[gmx-users] Cluster recommendations

Fri Jan 16 14:46:41 CET 2015

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