[gmx-users] About system requirement to gromacs

[Linus Östberg]

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 <ramadavidgroup at 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 at 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-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists