Re: Abe versus Lincoln

From: johan strumpfer (johanstr_at_ks.uiuc.edu)
Date: Thu Apr 07 2011 - 16:23:16 CDT

Hi Gianluca,

Using 4 Lincoln nodes with a 112580 atoms system I
get 9.3 hours/ns (stepsize 1, fullElectFrequency 1 and stepspercycle 20).

Cheers,
Johan

On Thu, Apr 7, 2011 at 4:40 PM, Gianluca Interlandi
<gianluca_at_u.washington.edu> wrote:
> 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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