From: Axel Kohlmeyer (
Date: Mon Jun 29 2009 - 13:46:51 CDT

On Mon, 2009-06-29 at 10:55 -0700, BIN ZHANG wrote:
> Dear all:
> I'm trying to run vmd on a linux amd64 cluster. Instead of overloading
> the head node, I would like to submit the jobs to computer nodes.
> However, simply using *qsub* vmd executable gives the following error :
> ======
> /home/bingo/vmd-1.8.6.ORIGINAL/LINUXAMD64/vmd_LINUXAMD64: error while
> loading shared libraries: cannot open shared object
> file: No such file or directory
> ======

this is a self-compiled VMD executable, right?
the one that can be downloaded from the VMD home
page should not have this problem.

> Does this mean I need to recompile vmd w/o linking to the library
> fltk, which, to my understanding, is only necessary for the GUI?

this is one option, you can also link FLTK, Tk/Tcl and so on statically
by using constructs like this:

and finally, you can copy all required shared libraries that are
not installed to some directory that is available
and then set LD_LIBRARY_PATH accordingly.

this is all pretty standard stuff.


> BTW, vmd runs fine on the head node.
> Thanks for your help,
> Best Wishes,
> Bin

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.