1.9

[mothur.git] / distancecommand.cpp

diff --git a/distancecommand.cpp b/distancecommand.cpp
index 2cc92a7d1599ac96309887d0c2e7b8a14f37a364..58302ddfbbc9e07de80747544217e79937c387ba 100644 (file)
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -199,12 +199,13 @@ int DistanceCommand::execute(){
                if (output != "lt") {
                        MPI_File outMPI;
                        int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY; 
-                       
-                       char filename[outputFile.length()];
-                       strcpy(filename, outputFile.c_str());
+
+                       char* filename = new char[outputFile.length()];\r
+                       memcpy(filename, outputFile.c_str(), outputFile.length());
                        
                        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 +248,12 @@ int DistanceCommand::execute(){
                                int amode=MPI_MODE_APPEND|MPI_MODE_WRONLY|MPI_MODE_CREATE; //
                                MPI_File outMPI;
                                MPI_File inMPI;
-                       
-                               char filename[outputFile.length()];
-                               strcpy(filename, outputFile.c_str());
+
+                               char* filename = new char[outputFile.length()];\r
+                               memcpy(filename, outputFile.c_str(), outputFile.length());
                        
                                MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
+                               delete filename;
 
                                //wait on chidren
                                for(int b = 1; b < processors; b++) { 
@@ -262,11 +264,13 @@ 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()];\r
+                                       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
@@ -483,11 +487,13 @@ 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];\r
+                       memcpy(buf, outputString.c_str(), length);
                        
                        MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
                        outputString = "";
+                       delete buf;
                        
                }
                
@@ -508,11 +514,12 @@ int DistanceCommand::driverMPI(int startLine, int endLine, string file, long& si
                
                MPI_File outMPI;
                int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY; 
-               
-               char filename[file.length()];
-               strcpy(filename, file.c_str());
+
+               char* filename = new char[file.length()];\r
+               memcpy(filename, file.c_str(), file.length());
                
                MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
+               delete filename;
 
                int startTime = time(NULL);
                
@@ -550,14 +557,13 @@ 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];\r
+                       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();