Separating Yourkit sessions

I have some segment of code I want to profile on many different inputs (~1000) so it doesn't make sense to manually run each test and save the results. I'm using yourkit in combination with Eclipse to profile. Is there any way to create "new sessions" for profiling? I want to be able to separate each run so that would make the most sense.

You don't really need to create "sessions" for each test. Instead, you have to capture a snapshot of the profiling data at the end of each test, and clear the profiling data before running the next test.

Using the yourkit API, you can do so in a manner similar to:

public void profile(String host, int port, List<InputData> inputDataSet) {
  Map<InputData, String> pathMap = new HashMap<InputData, String>(); //If you want to save the location of each file

  //Init profiling data collection
  com.yourkit.api.Controller controller = new Controller(host, port);
  controller.startCPUSampling(/*with your settings*/);
  controller.startAllocationRecording(/*With your settings*/);
  //controller.startXXX with whatever data you want to collect

  for (InputData input: inputDataSet) {
    //Run your test
    runTest(inputData);

    //Save profiling data
    String path = controller.captureSnapshot(/*With or without memory dump*/);
    pathMap.put(input, path);

    //Clear yourkit profiling data
    controller.clearAllocationData();
    controller.clearCPUData();
    //controller.clearXXX with whatever data you are collecting
  }
}

I don't think you need to stop collecting, capture snapshot, clear data, restart collecting, you can just capture and clear data, but please double-check. Once the tests are run, you can open the snapshots in yourkit and analyze the profiling data.