VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 09 2013 - 13:45:47 CDT

Hi,
  Thanks for the note. I'm CCing Jim Phillips to see if he has comments
on how we can improve this situation. Currently there's no way for
the namdenergy plugin to know if the NAMD binary is a CUDA binary or not,
so I'm not sure what the best long-term fix is. We'll see what Jim suggests.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Jun 30, 2013 at 04:42:38PM -0400, Alessandro Mascioni wrote:
> Hello,
> I noticed that the namdenergy plug-in in VMD 1.9.1 does not work on CUDA
> systems.
> I have NAMD_2.9_Linux-x86_64-multicore-CUDA, and when I try to run
> namdenergy from the VMD gui it gives me an error requiring the +idlepoll
> option.
> If I modify the namdenergy.tcl script to include +idlepoll (as suggested
> in an older post), then it complains that certain energy terms cannot be
> execuded on the GPU.
>
> The only way I could find to fix this issue is to download the non CUDA
> version of namd 2.9 (NAMD_2.9_Linux-x86_64-multicore) hard code the path
> inside the namdenergy.tcl scipt:
> if {$namdcmd == "DUMMY"} {
> set namdcmd "/home/me/NAMD_2.9_Linux-x86_64-multicore/namd2"
> # set namdcmd \
> # [::ExecTool::find -interactive \
> # -description "NAMD 2.x Molecular Dynamics Engine" \
> # -path [file join /usr/local/bin/namd2] namd2]
> }
>
> I don't know if other plugins are also affected by this and if there is a
> more elegant fix for it.
>
> Thanks,
>
> Al 

-- 
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/