[gmx-users] Question about scaling

[Thomas Schlesier]

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
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

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 
GROMACS-version.
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?

Greetings
Thomas