It looks like every MPI thread thinks it's the one-and-only master thread
-- that is, none of the threads knows about each other.
The only cause I've ever seen for this behavior is using an "mpirun" or
"mpiexec" that comes from a *different* MPI than the one that was used to
compile the program (for instance, using mpirun from mpich to run a program
built with OpenMPI).
This issue is being caused at the MPI layer (before ever reaching the pmemd
code itself) -- it's not a problem with Amber per se.
HTH,
Jason
On Fri, Nov 23, 2018 at 10:31 AM Bruno Falcone <brunofalcone.qo.fcen.uba.ar>
wrote:
> Hi! I'm trying to run a Hamiltonian Replica Exchange simulation using
> Amber 18. This, with the very same files, works with Amber 16, but it's
> not working with Amber 18. I attach the input and groupfile.
>
> I run it with the command:
>
> mpirun -np 8 pmemd.cuda.MPI -ng 8 -groupfile remd.gf
>
> I get the following error in the terminal and no output files are
> generated:
>
> #################
>
> setup_groups: MPI size is not a multiple of -ng
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> setup_groups: MPI size is not a multiple of -ng
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> setup_groups: MPI size is not a multiple of -ng
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> setup_groups: MPI size is not a multiple of -ng
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> setup_groups: MPI size is not a multiple of -ng
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> setup_groups: MPI size is not a multiple of -ng
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> setup_groups: MPI size is not a multiple of -ng
> setup_groups: MPI size is not a multiple of -ng
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> --------------------------------------------------------------------------
> mpirun noticed that the job aborted, but has no info as to the process
> that caused that situation.
> --------------------------------------------------------------------------
> ##################
>
> Any help would be greatly appreciated.
>
> Thanks!
>
> Bruno
>
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>
--
Jason M. Swails
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Received on Mon Nov 26 2018 - 08:30:02 PST
