Hi everyone, please I was running simulations with gromacs version 4.0.3 ,but I got the following error:<br>Average load imbalance: 12.1 %<br> Part of the total run time spent waiting due to load imbalance: 6.9 %<br> Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Y 9 %<br>
Average PME mesh/force load: 0.807<br> Part of the total run time spent waiting due to PP/PME imbalance: 5.3 %<br><br>NOTE: 6.9 % performance was lost due to load imbalance<br> in the domain decomposition.<br><br>NOTE: 5.3 % performance was lost because the PME nodes<br>
had less work to do than the PP nodes.<br> You might want to decrease the number of PME nodes<br> or decrease the cut-off and the grid spacing.<br><br>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:<br>
<br>#PBS -S /bin/bash<br>#PBS -N job_md6ns<br>#PBS -e job_md6ns.err<br>#PBS -o job_md6ns.log<br>#PBS -m ae -M <a href="mailto:carlajamous@gmail.com">carlajamous@gmail.com</a><br>#PBS -l select=2:ncpus=8:mpiprocs=8<br>#PBS -l walltime=024:00:00<br>
cd $PBS_O_WORKDIR<br>export GMXLIB=$GMXLIB:/scratch/carla/top:.<br>module load gromacs<br>chem="/opt/software/SGI/gromacs/4.5.4/bin/"<br>mdrunmpi="mpiexec /opt/software/SGI/gromacs/4.5.4/bin/"<br>${chem}grompp -v -f md6ns.mdp -c 1rlu_apo_mdeq.gro -o 1rlu_apo_md6ns.tpr -p 1rlu_apo.top<br>
${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<br><br>But now, I have the following error message: <br>
<br>Fatal error:<br>Library file residuetypes.dat not found in current dir nor in your GMXLIB path.<br><br>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.<br>
<br>Please does anyone have an idea of what it might be?<br><br>Do I have to run pdb2gmx, editconf, etc... with the gromacs 4.5.4 for it to work?<br><br>Thank you,<br><br>Carla<br>