working on nmds

[mothur.git] / chimerapintailcommand.cpp

diff --git a/chimerapintailcommand.cpp b/chimerapintailcommand.cpp
index b355f6da6ac5839a054d4503e4dbb4f43237c23a..c5e579e730e1cfbd3da0040359393ef08b497295 100644 (file)
--- a/chimerapintailcommand.cpp
+++ b/chimerapintailcommand.cpp
@@ -382,7 +382,7 @@ int ChimeraPintailCommand::execute(){
                        templateSeqsLength = chimera->getLength();
                
                #ifdef USE_MPI
-                       int pid, end, numSeqsPerProcessor; 
+                       int pid, numSeqsPerProcessor; 
                                int tag = 2001;
                                vector<unsigned long int> MPIPos;
                                
@@ -631,7 +631,7 @@ int ChimeraPintailCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_Fi
                                        if (m->control_pressed) {       delete candidateSeq; return 1;  }
                
                                        //print results
-                                       bool isChimeric = chimera->print(outMPI, outAccMPI);
+                                       chimera->print(outMPI, outAccMPI);
                                }
                        }
                        delete candidateSeq;
@@ -678,7 +678,11 @@ int ChimeraPintailCommand::createProcesses(string outputFileName, string filenam
                                out.close();
 
                                exit(0);
-                       }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); 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);
+                       }
                }
                
                //force parent to wait until all the processes are done