Re: [AMBER] Running Amber on a SGI cluster

From: George Tzotzos <gtzotzos.me.com>
Date: Wed, 25 Sep 2013 13:20:25 -0300

Hi Ross,

Using a 140 residue protein in thermostat (~ 4,000 HOHs).

Cheers

George

On Sep 25, 2013, at 12:53 PM, Ross Walker <ross.rosswalker.co.uk> wrote:

> 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
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber


_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 25 2013 - 09:30:03 PDT
Custom Search