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

Shay Teaching shay.teaching at gmail.com
Tue Jun 5 15:33:44 CEST 2012 

2012/6/5 Erik Marklund <erikm at xray.bmc.uu.se>

>
> 5 jun 2012 kl. 14.23 skrev Shay Teaching:
>
>
>
> 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?
>
>
> Yes, IIRC.
>
> If this is something that is useful for others, then perhaps you should
> aim at a more recent version than 4.0.7
>
> Best,
>
> Erik
>
> My research group is currently finishing up some projects that started
with 4.0.x, but I'll make sure to make it easily passable to the 4.5.x if
it seems useful.
Thanks,
-Shay

>
>
>>
>> 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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> -----------------------------------------------
> 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
> http://www2.icm.uu.se/molbio/elflab/index.html
>
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