[gmx-users] job error in cluster

[Mark Abraham]

That's extremely strange. There's a bug there to fix (48 cannot be correct
in both places it is used). Albert, can you please upload your .tpr to a
new issue at http://redmine.gromacs.org? Please also add what value of
OMP_NUM_THREADS is set (perhaps implicitly by the script or your mpirun or
mpirun setup).

Mark


On Tue, Jan 28, 2014 at 11:12 AM, Albert <mailmd2011 at gmail.com> wrote:

> Hello:
>
> I am submitting a gromacs job in a cluster with command:
>
>
> module load module load gromacs/4.6.5-intel13.1
> export MDRUN=mdrun_mpi
> #steepest MINI
> mpirun -np 1 grompp_mpi -f em.mdp -c ion-em.gro -p topol.top -o em.tpr -n
> mpirun -np 64 mdrun_mpi -s em.tpr -c em.gro -v -g em.log &>em.info
>
>
> but it failed with messages:
>
>
> ------------------------------------------------------------
> ----------------------------
> Reading file em.tpr, VERSION 4.6.5 (single precision)
>
> Will use 48 particle-particle and 16 PME only nodes
> This is a guess, check the performance at the end of the log file
> Using 64 MPI processes
> Using 12 OpenMP threads per MPI process
>
> -------------------------------------------------------
> Program mdrun_mpi, VERSION 4.6.5
> Source code file: /icm/home/magd/gromacs-4.6.5/src/mdlib/nbnxn_search.c,
> line: 2523
>
> Fatal error:
> 48 OpenMP threads were requested. Since the non-bonded force buffer
> reduction is prohibitively slow with more than
>  32 threads, we do not allow this. Use 32 or less OpenMP threads.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> "Everybody Lie Down On the Floor and Keep Calm" (KLF)
>
> Error on node 1, will try to stop all the nodes
> Halting parallel program mdrun_mpi on CPU 1 out of 64
>
> gcq#78: "Everybody Lie Down On the Floor and Keep Calm" (KLF)
>
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 1 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.
> --------------------------------------------------------------------------
> --------------------------------------------------------------------------
>
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