VMD-L Mailing List

From: Brendan Dennis (bdennis_at_physics.ucsd.edu)
Date: Tue Jan 31 2023 - 13:16:41 CST

Hi Josh,

Thanks for the link, from looking at your repo it looks like we both
figured out a lot of the same tweaks needed to get VMD building from source
on newer systems with newer versions of various dependencies and CUDA.
Unfortunately though, I don't think tweaking of the configure scripts or
similar will get VMD building against OptiX 7, as NVIDIA made some pretty
substantial changes in the OptiX 7.0.0 release that VMD's OptiX code
doesn't yet reflect. Although it looks like the relevant portions of code
in the most recent standalone release of Tachyon (0.99.5) have been
rewritten to support OptiX 7, those changes have not been ported over to
VMD's internal Tachyon renderer (or at least not as of VMD 1.9.4a57), and
sadly it's all a bit over my head to port it myself. 

--
Brendan Dennis (he/him/his)
Systems Administrator
UCSD Physics Computing Facility
https://urldefense.com/v3/__https://pcf.ucsd.edu/__;!!DZ3fjg!-uXuHquGUkYHh4eqrd4PbX85DPYEPk4et3FfNqqtNYxmRkM161lmHDt8DXfZrnWHNVEqJCLyi585WMUu01My8VGIaQ$ 
Mayer Hall 3410
(858) 534-9415
On Tue, Jan 31, 2023 at 6:58 AM Josh Vermaas <vermaasj_at_msu.edu> wrote:
> Hi Brendan,
>
> I've been running VMD with CUDA 12.0 and OptiX 6.5, so I think it can be
> done. I've put instructions for how to do this on github.
> https://urldefense.com/v3/__https://github.com/jvermaas/vmd-packaging-instructions__;!!DZ3fjg!-uXuHquGUkYHh4eqrd4PbX85DPYEPk4et3FfNqqtNYxmRkM161lmHDt8DXfZrnWHNVEqJCLyi585WMUu01NSeiZWQQ$ 
> <https://urldefense.com/v3/__https://github.com/jvermaas/vmd-packaging-instructions__;!!Mih3wA!CpCXGIkyDLgkiLgg6XYyO8rPhE9542sEIOdi43gpxDKn7YboDflWtoPUOT5kOJhsyyEB0p6PdIdEKB-amahcGR4$>.
> This set of instructions was designed with my own use case in mind, where I
> have multiple Ubuntu machines all updating from my own repository. This
> saves me time on installing across the multiple machines, while respecting
> the licenses to both OptiX and CUDA. There may be some modifications you
> need to do for your own purposes, as admittedly I haven't updated the
> instructions for more recent alpha versions of VMD.
>
> -Josh
>
> On 1/30/23 9:16 PM, Brendan Dennis wrote:
>
> Hi,
>
> I provide research IT support to a lab that makes heavy use of VMD. They
> recently purchased several new Linux workstations with NVIDIA RTX A5000
> GPUs, which are only compatible with CUDA 11.1 and above. If they attempt
> to use the binary release of VMD 1.9.4a57, which is built against CUDA 10
> and OptiX 6.5.0, then they run into problems with anything using GPU
> acceleration. Of particular note is rendering an image using the internal
> TachyonL-OptiX option; the image is rendered improperly, with a severe
> checkered pattern throughout.
>
> I have been attempting to compile VMD 1.9.4a57 from source for them in
> order to try and get GPU acceleration working. Although I am able to
> compile against CUDA 11.2 successfully, the maximum version of OptiX that
> appears to be supported by VMD is 6.5.0. When built against CUDA 11.2 and
> OptiX 6.5.0, the image checkering still occurs on render, but is not nearly
> as severe as it was with the CUDA 10 binary release. My guess is that some
> version of OptiX 7 is also needed to fix this for these newer GPUs.
>
> In researching OptiX 7 support, it appears that how one would use OptiX in
> one's code changed pretty substantially with the initial 7.0.0 release, but
> also that CUDA 11 was not supported until the 7.2.0 release. It
> additionally looks like Tachyon 0.99.5 uses OptiX 7, and I was able to
> build the libtachyonoptix.a library with every OptiX 7 version <= 7.4.0.
> However, there does not appear to be a way to use this external Tachyon
> OptiX library with VMD, as all of VMD's OptiX support is internal.
>
> Is there any way to use an external Tachyon OptiX library with VMD? If
> not, is there any chance that support for OptiX 7 in VMD is not too far off
> on the horizon, perhaps even in the form of a new alpha Linux binary
> release built against CUDA 11.1+ and OptiX 7.2.0+? For now, I've had to
> tell people that they'll need to make due with using the Intel OSPray or
> other CPU-based rendering options, but I imagine that's going to get
> frustrating fairly quickly as they watch renders take minutes on their
> brand new systems, while older workstations with older GPUs can do them in
> seconds.
> --
> Brendan Dennis (he/him/his)
> Systems Administrator
> UCSD Physics Computing Facility
> https://urldefense.com/v3/__https://pcf.ucsd.edu/__;!!DZ3fjg!-uXuHquGUkYHh4eqrd4PbX85DPYEPk4et3FfNqqtNYxmRkM161lmHDt8DXfZrnWHNVEqJCLyi585WMUu01My8VGIaQ$ 
> <https://urldefense.com/v3/__https://pcf.ucsd.edu/__;!!DZ3fjg!6Pk3uKQJXsVVUBSNiEN5nlGSFRbvhvd-zrWzv6WpfLenvQEvVvxE_ux5Q9DAtJmubWIicqFWxYWVawU-ciHx-3E1Yw$>
> Mayer Hall 3410
> (858) 534-9415
>
>
> --
> Josh Vermaas
> vermaasj_at_msu.edu
> Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
> Michigan State Universityvermaaslab.github.io
>
>