Add waitForMakers function and avoid segfaults when writing to file.

Use this to wait for any writing of markers to finish. Used when the dumping to file is stopped,
and when the I/O thread is stopped. Sometimes a marker was written after
closing the dump file. Check if the dumpfile is not nullptr both when
writing a marker and when writing power data

host/include/PowerSensor.hpp

@@ -82,6 +82,7 @@ class PowerSensor {
     int openDevice(std::string device);
     std::queue<char> markers;
     void writeMarker();
+    void waitForMarkers(int timeout=500);
 
     void initializeSensorPairs();
     void updateSensorPairs();

host/src/PowerSensor.cc

@@ -336,9 +336,11 @@ void PowerSensor::mark(char name) {
  *
  */
 void PowerSensor::writeMarker() {
-  std::unique_lock<std::mutex> lock(dumpFileMutex);
-  *dumpFile << "M " << markers.front() << std::endl;
-  markers.pop();
+  if (dumpFile != nullptr) {
+    std::unique_lock<std::mutex> lock(dumpFileMutex);
+    *dumpFile << "M " << markers.front() << std::endl;
+    markers.pop();
+  }
 }
 
 /**
@@ -357,6 +359,24 @@ void PowerSensor::mark(const State &startState, const State &stopState, std::str
   }
 }
 
+/**
+ * @brief Wait for all markers to be written to the dump file
+ *
+ * @param timeout maximum waiting time in milliseconds
+ */
+void PowerSensor::waitForMarkers(int timeout) {
+  std::chrono::duration<double, std::milli> elapsed;
+  auto tstart = std::chrono::high_resolution_clock::now();
+  while (markers.size() != 0) {
+    std::this_thread::sleep_for(std::chrono::milliseconds(10));
+    elapsed = std::chrono::high_resolution_clock::now() - tstart;
+    if (elapsed.count() > timeout) {
+        break;
+    }
+  }
+  std::cout << "Marker waiting time: " << elapsed.count() << std::endl;
+}
+
 /**
  * @brief thread to continuously read sensor values from device
  *
@@ -418,6 +438,8 @@ void PowerSensor::startIOThread() {
  *
  */
 void PowerSensor::stopIOThread() {
+  // first ensure there are no markers still to be sent from the device
+  waitForMarkers();
   if (thread != nullptr) {
     writeCharToDevice('X');
     thread->join();
@@ -432,6 +454,11 @@ void PowerSensor::stopIOThread() {
  * @param dumpFileName
  */
 void PowerSensor::dump(std::string dumpFileName) {
+  // if dumping should be stopped, first wait until all markers are written
+  if (dumpFileName.empty()) {
+    waitForMarkers();
+  }
+
   std::unique_lock<std::mutex> lock(dumpFileMutex);
   dumpFile = std::unique_ptr<std::ofstream>(dumpFileName.empty() ? nullptr: new std::ofstream(dumpFileName));
   if (!dumpFileName.empty()) {
@@ -449,6 +476,9 @@ void PowerSensor::dump(std::string dumpFileName) {
  *
  */
 void PowerSensor::dumpCurrentWattToFile() {
+  if (dumpFile == nullptr) {
+    return;
+  }
   std::unique_lock<std::mutex> lock(dumpFileMutex);
   double totalWatt = 0;
   double time = omp_get_wtime();