VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Sun May 18 2014 - 16:11:45 CDT

Hi Yeping,

What Axel is saying is that because you need to add +idlepoll to the
command line in NAMD 2.9 when running a GPU-enabled build, the error you
are getting is actually perfectly normal (although undesirable). What
you need to do to fix this is change a line in the tcl script that runs
the plugin. To do this, first figure out the directory where the
NAMDEnergy plugin is stored. env is your friend here. From the tkconsole
of VMD, the "env" command will give you a bunch of information, but you
want what is at the end, the plugin directories. Find the NAMDENERGYDIR
line, and open the namdenergy.tcl file in that directory. You'll find
many lines like this:

exec $namdcmd something.namd > something.log

I think its just a simple matter of adding +idlepoll between the
$namdcmd and the configuration file, and it should no longer give you
that error.

This was the technical solution. Most of the time non-technical
solutions are better. Neither the CPU-only version of NAMD nor the
current GPU-enabled CVS builds of NAMD need the +idlepoll argument, so
you could just try using those. :)
-Josh Vermaas

On 5/18/14, 1:00 PM, sunyeping wrote:
>
>
> Yeping Sun
>
> Institute of Microbiology, Chinese Academy of Sciences
>
>
> ------------------------------------------------------------------
> 发件人：Axel Kohlmeyer <akohlmey_at_gmail.com>
> 发送时间：2014年5月18日(星期日) 21:08
> 收件人：孙业平 <sunyeping_at_aliyun.com>
> 抄　送：vmd-l <vmd-l_at_ks.uiuc.edu>
> 主　题：Re: vmd-l: proper enviroment for the VMD namdenergy plugin
>
>
>
>
> On Sun, May 18, 2014 at 1:30 AM, sunyeping <sunyeping_at_aliyun.com
> <mailto:sunyeping_at_aliyun.com>> wrote:
>
> Dear VMD users,
>
>
> ​[...]​
>
>
> My cuda version is cuda_5.0.35_linux_64_rhel5.x-1.run, my
> VMD version is 1.9.1
>
> In order to run the namdenergy plugin properly, which version of
> cuda do I need? should I upgrade or downgrade it?
>
>
> ​neither. you obviously have to use a CPU version of NAMD.
>
> axel​
>
> Dear axel,
>
> Thank you for you reply! I have installed NAMD of CPU version:
> NAMD_CVS-2014-05-18_Linux-x86_64-multicore. But there is still one
> thing that I don't understand: how should I make the namdenergy.tcl
> get the path of namd2 in this CPU version of NAMD ( say,
> /opt/NAMD_CPU) rather than that of my previously installed NAMD of
> CUDA version (in /opt/NAMD_CUDA)? Should I fillful it by modifying the
> namdenergy.tcl script and how?
>
> Best regards,
>
>
> Yeping
>
>
>
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com <mailto:akohlmey_at_gmail.com>
> http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.