Hi Yan,
You may be running out of RAM. Try averaging every 3 movie frames upon
particle extraction. That way you end up with 20 frames, which is a more
reasonable number.
HTH,
S
> Hi all,
>
> I was trying to run movie processing in RELION 1.3 by using the command :
>
> relion_refine_mpi --o Refine3D/movie_60f_7f_ct26 --continue
> Refine3D/cont_run1_ct12_it026_optimiser.star --solvent_mask
> run1_class001_mask.mrc --oversampling 1 --healpix_order 2
> --auto_local_healpix_order 4 --offset_range 5 --offset_step 2
> --realign_movie_frames particles_ori_60f_movie_subset.star
> --movie_frames_running_avg 7 --sigma_off 1 --skip_rotate --skip_maximize
> --j 1
>
> Job was stuck at the step of 'Expanding current model for movie frames'
> for
> about 9 hours and then was killed by signal 9 like the following:
> --------------------------------------------------------------------------
> orterun noticed that process rank 6 with PID 91141 on node
> gcomp-08.cryoem.lsi.umich.edu exited on signal 9 (Killed).
> --------------------------------------------------------------------------
>
> There are 60 frames each micrographs and in total 52K particles for movie
> processing. 16Gb RAM was assigned to each thread.
>
> Any advice would be much appreciated.
>
> Thanks a lot,
> Yan
>
--
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
http://www2.mrc-lmb.cam.ac.uk/groups/scheres
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