X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=distancecommand.cpp;h=ec32ffeb9e2e28b7398f78c5dd5fd858de2326a0;hb=89d6711c2beed6ee75fb00e5e57f1a91564d3e89;hp=47e22ad47d21e9320dd5ee60bb6d40525793662d;hpb=fdc1f6eaf544f695fc1511f24bddd7e6069c33ba;p=mothur.git

diff --git a/distancecommand.cpp b/distancecommand.cpp
index 47e22ad..ec32ffe 100644
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -199,13 +199,15 @@ 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);
-			
-			if (m->control_pressed) {   MPI_File_close(&outMPI);  delete distCalculator;  return 0;  }
+			//delete filename;
 
 			if (pid == 0) { //you are the root process 
 			
@@ -249,11 +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++) { 
@@ -264,14 +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);
@@ -335,6 +342,14 @@ 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
@@ -485,11 +500,13 @@ 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;
 			
 		}
 		
@@ -510,11 +527,15 @@ 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);
 		
@@ -552,14 +573,13 @@ 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();