Re: Abe versus Lincoln

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Thu Apr 07 2011 - 15:40:11 CDT

Hi Axel,

Thanks, it makes it more clear. These are two typical system sizes I
normally work with on Abe:

Size [atoms] Time [hours/ns] # CPUs

127,000 9.7 32 CPUs
60,000 4.7 32 CPUs

Do you think I would get a similar or better performance on Lincoln? How
fast would these systems run on 2 or 4 Lincoln nodes?

Gianluca

On Thu, 7 Apr 2011, Axel Kohlmeyer wrote:

> On Thu, Apr 7, 2011 at 2:57 PM, Gianluca Interlandi
> <gianluca_at_u.washington.edu> wrote:
>> 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?
>
> that depends. GPU support will get better over time. but it is not predictable
> how much and how soon. in part, it also depends on the hardware (GPU and host).
> the biggest weakness of lincoln are the host nodes, TACC's longhorn has
> essentially the same GPUs but they give better performance.
>
> in general, the current status is the following. if you want to get the most
> out of your SUs (when using NAMD), then you want to run on GPUs, but
> only a very small number of nodes and share the GPU between two CPU tasks.
> so you get to run 3-4x faster _per SU_, but it will be overall slower.
>
> if you want to run faster, you are better off on kraken, lonestar and alike.
> which one exactly would be best depends on the typical size of the job
> and how far altogether you want to scale.
>
> does that make sense?
>
> axel.
>
>> 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.
>> -----------------------------------------------------
>
>
>
> --
> 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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