[gmx-users] PBS

Campbell Millar c.millar at elec.gla.ac.uk
Mon Dec 12 10:57:54 CET 2005


I've had the same problem when submitting to grid-engine.

The fix is that you have to make sure that you are exporting the 
LD_LIBRARY_PATH environment correctly and that the libraries are 
available on the slave nodes in your cluster. Our master node exports 
some folders to the workers so in grid-engine I usually have to do 
something like.

export LD_LIBRARY_PATH <path to libs>:$LD_LIBRARY_PATH

You can also use the -V flag (I think) in pbs to export paths.

If the folder that the libraries are in is not exported you'll either 
need to make sure that they are installed on the slave nodes or 
re-compile gromacs statically with the -static flag. This builds the 
libraries into the executable so they are not required to be loaded at 

Hope this helps,


On 12 Dec 2005, at 03:42, 主月 :) wrote:

> Hi every one!
> I've install the GM without parrel in /home/gromacs_s that have been 
> linked. So i can run it with "mdrun" on main node directly. But when i 
> use PBS the errors happened.My pbs script is as follows.
> #!/bin/sh
> ###Job name
> #PBS -N test
> ### Output files
> #PBS -o test.out
> #PBS -e test.err
> ### Queue name
> #PBS -q workq
> ### CPU number
> #PBS -l nodes=1:ppn=1
> #JRS -l walltime=2400:00:00
> ### Script Commands
> mdrun
> exit 0
> But some error happened that is :
> mdrun: error while loading shared libraries: libXm.so.3: cannot open 
> shared object file: No such file or directory
> how can i fix it !
> thanks all!
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
Dr Campbell Millar,
University of Glasgow,
Device Modelling Group,
Oakfield Avenue,
Glasgow G12 8LT
tel: +44 141 330 4792  fax: +44 141 330 4907 skype: campbell_millar

"Diplomacy is the art of saying 'nice doggy', till you can find a rock"
Larry Niven.
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: text/enriched
Size: 2208 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20051212/b0438710/attachment.bin>

More information about the gromacs.org_gmx-users mailing list