[gmx-users] g_tune_pme cannot be executed

zifeng li lizifeng7 at gmail.com
Mon Aug 20 17:07:56 CEST 2012

Dear Gromacs users,

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
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 :)


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