[gmx-users] gromacs installation and test set

Gu, Xiang xgu at cc.hut.fi
Thu Jun 3 14:31:51 CEST 2010

Hi, all,

I'm trying to install a parallel version of gromacs-4.0.7 under my own 
account (on our campus supercomputing center, configured with 
--enable-threads, --enable-float, --enable-mpi, and prefixed with 
specified directory), because I need to develop some new extensions for 
our research and will have to do code modification and debugging from 
time to time.

Now the installation went through (I felt there was no severe error 
information shown). But when I started running it parallely, the mdrun 
program seemed to crash at the first MPI command it encountered (the 
MPI_Bcast in line 372 of gmxlib/network.c). It is not yet addressed what 
has gone wrong in the installation and I was trying to run the test set 
to get some information. I wonder if I had put the gmxtest directory at 
proper place, since after I sourced GMXRC and ran gmxtest.pl, for all 
the cases I was told "No topol.tpr file in kernel ...".

It would be quite appreciated if someone could guess what might have 
been wrong with the installation; also is it worth running the test set 
for locating the problem? and what does the error information "No 
topol.tpr file in kernel ..." imply?

Thank you!

Xiang Gu

Xiang Gu, PhD, Postdoctoral Research Fellow
Department of Applied Physics
Helsinki University of Technology (TKK), Finland
Tel: +358-9-470 23137
Email: xgu at cc.hut.fi

More information about the gromacs.org_gmx-users mailing list