[gmx-users] Cluster recommendations

Tue Jan 20 12:12:04 CET 2015

Thank you very much Karsten.

2015-01-16 14:46 GMT+01:00 Carsten Kutzner <ckutzne at gwdg.de>:

> Hi David,
>
> On 16 Jan 2015, at 12:28, David McGiven <davidmcgivenn at gmail.com> wrote:
>
> > Hi Carsten,
> >
> > Thanks for your answer.
> >
> > 2015-01-16 11:11 GMT+01:00 Carsten Kutzner <ckutzne at gwdg.de>:
> >
> >> Hi David,
> >>
> >> we are just finishing an evaluation to find out which is the optimal
> >> hardware for Gromacs setups. One of the input systems is an 80,000 atom
> >> membrane channel system and thus nearly exactly what you want
> >> to compute.
> >>
> >> The biggest benefit you will get by adding one or two consumer-class
> GPUs
> >> to your nodes (e.g. NVIDIA GTX 980). That will typically double your
> >> performace-to-price ratio. This is true for Intel as well as for AMD
> >> nodes, however the best ratio in our tests was observed with 10-core
> >> Intel CPUs (2670v2, 2680v2) in combination with a GTX 780Ti or 980,
> >> ideally two of those CPUs with two GPUs on a node.
> >>
> >>
> > Was there a difference between 2670v2 (2.5 GHz) and 2680v2  (2.8 GHz) ?
> I'm
> > wondering if those 0,3 GHz are significative. Or the 0,5 GHz compared to
> > 2690v2 for the matter. There’s a significative difference in price
> indeed.
> Usually the percent improvement for Gromacs performance is not as much
> as the percent improvement in clock speed, so the cheaper ones will
> give you a higher performance-to-price ratio.
>
> >
> > I'm also wondering if the performance would be better with 16 core Intels
> > instead of 10 core. I.e E5-2698 v3.
> Didn’t test those.
>
> >
> > I would like to know which other tests have you done. What about AMD ?
> We tested AMD 6380 with 1-2 GTX 980 GPUs, which gives about the same
> performance-to-price ratio as a 10 core Intel 2680v2 node with one GTX 980.
> The Intel node gives you a higher per-node performance, though.
>
> >
> > Unless you want to buy expensive FDR14 Infiniband, scaling across two
> >> or more of those nodes won’t be good (~0.65 parallel efficiency across
> 2,
> >> ~0.45 across 4 nodes using QDR infiniband), so I would advise against
> >> it and go for more sampling on single nodes.
> >>
> >>
> > Well, that puzzles me. Why is it that you get poor performance ? Are you
> > talking about pure CPU jobs over infiniband, or are you talking about
> > CPU+GPU jobs over infiniband ?
> For a given network (e.g. QDR Infiniband), the scaling is better the lower
> the performance of the individual nodes. So for CPU-only nodes you
> will get a better scaling than for CPU+GPU nodes, which have a way higher
> per-node performance.
>
> > How come you won’t get good performance if a great percentage of
> The performance is good, it is just that the parallel efficiency is
> not optimal for an MD system <100,000 atoms, meaning you do not get two
> times the performance on two nodes in parallel as compared to the
> aggregated performance of two individual runs.
> Bigger systems will have a better parallel efficiency.
>
> > supercomputer centers in the world use InfiniBand ? And I'm sure lots of
> > users here in the list use gromacs over Infiniband.
> I do, too :)
> But you get more trajectory for your money if you can wait and run on
> a single node.
>
> Carsten
>
> >
> > Thanks again.
> >
> > Best Regards,
> > D
> >
> >
> >> Best,
> >>  Carsten
> >>
> >>
> >>
> >>
> >> On 15 Jan 2015, at 17:35, David McGiven <davidmcgivenn at gmail.com>
> wrote:
> >>
> >>> Dear Gromacs Users,
> >>>
> >>> We’ve got some funding to build a new cluster. It’s going to be used
> >> mainly
> >>> for gromacs simulations (80% of the time). We run molecular dynamics
> >>> simulations of transmembrane proteins inside a POPC lipid bilayer. In a
> >>> typical system we have ~100000 atoms, from which almost 1/3 correspond
> to
> >>> water molecules. We employ usual conditions with PME for electorstatics
> >> and
> >>> cutoffs for LJ interactions.
> >>>
> >>> I would like to hear your advice on which kind of machines are the best
> >>> bang-for-the-buck for that kind of simulations. For instance :
> >>>
> >>> - Intel or AMD ? My understanding is that Intel is faster but
> expensive,
> >>> and AMD is slower but cheaper. So at the end you almost get the same
> >>> performance-per-buck. Right ?
> >>>
> >>> - Many CPUs/Cores x machine or less ? My understanding is that the more
> >>> cores x machine the lesser the costs. One machine is always cheaper to
> >> buy
> >>> and maintain than various. Plus maybe you can save the costs of
> >> Infiniband
> >>> if you use large core densities ?
> >>>
> >>> - Should we invest in an Infiniband network to run jobs across multiple
> >>> nodes ? Will the kind of simulations we run benefit from multiple
> nodes ?
> >>>
> >>> - Would we benefit from adding GPU’s to the cluster ? If so, which
> ones ?
> >>>
> >>> We now have a cluster with 48 and 64 AMD Opteron cores x machine (4
> >>> processors x machine) and we run our gromacs simulations there. We
> don’t
> >>> use MPI because our jobs are mostly run in a single node. As I said,
> with
> >>> 48 or 64 cores x simulation in a single machine. So far, we’re quite
> >>> satisfied with the performance we get.
> >>>
> >>> Any advice will be greatly appreciated.
> >>>
> >>>
> >>> Best Regards,
> >>> D.
> >>> --
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> >>
> >>
> >> --
> >> 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
> >> http://www.mpibpc.mpg.de/grubmueller/sppexa
> >>
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>
> --
> 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
> http://www.mpibpc.mpg.de/grubmueller/sppexa
>
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