Re: [scipion-users] Java failed

[Pablo C. <pc...@cn...>]

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)
>
>
>
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-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*