[gmx-users] Writing and compiling new analyses for gromacs
Shay Teaching
shay.teaching at gmail.com
Tue Jun 5 14:22:09 CEST 2012
Thanks I'll try that
2012/6/5 Peter C. Lai <pcl at uab.edu>
> 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
> Programmer/Analyst | KAUL 752A
> Genetics, Div. of Research | 705 South 20th Street
> pcl at uab.edu | Birmingham AL 35294-4461
> (205) 690-0808 |
> ==================================================================
>
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