[gmx-users] compilation instructions, the gromacs wiki, documentation, and test suites

[Justin A. Lemkul]

chris.neale at utoronto.ca wrote:
> Dear Roland:
> 
> I am not sure what my barrier is electronically, only that there is a 
> barrier. The web site has changed since my last attempt to make 
> modifications, but I still can not add to the site as I once could when 
> it was simply a wiki. Currently, I have a tab labeled "[MISSING: 
> skin.common.this-page]" and if I click on it there is an edit page 
> option but it is commented out, even when I am logged in.
> 

To edit the wiki, you have to be added as a contributor by Rossen after you've 
created your account.  This process started when the Gromacs site transitioned over.

> My suggestion for the documentation and the test suite is that these 
> aspects of gromacs become part of the "vision" in the way that speed is 
> prioritized. A while back, myself and a colleague had a gromacs 
> pull-code extension turned down as a contribution because it would 
> negatively impact the overall performance of gromacs in the general 
> case. After I mulled that decision over for a while, I realized that it 
> was actually a very good and very important decision made by the 
> developers to keep gromacs as fast as possible over the long term even 
> if that meant losing out on some bells and whistles in the short term. 
> So I would suggest that this philosophy might be usefully applied to 
> code development and that modification acceptance would be dependent on 
> the provision of both documentation and a test suite. Not glamorous, I 
> know, but it's my two-cents and it's why I tend to stay more than a year 
> behind the release cycle with my important runs.
> 

I tend to be the same way.  I will usually play with new features, but I haven't 
done any production runs with any version post-4.0.7 (mostly due to the fact 
that I prefer continuity).  I agree with this assessment.  The need for a test 
suite that actually works has been debated for a long time, usually amounting to 
incremental progress at best, but it seems that other MD packages provide 
extensive tests, though Gromacs does not.  I know many are willing to help 
develop it, and I guess we're waiting on a way to effectively communicate, set 
priorities and to-do lists, and put it all in motion.  Is the Redmine 
infrastructure on the way?  Do we have an estimate on when that might be 
available?  I think it would really help.

-Justin

> Thanks again,
> Chris.
> 
> -- original message --
> 
> sorry I didn't pay attention (was in a hurry). I know that you have helped
> with the documentation and wouldn't have suggested to you to put it on the
> wiki if I recognized it was you. I thought it was a new user. And I didn't
> want to criticize but only point out (to the assumed new user) that the 
> wiki
> can be improved by everyone.
> 
> Do you have suggestion of how to improve the documentation or the test
> suite? What is the barrier to the wiki?
> I have mentioned that before (on the dev-list) but I think a monthly phone
> conference could help to coordinate those kind of issues.
> 
> Roland
> 
> On Mon, Dec 20, 2010 at 10:07 PM, <chris.neale at utoronto.ca> wrote:
> 
>> <<I have changed the topic to continue a conversation that started on
>> "cmake --> relocation R_X86_64_32S against `a local symbol' can not be 
>> used
>> when making a shared object;>>
>>
>> Dear Roland:
>>
>> It is not my intention to be confrontational, your assistance was very
>> useful, I appreciate it very much, and I realize that it's not your 
>> job to
>> comment everything (or even answer my questions on this mailing list).
>> Further, I have actually contributed significantly to the gromacs wiki in
>> the past, but it's not a wiki anymore and the barrier to posting is 
>> enough
>> that I'm not the only person who has given up on it.
>>
>> Second, I would like to mention that as a user I am extremely hesitant to
>> upgrade my gromacs version due to the lack of commenting and lack of a 
>> good
>> test suite. Anybody who used the free energy code with TIP4P in 
>> 2008/2009 or
>> used the pull code in the early versions of gromacs 4 will probably agree
>> with me that testing and documentation are at least as important as new
>> code.
>>
>> I'm not asking anybody else to add documentation or test suites. I'm 
>> simply
>> pointing out that gromacs is falling behind in these areas and it is not
>> necessarily a good thing. I think that there is a utility in simply 
>> noting
>> this.
>>
>> Sincerely,
>> Chris.
>>
>>
> 
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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