[gmx-users] Question about scaling
schlesi at uni-mainz.de
Mon Nov 12 17:18:01 CET 2012
i did some scaling tests for a cluster and i'm a little bit clueless
about the results.
So first the setup:
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
895 spce water molecules
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.
gmx-version 1cpu 2cpu 4cpu
4.0.7 4223 3384 3540
4.5.5 3780 3255 2878
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 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
Only other explaination, which comes to my mind, would be that something
went wrong during the installation of the programs...
Please, can somebody enlighten me?
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