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Re: [scipion-users] Java failed
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From: Dmitry S. <Sem...@gm...> - 2020-10-20 15:26:37
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Thank you Pablo - I put 10 Gb and it opened immediately! Kind regards, Dmitry > On 20. Oct 2020, at 17:05, Pablo Conesa <pc...@cn...> wrote: > > Try to increase the memory using the config file and giving more memory to JAVA: > > JAVA_MAX_MEMORY = 3 > > Note: units are in GB --> 3 equals 3GB of RAM > > I've seen the viewer coping with 8M particles but taking ages to load, so if there is no error, wait! > > > > Another option would be to use "split set" to split the set in smaller ones and review them and then join. > > > > Cheers! > > > > On 20/10/20 16:52, Dmitry Semchonok wrote: >> One more small question — >> >> >> I have 5 000 000 particles and java fails while opening the result of relion 2D. >> >> Any idea how to get the classes/particles that I want? >> >> Thank you! >> >> >> Sincerely, >> Dmitry >> >> >> ERROR loading project: scratch >> Project database not found at '/home/user/Data/ScipionUserData/projects/scratch/project.sqlite' >> >> java -Xmx2g -d64 -Djava.library.path=/usr/local/scipion/software/em/xmipp/lib -Dplugins.dir=/usr/local/scipion/software/em/xmipp/bindings/java/imagej/plugins -cp /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.242.b08-0.el7_7.x86_64/lib/*:/usr/local/scipion/software/em/xmipp/bindings/java/imagej/*:/usr/local/scipion/software/em/xmipp/bindings/java/lib/* xmipp.viewer.scipion.ScipionViewer -i "Runs/001802_ProtRelionClassify2D/classes2D.sqlite" --render _representative._filename --labels id _size --zoom 152 --visible enabled id _size _representative._filename _rlnclassDistribution _rlnAccuracyRotations _rlnAccuracyTranslations --sortby _size desc --order enabled id _size _representative._filename _rlnclassDistribution _rlnAccuracyRotations _rlnAccuracyTranslations --scipion 57898 1802 1712 >> Exception in thread "main" java.lang.OutOfMemoryError: Java heap space >> at java.util.Arrays.copyOfRange(Arrays.java:3664) >> at java.lang.String.<init>(String.java:207) >> at java.lang.String.toUpperCase(String.java:2810) >> at java.lang.String.toUpperCase(String.java:2833) >> at org.sqlite.RS.findColumn(RS.java:163) >> at org.sqlite.RS.getInt(RS.java:527) >> at xmipp.viewer.scipion.ScipionMetaData.loadValues(ScipionMetaData.java:207) >> at xmipp.viewer.scipion.ScipionMetaData.loadData(ScipionMetaData.java:151) >> at xmipp.viewer.scipion.ScipionMetaData.<init>(ScipionMetaData.java:91) >> at xmipp.viewer.scipion.ScipionMetaData.<init>(ScipionMetaData.java:68) >> at xmipp.viewer.windows.ImagesWindowFactory.openScipionMetadata(ImagesWindowFactory.java:223) >> at xmipp.viewer.scipion.ScipionViewer.openFile(ScipionViewer.java:71) >> at xmipp.viewer.scipion.ScipionViewer.main(ScipionViewer.java:52) >> >> >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users> > -- > Pablo Conesa - Madrid Scipion <http://scipion.i2pc.es/> team > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
