Re: [AMBER] Running Amber on a SGI cluster

From: Ross Walker <ross.rosswalker.co.uk>
Date: Wed, 25 Sep 2013 08:53:24 -0700

How many atoms is the system you are trying to simulate?

And what settings are you using? - Thermostat, barostat etc.

All the best
Ross


On 9/25/13 8:26 AM, "George Tzotzos" <gtzotzos.me.com> wrote:

>Jason,
>
>Many thanks. We have Infiniband running on the cluster. Is there another
>diagnostic to achieve better scaling?
>
>Any suggestion will be much appreciated.
>
>Regards
>
>George
>
>
>On Sep 25, 2013, at 8:52 AM, Jason Swails <jason.swails.gmail.com> wrote:
>
>> On Tue, Sep 24, 2013 at 3:32 PM, George Tzotzos <gtzotzos.me.com> wrote:
>>
>>> Hi everybody,
>>>
>>> I'm trying to run Amber on a cluster of the following specs
>>>
>>> SGI Specs SGI ICE X
>>> OS - SUSE Linux Enterprise Server 11 SP2
>>> Kernel Version: 3.0.38-0.5
>>> 2x6-Core Intel Xeon
>>>
>>> 16 blades 12 cores each
>>>
>>> Environment
>>> export AMBERHOME=/bio/georgios/MD/amber12
>>> export
>>>
>>>LD_LIBRARY_PATH=/opt/rpm_share/lib/lib64:/bio/george/amber12/lib:/bio/ge
>>>orge/MD/amber12/AmberTools/lib
>>>
>>> Command line
>>> mpirun -np 48 pmemd.MPI -O -i prod.in -o prod_12ns.out -p
>>> 2erb_bis_solv.prmtop -c prod_10ns.rst -r prod_12ns.rst -x
>>>prod_12ns.mdcrd
>>>
>>> Question
>>>
>>> No advantage in increasing the number of nodes beyond -np 24. The
>>> performance is reduced the more cores engaged. In fact it is similar or
>>> worse to that on a OSX 2 x 3.06 GHz 6-Core Intel Xeon
>>>
>>> I'd be very grateful for any suggestions on what may be wrong
>>>
>>
>> Your interconnect between nodes may be too slow. Also, the more cores
>>you
>> have on a single node, the more bandwidth you need between nodes to
>>avoid a
>> slow-down (this is why some supercomputers give faster timings for Amber
>> when you do not utilize the whole node). This does not paint the whole
>> picture (the topology of the inter-node connections also matters to some
>> extent), but it's probably the most important part.
>>
>> You really need Infiniband (QDR is typical, I think) to see good scaling
>> across nodes with Amber.
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
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>
>
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Received on Wed Sep 25 2013 - 09:00:03 PDT
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