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?
Xiang
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: x...@cc.hut.fi
http://tfy.tkk.fi/soft/
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