[gmx-users] Workstation choice

Benson Muite benson.muite at ut.ee
Fri Sep 7 16:15:17 CEST 2018

Check if the routines you will use have been ported to use GPUs. Time 
and profile a typical run you will perform on your current hardware to 
determine the bottlenecks, and then choose hardware that will perform 
best on these bottlenecks and is within your budget.

Note that benchmarking can be quite time consuming - even without 
performance optimization. If you have an idea of the simulations you 
will run and have profiled your code, and will primarily do these 
simulations, then it is probably easiest to go to a computer store where 
they have several available workstations, run your benchmark yourself 
and choose the best value system.

On 09/06/2018 08:09 PM, Olga Selyutina wrote:
>   Thank you,
> to use these tests isn’t a problem, but available workstation are too old,
> so test results won’t be helpful in choosing actual components. I have an
> access to high-performance cluster, but it also couldn’t be the basis
> because of its high cost. If it is hard to give the certain recommendation,
> I would to know at least how do performance correlate with the number of
> cores/threads and core frequency? What is more important the core frequency
> or number of cores? What is preferable, Intel or AMD? How should be
> correlated GPU and CPU performance?
> In the previous letters in mail-list I found recommendations on purchase of
> Threadripper 1950X+GeForce GTX-1080Ti, I think that more cheap and similar
> effective choice is TR 1950X+GeForce GTX-*1080*. Will there be significant
> differences with 1)TR 19*20*X+GeForce GTX-1080 2) Intel 7900x+GeForce
> GTX-1080?
> 2018-09-05 20:53 GMT+07:00 Benson Muite <benson.muite at ut.ee>:
>> Hi Olga,
>> The authors of:
>> https://github.com/bio-phys/MDBenchmark/tree/version-1.3.2
>> https://zenodo.org/record/1318123
>> May be helpful. If your data is not confidential, you may consider running
>> Gromacs remotely on a cloud high performance computing resource, or
>> benchmarking remotely and then purchasing a suitable configuration.
>> Some other information:
>> http://manual.gromacs.org/documentation/current/user-guide/
>> mdrun-performance.html#
>> http://www.gromacs.org/GPU_acceleration
>> https://extras.csc.fi/chem/courses/gmx2007/Erik_Talks/buildi
>> ng_clusters.pdf
>> http://www.gromacs.org/Documentation/Performance_checklist
>> On 09/05/2018 12:02 PM, Olga Selyutina wrote:
>>>    Hello,
>>> I need help in choice of the workstation for MD simulations using GROMACS.
>>> It is supposed to study systems consisting from 30-50k atoms, in
>>> particular, lipid bilayer models. Since the last generation of Intel and
>>> Ryzen CPU has made a big leap in performance, available workstation can’t
>>> be taken as a basis. Please, help to choose components of the workstation,
>>> particularly, GPU and CPU with total cost about $2000. What is better, to
>>> buy two GPUs(sli) or one GPU but more effective?
>> --
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