[gmx-users] multinode issue

[Mark Abraham]

On Fri, Dec 5, 2014 at 9:15 AM, Éric Germaneau <germaneau at sjtu.edu.cn>
wrote:

> Dear all,
>
> I use impi and when I submit o job (via LSF) to more than one node I get
> the following message:
>
>    Number of CPUs detected (16) does not match the number reported by
>    OpenMP (1).
>

That suggests this machine has not be set up to return information to the
standard sysconf() routine in the usual way. What kind of machine is this?

   Consider setting the launch configuration manually!
>    Reading file test184000atoms_verlet.tpr, VERSION 4.6.2 (single
>    precision)
>

I hope that's just a 4.6.2-era .tpr, but nobody should be using 4.6.2 mdrun
because there was a bug in only that version affecting precisely these
kinds of issues...

   [16:node319] unexpected disconnect completion event from [11:node328]
>    Assertion failed in file ../../dapl_conn_rc.c at line 1179: 0
>    internal ABORT - process 16
>
> I submit doing
>
>    mpirun -np 32 -machinefile nodelist $EXE -v -deffnm $INPUT
>
> The machinefile looks like this
>
>    node328:16
>    node319:16
>
> I'm running the release 4.6.7.
> I do not set anything about OpenMP for this job, I'd like to have 32 MPI
> process.
>
> Using one node it works fine.
> Any hints here?
>

Everything seems fine. What was the end of the .log file? Can you run
another MPI test program thus?

Mark


>                                                              Éric.
>
> --
> Éric Germaneau (艾海克), Specialist
> Center for High Performance Computing
> Shanghai Jiao Tong University
> Room 205 Network Center, 800 Dongchuan Road, Shanghai 200240 China
> M:germaneau at sjtu.edu.cn P:+86-136-4161-6480 W:http://hpc.sjtu.edu.cn
> --
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