From: Vermaas, Josh (vermaasj_at_msu.edu)
Date: Fri Mar 12 2021 - 07:54:43 CST
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 <vermaasj_at_msu.edu<mailto:vermaasj_at_msu.edu>> wrote:
Hi Michael,
I have NAMD3 running with CUDA 10 on my cluster. I got a copy of the
source from gitlab.
https://urldefense.com/v3/__https://gitlab.com/tcbgUIUC/namd__;!!DZ3fjg!raze168flmP6-dMKmU-wW8mx1OdK9l2JVR2t5nQdeDtoqT8L_6DAspneyEzJmbEwHA$ <https://urldefense.com/v3/__https://gitlab.com/tcbgUIUC/namd__;!!HXCxUKc!kaFRFX56GRcKdUYZ0OjCvfU7zm-gZXnckT52b_u2FUSSb9GGa80TmJaZzJnbRAY$>
It is in the devel branch, and it tagged as 3.0a9. I have compilation
instructions that are what I used (or at least what I think I used from
memory) on github.
https://urldefense.com/v3/__https://github.com/jvermaas/Software-Building-Instructions/blob/main/NAMD.md__;!!DZ3fjg!raze168flmP6-dMKmU-wW8mx1OdK9l2JVR2t5nQdeDtoqT8L_6DAspneyEy1mAqwHw$ <https://urldefense.com/v3/__https://github.com/jvermaas/Software-Building-Instructions/blob/main/NAMD.md__;!!HXCxUKc!kaFRFX56GRcKdUYZ0OjCvfU7zm-gZXnckT52b_u2FUSSb9GGa80TmJaZ4u2ZUac$>
Compilation with NAMD3 from there is basically the same as it would be
anywhere else. You need charm++ compiled, followed by NAMD itself. The
hardest part for me was actually sorting out which of the many openMPI
implementations installed on the cluster had the PMI backend so I could
just call srun if I wanted to do replica exchange stuff.
-Josh
On 3/11/21 7:42 PM, Michael Von Domaros wrote:
> Hi everyone,
>
> It appears that the namd 3 alpha 9 builds now require CUDA 11.0 (or
> something even newer? not sure.) Is this absolutely necessary? I'm
> asking because our compute cluster is stuck with CUDA 10 and CUDA 10
> compatible device drivers, because a pretty substantial software stack
> has been compiled against this version. The admins are somewhat
> hesitant to update the device drivers, because they don't think that
> running CUDA 10 apps with newer device drivers will be flawless.
>
> So, long story short: Could NAMD3 be compiled against CUDA 10? If so,
> is there any way to access the source code? As far as I can tell, only
> source codes for the 2.x series and nightly snapshots are available.
>
> Thanks a bunch,
> Michael
-- Josh Vermaas Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemisty and Molecular Biology vermaasj_at_msu.edu<mailto:vermaasj_at_msu.edu> https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!raze168flmP6-dMKmU-wW8mx1OdK9l2JVR2t5nQdeDtoqT8L_6DAspneyExZF2KpHQ$ -- Josh Vermaas Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemisty and Molecular Biology vermaasj_at_msu.edu<mailto:vermaasj_at_msu.edu> https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!raze168flmP6-dMKmU-wW8mx1OdK9l2JVR2t5nQdeDtoqT8L_6DAspneyExZF2KpHQ$
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