X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.cpp;h=8bf216a39ce9b6d8492e1e2ec10dedc70d46843e;hb=a86aff4f80701bf0d436f02c0095920114e1cba2;hp=ca1a40b32ddbd86e185ddee6e59366e4b3aace94;hpb=a8367302932de9be5434e77f6e5829d7609e2aec;p=mothur.git

diff --git a/mothurout.cpp b/mothurout.cpp
index ca1a40b..8bf216a 100644
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -1,154 +1,240 @@
-/*
- *  m->mothurOut.cpp
- *  Mothur
- *
- *  Created by westcott on 2/25/10.
- *  Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "mothurout.h"
-
-/******************************************************/
-MothurOut* MothurOut::getInstance() {
-	if( _uniqueInstance == 0) {
-		_uniqueInstance = new MothurOut();
-	}
-	return _uniqueInstance;
-}
-/*********************************************************************************************/
-void MothurOut::setFileName(string filename)  {
-	try {
-		logFileName = filename;
-		
-		#ifdef USE_MPI
-			int pid;
-			MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
-					
-			if (pid == 0) { //only one process should output to screen
-		#endif
-		
-		openOutputFile(filename, out);
-		
-		#ifdef USE_MPI
-			}
-		#endif
-	}
-	catch(exception& e) {
-		errorOut(e, "MothurOut", "setFileName");
-		exit(1);
-	}
-}
-/*********************************************************************************************/
-void MothurOut::closeLog()  {
-	try {
-		
-		#ifdef USE_MPI
-			int pid;
-			MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
-					
-			if (pid == 0) { //only one process should output to screen
-		#endif
-		
-		out.close();
-		
-		#ifdef USE_MPI
-			}
-		#endif
-	}
-	catch(exception& e) {
-		errorOut(e, "MothurOut", "closeLog");
-		exit(1);
-	}
-}
-
-/*********************************************************************************************/
-MothurOut::~MothurOut() {
-	try {
-		_uniqueInstance = 0;
-		
-	}
-	catch(exception& e) {
-		errorOut(e, "MothurOut", "MothurOut");
-		exit(1);
-	}
-}
-/*********************************************************************************************/
-void MothurOut::mothurOut(string output) {
-	try {
-		
-		#ifdef USE_MPI
-			int pid;
-			MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
-					
-			if (pid == 0) { //only one process should output to screen
-		#endif
-		
-		cout << output;
-		out << output;
-		
-		#ifdef USE_MPI
-			}
-		#endif
-	}
-	catch(exception& e) {
-		errorOut(e, "MothurOut", "MothurOut");
-		exit(1);
-	}
-}
-/*********************************************************************************************/
-void MothurOut::mothurOutEndLine() {
-	try {
-		#ifdef USE_MPI
-			int pid;
-			MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
-					
-			if (pid == 0) { //only one process should output to screen
-		#endif
-		
-		cout << endl;
-		out << endl;
-		
-		#ifdef USE_MPI
-			}
-		#endif
-	}
-	catch(exception& e) {
-		errorOut(e, "MothurOut", "MothurOutEndLine");
-		exit(1);
-	}
-}
-/*********************************************************************************************/
-void MothurOut::mothurOutJustToLog(string output) {
-	try {
-		#ifdef USE_MPI
-			int pid;
-			MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
-					
-			if (pid == 0) { //only one process should output to screen
-		#endif
-		
-		out << output;
-		
-		#ifdef USE_MPI
-			}
-		#endif
-	}
-	catch(exception& e) {
-		errorOut(e, "MothurOut", "MothurOutJustToLog");
-		exit(1);
-	}
-}
-/*********************************************************************************************/
-void MothurOut::errorOut(exception& e, string object, string function) {
-	mothurOut("Error: ");
-	mothurOut(toString(e.what()));
-	mothurOut(" has occurred in the " + object + " class function " + function + ". Please contact Pat Schloss at mothur.bugs@gmail.com, and be sure to include the mothur.logFile with your inquiry.");
-	mothurOutEndLine();
-}
-/*********************************************************************************************/
-
-
-
-
-
+/*
+ *  m->mothurOut.cpp
+ *  Mothur
+ *
+ *  Created by westcott on 2/25/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "mothurout.h"
+
+/******************************************************/
+MothurOut* MothurOut::getInstance() {
+	if( _uniqueInstance == 0) {
+		_uniqueInstance = new MothurOut();
+	}
+	return _uniqueInstance;
+}
+/*********************************************************************************************/
+void MothurOut::setFileName(string filename)  {
+	try {
+		logFileName = filename;
+		
+		#ifdef USE_MPI
+			int pid;
+			MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+					
+			if (pid == 0) { //only one process should output to screen
+		#endif
+		
+		openOutputFile(filename, out);
+		
+		#ifdef USE_MPI
+			}
+		#endif
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "setFileName");
+		exit(1);
+	}
+}
+/*********************************************************************************************/
+void MothurOut::closeLog()  {
+	try {
+		
+		#ifdef USE_MPI
+			int pid;
+			MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+					
+			if (pid == 0) { //only one process should output to screen
+		#endif
+		
+		out.close();
+		
+		#ifdef USE_MPI
+			}
+		#endif
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "closeLog");
+		exit(1);
+	}
+}
+
+/*********************************************************************************************/
+MothurOut::~MothurOut() {
+	try {
+		_uniqueInstance = 0;
+		
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "MothurOut");
+		exit(1);
+	}
+}
+/*********************************************************************************************/
+void MothurOut::mothurOut(string output) {
+	try {
+		
+		#ifdef USE_MPI
+			int pid;
+			MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+					
+			if (pid == 0) { //only one process should output to screen
+		#endif
+		
+		cout << output;
+		out << output;
+		
+		#ifdef USE_MPI
+			}
+		#endif
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "MothurOut");
+		exit(1);
+	}
+}
+/*********************************************************************************************/
+void MothurOut::mothurOutEndLine() {
+	try {
+		#ifdef USE_MPI
+			int pid;
+			MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+					
+			if (pid == 0) { //only one process should output to screen
+		#endif
+		
+		cout << endl;
+		out << endl;
+		
+		#ifdef USE_MPI
+			}
+		#endif
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "MothurOutEndLine");
+		exit(1);
+	}
+}
+/*********************************************************************************************/
+void MothurOut::mothurOutJustToLog(string output) {
+	try {
+		#ifdef USE_MPI
+			int pid;
+			MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+					
+			if (pid == 0) { //only one process should output to screen
+		#endif
+		
+		out << output;
+		
+		#ifdef USE_MPI
+			}
+		#endif
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "MothurOutJustToLog");
+		exit(1);
+	}
+}
+/*********************************************************************************************/
+void MothurOut::errorOut(exception& e, string object, string function) {
+	double vm, rss;
+	mem_usage(vm, rss);
+	
+	mothurOut("Error: ");
+	mothurOut(toString(e.what()));
+	mothurOut(" has occurred in the " + object + " class function " + function + ". Please contact Pat Schloss at mothur.bugs@gmail.com, and be sure to include the mothur.logFile with your inquiry.");
+	mothurOutEndLine();
+}
+/*********************************************************************************************/
+//The following was originally from http://stackoverflow.com/questions/669438/how-to-get-memory-usage-at-run-time-in-c 
+// process_mem_usage(double &, double &) - takes two doubles by reference,
+// attempts to read the system-dependent data for a process' virtual memory
+// size and resident set size, and return the results in KB.
+//
+// On failure, returns 0.0, 0.0
+int MothurOut::mem_usage(double& vm_usage, double& resident_set) {
+  #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+  
+	   vm_usage     = 0.0;
+	   resident_set = 0.0;
+
+	   // 'file' stat seems to give the most reliable results
+	   //
+	   ifstream stat_stream("/proc/self/stat",ios_base::in);
+
+	   // dummy vars for leading entries in stat that we don't care about
+	   //
+	   string pid, comm, state, ppid, pgrp, session, tty_nr;
+	   string tpgid, flags, minflt, cminflt, majflt, cmajflt;
+	   string utime, stime, cutime, cstime, priority, nice;
+	   string O, itrealvalue, starttime;
+
+	   // the two fields we want
+	   //
+	   unsigned long vsize;
+	   long rss;
+
+	   stat_stream >> pid >> comm >> state >> ppid >> pgrp >> session >> tty_nr
+				   >> tpgid >> flags >> minflt >> cminflt >> majflt >> cmajflt
+				   >> utime >> stime >> cutime >> cstime >> priority >> nice
+				   >> O >> itrealvalue >> starttime >> vsize >> rss; // don't care about the rest
+
+	   long page_size_kb = sysconf(_SC_PAGE_SIZE) / 1024; // in case x86-64 is configured to use 2MB pages
+	   vm_usage     = vsize / 1024.0;
+	   resident_set = rss * page_size_kb;
+	   
+	   mothurOut("Memory Usage: vm = " + toString(vm_usage) + " rss = " + toString(resident_set) + "\n");
+		return 0;
+
+	#else
+/*		//windows memory usage
+		// Get the list of process identifiers.
+		DWORD aProcesses[1024], cbNeeded, cProcesses;
+		
+		if ( !EnumProcesses( aProcesses, sizeof(aProcesses), &cbNeeded ) ){ return 1; }
+
+		// Calculate how many process identifiers were returned.
+		cProcesses = cbNeeded / sizeof(DWORD);
+
+		// Print the memory usage for each process
+		for (int i = 0; i < cProcesses; i++ ) {
+			DWORD processID = aProcesses[i];
+			
+			PROCESS_MEMORY_COUNTERS pmc;
+
+			HANDLE hProcess = OpenProcess((PROCESS_QUERY_INFORMATION | PROCESS_VM_READ), FALSE, processID);
+
+			// Print the process identifier.
+			printf( "\nProcess ID: %u\n", processID);
+			
+			if (NULL != hProcess) {
+
+				if ( GetProcessMemoryInfo( hProcess, &pmc, sizeof(pmc)) ) {
+					printf( "\tPageFaultCount: 0x%08X\n", pmc.PageFaultCount );
+					printf( "\tPeakWorkingSetSize: 0x%08X\n", pmc.PeakWorkingSetSize );
+					printf( "\tWorkingSetSize: 0x%08X\n", pmc.WorkingSetSize );
+					printf( "\tQuotaPeakPagedPoolUsage: 0x%08X\n", pmc.QuotaPeakPagedPoolUsage );
+					printf( "\tQuotaPagedPoolUsage: 0x%08X\n", pmc.QuotaPagedPoolUsage );
+					printf( "\tQuotaPeakNonPagedPoolUsage: 0x%08X\n", pmc.QuotaPeakNonPagedPoolUsage );
+					printf( "\tQuotaNonPagedPoolUsage: 0x%08X\n", pmc.QuotaNonPagedPoolUsage );
+					printf( "\tPagefileUsage: 0x%08X\n", pmc.PagefileUsage ); 
+					printf( "\tPeakPagefileUsage: 0x%08X\n", pmc.PeakPagefileUsage );
+				}
+				CloseHandle(hProcess);
+			}
+		}
+*/
+			return 0;
+
+	#endif
+}
+/*********************************************************************************************/
+
+
+
+
+