[gmx-users] gromacs installation and test set

Gu, Xiang xgu at cc.hut.fi
Thu Jun 3 15:19:14 CEST 2010

Dear Justin,

(1) sorry, my ignorance; threads was enabled when installing FFTW 
instead of Gromacs, I should have said "configured with --enable-float 
and --enable-mpi" (and actually this is what I did).

(2) I think I used OpenMPI.

(3) Thank you. Is there anyway to fix the grompp?


Justin A. Lemkul wrote:
> 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.
> -Justin
>> 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

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