[gmx-users] hardware setup for gmx

[Szilárd Páll]

Dear Michael,

On Wed, Jul 30, 2014 at 1:49 PM, Michael Brunsteiner <mbx0009 at yahoo.com> wrote:
>
> Dear Szilard,
>
> sorry for bothering you again ... regarding performance tuning by adjusting
> the VdW and Coulomb cut-offs you wrote:

No worries, I am happy to answer on the list whenever I can!

> The PP-PME load balancing - which acts as CPU-GPU load balancing - is
> meant to take care of that by  scaling only rcoulomb to adjust the
> real vs reciprocal space load while keeping rvdw fixed. This is not
> perfect, though as short- and long-range interaction cost scales quite
> differently and it does not always work perfectly either, bu
>
> hut here:
>
> http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x
>
> it says:
>
> "Made g_tune_pme honour the requirement that the van der Waals radius must
> equal the Coulomb radius with Verlet cut-off scheme #1460"

Unfortunately, that's a very crude and developer-centric commit
message that IMO should not end up straight in the release notes, but
let's not get off-topic.

> does this mean that what you wrote does not apply to the Verlet cut-off
> scheme?

No, the difference is that the user can't set rvdw != rcoulomb in the
mdp file, but mdrun itself can increase rcoulomb to shift work from
long- to short-range calculation. So the above commit message refers
to the mdp/tpr generated by g_tune_pme having to respect rvdw ==
rcoulomb.

Cheers,
--
Szilárd

> cheers
> mic
>
>
> ===============================
>
>
> Why be happy when you could be normal?
>
> ________________________________
> From: Szilárd Páll <pall.szilard at gmail.com>
> To: Michael Brunsteiner <mbx0009 at yahoo.com>
> Sent: Thursday, July 17, 2014 2:00 AM
> Subject: Re: [gmx-users] hardware setup for gmx
>
> Dear Michael,
>
> I'd appreciate if you kept the further discussion on the gmx-users list.
>
> On Thu, Jul 10, 2014 at 10:20 AM, Michael Brunsteiner <mbx0009 at yahoo.com>
> wrote:
>> Dear Szilard,
>>
>> Thank you for the two replies to my questions in gmx-users. I was
>> glad to learn that free energy calculations + GPU now work! (are you aware
>> of any tests/benchmarkls there?)
>
> What kind of tests are you referring to? "make check" does some
> regressiontests, benchmarks we don't have any. The performance will
> depend greatly on the kind of system used; the actual free energy
> kernels are still running on the CPU (and aren't super-optimized
> either), so the amount of GPU speedup will depend on the balance of
> normal vs perturbed non-bondeds.
>
>>
>> about the harware ... i figured as much .. what i keep worrying about ist
>> the
>> CPU-GPU balance ... this can only be adjusted through the cut-off length.
>
> Or by algorithmic changes and optimizations. :)
>
>> With PME/Ewald one can easily optimize this for electrostatics within
>> certain limits ... but the VdW cut-off is usually parameter that comes
>> with the force field and tinkering with this cutoff one might see
>> unexpeted
>> consequences, but then this is perhaps a minor issue ...
>
> The PP-PME load balancing - which acts as CPU-GPU load balancing - is
> meant to take care of that by  scaling only rcoulomb to adjust the
> real vs reciprocal space load while keeping rvdw fixed. This is not
> perfect, though as short- and long-range interaction cost scales quite
> differently and it does not always work perfectly either, bu
>
> Cheers,
> --
> Szilárd
>
>
>> thanks again & best regards
>> michael
>>
>>
>>
>>
>> ===============================
>> Why be happy when you could be normal?
>>
>>
>> On Tuesday, July 8, 2014 7:47 PM, Szilárd Páll <pall.szilard at gmail.com>
>> wrote:
>>
>>
>>
>> Hi,
>>
>> Please have a look at the gmx-users history, there has been recent
>> discussions about this topic.
>>
>> Brief answer:
>> * If you only/mostly run GROMACS using GPU, Intel CPUs with many fast
>> cores
>> combined with high-end Geforce GTX cards will give the best performance/$;
>> e.g. currently i7 4930K + GTX 770,780 is what I would recommend
>> * The ideal hardware balance depends on the kind of simulations you plan
>> to
>> do (e.g. system size, cut-off, #of concurrent simulations, etc.).
>>
>> Note however, that you could get much better perf/buck on e.g. AMD CPUs
>> with
>> middle-range GTX cards e.g. if you have many small simulations to run
>> concurrently (and especially if you want rack-mountable OEM servers).
>>
>> Cheers,
>>
>>
>> On Thu, Jul 3, 2014 at 3:46 PM, Michael Brunsteiner <mbx0009 at yahoo.com>
>> wrote:
>>
>>
>>
>> Hi,
>>
>> can anybody recommend a hardware setup to perform MD runs (with PME) that
>> has a good
>> price-performance ratio? ... in particular I'd be interested in learning
>> which combinations
>> of CPU and GPU can be expected to provide a good FLOPS-per-dollar ratio
>> with
>> the more
>> recent gmx versions (4.6 or 5.0)?
>>
>> thanks in advance for any recommendations!
>>
>> Michael
>>
>>
>>
>> ps: if your opinion is highly subjective and/or perhaps prone to make
>> particular hardware vendors
>> really sad, you might want to send your answer only to my email rather
>> than
>> to all gmx-users)
>>
>>
>>
>> ===============================
>> Why be happy when you could be normal?
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send
>> a
>> mail to gmx-users-request at gromacs.org.
>>
>>
>>
>>
>> --
>> Páll Szilárd
>>
>>
>
>