[gmx-developers] gsl

David van der Spoel spoel at xray.bmc.uu.se
Tue Mar 20 19:12:25 CET 2007

Jason de Joannis wrote:
> Quoting David van der Spoel <spoel at xray.bmc.uu.se>:
>> Jason de Joannis wrote:
>>> Are you sure? My gsl (v1.9) is located in /usr/local/lib. I ran 
>>> configure with --with-gsl. The output of make does not include the 
>>> -lgsl or -lgslcblas flags and it gives an error:
>>>  undefined reference to `gsl_rng_env_setup'
>>> I am not so knowledgable about inner workings of the auto-tools, so I 
>>> appreciate the help. I did not find gmx_kinetics in my gromacs 3.3.1. 
>>> There is a reference to this function in one of the header files though.
>>> Perhaps I have to add certain environment variables to the configure 
>>> arguments...
>>> /Jason
>> Hm, you could be right. In that case you should try the CVS 3.3 
>> version instead.
> I just tried it and the same error occurs. Although now I do see a 
> gmx_kinetics file, which produces the following:
> -------------------------------------------------------
> Program GROMACS, VERSION 3.3.99_development_20070215
> Source code file: gmx_kinetics.c, line: 889
> Fatal error:
> This program should be compiled with the GNU scientific library. Please 
> install the library and reinstall GROMACS.
> -------------------------------------------------------
> My GSL does work out of a simple 'hello world' program when compiled 
> with -lgsl -lgslcblas and either -static or LD_LIBRARY_PATH=/usr/local/lib.
> /Jason
How about the include files?
What does configure say? It should let you know whether or not gsl was 

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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