[gmx-users] Workstation choice

[Szilárd Páll]

On Fri, Sep 7, 2018 at 4:15 PM Benson Muite <benson.muite at ut.ee> wrote:

> 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.
>

Not a bad suggestion, but these days people shop online. Even if one would
opt for a physical store, benchmarking each candidate doesn't sound
feasible (or easily done). You'd need to have multiple systems assembled,
OS and benchmarks scripts ready on a bootable drive, and measure
performance of each system before buying.


>
> 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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> >
>
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