Modified ioctl and timing as part of stall debugging

src/Filter_Obs.cpp

@@ -306,7 +306,7 @@ int Filter_Obs::lowpass_PLASMON_1Hz(buffer_obs* buffer_in,
     // =================================================
     //      
     //int counter = 0;
-    //std::string datastr;
+    std::string datastr;
     while (1) {
 
         // Grab new data
@@ -318,16 +318,17 @@ int Filter_Obs::lowpass_PLASMON_1Hz(buffer_obs* buffer_in,
         this_msec = this_timespec.tv_nsec;
 
 	//counter++;
-	/*
+	
 	data->string(&datastr,5);
-	std::cerr << "INCOMING: " << std::endl;
+	// std::cerr << "INCOMING: " << std::endl;
     std::cerr << data->get_sec()
-		  << "."
+		//   << "."
+		  << " "
 		  << data->get_msec() << " "
 		  << datastr << " "
-		  << counter
+		//   << counter
 		  << std::endl;
-    */
+    
 
         // One data point is produced from filter1 for each block of 
         // data, corresponding to its output filter frequency

src/driver_serial.cpp

@@ -194,6 +194,7 @@ int driver_serial::receive(char *buf, int buflen, double timeout,
 
     // Starting time and current time
     struct timespec start_time, end_time;
+    // struct timespec test_time;
 
     //////////////////////////////////////////////////////////////////////////////
     //
@@ -209,21 +210,23 @@ int driver_serial::receive(char *buf, int buflen, double timeout,
 
     // Timeout in nanoseconds
     if (timeout>0){
-        clock_gettime(CLOCK_REALTIME, &start_time);
+        // clock_gettime(CLOCK_REALTIME, &start_time);
+        clock_gettime(CLOCK_MONOTONIC_RAW, &start_time);
 
     }
 
     // Repeat loop until all termination characters have been received
     while (n < termlen) {
 
-        //clock_gettime(CLOCK_REALTIME, &test_time);
-        //fprintf(stderr,"LOOP TIME: %d\n",(int)(test_time.tv_nsec/1e3));
+        // clock_gettime(CLOCK_MONOTONIC, &test_time);
+        // fprintf(stderr,"LOOP TIME: %d\n",(int)(test_time.tv_nsec/1e3));
         
         //
         // Check for timeout
         //
         if (timeout > 0) {
-            clock_gettime(CLOCK_REALTIME, &end_time);
+            // clock_gettime(CLOCK_REALTIME, &end_time);
+            clock_gettime(CLOCK_MONOTONIC_RAW, &end_time);
             if ( (end_time.tv_sec-start_time.tv_sec)+end_time.tv_nsec/1e9 >=
                 start_time.tv_nsec/1e9+timeout ) {
                 //flush();
@@ -699,7 +702,8 @@ int driver_serial::init() {
 	// O_NDELAY - Use no-blocking I/O. Ignore control characters and 
 	//            transmit raw data- REMOVED as it overwrites VMIN and VTIME
 
-	if ((fd = open((char *) port.c_str(), O_RDWR | O_NOCTTY | O_NDELAY)) < 0) {
+	// if ((fd = open((char *) port.c_str(), O_RDWR | O_NOCTTY | O_NDELAY)) < 0) {
+	if ((fd = open((char *) port.c_str(), O_RDWR )) < 0) {
 		std::cerr << "Couldn't open serial port " << port << std::endl;
 		return (-1);
 	}
@@ -736,14 +740,16 @@ int driver_serial::init() {
 
 	// IGNBRK    -  Ignore break conditions
 	// IGNPAR    -  Ignore parity errors
-	tio.c_iflag = IGNBRK | IGNPAR;
+	// tio.c_iflag = IGNBRK | IGNPAR;
+	tio.c_iflag &= (IGNBRK | IGNPAR);
 
 	//
 	// Set the output flags (c_oflag)
 	//
 
 	// No output processing.
-	tio.c_oflag = 0;
+	// tio.c_oflag = 0;
+	tio.c_oflag &= ~OPOST;
 
 	//
 	// Set the flag constants (c_cflag)
@@ -752,14 +758,15 @@ int driver_serial::init() {
 	// CS8     - Eight bits per byte
 	// CREAD   - Enable to receive data
 	// CLOCAL  - Ignore modem control lines
-	tio.c_cflag = CS8 | CREAD | CLOCAL;
-
+	// tio.c_cflag = CS8 | CREAD | CLOCAL;
+	tio.c_cflag &= (CS8 | CREAD | CLOCAL);
 	//   
 	// Set the local flags (c_lflag)
 	//
 
 	// No higher-level input processing, non-canonical.
-	tio.c_lflag = 0;
+	// tio.c_lflag = 0;
+	tio.c_lflag &= ~ICANON;
 
 	//
 	// Set some special characters (c_cc).