Dear all,
sometimes, I also got errors with CtfRefine, too.
The same job has run before with the exact same settings and the data is also from the recent relion version (I did not change the versions in between).
The error message is below.
in: /home/local/relion-3.0_beta/src/metadata_table.cpp, line 1074
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 3
srun: Job step aborted: Waiting up to 32 seconds for job step to finish.
and it appears when doing the loop over all micrographs:
...
+ Transforming references ...
+ Performing loop over all micrographs ...
000/??? sec ~~(,_,”>
The file, where the error comes from says this:
void MetaDataTable::write(const FileName &fn_out) const
{
std::ofstream fh;
fh.open((fn_out).c_str(), std::ios::out);
if (!fh)
REPORT_ERROR( (std::string)"MetaDataTable::write: cannot write to file: " + fn_out);
fh << "# RELION; version " << RELION_VERSION << std::endl;
write(fh);
fh.close();
}
It quite confuses me because relion does not seem to be able to write something to a file.
Is there any information what exact file that is?
And what could be the reason for that?
Thanks for your help,
Thomas
> On 7. Jan 2019, at 09:04, Sjors Scheres <[log in to unmask]> wrote:
>
> Dear Leo,
>
> I'm afraid this message does not provide a good starting point for a
> follow-up investigation on our side. The below is not only for you, but
> also for the community.
>
> When reporting errors, it is very useful for us to:
> 1) know the exact command line arguments
> 2) know the exact error
> 3) know when that error occurs and when not
> 4) (most useful) have a small test case you could share with us that
> quickly and reproducibly leads to the error.
>
> In such cases we can relatively quickly find the error. Otherwise, it may
> take a long time...
>
> HTH,
> Sjors
>
>
>> Hi, recently using Relion3 build from 04 Dec with CtfRefine I constantly
>> get cryptic errors which are different depending on whether I use several
>> mpi and several threads or one mpi and several threads or even if just 1
>> mpi and 1 thread. Larger set of particles from the same set of images
>> works fine, so that is really puzzling.
>> Any info on what may help highly appreciated.
>> Thanks!
>>
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>
>
> --
> Sjors Scheres
> MRC Laboratory of Molecular Biology
> Francis Crick Avenue, Cambridge Biomedical Campus
> Cambridge CB2 0QH, U.K.
> tel: +44 (0)1223 267061
> http://www2.mrc-lmb.cam.ac.uk/groups/scheres
>
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