[gmx-users] Writing and compiling new analyses for gromacs

Shay Teaching shay.teaching at gmail.com
Tue Jun 5 14:23:17 CEST 2012 

2012/6/5 Mark Abraham <Mark.Abraham at anu.edu.au>

> On 5/06/2012 9:11 AM, Peter C. Lai wrote:
>
>> The quick and dirty way is to post-patch Makefile in src/tools.
>>
>> I think patching the appropriate Makefile.in is sufficient for configure
>> to
>> pick up and automake into Makefile if all you need to do is append a make
>> target.
>>
>> As to your previous question, on our cluster, I use Intel ICC 11.1.056
>>
>> both openmpi and fftw3 are also built with icc but root builds those and
>> exposes their libs/headers through Modules, so I just module load them
>> and specify the appropriate CPPFLAGS, LDFLAGS, and MPICC to configure
>> (I'm still on 4.5.4 here).
>>
>> Btw: If you are patching 4.6 you should ask for someone else on here to
>> tell
>> you how to add it to the CMake config, since that's going to be the
>> default
>> build framework going forward.
>>
>
> That's easy with CMake - just add your tool to the list in
> src/tools/CMakeLists.txt and re-make (which I expect will trigger a
> re-cmake automatically).
>
How about in gromacs 4.0.7? Is it as Peter says?Just add it manually to the
Makefile in src/tools, or is there an automatic way to generate this make
file?


>
> Mark
>
>
>
>> On 2012-06-05 01:43:09AM +0300, Shay Teaching wrote:
>>
>>> One more question: How do I get my new g_whatever analysis to be included
>>> in the compilation?
>>> Simply placing my file in src/tools won't work of course. How to I place
>>> it
>>> correctly in the build?
>>> Thanks,
>>> -Shay
>>>
>>> 2012/6/5 Justin A. Lemkul<jalemkul at vt.edu>
>>>
>>>
>>>> On 6/4/12 5:16 PM, Shay Teaching wrote:
>>>>
>>>>
>>>>> 2012/6/4 Justin A. Lemkul<jalemkul at vt.edu<mailto:**jalemkul at vt.edu<jalemkul at vt.edu>
>>>>> >>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>    On 6/4/12 2:59 PM, Shay Teaching wrote:
>>>>>
>>>>>        Dear Gromacs users,
>>>>>
>>>>>        I want to write new analyses for gromacs and compile it (so I'll
>>>>> have
>>>>>        g_whatever) as part of the gromacs package.
>>>>>        Per the instructions I found on gromacs website, I installed
>>>>> kdevelop
>>>>>        and opened
>>>>>        the gromacs as a project using kdevelop. However I have two
>>>>> questions:
>>>>>        1) When I try to compile gromacs source, through kdevelop, I
>>>>> get a
>>>>>        "permission
>>>>>        denied" error. I think it is because gromacs installation
>>>>> requires
>>>>> root
>>>>>        privileges. Any suggestions on how to bypass that, so I won't
>>>>> have
>>>>> to use
>>>>>        kdevelop as root (which is a *really* bad idea)? (e.g.,
>>>>> installing
>>>>> gromacs
>>>>>        without root?)
>>>>>
>>>>>
>>>>>    Assuming you're trying to compile template.c in some system-level
>>>>> directory,
>>>>>    you're certain to run into that problem.  Compile in a different
>>>>> location.
>>>>>
>>>>> Actually, I tried installing Gromacs to my home directory, not system
>>>>> directory.
>>>>> You're saying that I'm not supposed to encounter this error?
>>>>>
>>>>>
>>>>>  You shouldn't have permission errors in your home directory.  I've
>>>> never
>>>> used KDevelop; what happens if you try to compile from a normal command
>>>> line?
>>>>
>>>>
>>>>
>>>>         2) Are there any guidelines for writing new g_whatever analyses?
>>>>> Or any
>>>>>        general
>>>>>        suggestions on how to approach it?
>>>>>
>>>>>
>>>>>    Write good code? ;)  I don't really know what you're asking here,
>>>>> but
>>>>> if you
>>>>>    want pointers for writing code, you'll need to at least state what
>>>>> you're doing.
>>>>>
>>>>> Write good code of course :-)
>>>>> What I mean is: Is there a proper list of gromacs functions used for
>>>>> 'common'
>>>>> operations? (such as, reading from trajectory, reading index file,
>>>>> documentation
>>>>> of types and data structures for dealing with gromacs trajectory: atom,
>>>>> molecule, their input and output, etc.)
>>>>> Of course I'll open existing analyses, and see how its done there
>>>>> (g_mindist,
>>>>> g_rms..) but it would be useful to have like... a list of methods so I
>>>>> won't
>>>>> waste time on stuff that's already been dealt with.
>>>>>
>>>>>
>>>>>  The only related information is probably on the website at
>>>> http://www.gromacs.org/****Developer_Zone/Programming_****Guide<http://www.gromacs.org/**Developer_Zone/Programming_**Guide>
>>>> <http://www.gromacs.org/**Developer_Zone/Programming_**Guide<http://www.gromacs.org/Developer_Zone/Programming_Guide>
>>>> >.
>>>>  I doubt you'll get a how-to for coding though.  The approach of
>>>> looking at
>>>> existing files for these routines is probably as efficient as it gets.
>>>>
>>>>
>>>> -Justin
>>>>
>>>> --
>>>> ==============================****==========
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Research Scientist
>>>> Department of Biochemistry
>>>> Virginia Tech
>>>> Blacksburg, VA
>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>> http://www.bevanlab.biochem.****vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>>>> <h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>>> >
>>>>
>>>> ==============================****==========
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