[gmx-users] gromacs installation and test set

Justin A. Lemkul jalemkul at vt.edu
Thu Jun 3 15:05:47 CEST 2010

Gu, Xiang wrote:
> 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.

There is no point to using --enable-threads in version 4.0.7 - there's no thread 
support yet.

> 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 ...".

What is your MPI implementation?  OpenMPI, MPICH, etc?

> 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?

The test set is not terribly useful, and certainly won't diagnose this issue for 
you.  If you've failed to generate the necessary .tpr file, then errors occurred 
in grompp that prevented the .tpr file from being generated.


> Thank you!
> Xiang Gu


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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