VMD-L Mailing List

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Tue Jul 09 2013 - 13:57:02 CDT

I checked in a fix for this on April 4. Current nightly builds available
for download should not require +idlepoll.

-Jim

On Tue, 9 Jul 2013, John Stone wrote:

> 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/
>