Hi,
I am not sure why relion_refine crashed (your log
contains only up to iteration 4 not 7), but one possibility
is shortage of GPU memory. What is your box size?
Please try again with 'Skip padding: Yes'.
Best regards,
Takanori Nakane
On 2018/09/02 3:19, Qian, Hongwu wrote:
> Dear all,
>
> I am a postdoc in Princeton University working on cryo-EM 3D reconstruction. Recently, I tried to used the 3D multi-body in RELION 3.0 to process one data set. However, an error appeared after the end of the 7th iteration. Could anyone help me to figure out what is wrong? My scripts to submit job are shown as below and the log file has been attached.
>
> srun -n 5 relion_refine_mpi --continue AP0814b2Refine3D/run1_it008_optimiser.star --o AP0814b2MBRefine3D/run1 --solvent_correct_fsc --multibody_masks AP0814b2Refine3D/run1_multiBody.star --reconstruct_subtracted_bodies --oversampling 1 --healpix_order 4 --auto_local_healpix_order 4 --offset_range 3 --offset_step 1.5 --dont_combine_weights_via_disc --pool 3 --no_parallel_disc_io --pad 1 --j 1 --gpu
> srun -n 5 relion_flex_analyse_mpi --PCA_orient --model AP0814b2MBRefine3D/run1_model.star --data AP0814b2MBRefine3D/run1_data.star --bodies AP0814b2Refine3D/run1_multiBody.star --o AP0814b2MBRefine3D/run1_analyse --do_maps --k 3
>
>
> Thanks a lot,
>
> Hongwu
>
>
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