Hi Zifeng,
have you tried to use
g_tune_pme -npstring none …
Carsten
On Aug 20, 2012, at 5:07 PM, zifeng li lizife...@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 hostsuse 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
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