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

[Peter C. Lai]

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.

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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Peter C. Lai			| University of Alabama-Birmingham
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