[gmx-developers] Modification of g_mdmat tool and compiling

Joshua Adelman jadelman at berkeley.edu
Fri Jan 16 20:41:50 CET 2009

Thank you all for your suggestions. I had inserted the corresponding  
gmx_mdmat2 and g_mdmat2 into the Makefile.am in src/tools As Mark  
suggested, I then went up to the top GROMACS directory and tried to run
On Jan 16, 2009, at 5:07 AM, Erik Lindahl wrote:

> Hi,
> On Jan 16, 2009, at 1:03 PM, Mark Abraham wrote:
>> Joshua Adelman wrote:
>>> I'm attempting to write a modified version of g_mdmat to do some  
>>> custom analysis of a simulation trajectory. Since what I'm trying  
>>> to do requires only slight modification of the code, I thought the  
>>> easiest thing to do is just copy g_mdmat.c and gmx_mdmat.c to  
>>> something like g_mdmat2.c and gmx_mdmat2.c and compile them in the  
>>> src/tools directory (as opposed to writing something from scratch  
>>> given the template in shared/template). I'm just having a little  
>>> bit of difficulty getting the modified versions compiled and was  
>>> hoping someone could point me in the right direction. Since the  
>>> Makefile and Makefile.in are auto-generated, I believe I shouldn't  
>>> be modifying them directly. I tried inserting duplicating the  
>>> enteries in Makefile.am that reference the g_mdmat files, and then  
>>> rerun ./configure, but I'm not getting any instructions for the  
>>> 'g_mdmat2' tool in Makefile and Makefile.in.
>> A more elegant solution than the one DvdS suggested, is to adapt  
>> Makefile.am suitably (wherever g_mdmat(.*) appears, modify suitably  
>> to add your version), return to the top-level GROMACS directory and  
>> invoke automake to create the Makefile.in files. Then invoke  
>> configure to create the Makefile files. Then things should work OK,  
>> and the GROMACS build process will build and install your utility.
>> You may run into versioning issues with the autotools. Invoking  
>> autom4te or autoconf in the top-level GROMACS directory may help  
>> resolve these. Test on a non-precious GROMACS build directory first!
>> If you're working in the CVS version, there's a "bootstrap" script  
>> that takes care of the invocation order for you. Grabbing a copy of  
>> it to apply to your modified 4.0.2 distribution may streamline  
>> things for you.
> In principle the autotools should actually detect and rebuild the  
> files automatically for you when necessary, so ideally a "make" is  
> enough even after modifying Makefile.am.
> One problem with this is that the build tools might end up re- 
> running the configure and automake commands separately for every  
> single subdirectory in your tree, and then it's much cheaper to do  
> as Mark says - go to the top directory and issue the commands there  
> manually.
> I've modified and included some libtool scripts in the release-4-0- 
> patches CVS branch to reduce the autotools versioning issues for  
> developers - in particular it should no longer matter whether you  
> have libtool-1.x or 2.x installed. This will be included in 4.0.3  
> that we in best case might get out today or tomorrow!
> Cheers,
> Erik
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Joshua L. Adelman
Biophysics Graduate Group              Lab: 510.643.2159
218 Wellman Hall                                Fax: 510.642.7428
University of California, Berkeley     http://nature.berkeley.edu/~jadelman
Berkeley, CA 94720 USA                   jadelman at berkeley.edu

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