Re: [scipion-users] particle polishing with movies error

[Carlos O. S. <co...@cn...>]

Dear Dmitry,

the problem seems to be related to the maximum memory limit for each of 
the working nodes. I'm not familiar with slurm but most queuing systems 
have an option to increase the maximum memory available to each node 
(this also seems to be the case of Slurm, 
https://slurm.schedmd.com/sbatch.html). This should go in Scipion host 
configuration file 
(https://github.com/I2PC/scipion/wiki/Host-Configuration, probably you 
have already edited this file to be able to submit jobs to Slurm).

Regarding threads or mpi, it is not a matter of the GUI interface but 
the program itself. Relion_polishing is implemented using mpi 
parallelization and not threads.

Kind regards, Carlos Oscar


On 12/06/16 13:08, Dmitry Semchonok wrote:
> 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
>
>
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Carlos Oscar Sánchez Sorzano                  e-mail:   co...@cn...
Biocomputing unit                             http://biocomp.cnb.csic.es
National Center of Biotechnology (CSIC)
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Campus Universidad Autónoma (Cantoblanco)     Tlf: 34-91-585 4510
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