[gmx-users] Gromacs on SGI Altix

[Mingfeng Yang]

David van der Spoel wrote:
> Florian Haberl wrote:
>
>> hi
>>
>> On Tuesday 03 January 2006 16:08, Mingfeng Yang wrote:
>>  
>>
>>> Happy new year to each gromacs user!
>>>
>>> I just finished installation of Gromacs 3.3 on our Itanium2 based SGI
>>> Altix. My configuration option is
>>>
>>> |./configure --prefix=/home/myang/usr/local/gromacs_intel --enable-mpi
>>>
>>> CC=icc F77=ifort|
>>> The intel C++ compiler 9.021 and intel fortran compiler 9.021 were 
>>> used.
>>> The OS is Red Hat Enterprise WS 3.0.
>>>
>>> The parallel efficiency is kind of disappointing. For the benchmark 
>>> case
>>> of villin, it took 97 seconds with one CPU, 55 seconds with two CPUs,
>>> and 35 seconds for 4 CPUs. From the benchmark pages of Gromacs website,
>>> I saw the parallel efficiency can go beyond 100% under 8 CPUs. Is there
>>> anything I missed? What supposed to be the best options when install
>>> gromacs on Itanium2 based machine?
>>>   
>>
>> I think that d.villin is not the right benchmark for more cpus and 
>> measering parallel speedup.
>> I would prefer here d.dppc as shown on gromacs webpage. Reason for 
>> this bad scalling is is small system size.
>>  
>>
>
> Apart from that, what interconnect are you using? And which MPI 
> library? I presume the Altix has some kind of nice interconnect, but 
> do you use it?
It's a 8 CPUs machine (I think these CPUs are on the same board). The 
mpi library is sgi-mpt. I just run the simulation by "mpirun -np 2 
mdrun". Did I miss anything here?
>
>>  
>>
>>> Thank you for any input!
>>>
>>> Mingfeng
>>>
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>>>   
>>
>> greetings,
>>
>> florian
>>
>>  
>>
>
>