[gmx-users] Details of 5.0 benchmark report?

[Szilárd Páll]

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
>>> --
>>> 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.
>>>
>> --
>> 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.
> --
> 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.