hi,
it seems you are using 1 process instead of 120.
with mpi you should use the relion_refine_mpi program.
do you run this directly or via s job submission system?
if you run this directly the call should be (depending on the mpi verson
- man mpirun):
mpirun -n 120 <here_comes the flag and name of a host or machinefile
with the node names> relion_refine_mpi ...
cheers,
wolfgang
On 03/15/2017 05:43 PM, Alok Sharma wrote:
> Dear All,
>
> I am running 3D classification for a set of ~100K particles on relion.
> The job is running extremely slowly. It takes more than 50 hours for
> each iteration. It already had been more than 30 days and so far only
> 14 iterations are complete. Is this common?
>
> I am using 5 nodes and 120 cores. Command which I am using is:
>
> mpirun relion_refine --o Class3D/job014/run --i
> ./Extract/job003/particles.star --ref volf_scaled.mrc --firstiter_cc
> --ini_high 60 --dont_combine_weights_via_disc --pool 3 --ctf --iter 25
> --tau2_fudge 4 --particle_diameter 200 --K 5 --flatten_solvent
> --zero_mask --oversampling 1 --healpix_order 2 --offset_range 5
> --offset_step 2 --sym C1 --norm --scale --j 1 --no_parallel_disc_io
>
> Thanks,
> Alok
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