Hi Thomas, On Nov 12, 2012, at 5:18 PM, Thomas Schlesier <[email protected]> wrote:
> Dear all, > i did some scaling tests for a cluster and i'm a little bit clueless about > the results. > So first the setup: > > Cluster: > Saxonid 6100, Opteron 6272 16C 2.100GHz, Infiniband QDR > GROMACS version: 4.0.7 and 4.5.5 > Compiler: GCC 4.7.0 > MPI: Intel MPI 4.0.3.008 > FFT-library: ACML 5.1.0 fma4 > > System: > 895 spce water molecules this is a somewhat small system I would say. > Simulation time: 750 ps (0.002 fs timestep) > Cut-off: 1.0 nm > but with long-range correction ( DispCorr = EnerPres ; PME (standard > settings) - but in each case no extra CPU solely for PME) > V-rescale thermostat and Parrinello-Rahman barostat > > I get the following timings (seconds), whereas is calculated as the time > which would be needed for 1 CPU (so if a job on 2 CPUs took X s the time > would be 2 * X s). > These timings were taken from the *.log file, at the end of the > 'real cycle and time accounting' - section. > > Timings: > gmx-version 1cpu 2cpu 4cpu > 4.0.7 4223 3384 3540 > 4.5.5 3780 3255 2878 Do you mean CPUs or CPU cores? Are you using the IB network or are you running single-node? > > I'm a little bit clueless about the results. I always thought, that if i have > a non-interacting system and double the amount of CPUs, i You do use PME, which means a global interaction of all charges. > would get a simulation which takes only half the time (so the times as > defined above would be equal). If the system does have interactions, i would > lose some performance due to communication. Due to node imbalance there could > be a further loss of performance. > > Keeping this in mind, i can only explain the timings for version 4.0.7 2cpu > -> 4cpu (2cpu a little bit faster, since going to 4cpu leads to more > communication -> loss of performance). > > All the other timings, especially that 1cpu takes in each case longer than > the other cases, i do not understand. > Probalby the system is too small and / or the simulation time is too short > for a scaling test. But i would assume that the amount of time to setup the > simulation would be equal for all three cases of one GROMACS-version. > Only other explaination, which comes to my mind, would be that something went > wrong during the installation of the programs… You might want to take a closer look at the timings in the md.log output files, this will give you a clue where the bottleneck is, and also tell you about the communication-computation ratio. Best, Carsten > > Please, can somebody enlighten me? > > Greetings > Thomas > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
