fixed an mpi bug in shhh.seqs

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index e4797253008a0057cc5562ddef17f0c4b4a8efa2..902e927e15ac79e725a1277fa67e891c237e7576 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -1625,7 +1625,7 @@
                        attributes = {
                                ORGANIZATIONNAME = "Schloss Lab";
                        };
-                       buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "mothur" */;
+                       buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */;
                        compatibilityVersion = "Xcode 3.1";
                        developmentRegion = English;
                        hasScannedForEncodings = 1;
@@ -2048,7 +2048,7 @@
                        defaultConfigurationIsVisible = 0;
                        defaultConfigurationName = Release;
                };
-               1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "mothur" */ = {
+               1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */ = {
                        isa = XCConfigurationList;
                        buildConfigurations = (
                                1DEB928A08733DD80010E9CD /* Debug */,

diff --git a/makefile b/makefile
index 7cc71f0e9a4064a2163707f3f7bc08da36af2b5e..6ac7e31c49b396397c946010777800a1e29993c2 100644 (file)
--- a/makefile
+++ b/makefile
@@ -9,7 +9,7 @@
 # Macros
 #
 
-USEMPI ?= no
+USEMPI ?= yes
 64BIT_VERSION ?= yes
 USEREADLINE ?= yes
 CYGWIN_BUILD ?= no

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 6833f5d4c1cae8f4ee0e3b6f3da3bd2474b31285..066a9c51f26b764f14fa3f9490e094748ad3e7b6 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -250,9 +250,6 @@ int ShhherCommand::execute(){
                int tag = 1976;
                MPI_Status status; 
 
-               double begClock = clock();
-               unsigned long int begTime = time(NULL);
-               
                if(pid == 0){
 
                        for(int i=1;i<ncpus;i++){
@@ -288,9 +285,10 @@ int ShhherCommand::execute(){
                        }
                        
                        for(int i=0;i<numFiles;i++){
-                               flowFileName = flowFileVector[i];
+                               double begClock = clock();
+                               unsigned long int begTime = time(NULL);
 
-                               
+                               flowFileName = flowFileVector[i];
                                
                                m->mothurOut("\n>>>>>\tProcessing " + flowFileName + " (file " + toString(i+1) + " of " + toString(numFiles) + ")\t<<<<<\n");
                                m->mothurOut("Reading flowgrams...\n");
@@ -370,7 +368,7 @@ int ShhherCommand::execute(){
                                                MPI_Send(&nSeqsPerOTU[0], numOTUs, MPI_INT, i, tag, MPI_COMM_WORLD);
                                                MPI_Send(&cumNumSeqs[0], numOTUs, MPI_INT, i, tag, MPI_COMM_WORLD);
                                        }
-                               
+                                       
                                        calcCentroidsDriver(0, numOTUsOnCPU);
                                        
                                        for(int i=1;i<ncpus;i++){
@@ -489,7 +487,6 @@ int ShhherCommand::execute(){
                }
                else{
                        int abort = 1;
-                       bool live = 1;
 
                        MPI_Recv(&abort, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
                        if(abort){      return 0;       }
@@ -499,6 +496,8 @@ int ShhherCommand::execute(){
 
                        for(int i=0;i<numFiles;i++){
                                //Now into the pyrodist part
+                               bool live = 1;
+
                                char fileName[1024];
                                MPI_Recv(&fileName, 1024, MPI_CHAR, 0, tag, MPI_COMM_WORLD, &status);
                                MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
@@ -554,12 +553,12 @@ int ShhherCommand::execute(){
                                int total;
 
                                while(live){
-
+                                       
                                        MPI_Recv(&total, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
                                        singleTau.assign(total, 0.0000);
                                        seqNumber.assign(total, 0);
                                        seqIndex.assign(total, 0);
-                                       
+
                                        MPI_Recv(&change[0], numOTUs, MPI_SHORT, 0, tag, MPI_COMM_WORLD, &status);
                                        MPI_Recv(&centroids[0], numOTUs, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
                                        MPI_Recv(&singleTau[0], total, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD, &status);
@@ -567,13 +566,12 @@ int ShhherCommand::execute(){
                                        MPI_Recv(&seqIndex[0], total, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
                                        MPI_Recv(&nSeqsPerOTU[0], total, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
                                        MPI_Recv(&cumNumSeqs[0], numOTUs, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
-                                       
+
                                        calcCentroidsDriver(startOTU, endOTU);
 
                                        MPI_Send(&centroids[0], numOTUs, MPI_INT, 0, tag, MPI_COMM_WORLD);
                                        MPI_Send(&change[0], numOTUs, MPI_SHORT, 0, tag, MPI_COMM_WORLD);
 
-                                       
                                        MPI_Recv(&centroids[0], numOTUs, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
                                        MPI_Recv(&weight[0], numOTUs, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD, &status);
                                        MPI_Recv(&change[0], numOTUs, MPI_SHORT, 0, tag, MPI_COMM_WORLD, &status);
@@ -592,8 +590,8 @@ int ShhherCommand::execute(){
                                }
                        }
                }               
-
                MPI_Barrier(MPI_COMM_WORLD);
+
                return 0;
 
        }
@@ -704,7 +702,6 @@ int ShhherCommand::execute(){
                        double begClock = clock();
                        unsigned long int begTime = time(NULL);
 
-                       
                        m->mothurOut("\nDenoising flowgrams...\n");
                        m->mothurOut("iter\tmaxDelta\tnLL\t\tcycletime\n");