VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jun 11 2020 - 21:56:17 CDT

Lorenzo,
  Awesome. Let me know how it goes as you continue testing.

Best,
  John

On Thu, Jun 11, 2020 at 04:26:03PM -0700, Lorenzo Casalino wrote:
> Hi John,
> Just to follow up, I just tested the 1.9.4 alpha 43 build and it has cured
> the problem.
> Best
> Lorenzo
> - - - - - - - - - - - - -
> Lorenzo Casalino, PhD
> Post-doctoral research scholar - Amaro Lab
> University of Califonia, San Diego
> 3210 Urey Hall
> 9500 Gilman Dr, La Jolla, CA 92093-0340
> [1]https://amarolab.ucsd.edu/
>
> On May 29, 2020, at 2:46 PM, John Stone <[2]johns_at_ks.uiuc.edu> wrote:
> Hi,
>
> I've posted the first round of VMD 1.9.4 alpha 42 builds, which has
>
> OptiX 6.5 and the code path that no longer tries to workaround the old
>
> broken drivers. The Linux build was done on CentOS 6.x and is a bit of
>
> an experiment due the bleeding edge libraries it is built on.
>
>
> If anyone encounters any trouble, I'll likely make a second Linux build
>
> using CentOS 7 or CentOS 8, but I'm planning to hold off on that unless
>
> it is needed, as my plan for CentOS 8 and Ubuntu 18/20 distro users is
>
> to do builds on CUDA 11 whenever it posts.
>
>
> Best,
>
> John
>
> On Wed, May 27, 2020 at 04:26:16PM -0500, John Stone wrote:
>
> Hi,
> Quick answer since I'm amidst zoom sessions:
> Yes, the older alpha builds had to not free some memory, or they would
> crash due to a driver bug, but this led to a huge memory leak, which
> also
> causes a crash, but not until you render a bunch of frames. The new
> test build I will be posting no longer does that, since the drivers
> were finally fixed, so you'll get the expected behavior.
>
> I'm finishing integrating new code and patches, and hope to have
> a new test build before the end of the week.
>
> Best,
> John
>
> On Wed, May 27, 2020 at 12:04:45PM -0700, Lorenzo Casalino wrote:
>
> Thank you John,
> I updated the driver to 440.82 and that fixed the problem!
> Now I was able to use 1.9.4a38 RTX, with significant performance
> improvement.
> However, while rendering a movie, it always fails after a few
> frames and
> similarly to a31.
> This doesn't happen with other vmd (nonRTX) like 1.9.3, 1.9.4a27
> or
> 1.9.4a35.
> I am rendering a scene with 240,000 atoms, with a transparent
> surface, new
> cartoons and a few graphics elements. I am using a user-defined
> procedure
> and running using a tcl script (text mode).
> It seems that when it reaches a view point and starts proceeding
> to the
> next one it crashes with the following error (vmd 1.9.4a38):
> ERROR) OptiXRenderer) ERROR: Unknown error (Details: Function
> "RTresult
> _rtContextLaunch2D(RTcontext, unsigned int, RTsize, RTsize)"
> caught
> exception: Assertion failed: "!m_enteredFromAPI : Memory manager
> already
> entered from API", file: <internal>, line: 1103)
> (OptiXRenderer.C:2621
> OptiXRenderer) Error during AS generation. Rendering aborted.
> I tried with a31 and crashes at the same point with this error:
> ERROR) OptiXRenderer) ERROR: Memory allocation failed (Details:
> Function
> "RTresult _rtContextLaunch2D(RTcontext, unsigned int, RTsize,
> RTsize)"
> caught exception: Out of memory) (OptiXRenderer.C:2597
> OptiXRenderer) Error during AS generation. Rendering aborted.
> I have a 24 GB RTX GPU so I believe it can handle the scene pretty
> easily
> memory-wise.
> Thank you,
> Best
> Lorenzo
> - - - - - - - - - - - - -
> Lorenzo Casalino, PhD
> Post-doctoral research scholar - Amaro Lab
> University of Califonia, San Diego
> 3210 Urey Hall
> 9500 Gilman Dr, La Jolla, CA 92093-0340
> [1][3]https://amarolab.ucsd.edu/
>
> On May 25, 2020, at 9:16 PM, John Stone
> <[2][4]johns_at_ks.uiuc.edu> wrote:
> Hi,
> The most likely cause of your problem is the out-of-date NVIDIA
> driver.
> Unlike prior versions of VMD, VMD 1.9.4 is compiled against a
> new
> generation
> of OptiX wherein a large fraction of the OptiX code lives as
> part of the
> driver rather than in the liboptix.so.* shared libraries. This
> change
> has the direct consequence that if you run an older driver,
> you're
> also running an older version of the OptiX code. The latest VMD
> 1.9.4
> test builds I'm making are compiled against OptiX 6.5, and the
> minimum
> driver version required is 436.02, which is quite a bit newer
> than
> your current driver.
>
> It gets more interesting however. Since a large part of the
> core
> OptiX implementation now lives in the driver, another issue is
> that
> bugs in OptiX now get fixed as part of driver releases. This
> means
> that it is much more important not only to have a new-enough
> driver,
> but also one that is "stable". In my mind, people using VMD
> 1.9.4 with
> OptiX should be using NVIDIA driver version 440.44 or later, as
> some
> issues VMD previously encountered memory management were cured
> in the
> later drivers.
>
> So, I'd go for version 440.44, or later. We have a bunch of
> machines
> running 440.44 with RTX cards, and they have been pretty stable
> for us.
>
> There will soon be a new set of drivers coming out with the
> release CUDA 11, I'm hopefull that the OptiX components in these
> new
> drivers will be good and solid, in which case that will be what
> I advise
> most people to use going forward (445.xx driver series).
>
> I expect to post new VMD 1.9.4 test binaries shortly, you'll
> also want
> to use these rather than the older a38 build.
>
> Best regards,
> John Stone
>
> On Mon, May 25, 2020 at 01:28:53PM -0700, Lorenzo Casalino
> wrote:
>
> Hi all,
>
> I am having some issues in getting Optix renderer compiled on
> a target
> GPU when using VMD OPTIX RTX versions, like 1.9.4a31 or the
> latest
> 1.9.4a38 (ERROR: Invalid value (OptiXRenderer.C:1214).
>
> First of all, I have 2 GPUs installed on my machine. This is
> the log
> when I run nvidia-smi:
>
> | NVIDIA-SMI 430.26 Driver Version: 430.26 CUDA
> Version:
> 10.2 |
> | 0 Quadro P6000 Off | 00000000:3B:00.0 On |
> Off |
> | 26% 57C P5 30W / 250W | 1846MiB / 24446MiB |
> 21%
> Default |
> +-------------------------------+----------------------+----------------------+
> | 1 TITAN RTX Off | 00000000:AF:00.0 Off |
> N/A |
> | 41% 42C P8 15W / 280W | 345MiB / 24220MiB |
> 0%
> Default |
> +-------------------------------+----------------------+----------------------+
>
> The GPUs are detected, but for some reason vmd1.9.4a38 fails
> in
> compiling Optix renderer on the TITAN RTX.
> This is the log when I try to run vmd 1.9.4a38:
>
> Info) VMD for LINUXAMD64, version 1.9.4a38 (October 20, 2019)
> Info)
> [3][5]https://urldefense.com/v3/__http://www.ks.uiuc.edu/Research/vmd/__;!!Mih3wA!Wc_2cph4f8JXiqRM6sFgFd7wqedSGncDH3YaNIdxJk96V7uocI1wGR6SeGBFTfg6$
> Info) Email questions and bug reports to [4][6]vmd_at_ks.uiuc.edu
> Info) Please include this reference in published work using
> VMD:
> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD -
> Visual
> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1,
> 33-38.
> Info)
> -------------------------------------------------------------
> Info) Multithreading available, 72 CPUs detected.
> Info) CPU features: SSE2 AVX AVX2 FMA AVX512F AVX512CD
> Info) Free system memory: 955GB (94%)
> Info) Creating CUDA device pool and initializing hardware...
> Info) Detected 2 available CUDA accelerators:
> Info) [0] TITAN RTX 72 SM_7.5 1.8 GHz, 24GB RAM
> SP32 AE3 ZC
> Info) [1] Quadro P6000 30 SM_6.1 1.6 GHz, 24GB RAM
> SP32 KT AE2
> ZC
> Warning) Detected X11 'Composite' extension: if incorrect
> display
> occurs
> Warning) try disabling this X server option. Most OpenGL
> drivers
> Warning) disable stereoscopic display when 'Composite' is
> enabled.
> Info) OpenGL renderer: Quadro P6000/PCIe/SSE2
> Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS
> GLSL(OVFGS)
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (32768x32768), 3-D (16384x16384x16384),
> Multitexture (4)
> Info) Using OptiX device mask '0x1'
> Info) Detected 1 available TachyonL/OptiX ray tracing
> accelerator
> Info) Compiling 1 OptiX shaders on 1 target GPU...
> ERROR) OptiXRenderer) ERROR: Invalid value
> (OptiXRenderer.C:1214
> ERROR) OptiXRenderer) Failed to create OptiX rendering context
> ERROR) OptiXRenderer) ERROR: Invalid value
> (OptiXRenderer.C:1214
> ERROR) OptiXRenderer) Failed to create OptiX rendering context
>
> I have set the environment variable to use only the first GPU
> recognized by VMD (e.g., [0] TITAN RTX): export
> VMDOPTIXDEVICEMASK=0x1
> It also fails if I try to use the QuadroP6000 (export
> VMDOPTIXDEVICEMASK=0x2).
>
> Instead, when I run vmd 1.9.3 or 1.9.4a27 everything works:
>
> Info) VMD for LINUXAMD64, version 1.9.4a27 (February 8, 2019)
> Info)
> [5][7]https://urldefense.com/v3/__http://www.ks.uiuc.edu/Research/vmd/__;!!Mih3wA!Wc_2cph4f8JXiqRM6sFgFd7wqedSGncDH3YaNIdxJk96V7uocI1wGR6SeGBFTfg6$
> Info) Email questions and bug reports to [6][8]vmd_at_ks.uiuc.edu
> Info) Please include this reference in published work using
> VMD:
> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD -
> Visual
> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1,
> 33-38.
> Info)
> -------------------------------------------------------------
> Info) Multithreading available, 72 CPUs detected.
> Info) CPU features: SSE2 AVX AVX2 FMA AVX512F AVX512CD
> Info) Free system memory: 956GB (94%)
> Info) Creating CUDA device pool and initializing hardware...
> Info) Detected 2 available CUDA accelerators:
> Info) [0] TITAN RTX 72 SM_7.5 1.77 GHz, 24GB RAM,
> AE3, ZCP
> Info) [1] Quadro P6000 30 SM_6.1 1.64 GHz, 24GB RAM,
> KTO, AE2,
> ZCP
> Warning) Detected X11 'Composite' extension: if incorrect
> display
> occurs
> Warning) try disabling this X server option. Most OpenGL
> drivers
> Warning) disable stereoscopic display when 'Composite' is
> enabled.
> Info) OpenGL renderer: Quadro P6000/PCIe/SSE2
> Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS
> GLSL(OVFGS)
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (32768x32768), 3-D (16384x16384x16384),
> Multitexture (4)
> Info) Using OptiX device mask '0x1'
> Info) Detected 1 available TachyonL/OptiX ray tracing
> accelerator
> Info) Compiling 1 OptiX shaders on 1 target GPU...
> Info) Using OptiX device mask '0x1'
> Info) Using OptiX device mask '0x1'
>
> Could it be a problem of compatibility of the TITAN RTX, or of
> the
> driver version?
> Thank you for your help,
>
> Best regards,
> Lorenzo
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> [7][9]https://urldefense.com/v3/__http://www.ks.uiuc.edu/*johns/__;fg!!Mih3wA!Wc_2cph4f8JXiqRM6sFgFd7wqedSGncDH3YaNIdxJk96V7uocI1wGR6SeIwfIk11$
> Phone:
> 217-244-3349
> [8][10]https://urldefense.com/v3/__http://www.ks.uiuc.edu/Research/vmd/__;!!Mih3wA!Wc_2cph4f8JXiqRM6sFgFd7wqedSGncDH3YaNIdxJk96V7uocI1wGR6SeGBFTfg6$
>
> References
>
> Visible links
> 1. [11]https://amarolab.ucsd.edu/
> 2. [12]mailto:johns_at_ks.uiuc.edu
> 3.
> [13]https://urldefense.com/v3/__http://www.ks.uiuc.edu/Research/vmd/__;!!Mih3wA!Wc_2cph4f8JXiqRM6sFgFd7wqedSGncDH3YaNIdxJk96V7uocI1wGR6SeGBFTfg6$
> 4. [14]mailto:vmd_at_ks.uiuc.edu
> 5.
> [15]https://urldefense.com/v3/__http://www.ks.uiuc.edu/Research/vmd/__;!!Mih3wA!Wc_2cph4f8JXiqRM6sFgFd7wqedSGncDH3YaNIdxJk96V7uocI1wGR6SeGBFTfg6$
> 6. [16]mailto:vmd_at_ks.uiuc.edu
> 7.
> [17]https://urldefense.com/v3/__http://www.ks.uiuc.edu/*johns/__;fg!!Mih3wA!Wc_2cph4f8JXiqRM6sFgFd7wqedSGncDH3YaNIdxJk96V7uocI1wGR6SeIwfIk11$
> 8.
> [18]https://urldefense.com/v3/__http://www.ks.uiuc.edu/Research/vmd/__;!!Mih3wA!Wc_2cph4f8JXiqRM6sFgFd7wqedSGncDH3YaNIdxJk96V7uocI1wGR6SeGBFTfg6$
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> [19]https://urldefense.com/v3/__http://www.ks.uiuc.edu/*johns/__;fg!!Mih3wA!SU37Z_s1jwlJAwSQNZUc6oaMrLqgjy7qLEqtAk-x6KPgQ741YfOlXdEvAYKbPX_v$ Phone:
> 217-244-3349
> [20]https://urldefense.com/v3/__http://www.ks.uiuc.edu/Research/vmd/__;!!Mih3wA!SU37Z_s1jwlJAwSQNZUc6oaMrLqgjy7qLEqtAk-x6KPgQ741YfOlXdEvARwlFOJV$
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> [21]https://urldefense.com/v3/__http://www.ks.uiuc.edu/*johns/__;fg!!Mih3wA!SU37Z_s1jwlJAwSQNZUc6oaMrLqgjy7qLEqtAk-x6KPgQ741YfOlXdEvAYKbPX_v$ Phone:
> 217-244-3349
> [22]https://urldefense.com/v3/__http://www.ks.uiuc.edu/Research/vmd/__;!!Mih3wA!SU37Z_s1jwlJAwSQNZUc6oaMrLqgjy7qLEqtAk-x6KPgQ741YfOlXdEvARwlFOJV$
>
> References
>
> Visible links
> 1. https://amarolab.ucsd.edu/
> 2. mailto:johns_at_ks.uiuc.edu
> 3. https://amarolab.ucsd.edu/
> 4. mailto:johns_at_ks.uiuc.edu
> 5. https://urldefense.com/v3/__http://www.ks.uiuc.edu/Research/vmd/__;!!Mih3wA!Wc_2cph4f8JXiqRM6sFgFd7wqedSGncDH3YaNIdxJk96V7uocI1wGR6SeGBFTfg6$
> 6. mailto:vmd_at_ks.uiuc.edu
> 7. https://urldefense.com/v3/__http://www.ks.uiuc.edu/Research/vmd/__;!!Mih3wA!Wc_2cph4f8JXiqRM6sFgFd7wqedSGncDH3YaNIdxJk96V7uocI1wGR6SeGBFTfg6$
> 8. mailto:vmd_at_ks.uiuc.edu
> 9. https://urldefense.com/v3/__http://www.ks.uiuc.edu/*johns/__;fg!!Mih3wA!Wc_2cph4f8JXiqRM6sFgFd7wqedSGncDH3YaNIdxJk96V7uocI1wGR6SeIwfIk11$
> 10. https://urldefense.com/v3/__http://www.ks.uiuc.edu/Research/vmd/__;!!Mih3wA!Wc_2cph4f8JXiqRM6sFgFd7wqedSGncDH3YaNIdxJk96V7uocI1wGR6SeGBFTfg6$
> 11. https://amarolab.ucsd.edu/
> 12. mailto:johns_at_ks.uiuc.edu
> 13. https://urldefense.com/v3/__http://www.ks.uiuc.edu/Research/vmd/__;!!Mih3wA!Wc_2cph4f8JXiqRM6sFgFd7wqedSGncDH3YaNIdxJk96V7uocI1wGR6SeGBFTfg6$
> 14. mailto:vmd_at_ks.uiuc.edu
> 15. https://urldefense.com/v3/__http://www.ks.uiuc.edu/Research/vmd/__;!!Mih3wA!Wc_2cph4f8JXiqRM6sFgFd7wqedSGncDH3YaNIdxJk96V7uocI1wGR6SeGBFTfg6$
> 16. mailto:vmd_at_ks.uiuc.edu
> 17. https://urldefense.com/v3/__http://www.ks.uiuc.edu/*johns/__;fg!!Mih3wA!Wc_2cph4f8JXiqRM6sFgFd7wqedSGncDH3YaNIdxJk96V7uocI1wGR6SeIwfIk11$
> 18. https://urldefense.com/v3/__http://www.ks.uiuc.edu/Research/vmd/__;!!Mih3wA!Wc_2cph4f8JXiqRM6sFgFd7wqedSGncDH3YaNIdxJk96V7uocI1wGR6SeGBFTfg6$
> 19. https://urldefense.com/v3/__http://www.ks.uiuc.edu/*johns/__;fg!!Mih3wA!SU37Z_s1jwlJAwSQNZUc6oaMrLqgjy7qLEqtAk-x6KPgQ741YfOlXdEvAYKbPX_v$
> 20. https://urldefense.com/v3/__http://www.ks.uiuc.edu/Research/vmd/__;!!Mih3wA!SU37Z_s1jwlJAwSQNZUc6oaMrLqgjy7qLEqtAk-x6KPgQ741YfOlXdEvARwlFOJV$
> 21. https://urldefense.com/v3/__http://www.ks.uiuc.edu/*johns/__;fg!!Mih3wA!SU37Z_s1jwlJAwSQNZUc6oaMrLqgjy7qLEqtAk-x6KPgQ741YfOlXdEvAYKbPX_v$
> 22. https://urldefense.com/v3/__http://www.ks.uiuc.edu/Research/vmd/__;!!Mih3wA!SU37Z_s1jwlJAwSQNZUc6oaMrLqgjy7qLEqtAk-x6KPgQ741YfOlXdEvARwlFOJV$ 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/