Re: 3.0alpha9 CUDA version

From: David Hardy (
Date: Tue Mar 16 2021 - 13:20:22 CDT

Hi Michael,

I just wanted to follow up in support of what Josh said. The NAMD License that we developed years ago with the university legal department allows much freedom to users, including monetarily free access to run the software and view the source code, along with some amount of reuse of the code. However, in order for us to not to be in violation of our own license when distributing NAMD, the license must be presented to the user in a ‚Äúclick-through‚ÄĚ form, which is why access to the GitLab repository is protected in the way that it is.

As Josh stated, it is fine for you to obtain the NAMD source code through GitLab, even when your intention is simply to build NAMD yourself.

Best regards,

David J. Hardy, Ph.D.
Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews Ave., Urbana, IL 61801,
> On Mar 12, 2021, at 7:54 AM, Vermaas, Josh <> wrote:
> Hi Michael,
> Developers are certainly one audience, but really the reason behind the gitlab wall is due to needing to be able to track users for reporting usage statistics back to funding agencies, and to make sure folks have agreed to the NAMD license. That is why the user registration form is one of the prerequisites, so that the developers can report back to NIH the percentage of users that have NIH funding. Being able to download the source so you can compile it on your own hardware is totally a legit reason to get access through gitlab IMHO. I believe this opinion is shared by the folks that actually have decision making power.
> -Josh
> On 3/11/21 9:52 PM, Michael Von Domaros wrote:
>> Thanks, Josh! That's quite encouraging. Does that mean it's possible to request Gitlab access for this reason? I was operating under the assumption that this is just for developers.
>> Michael
>> On Thu, Mar 11, 2021 at 5:28 PM Vermaas, Josh < <>> wrote:
>> Hi Michael,
>> I have NAMD3 running with CUDA 10 on my cluster. I got a copy of the
>> source from gitlab.
>> <;!!HXCxUKc!kaFRFX56GRcKdUYZ0OjCvfU7zm-gZXnckT52b_u2FUSSb9GGa80TmJaZzJnbRAY$>
>> It is in the devel branch, and it tagged as 3.0a9. I have compilation
>> instructions that are what I used (or at least what I think I used from
>> memory) on github.
>> <;!!HXCxUKc!kaFRFX56GRcKdUYZ0OjCvfU7zm-gZXnckT52b_u2FUSSb9GGa80TmJaZ4u2ZUac$>
>> Compilation with NAMD3 from there is basically the same as it would be
>> anywhere else. You need charm++ compiled, followed by NAMD itself. The
>> hardest part for me was actually sorting out which of the many openMPI
>> implementations installed on the cluster had the PMI backend so I could
>> just call srun if I wanted to do replica exchange stuff.
>> -Josh
>> On 3/11/21 7:42 PM, Michael Von Domaros wrote:
>> > Hi everyone,
>> >
>> > It appears that the namd 3 alpha 9 builds now require CUDA 11.0 (or
>> > something even newer? not sure.) Is this absolutely necessary? I'm
>> > asking because our compute cluster is stuck with CUDA 10 and CUDA 10
>> > compatible device drivers, because a pretty substantial software stack
>> > has been compiled against this version. The admins are somewhat
>> > hesitant to update the device drivers, because they don't think that
>> > running CUDA 10 apps with newer device drivers will be flawless.
>> >
>> > So, long story short: Could NAMD3 be compiled against CUDA 10? If so,
>> > is there any way to access the source code? As far as I can tell, only
>> > source codes for the 2.x series and nightly snapshots are available.
>> >
>> > Thanks a bunch,
>> > Michael
>> -- 
>> Josh Vermaas
>> Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemisty and Molecular Biology
>> <>
>> <;!!DZ3fjg!raze168flmP6-dMKmU-wW8mx1OdK9l2JVR2t5nQdeDtoqT8L_6DAspneyExZF2KpHQ$>
> -- 
> Josh Vermaas
> Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemisty and Molecular Biology
> <>
> <;!!DZ3fjg!raze168flmP6-dMKmU-wW8mx1OdK9l2JVR2t5nQdeDtoqT8L_6DAspneyExZF2KpHQ$>

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