added fontsize to heatmap.sim, paralellized chimera.slayer byGroup for all os's,...

[mothur.git] / screenseqscommand.cpp

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index cedb74a9b6c7f0a4162cdc96d9b774105e6cc1d0..9a6998e28fdb7f41a8c7be6b00b86a7f0c5be8ee 100644 (file)
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -295,7 +295,7 @@ int ScreenSeqsCommand::execute(){
                int numFastaSeqs = 0;
                set<string> badSeqNames;
                int start = time(NULL);
-               
+       
 #ifdef USE_MPI 
                        int pid, numSeqsPerProcessor; 
                        int tag = 2001;
@@ -304,7 +304,7 @@ int ScreenSeqsCommand::execute(){
                        MPI_Status status; 
                        MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
                        MPI_Comm_size(MPI_COMM_WORLD, &processors); 
-
+       
                        MPI_File inMPI;
                        MPI_File outMPIGood;
                        MPI_File outMPIBadAccnos;
@@ -667,13 +667,11 @@ int ScreenSeqsCommand::getSummary(vector<unsigned long long>& positions){
                
                
 #ifdef USE_MPI
+               int pid;
                MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
                
-               if (pid == 0) { //only one process should fix files
+               if (pid == 0) { 
                        driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
-               }
-               
-               MPI_Barrier(MPI_COMM_WORLD); //make everyone wait
 #else
                int numSeqs = 0;
                #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
@@ -707,6 +705,33 @@ int ScreenSeqsCommand::getSummary(vector<unsigned long long>& positions){
                        else if (optimize[i] == "maxlength") { maxLength = seqLength[criteriaPercentile]; m->mothurOut("Optimizing maxlength to " + toString(maxLength) + "."); m->mothurOutEndLine(); }
                }
 
+#ifdef USE_MPI
+               }
+               
+               MPI_Status status; 
+               MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+               MPI_Comm_size(MPI_COMM_WORLD, &processors); 
+                       
+               if (pid == 0) { 
+                       //send file positions to all processes
+                       for(int i = 1; i < processors; i++) { 
+                               MPI_Send(&startPos, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+                               MPI_Send(&endPos, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+                               MPI_Send(&maxAmbig, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+                               MPI_Send(&maxHomoP, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+                               MPI_Send(&minLength, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+                               MPI_Send(&maxLength, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+                       }
+               }else {
+                       MPI_Recv(&startPos, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+                       MPI_Recv(&endPos, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+                       MPI_Recv(&maxAmbig, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+                       MPI_Recv(&maxHomoP, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+                       MPI_Recv(&minLength, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+                       MPI_Recv(&maxLength, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+               }
+               MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
+#endif
                return 0;
        }
        catch(exception& e) {