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ipb-halle / MetFrag

Repo hosting the MetFrag website
https://ipb-halle.github.io/MetFrag/
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MetFrag Web beta Issue #11

Closed JoaquinWojciech closed 5 years ago

JoaquinWojciech commented 6 years ago

Hi, no results shown for the processed candidates.

screenshot_2018-09-20 metfrag issue

Regards, Joaquin

schymane commented 6 years ago

There should be a feedback button where you can submit your settings, so that they can try and reproduce the issue and get back to you.

[cid:image002.jpg@01D450BB.04F49030]

schymane commented 6 years ago

I can confirm that I do not see any results for the queries I have tried as well.

JoaquinWojciech commented 6 years ago

Thanks Emma, feedback submitted.

sneumann commented 6 years ago

We're looking into it. Yours, Steffen

sneumann commented 5 years ago

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

JoaquinWojciech commented 5 years ago

Thank you Steffen.

JoaquinWojciech commented 5 years ago

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

Regards, Joaquin

schymane commented 5 years ago

It seems to work fine for me at the moment, can you try again?

JoaquinWojciech commented 5 years ago

It's working fine for now. Thanks!

david3231 commented 5 years ago

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

Thanks, David

korseby commented 5 years ago

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

david3231 commented 5 years ago

Hi @korseby , thanks but its not responding again.

korseby commented 5 years ago

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```
david3231 commented 5 years ago

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.

JoaquinWojciech commented 5 years ago

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

schymane commented 5 years ago

MetFragR should be independent of the web server …

korseby commented 5 years ago

It should be running again.

david3231 commented 5 years ago

image

@korseby Hi, the metfrag web is showing "Error fetching candidates" on both KEGG and Pubchem database..

korseby commented 5 years ago

Hi David,

I can see that MetFragBeta does not retrieve candidates.

Can you use the stable version (The Beta just went to stable last month)? I just tested it and it should work as expected.

https://msbi.ipb-halle.de/MetFrag/

Best wishes

david3231 commented 5 years ago

Hi Korseby,

ok noted. thank you so much!

sneumann commented 5 years ago

Database on MetFragBeta has also been restarted. Yours, Steffen

JoaquinWojciech commented 5 years ago

@korseby Hi, we're encountering database candidates fetching error in MetFrag Web. Regards.

korseby commented 5 years ago

Hi @JoaquinWojciech ,

we know. Our worker nodes rebooted and we are working on the issue. As this is not related to MetFrag development, can you send a mail to denbi-mash ÄT ipb-halle.de in the future? This way, you can reach us (Rene, Steffen, Hendrik and me) directly.

Best wishes

JoaquinWojciech commented 5 years ago

Noted and thank you @korseby.