Hi,
This is probably a problem with your MPI runtime, not RELION.
Your MPI runtime is not aware that you may use 8 processes.
If this is on a cluster, you should ask your cluster administrator
how to properly submit a job. If this is your own machine,
you can edit your 'machinefile' or force 'oversubscribing'.
See https://www.open-mpi.org/faq/?category=running#oversubscribing.
(Don't do this on a cluster, because it might affect other users!)
Best regards,
Takanori Nakane
On 2019/06/26 5:22, Joel Meyerson wrote:
> I am unable to run Relion jobs with MPI procs on all available threads. For example, if running CTFFIND4 on our 4 core / 8 hyperthread machine, the job runs successfully with 4x MPI procs, but fails with 8x MPI procs. The error message reports: "Either request fewer slots for your application, or make more slots available for use".
>
> One suspicion is that this problem may have arisen during compiling, so I've provided commands for "cmake" and "make" below, used when building Relion. I've also attached the output for the two commands. The system has Relion 3, Centos 7, openmpi3.
>
> sudo cmake -DCUDA_ARCH=61 -DMPI_CXX_COMPILER=/usr/lib64/openmpi3/bin/mpicxx -DMPI_C_COMPILER=/usr/lib64/openmpi3/bin/mpicc ..
>
> sudo make -j 8
>
> Any suggestions on how to solve this?
>
> Thanks,
> Joel
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