VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jun 23 2014 - 09:51:14 CDT

Hi,
  Since you are using an NVIDIA K20m, you will need to download one of the
recent VMD test builds, as K20m is a Kepler-based GPU, and the old VMD 1.9.1
release was compiled without the necessary flags to support Kepler GPUs.

The other error you're getting below seems to indicate that you may have
some kind of issue with VMD finding it's Tcl startup scripts.

Neither of these problems should have anything to do with running
VMD from a bash script or in the background. Do you set any environment
variables differently when you run VMD in the background from this script?

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Jun 21, 2014 at 09:08:51AM -0700, Jim wrote:
> I want to start multiple VMD processes in background from within a bash
> script, e.g.:
> #--------------------------
> files="dd-*"
> for f in $files; do
> A A A
> A A A vmd -dispdev text -e script.tcl -args $pdbf $trajf $atomids $f
> out-$f > vmdout-$f 2>&1 &
> done
> #--------------------------
> but it does not work. I'm usually getting an error like this (not
> consistently):
> #--------------------------
> Info) Multithreading available, 32 CPUs detected.
> Info) Free system memory: 114631MB (88%)
> Info) Creating CUDA device pool and initializing hardware...
> CUDA error: invalid device symbol, CUDAClearDevice.cu line 62
> Info) Detected 1 available CUDA accelerator:
> Info) [0] Tesla K20m A A A A 13 SM_3.5 @ 0.71 GHz, 4.7GB RAM, OIO, ZCP
> ERROR) Tcl startup error:
> Info) Dynamically loaded 2 plugins in directory:
> Info) /home/jim/mymodules/VMD/1.9.1/lib/vmd/plugins/LINUXAMD64/molfile
> ERROR) Could not read the vmd initialization file -
> ERROR) A source
> {/home/jim/mymodules/VMD/1.9.1/lib/vmd/scripts/vmd/vmdinit.tcl}
> ERROR) can't find package http 2.4
> ERROR) The VMDDIR environment variable is set by the startup
> ERROR) script and should point to the top of the VMD hierarchy.
> ERROR) VMD will continue with limited functionality.
> Info) VMD for LINUXAMD64, version 1.9.1 (February 1, 2012)
> Info) Exiting normally.
> #--------------------------
> When I remove the "&", it works (in serial though).A
> If I run this loop with the "&" directly in the terminal, it also works.
> I cannot figure out what is wrong.
> Thanks. 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/