[gmx-users] gmx_blast error when attempting to run in parallel

Justin A. Lemkul jalemkul at vt.edu
Thu Jun 11 14:24:01 CEST 2009

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.


> 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    gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> 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


More information about the gromacs.org_gmx-users mailing list