Hi all, I recently ran 20ns simulation in linux cluster.
Used following script for MD simulation #This is the first simulation MD.mdp file contains 20 ns setup grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o MD_first10.tpr mpirun -n 16 mdrun -s MD_first10.tpr -deffnm MD_first10 -np 16 #This extends 10 ns simulation tpbconv -s MD_first10.tpr -o md_extended.tpr -extend 10000 mpirun -n 16 mdrun -s md_extended.tpr -deffnm MD_first10 -cpi MD_first10.cpt -append -np 16 and bsub file #!/bin/bash #BSUB -J testgromacs # the job's name/array job #BSUB -W 120:00 # max. wall clock time in hh:mm #BSUB -n 16,16 # number of processors Min,Max #BSUB -o /home/sample/output_%J.log # output file #BSUB -e /home/sample/errors_%J.log # error file #BSUB -M 8192 #Memory limit in MB echo "Started at `date`" echo cd /home/sample/ echo "Running gromacs test in `pwd`" ./MD.sh echo "Finished at `date`" * * * * *It ran for total 5 days but didnt give all 20ns simulation ..So i checked log file for performance * *Parallel run - timing based on wallclock.* * * * NODE (s) Real (s) (%)* * Time: 359019.178 359019.178 100.0* * 4d03h43:39* * (Mnbf/s) (GFlops) (ns/day) (hour/ns)* *Performance: 445.015 24.708 2.407 9.973* * * * * *It looks like this gave very performance 2.4 ns per 9 hours..this looks very low for me.. Can any body tell me how to increase performance of simulation* Thanks Nitin -- 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