Hi Valérie,
When you say "returned no result", it sounds like you were
not running it as intended;
Relion will output files every iteration which can be used to
continue a job. --continue fileName_it010_optimiser.star will for
instance continue from the 10th iteration.
My advice is to use something like
mpirun -n 3 relion_refine_mpi --gpu --j 8 <all other flags>
[log in to unmask]">dear Relion users, I am new to cryo-EM and Relion and I am lucky enough to have access to a bioinformatics cluster with GPUs to perform calculations. It has a 24h wall time that might be doubled if really needed, but other people are running MD simulations and also need to access the machine. Calculations up to auto_refine worked ok. However, 3D auto_refine returned no result after 24 hours, so I have no idea how many cycles it performed. The option "relion_refine —continue" seems to allow programming the number of cycles and restart afterwards. however, it is not listed in the standard "relion_refine —help" result and it returns options that are marked OLD. Is it really obsolete or could we use it with re-entry after a few cycles? if yes, which options should we use? In summary, I would like to know how people run their 3D refinements. Do people use GPU clusters with longer time walls, or individual machines ? thanks for sharing your experience. all the best, Valérie