[gmx-users] gromacs installation and test set
Justin A. Lemkul
jalemkul at vt.edu
Thu Jun 3 15:24:53 CEST 2010
Gu, Xiang wrote:
> 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.
The use of "think" does not inspire confidence. Knowing your implementation
(including its version) will help decipher if this is a bug in MPI, since some
versions have known issues.
> (3) Thank you. Is there anyway to fix the grompp?
I doubt grompp is broken. Did you compile the entire Gromacs suite with
--enable-mpi? If so, you might be getting weird behavior, since mdrun is the
only program that is MPI-aware. Otherwise, I'd suspect that the gmxtest
directory is in the wrong place. It should be a subdirectory of the "gromacs"
directory of your installation. If in the default /usr/local/gromacs, then you
should have /usr/local/gromacs/gmxtest.
> 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
>>> Thank you!
>>> Xiang Gu
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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