X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=distancecommand.cpp;h=8be3ad4f8e084c688ab7e4937944f97f52ed521c;hb=60928795782d8f8648ec373d6a96b53032a77429;hp=73a38bfe023025be8b5533e20f72d28539a09cde;hpb=deba0af0ccdcb6005ed5b2b82649b137c63fbdf7;p=mothur.git

diff --git a/distancecommand.cpp b/distancecommand.cpp
index 73a38bf..8be3ad4 100644
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -540,8 +540,8 @@ void DistanceCommand::createProcesses(string filename) {
 				processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 				process++;
 			}else if (pid == 0){
-				if (output != "square") {  driver(lines[process].start, lines[process].end, filename + toString(getpid()) + ".temp", cutoff); }
-				else { driver(lines[process].start, lines[process].end, filename + toString(getpid()) + ".temp", "square"); }
+				if (output != "square") {  driver(lines[process].start, lines[process].end, filename + m->mothurGetpid(process) + ".temp", cutoff); }
+				else { driver(lines[process].start, lines[process].end, filename + m->mothurGetpid(process) + ".temp", "square"); }
 				exit(0);
 			}else { 
 				m->mothurOut("[ERROR]: unable to spawn the necessary processes. Error code: " + toString(pid)); m->mothurOutEndLine(); 
@@ -594,6 +594,9 @@ void DistanceCommand::createProcesses(string filename) {
 		
 		//Close all thread handles and free memory allocations.
 		for(int i=0; i < pDataArray.size(); i++){
+            if (pDataArray[i]->count != (pDataArray[i]->endLine-pDataArray[i]->startLine)) {
+                m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->endLine-pDataArray[i]->startLine) + " sequences assigned to it, quitting. \n"); m->control_pressed = true; 
+            }
 			CloseHandle(hThreadArray[i]);
 			delete pDataArray[i];
 		}
@@ -672,11 +675,11 @@ int DistanceCommand::driver(int startLine, int endLine, string dFileName, float
 			if (output == "lt") { outFile << endl; }
 			
 			if(i % 100 == 0){
-				m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
+				m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n"); 
 			}
 			
 		}
-		m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
+		m->mothurOutJustToScreen(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)+"\n");
 		
 		outFile.close();
 		delete distCalculator;
@@ -742,11 +745,11 @@ int DistanceCommand::driver(int startLine, int endLine, string dFileName, string
 			outFile << endl; 
 			
 			if(i % 100 == 0){
-				m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
+				m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n");
 			}
 			
 		}
-		m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
+		m->mothurOutJustToScreen(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)+"\n");
 		
 		outFile.close();
 		delete distCalculator;
@@ -809,8 +812,7 @@ int DistanceCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, flo
 			}
 			
 			if(i % 100 == 0){
-				//m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
-				cout << i << '\t' << (time(NULL) - startTime) << endl;
+				m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n"); 
 			}
 			
 			 
@@ -826,8 +828,7 @@ int DistanceCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, flo
 			
 		}
 		
-		//m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
-		cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;	
+		m->mothurOutJustToScreen(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)+"\n");
 		delete distCalculator;
 		return 1;
 	}
@@ -904,9 +905,7 @@ int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned
 
 		
 			if(i % 100 == 0){
-				//m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
-				cout << i << '\t' << (time(NULL) - startTime) << endl;
-			}
+				m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n"); 			}
 			
 			
 			//send results to parent
@@ -920,8 +919,8 @@ int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned
 			delete buf;
 		}
 		
-		//m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
-		cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
+		m->mothurOutJustToScreen(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)+"\n");
+		
 		MPI_File_close(&outMPI);
 		delete distCalculator;
 		
@@ -999,8 +998,7 @@ int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned
 
 		
 			if(i % 100 == 0){
-				//m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
-				cout << i << '\t' << (time(NULL) - startTime) << endl;
+				m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n"); 
 			}
 			
 			
@@ -1015,8 +1013,8 @@ int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned
 			delete buf;
 		}
 		
-		//m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
-		cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
+		m->mothurOutJustToScreen(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)+"\n");
+		
 		MPI_File_close(&outMPI);
 		delete distCalculator;
 		return 1;