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 %
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:
#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.
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
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