[gmx-developers] Modification of g_mdmat tool and compiling
lindahl at cbr.su.se
Fri Jan 16 14:07:28 CET 2009
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!
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