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
You did not compile with MPI.
-------------------------------------------------------
"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
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
------------------------------------------------------------------------
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[email protected] [email protected] http://folding.bmc.uu.se
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