Hi,
Your are too finely fractionating the frames.
Please read https://relion.readthedocs.io/en/latest/Reference/MovieCompression.html#falcon4-eer.
Especially, "Fractionate such that each fraction has about 0.5 to 1.25 e/A2".
Best regards,
Takanori Nakane
On 2021/04/08 18:42, Richard Baxter wrote:
> Dear CCPEM,
>
> I am trying to perform motion correction of EER images (677 MB each) on a cluster using relion_run_motioncorr_mpi, but the job crashes with more than
> two images. Any advice on how to do it for ~6000 images - using RELION or other program - is *most* welcome.
>
> RELION was built on the cluster from git clone with -DGUI=OFF. The I am running a single node job with 28 CPUs:
>
> Dual socket Intel Xeon E5-2690v4, 28 CPU cores / node, 128GB RAM.
>
> using this in the PBS script header
>
> #PBS -l nodes=1:ppn=28
>
> and the command
> mpirun `which relion_run_motioncorr_mpi` --i Import/job001/movies1.star --o MotionCorr/job002 --first_frame_sum 1 --last_frame_sum 0 --use_own
> --bin_factor 1 --bfactor 150 --dose_per_frame 1.16 --preexposure 0 --patch_x 5 --patch_y 5 --eer_grouping 4 --gainref
> 20210311_125138_EER_GainReference.gain --gain_rot 0 --gain_flip 0 --dose_weighting --grouping_for_ps 4 --pipeline_control MotionCorr/job002
>
> I wonder if it is a memory issue because that appears to scale with the # movies in movies.star from the PBS output:
>
> movies1 movies2 movies3
> cput 3:29:55 3:28:59 02:24:18 PID 0 exited on signal 15 (Termination)
> wallt 00:07:33 00:07:31 00:05:16
> vmem 58.4 GB 98.3 GB 135 GB
> mem 40.4 GB 79.6 GB 114 GB
>
> adding threads with option --j N has no effect, so assuming it is memory the question is how to manage memory use and/or calculate how much is needed
> to complete the job (different cluster queues offer 512 GB, 1.5 TB. 3.0 TB RAM).
>
>
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