();