[gmx-users] Re: intel or gcc for opteron

[David van der Spoel]

Myunggi Yi wrote:
> Thank you for the answer.
> 
> I compiled gmx with gcc and gnu onpempi.
> 
> I have seen very good performance with 16 cpus (about 12,000 atoms).
> 
> +++++++++++++++++++++++++++++++++++
>                (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
> Performance:     50.828     19.920     14.648      1.638
> Total Scaling: 95% of max performance
> +++++++++++++++++++++++++++++++++++
> 
> Now I just submit a job with 32 cpus (about 48,000 atoms).
> It looks very very slow.
> 
> 
> Would you recommend the optimal numer of cpus?
No. You have to test for yourself (as you are doing right now).
It is very dependent on simulation size, network etc.
> 
> 
> 
> 
> On Nov 24, 2007 10:53 AM, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>> Myunggi Yi wrote:
>>> Sorry. Here is more information.
>>>
>>>
>>> GNU C/C++     3.4.6
>>> Intel C/C++   10.0.026
>>> and
>>> OpenMPI GNU   1.2.4
>>> OpenMPI Intel         1.2.4
>> Everything will probably be easier with the gcc compiler, and the
>> performance difference is negligible for gromacs.
>>
>>>
>>>
>>> On Nov 24, 2007 10:31 AM, Myunggi Yi <myunggi at gmail.com> wrote:
>>>> Dear gromacs users,
>>>>
>>>> I'm a beginner.
>>>> I'm trying to compile gromacs 3.3.1 or 3.3.2 on the following linux
>>>> cluster (centOS).
>>>> Dual, Dual-Core 2220 2.8 GHz Opterons, 2 GB RAM per core, 64-bit.
>>>> I will use 16 to 32 (64) cpus for the parallel simulations.
>>>>
>>>> I tested mpich2, but there is a problem with infiniband communications.
>>>>
>>>> I have intel and GNU compilers and openMPI.
>>>>
>>>> Which option will give me the best performance?
>>>>
>>>> Have a nice weekend.
>>>>
>>>>
>>>> --
>>>> Best wishes,
>>>>
>>>> MYUNGGI YI
>>>> ==================================
>>>> KLB 419
>>>> Institute of Molecular Biophysics
>>>> Florida State University
>>>> Tallahassee, FL 32306
>>>>
>>>> Office: (850) 645-1334
>>>> http://www.scs.fsu.edu/~myunggi
>>>>
>>>
>>>
>>
>> --
>> David.
>> ________________________________________________________________________
>> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>> Dept. of Cell and Molecular Biology, Uppsala University.
>> Husargatan 3, Box 596,          75124 Uppsala, Sweden
>> phone:  46 18 471 4205          fax: 46 18 511 755
>> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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> 
> 
> 


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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