VMD-L Mailing List

From: Vermaas, Josh (vermaasj_at_msu.edu)
Date: Tue Jan 31 2023 - 14:04:57 CST

Hi Brendan,

My point is that OptiX 6.5 works just fine with newer versions of CUDA. That is what we use in my lab here, and we haven’t noticed any graphical distortions. As you noted, porting VMD’s innards to a newer version of OptiX is something beyond the capabilities of a single scientist with other things to do for a dayjob. 😃 Do you have a minimal working example of something that makes a checkerboard in your setup? I’d be happy to render something here just to demonstrate that 6.5 works just fine, even with more modern CUDA libraries.

-Josh

From: Brendan Dennis <bdennis_at_physics.ucsd.edu>
Date: Tuesday, January 31, 2023 at 2:17 PM
To: "Vermaas, Josh" <vermaasj_at_msu.edu>
Cc: "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: Running VMD 1.9.4alpha on newer GPUs that require CUDA 11+ and OptiX 7+

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!89UBEQ4G7yu6u53QW2xxTzloqlocpYFIT6hrp6P59GYY09f9zF-OtugqTyu6gYKDm9XdYkXwt_zg32l6w3Q$ <https://urldefense.com/v3/__https:/pcf.ucsd.edu/__;!!HXCxUKc!y2kuOQIcWLv8EUaV3wpNMykOrLfVi5PJhmvm_sXJ5RCLM8fdDhHB6Zb_01wcuCnk3RMahrrqkmic6Yge5Vo5-OE$>
Mayer Hall 3410
(858) 534-9415
On Tue, Jan 31, 2023 at 6:58 AM Josh Vermaas <vermaasj_at_msu.edu<mailto:vermaasj_at_msu.edu>> wrote:
Hi Brendan,
I've been running VMD with CUDA 12.0 and OptiX 6.5, so I think it can be done. I've put instructions for how to do this on github. https://urldefense.com/v3/__https://github.com/jvermaas/vmd-packaging-instructions__;!!DZ3fjg!89UBEQ4G7yu6u53QW2xxTzloqlocpYFIT6hrp6P59GYY09f9zF-OtugqTyu6gYKDm9XdYkXwt_zgoEI-ZUE$ <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!89UBEQ4G7yu6u53QW2xxTzloqlocpYFIT6hrp6P59GYY09f9zF-OtugqTyu6gYKDm9XdYkXwt_zg32l6w3Q$ <https://urldefense.com/v3/__https:/pcf.ucsd.edu/__;!!DZ3fjg!6Pk3uKQJXsVVUBSNiEN5nlGSFRbvhvd-zrWzv6WpfLenvQEvVvxE_ux5Q9DAtJmubWIicqFWxYWVawU-ciHx-3E1Yw$>
Mayer Hall 3410
(858) 534-9415
--
Josh Vermaas
vermaasj_at_msu.edu<mailto:vermaasj_at_msu.edu>
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University
vermaaslab.github.io<https://urldefense.com/v3/__http:/vermaaslab.github.io__;!!HXCxUKc!y2kuOQIcWLv8EUaV3wpNMykOrLfVi5PJhmvm_sXJ5RCLM8fdDhHB6Zb_01wcuCnk3RMahrrqkmic6YgenUOnTvw$>