From: Sarah Westcott <mothur.westcott@gmail.com>
Date: Wed, 9 Apr 2014 13:18:00 +0000 (-0400)
Subject: pre.cluster unable to spawn necessary processes adjustment.
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=63befd5322a476436f08d9ae24954f06fa191395

pre.cluster unable to spawn necessary processes adjustment.
---

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index def5325..10ed825 100644
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -363,7 +363,8 @@ int PreClusterCommand::createProcessesGroups(string newFName, string newNName, s
 		vector<int> processIDS;
 		int process = 1;
 		int num = 0;
-		
+		bool recalc = false;
+        
 		//sanity check
 		if (groups.size() < processors) { processors = groups.size(); }
 		
@@ -401,12 +402,57 @@ int PreClusterCommand::createProcessesGroups(string newFName, string newNName, s
                 outTemp.close();
                 
 				exit(0);
-			}else { 
-				m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); 
-				for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
-				exit(0);
+			}else {
+                m->mothurOut("[ERROR]: unable to spawn the number of processes you requested, reducing number to " + toString(process) + "\n"); processors = process;
+                for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+                recalc = true;
+				break;
 			}
 		}
+        
+        if (recalc) {
+            lines.clear();
+            num = 0;
+            processIDS.resize(0);
+            process = 1;
+            
+            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;
+            }
+            
+            while (process != processors) {
+                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 + m->mothurGetpid(process) + ".temp", newNName + m->mothurGetpid(process) + ".temp", newMFile, lines[process].start, lines[process].end, groups);
+                    
+                    string tempFile = m->mothurGetpid(process) + ".outputNames.temp";
+                    ofstream outTemp;
+                    m->openOutputFile(tempFile, outTemp);
+                    
+                    outTemp << outputNames.size();
+                    for (int i = 0; i < outputNames.size(); i++) { outTemp << outputNames[i] << endl; }
+                    outTemp.close();
+                    
+                    exit(0);
+                }else {
+                    m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
+                    for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+                    exit(0);
+                }
+            }
+        }
+
 		
 		//do my part
 		num = driverGroups(newFName, newNName, newMFile, lines[0].start, lines[0].end, groups);