From: Michael Von Domaros (mvondoma_at_uci.edu)
Date: Tue Mar 16 2021 - 20:47:26 CDT
Thanks for clarifying this, Dave! And thanks to everyone else for their
help, too. I have it working now and our admins are relieved :)
On Tue, Mar 16, 2021 at 11:21 AM David Hardy <dhardy_at_ks.uiuc.edu> wrote:
> 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
> “click-through” 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,
> Dave
>
> --
> David J. Hardy, Ph.D.
> Beckman Institute
> University of Illinois at Urbana-Champaign
> 405 N. Mathews Ave., Urbana, IL 61801
> dhardy_at_ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/
>
> On Mar 12, 2021, at 7:54 AM, Vermaas, Josh <vermaasj_at_msu.edu> 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 <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!srKSpjcmbaw8r4qFlcV6ANlGmRzm2eWt-nIUQ2RDvcTTbX1_otEf3LsT7SJm_3qAQQ$
>> <https://urldefense.com/v3/__https://gitlab.com/tcbgUIUC/namd__;!!HXCxUKc!kaFRFX56GRcKdUYZ0OjCvfU7zm-gZXnckT52b_u2FUSSb9GGa80TmJaZzJnbRAY$>
>>
>> It is in the devel branch, and it tagged as 3.0a9. I have compilation
>> instructions that are what I used (or at least what I think I used from
>> memory) on github.
>>
>> https://urldefense.com/v3/__https://github.com/jvermaas/Software-Building-Instructions/blob/main/NAMD.md__;!!DZ3fjg!srKSpjcmbaw8r4qFlcV6ANlGmRzm2eWt-nIUQ2RDvcTTbX1_otEf3LsT7SJZ7lghhQ$
>> <https://urldefense.com/v3/__https://github.com/jvermaas/Software-Building-Instructions/blob/main/NAMD.md__;!!HXCxUKc!kaFRFX56GRcKdUYZ0OjCvfU7zm-gZXnckT52b_u2FUSSb9GGa80TmJaZ4u2ZUac$>
>>
>> Compilation with NAMD3 from there is basically the same as it would be
>> anywhere else. You need charm++ compiled, followed by NAMD itself. The
>> hardest part for me was actually sorting out which of the many openMPI
>> implementations installed on the cluster had the PMI backend so I could
>> just call srun if I wanted to do replica exchange stuff.
>>
>> -Josh
>>
>> On 3/11/21 7:42 PM, Michael Von Domaros wrote:
>> > Hi everyone,
>> >
>> > It appears that the namd 3 alpha 9 builds now require CUDA 11.0 (or
>> > something even newer? not sure.) Is this absolutely necessary? I'm
>> > asking because our compute cluster is stuck with CUDA 10 and CUDA 10
>> > compatible device drivers, because a pretty substantial software stack
>> > has been compiled against this version. The admins are somewhat
>> > hesitant to update the device drivers, because they don't think that
>> > running CUDA 10 apps with newer device drivers will be flawless.
>> >
>> > So, long story short: Could NAMD3 be compiled against CUDA 10? If so,
>> > is there any way to access the source code? As far as I can tell, only
>> > source codes for the 2.x series and nightly snapshots are available.
>> >
>> > Thanks a bunch,
>> > Michael
>>
>> --
>> Josh Vermaas
>> Assistant Professor, MSU-DOE Plant Research Lab and Department of
>> Biochemisty and Molecular Biology
>> vermaasj_at_msu.edu
>> https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!srKSpjcmbaw8r4qFlcV6ANlGmRzm2eWt-nIUQ2RDvcTTbX1_otEf3LsT7SJw-8BqoA$
>> <https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!raze168flmP6-dMKmU-wW8mx1OdK9l2JVR2t5nQdeDtoqT8L_6DAspneyExZF2KpHQ$>
>>
>>
> --
> Josh Vermaas
> Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemisty and Molecular Biologyvermaasj_at_msu.eduhttps://prl.natsci.msu.edu/people/faculty/josh-vermaas/ <https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!raze168flmP6-dMKmU-wW8mx1OdK9l2JVR2t5nQdeDtoqT8L_6DAspneyExZF2KpHQ$>
>
>
>
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