[gmx-developers] help needed: gmx_hbond cleanup

[David van der Spoel]

On 2012-06-19 11:57, Erik Marklund wrote:
> Hi,
>
> I agree. A more thorough cleanup of the code, which is a very good idea,
> would take (me)longer than a week or so. That said, I'm going through
> the code now to figure out the source of an error so I guess I could
> clean up the code in the meantime. But as I said, it may take longer
> than a week so that means that it will not go into 4.6 then.
I just discussed this with Berk. It would be great if bugs are fixed, 
but to do more than that we probably want to re-build it based on 
Teemu's framework.
>
> Best,
>
> Erik
>
> 19 jun 2012 kl. 08.53 skrev Berk Hess:
>
>> Hi,
>>
>> g_hbond is a critical tool for Gromacs. As for any tool, all options
>> should give correct output or be removed. I heard from Gerrit that
>> people get different results with different compilations.
>> Coding wise we should try to avoid different code paths and lots of
>> defines in the code. Ideally the OpenMP and non OpenMP versions should
>> use the same code path and the same functions.
>>
>> Mainly the code complexity should be significantly reduced. We would
>> rather have basic functionality that works reliably than lots of
>> functionality with unreliable compilation/output.
>>
>> Cheers,
>>
>> Berk
>>
>> ----- Reply message -----
>> From: "Erik Marklund" <erikm at xray.bmc.uu.se <mailto:erikm at xray.bmc.uu.se>>
>> To: "Discussion list for GROMACS development"
>> <gmx-developers at gromacs.org <mailto:gmx-developers at gromacs.org>>
>> Subject: [gmx-developers] help needed: gmx_hbond cleanup
>> Date: Thu, Jun 14, 2012 15:39
>>
>>
>> I might be able to do that. I did the OpenMP parallelization and are
>> going through the code now anyway. I'll just have to think hard about
>> actually having the time to do this within a week.
>>
>> What is the current restrictions/framework/wrappers/macros for OpenMP
>> in gromacs? Essentially: what do I need to know to adhere to our
>> coding standards in this case?
>>
>> Erik
>>
>> 14 jun 2012 kl. 15.30 skrev Szilárd Páll:
>>
>>> Hi,
>>>
>>> Although it's a little late, we've just realized that it would be
>>> beneficial to have gmx_hbond cleaned up a bit and fixed to adhere to
>>> the new OpenMP setup. Would there be anyone willing to pitch in with
>>> this say within a week?
>>>
>>> I know we don' twant to accept new features/"features", but this is an
>>> essential tool which people do. Moreover, does have OpenMP
>>> parallelization, so it only needs cleanup and a bit of adjustments. So
>>> we thought with Berk that this can go into 4.6 without interfering
>>> with anything if it gets done in time.
>>>
>>> Contact me or Berk if you would like to help!
>>>
>>> Cheers,
>>> --
>>> Szilárd
>>> --
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>>
>> -----------------------------------------------
>> Erik Marklund, PhD
>> Dept. of Cell and Molecular Biology, Uppsala University.
>> Husargatan 3, Box 596, 75124 Uppsala, Sweden
>> phone: +46 18 471 6688 fax: +46 18 511 755
>> erikm at xray.bmc.uu.se <mailto:erikm at xray.bmc.uu.se>
>> http://www2.icm.uu.se/molbio/elflab/index.html
>>
>> --
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>
> -----------------------------------------------
> Erik Marklund, PhD
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: +46 18 471 6688 fax: +46 18 511 755
> erikm at xray.bmc.uu.se <mailto:erikm at xray.bmc.uu.se>
> http://www2.icm.uu.se/molbio/elflab/index.html
>
>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se