Re: [scipion-users] 2Dclasses with millions of particles

[Ipsita B. <ips...@bi...>]

Hi

I see this kind of error..

matplotlib.use('TkAgg')
java -Xmx2g -d64 -Djava.library.path=/pfs/software/eb/amd64_ubuntu1604_bdw/software/MPI/GCC-CUDA/7.3.0-2.30-9.2.88/OpenMPI/3.1.1/Scipion/1.2.1/software/em/xmipp/lib -Dplugins.dir=/pfs/software/eb/amd64_ubuntu1604_bdw/software/MPI/GCC-CUDA/7.3.0-2.30-9.2.88/OpenMPI/3.1.1/Scipion/1.2.1/software/em/xmipp/external/imagej/plugins -cp /hpc2n/eb/software/Core/Java/1.8.0_181/lib/*:/pfs/software/eb/amd64_ubuntu1604_bdw/software/MPI/GCC-CUDA/7.3.0-2.30-9.2.88/OpenMPI/3.1.1/Scipion/1.2.1/software/em/xmipp/external/imagej/*:/pfs/software/eb/amd64_ubuntu1604_bdw/software/MPI/GCC-CUDA/7.3.0-2.30-9.2.88/OpenMPI/3.1.1/Scipion/1.2.1/software/em/xmipp/java/lib/* xmipp.viewer.scipion.ScipionViewer -i "Runs/004703_ProtRelionClassify2D/extra/relion_it015_classes_scipion.sqlite" --render _representative._filename --labels id _size --zoom 100 --visible enabled id _size _representative._filename _rlnclassDistribution _rlnAccuracyRotations _rlnAccuracyTranslations --sortby _size desc --order enabled id _size _representative._filename _rlnclassDistribution _rlnAccuracyRotations _rlnAccuracyTranslations --scipion 42855 4703 3748
#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007fb09dc69746, pid=170444, tid=0x00007fb09e7cb700
#
# JRE version: Java(TM) SE Runtime Environment (8.0_181-b13) (build 1.8.0_181-b13)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (25.181-b13 mixed mode linux-amd64 compressed oops)
# Problematic frame:
# C  [libc.so.6+0x8b746]  strlen+0x26
#
# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# An error report file with more information is saved as:
# /pfs/nobackup/home/s/swami63/ScipionUserData/projects/cem00264_00022_scipion_20190523/hs_err_pid170444.log
#
# If you would like to submit a bug report, please visit:
#   http://bugreport.java.com/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#


/Ipsita

On 5 Jul 2019, at 23:03, Jose Miguel de la Rosa Trevin <del...@gm...<mailto:del...@gm...>> wrote:

Dear Ipsita,

Do you see any error in the terminal after clicking "Show classification with Scipion" ??

Best,
Jose Miguel


On Fri, Jul 5, 2019 at 9:48 PM Ipsita Banerjee <ips...@bi...<mailto:ips...@bi...>> wrote:
Dear Scipion Users,

I have a dataset where I have about 2 million picked particles.. I could run relion2D classification for these particles..
However, when I click on the Analyze results button, and try to open the tab "Show classification in Scipion", I don't see anything..
When i click on the tab "show classes only", I can see the classes only..
Please, I need some help as to what I can do to continue with the processing...

Thanks so much...

Best regards,
Ipsita
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