Re: which namd versions compatible with CUDA 5.5 and other CUDA woes

From: Robert Wohlhueter (
Date: Sun Sep 28 2014 - 12:00:17 CDT

Glory be to god, and Jim Philips!

I didn't quite follow you advice, which suggested that compiling from
source should work with cuda5.5. Rather, I bit the bullet, upgraded to
cuda6.5, followed some advice from the Ubuntu community to work around
the incompatibility of nvidia's libopencli and wine, and tweaked my

And, voila!, everything worked (using pre-compiled
NAMD_CVS-2014-09-20_Linux-x86_64-multicore-CUDA) -- using 4 cores and
cuda acceleration on my 660Ti card.

Thanks a bunch,

Bob Wohlhueter

On 9/26/14, 6:25 PM, Jim Phillips wrote:
> NAMD 2.9 binaries should run with newer CUDA releases as long as the
> LD_LIBRARY_PATH is set to the included
> Also, NAMD 2.10b1 or nightly build source code will compile with CUDA
> 5.5 (which is the latest available for Cray XK7), and I think it works
> with everything back to CUDA 4.0. The compilations directions are
> relatively straightforward, and probably simpler than debugging WINE.
> Jim
> On Mon, 22 Sep 2014, Robert Wohlhueter wrote:
>> I am now running Ubuntu 14.04 on an AMD64 machine with a GTX 660Ti
>> graphics board. The out-of-the-box instalation of 14.04 includes
>> CUDA version 5.5. After my upgrade to 14.04 my previous installation
>> of namd2 (NAMD_2.9_Linux-x86_64-CUDA) seems to be broken.
>> My first impulse was to install a newer namd build, namely
>> NAMD_CVS-2014-09-20_Linux-x86_64-multicore-CUDA. Running that
>> version presents cuda errors -- which is doubtless explained from the
>> note in the namd-user-manual that v. 2.10b1 (and newer?) "supports"
>> CUDA 6.0 (probably implying that it does not support CUDA 5.5).
>> Following the manual's advice to make sure the delivered
>> with NAMD_CVS-2014-09-20_Linux-x86_64-multicore-CUDA is out-front in
>> LD_LIBRRY_PATH is of no avail.
>> My next idea was thus to upgrade my cuda support. NVIDIA's website
>> has a recipe for that:
>> I downloaded
>> "cuda-repo-ubuntu1404_6.5-14_amd64.debcuda-repo-ubuntu1404_6.5-14_amd64.deb",
>> ran "sudo -i " on that deb package, then "sudo apt-get update", then
>> "sudo apt-get install cuda" and got complains, most saliently that
>> dependencies were not met. Exploring this approach a little more
>> with synaptic, I find synaptic lists "cuda" and claims a latest
>> version as 6,5-14. But when I mark it for install, it tells me that
>> it will uninstall a bunch of things, including ocl-icd libs and
>> wine! Those removals would cause me a lot of grief.
>> So it seems the path of least resistance would be to try to revert to
>> a previous version of namd-cuda which would be compatible with v. 5.5
>> of cuda. Which is that?
>> Or perhaps one can suggest a slick way of installing getting to CUDA
>> 6.5 without destroying WINE, etc.
>> Thanks,
>> Bob Wohhueter

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