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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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