Re: Abe versus Lincoln

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Thu Apr 07 2011 - 13:57:41 CDT

Hi Axel,

Yes, I am aware of this retirement. This is part of the reason why I am
posting this. I need to evaluate whether it is worth moving my remaining
SUs to Lincoln or another CPU only cluster like ranger. Also, for the
future, is it better to apply for computational time on a heterogenous
(GPU+CPU) cluster like the new one which will be available at NCSA
starting in July (Forge) or on a CPU-only cluster like ranger or kraken?

Thanks,

      Gianluca

On Thu, 7 Apr 2011, Axel Kohlmeyer wrote:

> On Thu, Apr 7, 2011 at 2:40 PM, johan strumpfer <johanstr_at_ks.uiuc.edu> wrote:
>> Hi Gianluca,
>>
>> I've been running on both. Some benchmarks (system size ~120000 atoms):
>> Using lincoln 32 CPU's (i.e. 4 nodes) I get ~0.034 s/step and using
>> 160 CPU's on Abe I get ~0.017 s/step.
>>
>> Note that using CUDA NAMD, the scaling is good up to a point and then
>> drops dramatically. E.g. running on 5 nodes on Lincoln also gets me
>> approximate 0.034 s/step. So you'll be able to run faster on Abe, but
>> it will use up many more SU's.
>
> FYI:
>
> http://www.ncsa.illinois.edu/UserInfo/Resources/Hardware/Intel64Cluster/Retirement.html
>
> axel.
>
>
>>
>> Hope this helps,
>> Johan
>>
>> On Thu, Apr 7, 2011 at 2:22 PM, Gianluca Interlandi
>> <gianluca_at_u.washington.edu> wrote:
>>> Hi!
>>>
>>> Are there any benchmarks available which compare the performance of NAMD on
>>> Lincoln (CUDA heterogenous cluster) with its performance on a traditional
>>> CPU only cluster like Abe?
>>>
>>> Thanks!
>>>
>>>     Gianluca
>>>
>>> -----------------------------------------------------
>>> Gianluca Interlandi, PhD gianluca_at_u.washington.edu
>>>                    +1 (206) 685 4435
>>>                    http://artemide.bioeng.washington.edu/
>>>
>>> Postdoc at the Department of Bioengineering
>>> at the University of Washington, Seattle WA U.S.A.
>>> -----------------------------------------------------
>>>
>>>
>>
>>
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com  http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>

-----------------------------------------------------
Gianluca Interlandi, PhD gianluca_at_u.washington.edu
                     +1 (206) 685 4435
                     http://artemide.bioeng.washington.edu/

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------

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