示例#1
0
  /**
   * Start up the progress meter, printing initialization message and starting up the daemon thread
   * for periodic printing.
   */
  @Requires("progressMeterDaemon != null")
  private synchronized void start() {
    timer.start();
    lastProgressPrintTime = timer.currentTime();

    logger.info("[INITIALIZATION COMPLETE; STARTING PROCESSING]");
    logger.info(
        String.format(
            "%15s processed.%s  runtime per.1M.%s completed total.runtime remaining",
            "Location", processingUnitName, processingUnitName));

    progressMeterDaemon.start();
  }
示例#2
0
  /** Should be called when processing is done */
  public void notifyDone(final long nTotalRecordsProcessed) {
    // print out the progress meter
    this.nTotalRecordsProcessed = nTotalRecordsProcessed;
    this.positionMessage = "done";
    printProgress(true);

    logger.info(
        String.format(
            "Total runtime %.2f secs, %.2f min, %.2f hours",
            timer.getElapsedTime(), timer.getElapsedTime() / 60, timer.getElapsedTime() / 3600));

    if (performanceLog != null) performanceLog.close();

    // shutdown our daemon thread
    progressMeterDaemon.done();
  }
示例#3
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 /**
  * Creates a new ProgressData object recording a snapshot of our progress at this instant
  *
  * @param loc our current position. If null, assumes we are done traversing
  * @param nTotalRecordsProcessed the total number of records we've processed
  * @return
  */
 private ProgressMeterData takeProgressSnapshot(
     final GenomeLoc loc, final long nTotalRecordsProcessed) {
   // null -> end of processing
   final long bpProcessed =
       loc == null ? targetSizeInBP : regionsBeingProcessed.sizeBeforeLoc(loc);
   return new ProgressMeterData(timer.getElapsedTime(), nTotalRecordsProcessed, bpProcessed);
 }
示例#4
0
  /**
   * Actually try to print out progress
   *
   * <p>This function may print out if the progress print is due, but if not enough time has elapsed
   * since the last print we will not print out information.
   *
   * @param mustPrint if true, progress will be printed regardless of the last time we printed
   *     progress
   */
  protected synchronized void printProgress(final boolean mustPrint) {
    final long curTime = timer.currentTime();
    final boolean printProgress =
        mustPrint
            || maxElapsedIntervalForPrinting(
                curTime, lastProgressPrintTime, progressPrintFrequency);
    final boolean printLog =
        performanceLog != null
            && maxElapsedIntervalForPrinting(
                curTime, lastPerformanceLogPrintTime, PERFORMANCE_LOG_PRINT_FREQUENCY);

    if (printProgress || printLog) {
      final ProgressMeterData progressData =
          takeProgressSnapshot(maxGenomeLoc, nTotalRecordsProcessed);

      final AutoFormattingTime elapsed = new AutoFormattingTime(progressData.getElapsedSeconds());
      final AutoFormattingTime bpRate = new AutoFormattingTime(progressData.secondsPerMillionBP());
      final AutoFormattingTime unitRate =
          new AutoFormattingTime(progressData.secondsPerMillionElements());
      final double fractionGenomeTargetCompleted =
          progressData.calculateFractionGenomeTargetCompleted(targetSizeInBP);
      final AutoFormattingTime estTotalRuntime =
          new AutoFormattingTime(elapsed.getTimeInSeconds() / fractionGenomeTargetCompleted);
      final AutoFormattingTime timeToCompletion =
          new AutoFormattingTime(estTotalRuntime.getTimeInSeconds() - elapsed.getTimeInSeconds());

      if (printProgress) {
        lastProgressPrintTime = curTime;
        updateLoggerPrintFrequency(estTotalRuntime.getTimeInSeconds());

        logger.info(
            String.format(
                "%15s        %5.2e %s     %s    %5.1f%%      %s  %s",
                positionMessage,
                progressData.getUnitsProcessed() * 1.0,
                elapsed,
                unitRate,
                100 * fractionGenomeTargetCompleted,
                estTotalRuntime,
                timeToCompletion));
      }

      if (printLog) {
        lastPerformanceLogPrintTime = curTime;
        performanceLog.printf(
            "%.2f\t%d\t%.2e\t%d\t%.2e\t%.2e\t%.2f\t%.2f%n",
            elapsed.getTimeInSeconds(),
            progressData.getUnitsProcessed(),
            unitRate.getTimeInSeconds(),
            progressData.getBpProcessed(),
            bpRate.getTimeInSeconds(),
            fractionGenomeTargetCompleted,
            estTotalRuntime.getTimeInSeconds(),
            timeToCompletion.getTimeInSeconds());
      }
    }
  }
示例#5
0
 /** @return the current runtime in nanoseconds */
 @Ensures("result >= 0")
 public long getRuntimeInNanoseconds() {
   return timer.getElapsedTimeNano();
 }