[gmx-users] Details of 5.0 benchmark report?

[Adam Huffman]

Hi Szilárd,

Yes, it's certainly not worth a large effort to try and recover the information.

Thanks for the link, which should be very useful.

The next time you're looking at something like this, it might be worth
trying to capture what might be useful for others to run tests
themselves.

Thanks again,
Adam


On Tue, Apr 12, 2016 at 5:36 PM, Szilárd Páll <pall.szilard at gmail.com> wrote:
> Adam,
>
> The job scripts used in those benchmarks are all specific to the
> machines, and while admittedly the launch configuration information
> could be useful to have next to each data point, I'm afraid we don't
> have such data readily extracted from the run logs, I believe. I did
> not compile the document myself, but unless such data has been parsed
> and it's just not presented, it would be a quite large effort to go
> back and extract such information for quite little benefit (as the
> exact ranks/thread configurations will change with GROMACS versions,
> compilers, libraries, machine load, etc.)
>
> I recommend you to have a look at recent benchmark papers that contain
> detailed information on what to tune and how to run parallel jobs,
> e.g.
> http://onlinelibrary.wiley.com/doi/10.1002/jcc.24030/full
> Scaling of the GROMACS 4.6 molecular dynamics code on SuperMUC.
>
> Cheers,
> --
> Szilárd
>
>
> On Mon, Apr 11, 2016 at 2:00 PM, Adam Huffman <adam.huffman at gmail.com> wrote:
>> Hello
>>
>> Ideal would be to have the command-lines that were used, for those of
>> us that aren't GROMACS experts.
>>
>> Cheers,
>> Adam
>>
>> On Tue, Mar 8, 2016 at 5:08 PM, Szilárd Páll <pall.szilard at gmail.com> wrote:
>>> Hi,
>>>
>>> What details are you interested in? IIRC the inputs are clearly specified
>>> (although perhaps not provided there).
>>>
>>> --
>>> Szilárd
>>>
>>> On Fri, Mar 4, 2016 at 5:15 PM, Adam Huffman <adam.huffman at gmail.com> wrote:
>>>
>>>> Hello
>>>>
>>>> Are details of the running of the benchmarks reported for version 5.0
>>>> available anywhere?
>>>>
>>>> I'm referring to the report published at:
>>>>
>>>> http://www.gromacs.org/@api/deki/files/240/=gromacs-5.0-benchmarks.pdf
>>>>
>>>> I would like to be able to run these myself, on three different systems.
>>>>
>>>>
>>>> Cheers,
>>>> Adam
>>>> --
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