Sashank Karri wrote:
Hi, I'm running gromacs-4.0.3 on a cluster. I am testing gromacs on
it. We are currently getting this error when I run with 4 nodes with
one dedicated to PME calculations.
Back Off! I just backed up md.log to ./#md.log.5#
Reading file ionsol_minim96-1.tpr, VERSION 4.0.3 (single precision)
------------------------------
-------------------------
Program mdrun, VERSION 4.0.3
Source code file: network.c, line: 357
Routine should not have been called:
gmx_bast
-------------------------------------------------------
"I'll Match Your DNA" (Red Hot Chili Peppers).
Here is my job that I'm submitting to the cluster.
#PBS -N ionsol_karri
#PBS -l walltime=24:00:00
#PBS -l nodes=4:ppn=4:quad
#PBS -j oe
module load mpich
module load gromacs-4.0.3
cd /home/srk18/newplcre/
mpirun -nodes 4 /usr/local/gromacs/gromacs-4.0.3/bin/mdrun -npme 1 -s
ionsol_minim96-1.tpr -o finminim96_traj.trr -x finminim96_traj.xtc -c
final_minim.g96 -e enermin_fin.edr -cpo state96.cpt
Is your mdrun truly MPI-enabled? Typically the configure script advises you to
append _mpi to the parallel version.
Also, upgrade to the newest version of Gromacs, 4.0.5, and try again. That way,
if it is a bug, then changes can be made to the newest version, and not one that
is five months old.
-Justin
When discussing the installation of gromacs earlier with the cluster
admin, he sent the following message:
>I remember I seeing your error (not the present error) while I tried
to make the dynamic version of the GROMACS. So I used the
--enable-static while building parallel version of the GROMACS. That
build the executable and most of the inbuilt test were successful. If
you think we need dynamic build let me know, I might have to struggle a
bit. Also It would be good if you share information you have regarding
building.
Do you folks have any idea as to how to fix the above error?
Thanks,
Sashank Karri
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
