"GC overhead limit exceeded" from v7.6.2 #245
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Assignee should verify the issue and try to reproduce it.
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Thanks Kota for your kind words. Can you try to remove all the |
tinevez
added
the
investigate
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Hi @tinevez Great suggestion! so I tried:
So what was the change between v7.6.1 and v7.6.2? I cannot see the tag Cheers, |
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here is the stdout |
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Ok then it's definitely an issue with the memory not clearing between iterations. In you Java code I see that we always use the same Img<UnsignedByteType> img = ImageJFunctions.wrap(pmimp);outside of the loop? |
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OK, so I tried compacting the loop content more and using the import org.scijava.command.Command;
import org.scijava.log.Logger;
import org.scijava.plugin.Parameter;
import org.scijava.plugin.Plugin;
import fiji.plugin.trackmate.detection.DogDetector;
import ij.ImagePlus;
import net.imagej.ImageJ;
import net.imglib2.img.Img;
import net.imglib2.img.display.imagej.ImageJFunctions;
import net.imglib2.type.numeric.integer.UnsignedByteType;
@Plugin(type = Command.class, menuPath = "Tutorials>TrackMate test")
public class TrackMateTest20230228v3 implements Command {
@Parameter
private Logger logger;
@Override
public void run() {
logger.info("test");
String pp = "/Users/miura/samples/test5dots.tif";
final ImagePlus ccimpG = new ImagePlus(pp);
final int radius = 3;
final int threshold = 5;
final boolean doSubpixel = false;
final boolean doMedian = true;
final Img<UnsignedByteType> img = ImageJFunctions.wrap(ccimpG);
final Img<UnsignedByteType> interval = img;
final double[] calibration = { 1, 1, 1 };
for (int i = 0; i < 1000; i++) {
logger.info("=== count:" + Integer.toString(i));
final DogDetector<UnsignedByteType> detector = new DogDetector<UnsignedByteType>(
img, interval, calibration, radius, threshold,
doSubpixel, doMedian);
// detector.setNumThreads(1);
detector.process();
}
}
public static void main(String[] args) throws Exception {
System.out.println(System.getProperty("java.vm.name"));
System.out.println(System.getProperty("java.vm.version"));
System.out.println(System.getProperty("java.vm.info"));
final ImageJ ij = new ImageJ();
// ij.launch(args);
// ij.ui().showUI();
ij.command().run(TrackMateTest20230228v3.class, true);
}
} |
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Hi JY @tinevez
I encountered the following error starting from the v7.6.2-snapshot, while the v7.6.1-snapshot or earlier versions do not show this memory handling problem.
The above error is just an example and can be different as memory exhaustion causes this:
To reproduce this error, please try the following code with two different versions. I start to see the slowing down around 500th iteration, and often stops by 750th iteration. This is not affected by the VM setting such as
-xmx.I will add a download link to the sample image (hardcoded in the
main) below the code.The sample image:
https://www.dropbox.com/s/deu2vc6ftkp9wle/test5dots.tif?dl=0
Just as additional information: when similar processing is done using Jython, there is no problem. Interesting...
I hope this can be somehow fixed, as this is causing crashes when many spots are analyzed. Until this is fixed, I will use v7.6.1 to avoid the problem.
... and last but not least, big thanks to your masterpiece plugin!
Cheers,
Kota
ps: following versions were tested.
7.1.1 OK
7.5.1 OK
7.6.1 OK
7.6.2 failed
7.7.1 failed
7.10.2 failed
7.10.3 failed
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