Both are probably using 4 cores, the first one as threads, the second via mpi.
However, in the second one you are using 16 threads to run 4 copies of the same simulation, 4 threads each, thus getting performance similar (or less) to using only one core. When using mpi, you should use mdrun_mpi instead, ie: mpirun -np 4 mdrun_mpi -v -deffnm topol1 / Linus On Wed, Aug 1, 2012 at 12:36 PM, rama david <ramadavidgr...@gmail.com> wrote: > Thank you Mark for reply...... > > I run mdrun and mpirun with following command. I pasted output also.. > Please help me to parse it.. > > > 1. mdrun -v -deffnm topol1 > 2. mpirun -np 4 mdrun -v -deffnm topol1 > > > 1. mdrun -v -deffnm topol1 > > > step 30, will finish Wed Aug 1 16:49:28 2012 > Average load imbalance: 12.3 % > Part of the total run time spent waiting due to load imbalance: 5.1 % > > NOTE: 5.1 % performance was lost due to load imbalance > in the domain decomposition. > You might want to use dynamic load balancing (option -dlb.) > > > Parallel run - timing based on wallclock. > > NODE (s) Real (s) (%) > Time: 2.035 2.035 100.0 > (Mnbf/s) (GFlops) (ns/day) (hour/ns) > Performance: 109.127 5.744 2.632 9.117 > > gcq#98: "You're About to Hurt Somebody" (Jazzy Jeff) > > > > 2. mpirun -np 4 mdrun -v -deffnm topol1 > > Getting Loaded... > Reading file topol1.tpr, VERSION 4.5.5 (single precision) > Starting 4 threads > Starting 4 threads > Starting 4 threads > Starting 4 threads > Loaded with Money > > Loaded with Money > > Loaded with Money > > Loaded with Money > > Making 1D domain decomposition 4 x 1 x 1 > Making 1D domain decomposition 4 x 1 x 1 > > > Making 1D domain decomposition 4 x 1 x 1 > Making 1D domain decomposition 4 x 1 x 1 > > starting mdrun 'Protein in water' > 50000 steps, 100.0 ps. > starting mdrun 'Protein in water' > 50000 steps, 100.0 ps. > > starting mdrun 'Protein in water' > 50000 steps, 100.0 ps. > starting mdrun 'Protein in water' > 50000 steps, 100.0 ps. > > NOTE: Turning on dynamic load balancing > > > NOTE: Turning on dynamic load balancing > > step 0 > NOTE: Turning on dynamic load balancing > > step 100, will finish Wed Aug 1 19:36:10 2012vol 0.83 imb F 2% vol > 0.84 imb step 200, will finish Wed Aug 1 19:32:37 2012vol 0.87 imb > F 16% vol 0.86 imb step 300, will finish Wed Aug 1 19:34:59 2012vol > 0.88 imb F 4% vol 0.85 imb step 400, will finish Wed Aug 1 > 19:36:27 2012^Cmpirun: killing job... > > -------------------------------------------------------------------------- > mpirun noticed that process rank 0 with PID 4257 on node VPCEB34EN > exited on signal 0 (Unknown signal 0). > -------------------------------------------------------------------------- > 4 total processes killed (some possibly by mpirun during cleanup) > mpirun: clean termination accomplished > > > > > As you can also see the mdun command estimate to complete Aug 1 16:49:28 2012 > while mpirun taking the time Wed Aug 1 19:36:10 2012vol.... > > Mpirun command taking more time... > > so from above output I can guess In mpirun 4 processor are used > > > Sorry if I take any wrong meaning from output.. > > Thank you for giving your valuable time.. > > > With best wishes and regards > > Rama David > -- > 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 -- 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
