Hi,
I don't know.
As written in the FAQ, this kind of problems is often very specific to the
system and almost impossible to investigate remotely.
> Please note that due to limited resources we cannot provide support related to high-performance computing
> issues. If your jobs seem to die at seemingly random points, please do not email us, but speak to your system > administrator. RELION makes use of
some pretty intensive high-performance computing, and setting this up
> satisfactorily is not always straightforward.
What happens with other MPI runtime? Different versions of OpenMPI,
Intel MPI, or MPICH?
Takanori
On 2020/11/30 17:47, Karl Herbine wrote:
> Hi Takanori,
>
> Thank you for the suggestion. However, I am still getting this error even when I use the option "Combine iterations through disc? Yes". I have also tried using this suggestion on FAQs page of RELION's wiki with no success (https://www3.mrc-lmb.cam.ac.uk/relion//index.php?title=FAQs#My_runs_keep_crashing_at_seemingly_random_points_in_the_refinement).
>
> >> My runs keep crashing at seemingly random points in the refinement
>
>>> We noticed similar problems on our Dell cluster. Things became much more stable when we switched off TCP segmentation offloading, by using the command mentioned on this linux page.
>
> Do you have any other recommendations or suggestions I can try to fix this?
>
> I should note that this problem did start occurring when we established an ethernet connection to our university's network. Moreover, when I disconnect the connection by physically removing the ethernet wire from the port, we still get this problem.
>
> Thanks,
> Karl H
>
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