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

Erik Marklund erikm at xray.bmc.uu.se
Tue Jun 5 14:33:07 CEST 2012 

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

>  
> 
> 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>>
> 
> 
> 
> 
>    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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-----------------------------------------------
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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