Re: [scipion-users] Java failed

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

wow! good to know it can be fast with 10GB (not available in some machines)

On 20/10/20 17:26, Dmitry Semchonok wrote:
> 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... 
>> <mailto: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...
>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>> -- 
>> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es/> team*
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>
>
>
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-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*