[gmx-developers] Modification of g_mdmat tool and compiling

[Joshua Adelman]

Please ignore that last email. I hit send accidently on an old draft.

Thank you to David, Erik and Mark for their suggestions. I was able to  
get things working after downloading the bootstrap script from the  
current cvs version.

Josh

On Jan 16, 2009, at 11:41 AM, Joshua Adelman wrote:

> 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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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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