some bug fixes

[mothur.git] / distancecommand.cpp

diff --git a/distancecommand.cpp b/distancecommand.cpp
index 2cc92a7d1599ac96309887d0c2e7b8a14f37a364..05ed87cb960c5c61fff158384723ff9d3b2a1e3a 100644 (file)
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -32,7 +32,7 @@ DistanceCommand::DistanceCommand(string option) {
                        OptionParser parser(option);
                        map<string, string> parameters = parser.getParameters();
                        
-                       ValidParameters validParameter;
+                       ValidParameters validParameter("dist.seqs");
                        map<string, string>::iterator it2;
                
                        //check to make sure all parameters are valid for command
@@ -199,12 +199,16 @@ int DistanceCommand::execute(){
                if (output != "lt") {
                        MPI_File outMPI;
                        int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY; 
+
+                       //char* filename = new char[outputFile.length()];
+                       //memcpy(filename, outputFile.c_str(), outputFile.length());
                        
-                       char filename[outputFile.length()];
+                       char filename[1024];
                        strcpy(filename, outputFile.c_str());
                        
                        MPI_File_open(MPI_COMM_WORLD, filename, amode, MPI_INFO_NULL, &outMPI);
-                       
+                       //delete filename;
+
                        if (pid == 0) { //you are the root process 
                        
                                //do your part
@@ -247,11 +251,15 @@ int DistanceCommand::execute(){
                                int amode=MPI_MODE_APPEND|MPI_MODE_WRONLY|MPI_MODE_CREATE; //
                                MPI_File outMPI;
                                MPI_File inMPI;
-                       
-                               char filename[outputFile.length()];
+
+                               //char* filename = new char[outputFile.length()];
+                               //memcpy(filename, outputFile.c_str(), outputFile.length());
+                               
+                               char filename[1024];
                                strcpy(filename, outputFile.c_str());
-                       
+
                                MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
+                               //delete filename;
 
                                //wait on chidren
                                for(int b = 1; b < processors; b++) { 
@@ -262,14 +270,15 @@ int DistanceCommand::execute(){
                                        MPI_Recv(&fileSize, 1, MPI_LONG, b, tag, MPI_COMM_WORLD, &status); 
                                        
                                        string outTemp = outputFile + toString(b) + ".temp";
-                                       char buf[outTemp.length()];
-                                       strcpy(buf, outTemp.c_str());
+
+                                       char* buf = new char[outTemp.length()];
+                                       memcpy(buf, outTemp.c_str(), outTemp.length());
                                        
                                        MPI_File_open(MPI_COMM_SELF, buf, MPI_MODE_DELETE_ON_CLOSE|MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
-                                       
+                                       delete buf;
+
                                        int count = 0;
-                                       while (count < fileSize) { //read 1000 characters at a time
-                                               //send freqs
+                                       while (count < fileSize) { 
                                                char buf2[1];
                                                MPI_File_read(inMPI, buf2, 1, MPI_CHAR, &status);
                                                MPI_File_write(outMPI, buf2, 1, MPI_CHAR, &status);
@@ -291,6 +300,7 @@ int DistanceCommand::execute(){
                                MPI_Send(&size, 1, MPI_LONG, 0, tag, MPI_COMM_WORLD);
                        }
                }
+               MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 #else          
                                
        #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
@@ -333,6 +343,14 @@ int DistanceCommand::execute(){
                
                if (output == "square") {  convertMatrix(outputFile); }
                
+               ifstream fileHandle;
+               fileHandle.open(outputFile.c_str());
+               if(fileHandle) {
+                       gobble(fileHandle);
+                       if (fileHandle.eof()) { m->mothurOut(outputFile + " is blank. This can result if there are no distances below your cutoff.");  m->mothurOutEndLine(); }
+               }
+
+               
                #ifdef USE_MPI
                        }
                #endif
@@ -483,11 +501,13 @@ int DistanceCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, flo
                         
                        //send results to parent
                        int length = outputString.length();
-                       char buf[length];
-                       strcpy(buf, outputString.c_str()); 
+
+                       char* buf = new char[length];
+                       memcpy(buf, outputString.c_str(), length);
                        
                        MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
                        outputString = "";
+                       delete buf;
                        
                }
                
@@ -508,11 +528,15 @@ int DistanceCommand::driverMPI(int startLine, int endLine, string file, long& si
                
                MPI_File outMPI;
                int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY; 
+
+               //char* filename = new char[file.length()];
+               //memcpy(filename, file.c_str(), file.length());
                
-               char filename[file.length()];
+               char filename[1024];
                strcpy(filename, file.c_str());
-               
+
                MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
+               //delete filename;
 
                int startTime = time(NULL);
                
@@ -550,14 +574,13 @@ int DistanceCommand::driverMPI(int startLine, int endLine, string file, long& si
                        
                        //send results to parent
                        int length = outputString.length();
-                       char buf[length];
-                       strcpy(buf, outputString.c_str()); 
+                       char* buf = new char[length];
+                       memcpy(buf, outputString.c_str(), length);
                        
                        MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
                        size += outputString.length();
                        outputString = "";
-                       
-                       
+                       delete buf;
                }
                
                //m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();