Thanks Emma, feedback submitted.

We're looking into it. Yours, Steffen

Fixed. That was a fallout of an earlier failure of the server.
Mitigation measures have been conjured, but not yet implemented.
Sorry for the inconvenience. Yours, Steffen

Thank you Steffen.

Hi, it's the same issue again on MetFrag Web beta.

Regards,
Joaquin

It's working fine for now. Thanks!

Hi, the website is not responding. May I know when will the current issue be fixed?

Thanks,
David

Hi @david3231 , I have restarted the docker container and MetFrag is running again.

In case there are any issues in the future, please tag me in GitHub so I can take any actions more quickly.

Best wishes

Hi @korseby , thanks but its not responding again.

Hm. Seems like MetFrag is crashing because it is out of memory. Normally it should restart but it doesn't. I'll attach the log.

Can you try to reduce the number of candidates? 17000 compounds is probably too much for the computer where MetfRag is currently running on. (If that request was coming from you, of course. - We do not save any personal information.) We will merge MetFrag to our cluster sometime in February - which has much more memory.

checkDatabaseThread thread is dead
17977 compound(s)
init scores
checks before processing
start processing
ProcessCompoundsThreadRunner run
prepareDatabaseSettings
prepareCompoundFilterSettings
prepareCompoundScoreSettings
prepareFragmenterSettings
INFO  de.ipbhalle.metfraglib.process.ProcessingStatus - 10 %
INFO  de.ipbhalle.metfraglib.process.ProcessingStatus - 20 %
INFO  de.ipbhalle.metfraglib.process.ProcessingStatus - 30 %
INFO  de.ipbhalle.metfraglib.process.ProcessingStatus - 40 %
INFO  de.ipbhalle.metfraglib.process.ProcessingStatus - 50 %
INFO  de.ipbhalle.metfraglib.process.ProcessingStatus - 60 %
INFO  de.ipbhalle.metfraglib.process.ProcessingStatus - 70 %
INFO  de.ipbhalle.metfraglib.process.ProcessingStatus - 80 %
INFO  de.ipbhalle.metfraglib.process.ProcessingStatus - 90 %
INFO  de.ipbhalle.metfraglib.process.ProcessingStatus - 100 %
Exception in thread "Thread-30" java.lang.OutOfMemoryError: GC overhead limit exceeded
	at javolution.util.internal.map.MapView$KeySet.<init>(MapView.java:157)
	at javolution.util.internal.map.MapView.keySet(MapView.java:273)
	at javolution.util.FastSet.<init>(FastSet.java:59)
	at javolution.util.FastSet.<init>(FastSet.java:51)
	at javolution.util.FastBitSet.<init>(FastBitSet.java:39)
	at de.ipbhalle.metfraglib.FastBitArray.<init>(FastBitArray.java:81)
	at de.ipbhalle.metfraglib.scoreinitialisation.AutomatedLossFingerprintAnnotationScoreInitialiser.addNonExplainedLosses(AutomatedLossFingerprintAnnotationScoreInitialiser.java:407)
	at de.ipbhalle.metfraglib.scoreinitialisation.AutomatedLossFingerprintAnnotationScoreInitialiser.postProcessScoreParameters(AutomatedLossFingerprintAnnotationScoreInitialiser.java:234)
	at de.ipbhalle.metfraglib.process.CombinedMetFragProcess.postProcessScoresGlobal(CombinedMetFragProcess.java:420)
	at de.ipbhalle.metfraglib.process.CombinedMetFragProcess.run(CombinedMetFragProcess.java:202)
	at de.ipbhalle.metfragweb.container.BeanSettingsContainer.startCandidateProcessing(BeanSettingsContainer.java:1754)
	at de.ipbhalle.metfragweb.helper.ProcessCompoundsThreadRunner.run(ProcessCompoundsThreadRunner.java:71)
	at java.lang.Thread.run(Thread.java:748)
Exception in thread "http-bio-8080-AsyncTimeout" java.lang.OutOfMemoryError: GC overhead limit exceeded
	at java.util.concurrent.ConcurrentLinkedQueue.iterator(ConcurrentLinkedQueue.java:669)
Exception in thread "http-bio-8080-exec-8" 	at org.apache.tomcat.util.net.JIoEndpoint$AsyncTimeout.run(JIoEndpoint.java:158)
	at java.lang.Thread.run(Thread.java:748)
java.lang.OutOfMemoryError: GC overhead limit exceeded
Exception in thread "http-bio-8080-exec-19" Exception in thread "http-bio-8080-exec-5" java.lang.OutOfMemoryError: GC overhead limit exceeded
java.lang.OutOfMemoryError: GC overhead limit exceeded
Exception in thread "http-bio-8080-exec-14" java.lang.OutOfMemoryError: GC overhead limit exceeded
Exception in thread "http-bio-8080-exec-27" java.lang.OutOfMemoryError: GC overhead limit exceeded
Exception in thread "http-bio-8080-exec-7" java.lang.OutOfMemoryError: GC overhead limit exceeded
Jan 15, 2019 4:44:20 AM org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor run
SEVERE: Unexpected death of background thread ContainerBackgroundProcessor[StandardEngine[Catalina]]
java.lang.OutOfMemoryError: GC overhead limit exceeded

Exception in thread "ContainerBackgroundProcessor[StandardEngine[Catalina]]" java.lang.OutOfMemoryError: GC overhead limit exceeded
Exception in thread "http-bio-8080-exec-24" java.lang.OutOfMemoryError: GC overhead limit exceeded
Exception in thread "http-bio-8080-exec-34" java.lang.OutOfMemoryError: GC overhead limit exceeded
Exception in thread "http-bio-8080-exec-22" java.lang.OutOfMemoryError: GC overhead limit exceeded
Exception in thread "http-bio-8080-exec-2" java.lang.OutOfMemoryError: GC overhead limit exceeded
Exception in thread "http-bio-8080-exec-30" java.lang.OutOfMemoryError: GC overhead limit exceeded
Exception in thread "http-bio-8080-exec-20" Exception in thread "http-bio-8080-exec-44"
Exception: java.lang.OutOfMemoryError thrown from the UncaughtExceptionHandler in thread "http-bio-8080-exec-20"
java.lang.OutOfMemoryError: GC overhead limit exceeded

Exception: java.lang.OutOfMemoryError thrown from the UncaughtExceptionHandler in thread "http-bio-8080-exec-42"
Exception in thread "http-bio-8080-exec-4"
Exception: java.lang.OutOfMemoryError thrown from the UncaughtExceptionHandler in thread "http-bio-8080-exec-4"
Exception in thread "http-bio-8080-exec-26" Exception in thread "http-bio-8080-exec-46" java.lang.OutOfMemoryError: GC overhead limit exceeded
java.lang.OutOfMemoryError: GC overhead limit exceeded
Exception in thread "http-bio-8080-exec-49" java.lang.OutOfMemoryError: GC overhead limit exceeded
Exception in thread "http-bio-8080-exec-43" java.lang.OutOfMemoryError: GC overhead limit exceeded
Exception in thread "http-bio-8080-exec-29" java.lang.OutOfMemoryError: GC overhead limit exceeded
Exception in thread "http-bio-8080-Acceptor-0" java.lang.OutOfMemoryError: GC overhead limit exceeded
Exception in thread "http-bio-8080-exec-47" java.lang.OutOfMemoryError: GC overhead limit exceeded
Exception in thread "http-bio-8080-exec-32" java.lang.OutOfMemoryError: GC overhead limit exceeded
Exception in thread "http-bio-8080-exec-21" java.lang.OutOfMemoryError: GC overhead limit exceeded
Jan 15, 2019 4:55:09 AM com.sun.faces.application.ApplicationImpl newThing
SEVERE: Unable to load class:
java.lang.OutOfMemoryError: GC overhead limit exceeded

Jan 15, 2019 4:55:33 AM com.sun.faces.application.ApplicationImpl createComponentApplyAnnotations
SEVERE: JSF1068: Cannot instantiate component with component-type javax.faces.HtmlPanelGrid```

Hi @korseby , thanks for the information but that wasn't from me. I was just about to log on the website.

Ok great, I'm looking forward to it. Thank you very much.

@korseby
Hi, the webpage is down. I'm planning to use MetFragR. I wonder if MetFrag Web & R share the same server?
Regards.

It should be running again.