Hi Carla, On Jul 28, 2011, at 9:38 AM, Carla Jamous wrote:
> Hi everyone, please I was running simulations with gromacs version 4.0.3 ,but > I got the following error: > Average load imbalance: 12.1 % > Part of the total run time spent waiting due to load imbalance: 6.9 % > Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % > Y 9 % > Average PME mesh/force load: 0.807 > Part of the total run time spent waiting due to PP/PME imbalance: 5.3 % > This is not an error but just a hint how you could optimize your performance. > NOTE: 6.9 % performance was lost due to load imbalance > in the domain decomposition. > > NOTE: 5.3 % performance was lost because the PME nodes > had less work to do than the PP nodes. > You might want to decrease the number of PME nodes > or decrease the cut-off and the grid spacing. > > After searching the archive mailing list and reading the manual , I decided > to use g_tune_pme so I switched to gromacs 4.5.4. Here's my script: Note that there is also a g_tune_pme version for 4.0.7: http://www.mpibpc.mpg.de/home/grubmueller/projects/MethodAdvancements/Gromacs/index.html As another possibility, you can use the tpr file you created with 4.0.x as input for Gromcas 4.5.x, also for g_tune_pme, this is probably the easiest solution. > > #PBS -S /bin/bash > #PBS -N job_md6ns > #PBS -e job_md6ns.err > #PBS -o job_md6ns.log > #PBS -m ae -M carlajam...@gmail.com > #PBS -l select=2:ncpus=8:mpiprocs=8 > #PBS -l walltime=024:00:00 > cd $PBS_O_WORKDIR > export GMXLIB=$GMXLIB:/scratch/carla/top:. > module load gromacs > chem="/opt/software/SGI/gromacs/4.5.4/bin/" > mdrunmpi="mpiexec /opt/software/SGI/gromacs/4.5.4/bin/" > ${chem}grompp -v -f md6ns.mdp -c 1rlu_apo_mdeq.gro -o 1rlu_apo_md6ns.tpr -p > 1rlu_apo.top > ${mdrunmpi}g_tune_pme -v -s 1rlu_apo_md6ns.tpr -o 1rlu_apo_md6ns.trr -cpo > state_6ns.cpt -c 1rlu_apo_md6ns.gro -x 1rlu_apo_md6ns.xtc -e md6ns.edr -g > md6ns.log -np 4 -ntpr 1 -launch > > But now, I have the following error message: > > Fatal error: > Library file residuetypes.dat not found in current dir nor in your GMXLIB > path. Why don't you build your tpr file on your workstation and then switch over to the cluster? I guess this will make life easier for you. Also note that you must not call g_tune_pme in parallel (which you do by ${mdrunmpi}g_tune_pme. g_tune_pme will spawn its own MPI processes with the help of the MPIRUN and MDRUN environment variables. See g_tune_pme -h, probably you need do set export MDRUN=/opt/software/SGI/gromacs/4.5.4/bin/mdrun export MPIRUN=`which mpiexec` Hope that helps, Carsten > > Except that I'm using amber94 force-field and that my topology files are in a > special directory called top where I modified certain things. With gromacs > 4.0.3, it always worked so I don't know what is happening here. > > Please does anyone have an idea of what it might be? > > Do I have to run pdb2gmx, editconf, etc... with the gromacs 4.5.4 for it to > work? > > Thank you, > > Carla > -- > 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 -- 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://www.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