Dear Fuxing,
As before, I don't think it's an issue of the relion code. Your sys
admin on that system might be able to help.
HTH,
S
On 09/08/2016 04:32 AM, Fuxing Zeng wrote:
> Hi Sjors,
>
> According the Bluewaters website, I tried:
> aprun –n 5 –d 8 relion_refine_mpi
> aprun –n 5 –N 2 –d 8 relion_refine_mpi
> aprun –n 5 –S 2 –d 8 relion_refine_mpi
> All these three gave the error as below. Seems like the relion_refine_mpi didn’t take the number from aprun:
>
> === RELION MPI setup ===
> === RELION MPI setup ===
> + Number of MPI processes = 1
> + Number of MPI processes = 1
> + Number of threads per MPI process = 8
> + Number of threads per MPI process = 8
> + Total number of threads therefore = 8
> + Total number of threads therefore = 8
> + Master (0) runs on host = nid25211
> + Master (0) runs on host = nid25211
> =================
> =================
> Running in double precision.
> Running in double precision.
> Running in double precision.
> Running in double precision.
> Running in double precision.
> MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program
> File: src/ml_optimiser_mpi.cpp line: 173
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
>
>
> Thanks,
> Fuxing
>
>
> On 9/1/16, 13:42, "Sjors Scheres" <[log in to unmask]> wrote:
>
> Hi Fuxing,
> Perhaps the sys admin for that system may be able to help you with this.
> From here: https://bluewaters.ncsa.illinois.edu/using-aprun
> I understand that
>
> aprun -n XX -d YY relion_command
>
> should work for a hybrid job with XX MPI processes and YY threads.
>
> HTH,
> Sjors
>
> > Hello everyone,
> >
> > I installed Relion in the supercomputer, Blue waters. But it can only use
> > aprun instead of mpirun. How can I use aprun for Relion? It doesn't work
> > if use aprun -n 200 relion_command.
> >
> > Thanks,
> > Fuxing
> >
>
>
> --
> 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
>
>
--
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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