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 hosts" use my account > name as the "hosts" here. > > > Thanks in advance! > > Good day :) > > -Zifeng > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
