How big are the images? How many movie frames does each image have? What
are the command line arguments of the job that crashes?
S
On 10/17/2014 08:53 AM, SUBSCRIBE CCPEM SIddhanta wrote:
> Hi all,
>
> I am new to Relion. I have been following the tutorial closely to process around 12000 particles. Processing is done on a cluster (details given below). At almost every job (mainly for movie processing) we have faced memory issues or other problems which are causing the program to crash. However, after extensive trial and error with the cluster admin, we managed to find optimum settings for MPI processes and threads for each job.
>
> Unfortunately, now in particle polishing none of the configurations are working. I've tried many. It mostly exits with the error 'segmentation fault' at the particle writing stage or some times with 'std:bad_alloc()' right at the beginning.
>
> Cluster details: 8 nodes, each with 64 cores and 128 GB ram.
>
> I'm giving a little extra info which might help in trouble shooting. (these are all for movie processing)
> Optimal settings determined for
>
> 3D Classification: 128 MPI processes, 4 threads, 2 GB per thread
> 3D Auto refine: 32 MPI processes, 16 threads, 2 GB per thread
>
> For particle polishing, I've tried everything, from 8 MPI and 32 threads to 32 MPI and 4 threads. They all return with segmentation fault. And higher settings than 32 MPI or lower than 8 MPI cause the program to crash immediately.
>
> I hope I can get some help on this. Thanks in advance.
--
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
|