[scipion-users] particle polishing with movies error

[Dmitry S. <sem...@gm...>]

Dear colleagues,

I have a problem running particle polishing.

Every time I try to run it (with movies) I get an error:

In the run file I have the following notification:

*run.stdout:*
....................................

slurmstepd: Exceeded step memory limit at some point....
.......................................

*Log file:*

Protocol failed: Command 'srun  `which relion_particle_polish_mpi`  --i
Runs/015602_ProtRelionPolish/extra/relion_it032_data.star --o shiny
--angpix 1.108 --movie_frames_running_avg 5 --dont_read_old_files --sym c2
--sigma_nb 100 --perframe_highres 3.000 --autob_lowres 20.000 --bg_radius
155 --mask Runs/015357_ProtRelionPostprocess/extra/postprocess_automask.mrc
' returned non-zero exit status 137

Any recommendations?

In the gui is only MPI available (no threads).

What are the working settings?

Than you!

Sincerely,
Dmitry