Hi,
Which EMPIAR dataset did you get this error?
Does it happen even if you process only a few (say 10) movies?
> Is it possible to switch off pdf report during this step?
There is no such option, but since PDF generation happens at the
very last step, you can safely ignore the error.
You can simply 'mark as finished'.
Best regards,
Takanori Nakane
> Hello,
>
> I wanted to do the motion correction using Relion internal MotionCorr
> implementation. For some datasets I get segmentation fault - not during
> processing the data but at the end when the pdf log is generated. This is
> the error message:
>
> ---------------------
> Generating logfile.pdf ...
> 0/ 0 sec .................................~~(,_,">[witcher:33237] ***
> Process received signal ***
> [witcher:33237] Signal: Segmentation fault (11)
> [witcher:33237] Signal code: (128)
> [witcher:33237] Failing at address: (nil)
> --------------------------------------------------------------------------
> mpirun noticed that process rank 0 with PID 0 on node witcher exited on
> signal 11 (Segmentation fault).
> ----------------------
>
>
> When I check the micrographs everything seems to be processed and I can
> import aligned mrc files from MotionCorr job folder. Is it possible to
> switch off pdf report during this step? All other pdf reports (CTFfind,
> autopick) work well. Am I maybe something missing? I tried with my own
> datasets and also from EMPIAR - in most cases I get this error.
>
> PS. I also tried external MotionCorr2 and the results seems to be the same
> (error).
>
> Best,
> Dawid
>
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