[gmx-users] g_tune_pme cannot be executed

[Carsten Kutzner]

Hi Zifeng,

have you tried to use 

g_tune_pme -npstring none …

Carsten


On Aug 20, 2012, at 5:07 PM, zifeng li <lizifeng7 at gmail.com> wrote:

> Dear Gromacs users,
> 
> Morning!
> I am using Gromacs 4.5.4 version and tries to use the magic power of
> g_tune_pme. However, it cannot be executed with the error in
> benchtest.log file:
> 
> "mpirun error: do not specify a -np argument.  it is set for you."
> 
> The cluster I use needs to submit mpirun job though PBS script, which
> looks like following:
> 
> #PBS -l nodes=8
> #PBS -l walltime=2:00:00
> #PBS -l pmem=2gb
> cd $PBS_O_WORKDIR
> #
> echo " "
> echo " "
> echo "Job started on `hostname` at `date`"
> g_tune_pme -s npt
> echo " "
> echo "Job Ended at `date`"
> echo " "
> ~
> I can run the command "mpirun mdrun_mpi  -deffnm npt " using this PBS
> script before and as you notice, -np for g_tune_mpe is not used.  Any
> suggestions about this issue?
> 
> What I have tried for your reference:
> 1. to delete the first line. well...it won't help.
> 2. to set the environmental variable as Manual suggests curiously:
> export MPIRUN="/usr/local/mpirun -machinefile hosts"    use my account
> name as the "hosts" here.
> 
> 
> Thanks in advance!
> 
> Good day :)
> 
> -Zifeng
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www3.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne