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Re: [ESPResSo-users] different simulation scenario on desktop or cluster

From: Axel Arnold
Subject: Re: [ESPResSo-users] different simulation scenario on desktop or cluster
Date: Wed, 07 Aug 2013 23:01:08 +0200
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Bonded interactions are only computed for particles that are located on the same CPU. If you increase the number of cores, the range over which a bond can be computed, gets shorted. However, any reasonable bond is much shorter than your box dimensions, so that bond broken errors definitely point to excessive forces. That it "works" on your desktop probably simply means that on that machine, the long bonds can still be accommodated, but it is very likely that your simulation is still aphysical. In particular, I doubt that the problem is due to MPI or the machine, but rather a problem of your setup. An easy check would be to run just with 6 cores or even one core on the cluster, just as on your desktop.

To check the physics of your simulation, just write out the energies, and check that in particular the kinetic energy fluctuates around 1/2 N k_BT, where N is the number of degrees of freedom. Although, there should be no other strong energy drift.

Under most circumstances, it is very likely that you actually need a warmup phase. However, when combined with walls, capping the wall forces is usually not a good idea, since particles are then not hindered from penetrating the hard core of the wall constraint. Therefore, you should use the individual force cap feature, and only set a cap radius for the particle-particle interactions, see the User's guide for details on "inter forcecap individual".

On 07.08.13 12:36, Arash Azari wrote:

Hello everyone, 

I have a very strange situation and I cannot find any proper solution for it; I highly appreciate any recommendations.
Here is the problem:
I have a simulation system (polymer and ions with repulsive wall) and when I run this simulation on my desktop everything is fine (run on single CPU with 6 cores) regardless of skin parameter (0.4) and the warm up steps; it works even with a very short warm up.

When I try to run this simulation on a cluster, a few steps after warm up it crashes with the sometimes bond broken error or wall constraint violation error. I tried different nodes and cores combinations and even on a single node with 2 CPUs (run on 12 cores) it crashes. I have changed the skin parameter up to 2.0 and very long warm up and still I get the same error messages a few steps after the warm up.
I should mention that I did not cap the interactions between the particles (polymer or ion) and the walls during the warm up.
I am not sure whether it is because of the MPI settings on the cluster or not, but the cluster administrators are not helpful at all to ask anything about the system settings and configuration.
I attached the config.log file if it helps.
Thank you very much,

Best regards,
Arash Azari

JP Dr. Axel Arnold
ICP, Universität Stuttgart
Allmandring 3
70569 Stuttgart, Germany
Email: address@hidden
Tel: +49 711 685 67609

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