X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=preclustercommand.cpp;h=def53255b1c124c2d40ae76120723f78f47a7bec;hb=cac38e9e251998fa0b825d00189534534948d226;hp=bd3f172c2bcaa3e13ced0b5c57d92e39c9073969;hpb=ac663461b19ad1436a06aa63f97221d1ff105482;p=mothur.git

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index bd3f172..def5325 100644
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -192,7 +192,7 @@ PreClusterCommand::PreClusterCommand(string option) {
 			else if (countfile == "not open") { abort = true; countfile =  ""; }	
 			else {   
                 m->setCountTableFile(countfile); 
-                ct.readTable(countfile, true);
+                ct.readTable(countfile, true, false);
                 if (ct.hasGroupInfo()) { bygroup = true; }
                 else { bygroup = false;  }
             }
@@ -300,6 +300,7 @@ int PreClusterCommand::execute(){
 			m->mothurOut("It took " + toString(time(NULL) - start) + " secs to run pre.cluster."); m->mothurOutEndLine(); 
 				
 		}else {
+            if (processors != 1) { m->mothurOut("When using running without group information mothur can only use 1 processor, continuing."); m->mothurOutEndLine(); processors = 1; }
 			if (namefile != "") { readNameFile(); }
 		
 			//reads fasta file and return number of seqs
@@ -368,28 +369,30 @@ int PreClusterCommand::createProcessesGroups(string newFName, string newNName, s
 		
 		//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){
                 outputNames.clear();
-				num = driverGroups(newFName + toString(getpid()) + ".temp", newNName + toString(getpid()) + ".temp", newMFile, lines[process].start, lines[process].end, groups);
+				num = driverGroups(newFName + m->mothurGetpid(process) + ".temp", newNName + m->mothurGetpid(process) + ".temp", newMFile, lines[process].start, lines[process].end, groups);
                 
-                string tempFile = toString(getpid()) + ".outputNames.temp";
+                string tempFile = m->mothurGetpid(process) + ".outputNames.temp";
                 ofstream outTemp;
                 m->openOutputFile(tempFile, outTemp);