[gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P

[Mark Abraham]

Nope. Need a back trace.

Mark
On Mar 13, 2014 4:59 AM, "arrow50311" <linxingcheng50311 at gmail.com> wrote:

> Hi,
>
> Gromacs 4.0.7 is different story, and I did not test it with the same
> system
> though.
>
> The job script is as follows
>
> #@ job_name = job4.6
> #@ comment = "Hello World Job"
> #@ error = $(job_name).$(jobid).err
> #@ output = $(job_name).$(jobid).out
> #@ environment = COPY_ALL
> #@ wall_clock_limit = 10:00:00
> #@ notification = error
> #@ job_type = bluegene
> #@ class = compute
> #@ bg_size = 128
> # #@ bg_connection = torus
> #@ queue
> dir=/home/user/test
> GROM=4.6
> DDIR=/bgpscratch/user/test.$GROM
> mkdir -p $DDIR
> cd $DDIR
> MDRUN=/opt/apps/gromacs/$GROM/bin/mdrun_mpi
>
> ln -s $dir/run.tpr run.tpr
>
> /bgsys/drivers/ppcfloor/bin/mpirun -cwd $DDIR -mode VN -np 512 -exe $MDRUN
> -args "-s run.tpr -pd"
>
>
> With domain decomposition, it will be killed by signal 6, with particle
> decomposition, it will be killed by signal 11. I have no idea why it is
> like
> that.
>
> Do you have any suggestions?
>
> Thank you,
>
>
>
>
>
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