[gmx-users] Gromacs Installation troubles

Mark Abraham Mark.Abraham at anu.edu.au
Tue Nov 18 03:24:28 CET 2008

Nicholas Geraedts wrote:
> I'm trying to get Gromacs installed on our systems, but I've been 
> running into one error after another. We are running CentOS5 x86-64 with 
> all the latest updates.
> I've got the following packages downloaded
> lam-7.1.4
> fftw-3.2
> gsl-1.11
> gromacs-4.0
> I installed them in the following order with the following commands:
> cd lam-7.1.4 && ./configure && make && make install
> cd ../fftw-3.2 && ./configure --enable-float && make && make install
> cd ../gsl-1.11 && ./configure && make && make install
> cd ../gromacs-4.0 && ./configure --enable-mpi && make && make install && 
> make links
> I've got two problems when I try to run an MPI-based simulation. First, 
> the system complains that libgslcblas.so.0 is missing. Searching for 
> this finds that it has been installed in /usr/local/lib. 'ldconfig -p' 
> doesn't show the library installed, and from what I understand, the 
> library should be installed in /usr/local/lib64.

Well, adjust your configuration to make it work, or follow the gsl 
advice here http://wiki.gromacs.org/index.php/quick_and_dirty_installation

> Secondly, shouldn't the configure option of '--enable-mpi' create an 
> executable named mdrun_mpi? I have used this in previous installations, 
> but it doesn't seem to have been compiled.

It should, though since I'm always applying my own --program-suffix 
flags, I haven't observed it to work. You can always re-run "make 
install" and look at the tail of the output to deduce the filenames that 
are actually being installed. In any case, for MPI, you should not 
bother doing a complete make. See 


More information about the gromacs.org_gmx-users mailing list