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

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jun 5 03:13:29 CEST 2012

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).


> 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>>
>>>>     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>.
>>>   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://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>> ==============================**==========
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