 |
 |
Hi, What is the pixel size and the box size? Did you use fast subsets? > - MPI=16 > - Threads=1 > - Cores per node=1 Don't you have any GPU nodes or CPU nodes with more cores? Use more threads (if you have only 16 cores, try 4 MPI x 4 threads or 2 MPI x 8 threads). Set the number of threads per MPI to the "dedicated cores per node". Best regards, Takanori Nakane > Hi All, > > Been having some trouble running the 2D classification job in Relion 3.0. > > I have been submitting to a queue and everything has been running fine - > 2D classification to produce templates for autopick worked fine, as did > the autopicking but the 2D classification of the extracted autopicked > particles doesnt run. it just gets aborted for exceeding the walltime > (which I have set to 60hrs) - if I go back to the GUI to continue when I > browse there's only run_it000_optimiser.star so it doesnt look like it > ever gets started. And there are no error messages....... > > Input parameters; > > I/O - Extract/job13/particles.star (21395 particles) > CTF - No (negative staining) > Optimsation > - Classes 50 (I tried 100 first) > - T=2 > - Iteration = 20 (I tried 25 first) > - Mask =250 > > Sampling - default settings > Helix - default settings > Compute - default settings > > Running > - MPI=16 > - Threads=1 > - Queue=yes > - Name=batch > - Command=qsub > - Max hrs= 60 (I've tried 20, 30, 40) > - Submission = /local/software/relion/3.0/bin/qsub.bash (I was asked by my > IT dept to remove the 'double' in order to get it to submit - could this > be the problem?) > - Cores per node=1 > > Any suggestions? > > Thanks > Sonya > > ######################################################################## > > To unsubscribe from the CCPEM list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1 > ######################################################################## To unsubscribe from the CCPEM list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1