Re: namd2 CUDA errors for non-superusers in Debian

From: Blake Mertz (
Date: Fri Feb 15 2013 - 08:42:57 CST


Sorry for the confusion -- I knew I should have mentioned that I had
the correct LD_LIBRARY_PATH in my previous email (they are identical
for myself and the other user). That was actually my first
inclination, was that it was an improperly referenced variable. The
gist of the situation is this:

1) When the second user logs on and tries to run namd, she gets the CUDA error.

2) When the second user logs on and runs namd as a superuser, namd
will properly run.

So there is some disconnect with Debian recognizing this second user
as having the correct privileges to run namd. I've got the namd binary
soft-linked to the source directory.....I'm sure this is a linux
issue, and not namd. I was hoping that someone had run into this issue
before, but it looks like I'll need to troubleshoot it myself. Thanks
for putting in your two cents, Aron. I really appreciate it, and
didn't get the chance to thank you last fall -- you did help me on
another CUDA-related issue, just forgot to reply back then.


On Thu, Feb 14, 2013 at 6:31 PM, Aron Broom <> wrote:
> I'm a bit confused.
> 1) I don't see any errors
> 2) You are saying the SU gets errors? but your subject line says the non-SU
> gets errors?
> Either way, I can imagine it might simply be a problem with the library
> path. You should be running NAMD using the cuda library that is shipped
> with it, rather than the one that is part of the cuda libs. So if one of
> you has set your LD_LIBRARY_PATH to be the NAMD install directory, and the
> other hasn't, this kind of problem could occur. That's my best guess at
> this point.
> ~Aron
> On Thu, Feb 14, 2013 at 5:28 PM, Blake Mertz <>
> wrote:
>> Hello,
>> I realize this may be an Nvidia-related issue, but I wanted to see if
>> any namd users had run up against this problem as well. I'm running
>> Debian wheezy with native Nvidia drivers and cuda libraries, and can
>> run CUDA-accelerated pre-compiled binaries with the apoa1 benchmark
>> system myself. I have another user who has superuser privileges. She
>> gets the following error when running namd after ssh'ing in:
>> namd2 +idlepoll +p4 +devices 0 apoa1.namd
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo

Assistant Professor
C. Eugene Bennett Department of Chemistry
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