VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed May 19 2021 - 09:13:43 CDT
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Stefan,
Thanks for the followup on this, that's helpful.
Best regards,
John Stone
On Wed, May 19, 2021 at 10:28:31AM +0200, Stefan Boresch wrote:
> Dear John,
>
> just to confirm your suspicion in this 'ancient' thread: The most recent
> firmware(?) update to my Surface Book 3 bumbed the version of the nvidia
> driver considerably (to 461.40). The quicksurf error is now gone, as you
> anticipated.
>
> VMDNOSPRAY is still needed though (but that's obviously not an nvidia issue)
>
> Best regards,
>
> Stefan
>
> On Wed, Dec 16, 2020 at 02:20:44PM -0600, John Stone wrote:
> > Stefan,
> > Yeah, I would never advise a driver update except when one has
> > some "downtime" to deal with unplanned bugs/issues. For now,
> > just keep it on your TODO list for some later time and let me know
> > when you have had a chance to do it.
> >
> > On my side, I need to look at why the QuickSurf code was still trying
> > to run after the initial driver mismatch warning, it's possible
> > I need to add an additional safety check there.
> >
> > Best,
> > John
> >
> > On Wed, Dec 16, 2020 at 09:16:41PM +0100, Stefan Boresch wrote:
> > > John,
> > >
> > > thank you for the explanation, which makes sense. I'll try the driver
> > > update when I have (spare) time to recover should this blow up in my
> > > face. (I am a little bit wary that stuff may break on this dual gpu
> > > machine, hence I take driver updates when Windows offers them to me
> > > ..)
> > >
> > > And the Linux machine I remembered also had some cuda/driver mismatch, which
> > > didn't harm otherwise, so I didn't care/investigate at the time.
> > >
> > > Best,
> > > Stefan
> > >
> > > PS: Posting the driver recommendation might help others though!
> > >
> > > On Wed, Dec 16, 2020 at 02:07:55PM -0600, John Stone wrote:
> > > > Stefan,
> > > > I think the issue is that you're using NVIDIA driver version 451.77,
> > > > which is for the older CUDA 11.0 release.
> > > > The VMD 64-bit windows builds I've made used CUDA 11.1, so they need
> > > > driver series 455.x. I'm running driver 456.71 on my test machine and
> > > > it works fine, I'd recommend updating at some point when you have
> > > > the opportunity.
> > > >
> > > > Regarding memory use:
> > > > QuickSurf is significantly more memory intensive than the OptiX renderer is,
> > > > so the fact that you can do a rendering and not encounter problems may not
> > > > be a predictor of success for QuickSurf (on the GPU).
> > > > Most GPUs don't have enough memory to do a QuickSurf calculation in a
> > > > single pass, so VMD automatically breaks up the QuickSurf calculation
> > > > into many smaller "chunks" and loops until finished. This is normally
> > > > successful however, so the error you're getting is not what I'd expect
> > > > in general, and especially for a structure as small as 1CRN with a
> > > > tiny 42x36x42 grid size. That leads me to believe that this is purely
> > > > an NVIDIA driver version issue, as indicated by the startup message.
> > > >
> > > > Best regards,
> > > > John Stone
> > > > vmd_at_ks.uiuc.edu
> > > >
> > > > On Wed, Dec 16, 2020 at 08:49:53PM +0100, Stefan Boresch wrote:
> > > > > I will test the GPU memory issue when I can easily reboot, though I doubt
> > > > > it. This is a dual GPU machine (Intel integrated, NVIDIA for highend tasks,
> > > > > and the NVIDIA card has 4GB (discrete, at least so I believe) RAM).
> > > > >
> > > > > I checked before starting VMD right now -- nvidia-smi.exe shows no other
> > > > > process using the GPU, and the Windows taskmanager shows no program
> > > > > using the GPU. (Chrome is running, but only has my gdrive folder and
> > > > > gmail inbox). GPU and CPU are shown as idle (load < 1%)
> > > > >
> > > > > Also, just rendered the scene with the GPU accelerated Optixrenderer, which
> > > > > seems to work without a glitch -- and that would not fall back to the CPU, right? I will test this on my Linux box tomorrow -- I believe I have seen this
> > > > > error on Linux, too, in the not too distant past .. Since quicksurf works
> > > > > nevertheless, I did not investigate.
> > > > >
> > > > > Anyways, here is the output from VMDQUICKSURFVERBOSE (using 1crn.pdb as before)
> > > > >
> > > > > QuickSurf: R*1.0, I=0.5, H=1.0 Pad: 7.1 minR: 1.5 maxR: 1.8)
> > > > > GridSZ: ( 42 36 42) BBox: (-10.2 -7.6 -14.5)->(30.8 27.4 26.5)
> > > > > CUDA Thrust sort_by_key() failed: C:/Users/johns/Desktop/build/vmd/src/CUDASort.cu line 190
> > > > > dev_radix_sort_by_key() failed: C:/Users/johns/Desktop/build/vmd/src/CUDASpatialSearch.cu line 259
> > > > > Computing density map grid on CPUs vmd_gaussdensity_avx2()
> > > > > .Running marching cubes on CPU...
> > > > > Info) QuickSurf: 0.031 [pre:0.000 vol:0.031 gr:0.000 mc:0.00 mcv:0.000]
> > > > > Done.
> > > > >
> > > > > One thing I noted: if the atom selection in Graphics->Represenations is
> > > > > set to 'all', then the quicksurf command hangs (I see the hourglass in
> > > > > the Representation window), and I needed to hit Enter in the cmd window
> > > > > from which I started vmd. Repeating with the selection 'protein' worked
> > > > > instantenously -- the debug output, however, is exactly the same as copied
> > > > > above -- not surprsing, as 1crn.pdb contains only protein.
> > > > >
> > > > > Best,
> > > > > Stefan
> > > > >
> > > > > On Wed, Dec 16, 2020 at 10:57:22AM -0600, John Stone wrote:
> > > > > > Stefan,
> > > > > > The error message indicates that the GPU code path encountered a failure,
> > > > > > possibly due to running out of GPU memory. When this happens, VMD then
> > > > > > goes through an error fall-back to run the CPU version of QuickSurf instead,
> > > > > > to complete the rendering. Depending on the cause of the error, it may
> > > > > > prevent further invocations of QuickSurf from trying to use the GPU
> > > > > > code path and will continue to revert to using the CPU.
> > > > > > Since I'm able to run 1CRN on my machines without trouble, I'm assuming
> > > > > > that this is a GPU memory capacity shortfall. This sort of situation can
> > > > > > be caused or exacerbated by the simultaneous use of other graphics-intensive
> > > > > > applications. On Windows in particular, if you're using the Google Chrome
> > > > > > browser, it has a tendency to rack up significant GPU memory use. You might
> > > > > > try running VMD w/ QuickSurf again when the machine is otherwise devoid of
> > > > > > other running apps, and see if the problem recurs or not.
> > > > > >
> > > > > > If you want, you can enable much more detailed QuickSurf info logging
> > > > > > by setting the environment variable VMDQUICKSURFVERBOSE either before
> > > > > > launching VMD (the same way you're setting VMDNOOSPRAY), or within
> > > > > > VMD via: "set env(VMDQUICKSURFVERBOSE) 1" before computing the QuickSurf
> > > > > > surfaces. I would be curious to see what your system outputs in the case
> > > > > > that leads to the Thrust errors.
> > > > > >
> > > > > > Best,
> > > > > > John Stone
> > > > > > vmd_at_ks.uiuc.edu
> > > > > >
> > > > > > On Wed, Dec 16, 2020 at 05:31:30PM +0100, Stefan Boresch wrote:
> > > > > > > John,
> > > > > > >
> > > > > > > concerning Quicksurf: My test is 1crn.pdb as downloaded right now from
> > > > > > > https://urldefense.com/v3/__http://www.rcsb.org/structure/1CRN__;!!DZ3fjg!u9iV_oE89LbBva2N-zf5GohNp2gWNZtSXa4mbiagcYPeDu0KQsYHOB5PVedpCUJajA$
> > > > > > >
> > > > > > > Then, in /User/stefa/Downloads, I start vmd, console output follows.
> > > > > > > After loading, I just change the representation from Lines to Quicksurf.
> > > > > > > Note: I get a picture, which looks fine and which I can manipulate; just
> > > > > > > the error message is fishy.
> > > > > > >
> > > > > > > Thanks, best regards,
> > > > > > >
> > > > > > > Stefan
> > > > > > >
> > > > > > > PS: Is there anything I can do to turn on additional logging etc?
> > > > > > >
> > > > > > > ------------------------------------------------------------------
> > > > > > >
> > > > > > > Microsoft Windows [Version 10.0.19042.685]
> > > > > > > (c) 2020 Microsoft Corporation. All rights reserved.
> > > > > > >
> > > > > > > C:\Users\stefa>cd Downloads
> > > > > > >
> > > > > > > C:\Users\stefa\Downloads>set VMDNOOSPRAY=1
> > > > > > >
> > > > > > > C:\Users\stefa\Downloads>"\Program Files\VMD\vmd.exe" 1crn.pdb
> > > > > > > Info) VMD for WIN64, version 1.9.4a50 (December 14, 2020)
> > > > > > > Info) http://www.ks.uiuc.edu/Research/vmd/
> > > > > > > Info) Email questions and bug reports to 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, 8 CPUs detected.
> > > > > > > Info) CPU features: SSE2 SSE4.1 AVX AVX2 FMA F16 AVX512F AVX512CD HT
> > > > > > > Info) Detected VM or hypervisor execution environment
> > > > > > > Info) Free system memory: 20GB (62%)
> > > > > > > Warning) Detected a mismatch between CUDA runtime and GPU driver
> > > > > > > Warning) Check to make sure that GPU drivers are up to date.
> > > > > > > Info) No CUDA accelerator devices available.
> > > > > > > Info) OpenGL renderer: GeForce GTX 1650 with Max-Q Design/PCIe/SSE2
> > > > > > > Info) Features: STENCIL 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) No joysticks found. Joystick interface disabled.
> > > > > > > Info) Detected 1 available TachyonL/OptiX ray tracing accelerator
> > > > > > > Info) Compiling OptiX shaders on 1 target GPU...
> > > > > > > Info) Dynamically loaded 76 plugins in directory:
> > > > > > > Info) C:/Program Files/VMD/plugins/WIN64/molfile
> > > > > > > Info) File loading in progress, please wait.
> > > > > > > Info) Using plugin pdb for structure file 1crn.pdb
> > > > > > > Info) Using plugin pdb for coordinates from file 1crn.pdb
> > > > > > > Info) Determining bond structure from distance search ...
> > > > > > > Info) Eliminating bonds duplicated from existing structure...
> > > > > > > Info) Finished with coordinate file 1crn.pdb.
> > > > > > > Info) Analyzing structure ...
> > > > > > > Info) Atoms: 327
> > > > > > > Info) Bonds: 337
> > > > > > > Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
> > > > > > > Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
> > > > > > > Info) Residues: 46
> > > > > > > Info) Waters: 0
> > > > > > > Info) Segments: 1
> > > > > > > Info) Fragments: 1 Protein: 1 Nucleic: 0
> > > > > > > vmd > CUDA Thrust sort_by_key() failed: C:/Users/johns/Desktop/build/vmd/src/CUDASort.cu line 190
> > > > > > > dev_radix_sort_by_key() failed: C:/Users/johns/Desktop/build/vmd/src/CUDASpatialSearch.cu line 259
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > On Wed, Dec 16, 2020 at 09:12:02AM -0600, John Stone wrote:
> > > > > > > > Stefan,
> > > > > > > > Great. Regarding QuickSurf, if you can provide me with input file(s)
> > > > > > > > and parameters that cause QuickSurf to generate those Thrust errors,
> > > > > > > > that would be very helpful for me. Without the specific inputs that trigger
> > > > > > > > the issue it's very hard for me to address that kind of runtime fault.
> > > > > > > >
> > > > > > > > I hope to address the OSPRay startup failure issue in a more
> > > > > > > > graceful and automatic way so that at least no user-set environment
> > > > > > > > variable would be required to get past the problem. It's still
> > > > > > > > not clear why OSPRay has trouble on your system, but I'm hoping that
> > > > > > > > as more people start running the 64-bit Windows build a pattern may
> > > > > > > > emerge there that clarifies what's happening with OSPRay. This particular
> > > > > > > > issue has never arisen with OSPRay on the Linux or Mac builds, so it's
> > > > > > > > somehow unique to Windows thus far.
> > > > > > > >
> > > > > > > > Best,
> > > > > > > > John Stone
> > > > > > > > vmd_at_ks.uiuc.edu
> > > > > > > >
> > > > > > > >
> > > > > > > > On Wed, Dec 16, 2020 at 11:44:38AM +0100, Stefan Boresch wrote:
> > > > > > > > > John,
> > > > > > > > >
> > > > > > > > > rapidly tested V3.
> > > > > > > > >
> > > > > > > > > Stride works.
> > > > > > > > >
> > > > > > > > > QUICKSURF works (throwing the same error messages as before)
> > > > > > > > >
> > > > > > > > > SURF works. Though, here I should note that I got one of these
> > > > > > > > > 'hangs', where VMD seems frozen (nothing displayed yet), hitting Enter
> > > > > > > > > / Ctrl-C in the cmd Window from which I started vmd interupts this,
> > > > > > > > > and then the surface is displayed just fine.Running SURF again then
> > > > > > > > > works just fine without freezing. (Note: I have seen this behavior
> > > > > > > > > under Windows with 1.9.3 as well).
> > > > > > > > >
> > > > > > > > > VMDNOOSPRAY=1 is still needed, but that fix wasn't in the "release
> > > > > > > > > notes".
> > > > > > > > >
> > > > > > > > > I definitely seem to be able to do "quick and dirty" visualization (if
> > > > > > > > > needed) without switching to my Linux machine.
> > > > > > > > >
> > > > > > > > > Anyways, a big thank you!
> > > > > > > > >
> > > > > > > > > Stefan
> > > > > > > > >
> > > > > > > > > On Wed, Dec 16, 2020 at 01:57:17AM -0600, John Stone wrote:
> > > > > > > > > > Stefan,
> > > > > > > > > > I've posted a V3 installer with Stride and Surf fixed.
> > > > > > > > > >
> > > > > > > > > > Best,
> > > > > > > > > > John
> > > > > > > > > >
> > > > > > > > > > On Tue, Dec 15, 2020 at 10:27:01PM +0100, Stefan Boresch wrote:
> > > > > > > > > > > Hi John,
> > > > > > > > > > >
> > > > > > > > > > > 1) The QUICKSURF error/warning is reproducible, I'll paste the full
> > > > > > > > > > > console output below. Curiously, by mis-clicking I seem to have triggered
> > > > > > > > > > > a different error; no STRIDE executable is found:
> > > > > > > > > > >
> > > > > > > > > > > Info) assignment. Proteins: structure, function and genetics, 23, 566-579.
> > > > > > > > > > > ERROR) STRIDE binary "C:\Program Files\VMD\stride_WIN64.exe" cannot be run; check permissions.
> > > > > > > > > > > ERROR) Call to Stride program failed.
> > > > > > > > > > >
> > > > > > > > > > > (No stride_WIN64.exe in/at this path)
> > > > > > > > > > >
> > > > > > > > > > > 2) GPU is whatever version of a GTX1650 Microsoft used for the Surface Book
> > > > > > > > > > >
> > > > > > > > > > > Output from \Windows\System32\nvidia-smi.exe (running the new vmd alpha
> > > > > > > > > > > build)
> > > > > > > > > > >
> > > > > > > > > > > ~ $ C:\Windows\System32\nvidia-smi.exe
> > > > > > > > > > > Tue Dec 15 22:14:54 2020
> > > > > > > > > > > +-----------------------------------------------------------------------------+
> > > > > > > > > > > | NVIDIA-SMI 451.77 Driver Version: 451.77 CUDA Version: 11.0 |
> > > > > > > > > > > |-------------------------------+----------------------+----------------------+
> > > > > > > > > > > | GPU Name TCC/WDDM | Bus-Id Disp.A | Volatile Uncorr. ECC |
> > > > > > > > > > > | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. |
> > > > > > > > > > > |===============================+======================+======================|
> > > > > > > > > > > | 0 GeForce GTX 165... WDDM | 00000000:02:00.0 Off | N/A |
> > > > > > > > > > > | N/A 34C P8 1W / N/A | 132MiB / 4096MiB | 0% Default |
> > > > > > > > > > > +-------------------------------+----------------------+----------------------+
> > > > > > > > > > >
> > > > > > > > > > > +-----------------------------------------------------------------------------+
> > > > > > > > > > > | Processes: |
> > > > > > > > > > > | GPU GI CI PID Type Process name GPU Memory |
> > > > > > > > > > > | ID ID Usage |
> > > > > > > > > > > |=============================================================================|
> > > > > > > > > > > | 0 N/A N/A 7124 C+G C:\Program Files\VMD\vmd.exe N/A |
> > > > > > > > > > > +-----------------------------------------------------------------------------+
> > > > > > > > > > >
> > > > > > > > > > > Note: these are (this is) the driver(s) installed by the Windows
> > > > > > > > > > > update mechanism, I haven't touched anything nvidia related by hand. I did not
> > > > > > > > > > > install any CUDA development libraries/tools on this machine.
> > > > > > > > > > >
> > > > > > > > > > > 3) Processor, one of the cores (as reported by /proc/cpuinfo in WSL):
> > > > > > > > > > >
> > > > > > > > > > > processor : 1
> > > > > > > > > > > vendor_id : GenuineIntel
> > > > > > > > > > > cpu family : 6
> > > > > > > > > > > model : 126
> > > > > > > > > > > model name : Intel(R) Core(TM) i7-1065G7 CPU @ 1.30GHz
> > > > > > > > > > > stepping : 5
> > > > > > > > > > > microcode : 0xffffffff
> > > > > > > > > > > cpu MHz : 1497.604
> > > > > > > > > > > cache size : 8192 KB
> > > > > > > > > > > physical id : 0
> > > > > > > > > > > siblings : 2
> > > > > > > > > > > core id : 0
> > > > > > > > > > > cpu cores : 1
> > > > > > > > > > > apicid : 1
> > > > > > > > > > > initial apicid : 1
> > > > > > > > > > > fpu : yes
> > > > > > > > > > > fpu_exception : yes
> > > > > > > > > > > cpuid level : 21
> > > > > > > > > > > wp : yes
> > > > > > > > > > > flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ss ht syscall nx pdpe1gb rdtscp lm constant_tsc rep_good nopl xtopology cpuid pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand hypervisor lahf_lm abm 3dnowprefetch invpcid_single ssbd ibrs ibpb stibp ibrs_enhanced fsgsbase bmi1 avx2 smep bmi2 erms invpcid avx512f avx512dq rdseed adx smap avx512ifma clflushopt avx512cd sha_ni avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves avx512vbmi umip avx512_vbmi2 gfni vaes vpclmulqdq avx512_vnni avx512_bitalg avx512_vpopcntdq rdpid flush_l1d arch_capabilities
> > > > > > > > > > > bugs : spectre_v1 spectre_v2 spec_store_bypass swapgs itlb_multihit
> > > > > > > > > > > bogomips : 2995.20
> > > > > > > > > > > clflush size : 64
> > > > > > > > > > > cache_alignment : 64
> > > > > > > > > > > address sizes : 39 bits physical, 48 bits virtual
> > > > > > > > > > > power management:
> > > > > > > > > > >
> > > > > > > > > > > (This is the more or less fully maxed out configuration of the 13.5" Surface
> > > > > > > > > > > Book 3 laptop/convertible -- whatever this thing is ;-)
> > > > > > > > > > > See, e.g.,
> > > > > > > > > > > https://urldefense.com/v3/__https://www.microsoft.com/en-us/surface/devices/surface-book-3/tech-specs__;!!DZ3fjg!u9iV_oE89LbBva2N-zf5GohNp2gWNZtSXa4mbiagcYPeDu0KQsYHOB5PVeftOOPX9g$
> > > > > > > > > > >
> > > > > > > > > > > Copy of output in console window follows.
> > > > > > > > > > >
> > > > > > > > > > > And, yes, this is amazing progress -- thanks!
> > > > > > > > > > >
> > > > > > > > > > > Stefan
> > > > > > > > > > >
> > > > > > > > > > > PS: All I did was load PDB 1crn directly from the PDB, and trying to activate
> > > > > > > > > > > QUICKSURF must have by accident hit (New)Cartoon first ..
> > > > > > > > > > >
> > > > > > > > > > > C:\Users\stefa>"\Program Files\VMD\vmd.exe"
> > > > > > > > > > > Info) VMD for WIN64, version 1.9.4a50 (December 14, 2020)
> > > > > > > > > > > Info) http://www.ks.uiuc.edu/Research/vmd/
> > > > > > > > > > > Info) Email questions and bug reports to 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, 8 CPUs detected.
> > > > > > > > > > > Info) CPU features: SSE2 SSE4.1 AVX AVX2 FMA F16 AVX512F AVX512CD HT
> > > > > > > > > > > Info) Detected VM or hypervisor execution environment
> > > > > > > > > > > Info) Free system memory: 22GB (69%)
> > > > > > > > > > > Warning) Detected a mismatch between CUDA runtime and GPU driver
> > > > > > > > > > > Warning) Check to make sure that GPU drivers are up to date.
> > > > > > > > > > > Info) No CUDA accelerator devices available.
> > > > > > > > > > > Info) OpenGL renderer: GeForce GTX 1650 with Max-Q Design/PCIe/SSE2
> > > > > > > > > > > Info) Features: STENCIL 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) No joysticks found. Joystick interface disabled.
> > > > > > > > > > > Info) Detected 1 available TachyonL/OptiX ray tracing accelerator
> > > > > > > > > > > Info) Compiling OptiX shaders on 1 target GPU...
> > > > > > > > > > > Info) Dynamically loaded 76 plugins in directory:
> > > > > > > > > > > Info) C:/Program Files/VMD/plugins/WIN64/molfile
> > > > > > > > > > > vmd > The PDB is supported by RCSB, the NSF, US PHS, NIH, NCRP, NIGMS, NLM,
> > > > > > > > > > > and US DoE, who are not liable for the data. PDB files shall not be
> > > > > > > > > > > sold. See https://urldefense.com/v3/__ftp://ftp.rcsb.org/advisory.doc__;!!DZ3fjg!u9iV_oE89LbBva2N-zf5GohNp2gWNZtSXa4mbiagcYPeDu0KQsYHOB5PVecdHiAfww$ for full details.
> > > > > > > > > > > Info) Using plugin webpdb for structure file 1crn
> > > > > > > > > > > Info) Using plugin webpdb for coordinates from file 1crn
> > > > > > > > > > > Info) Determining bond structure from distance search ...
> > > > > > > > > > > Info) Analyzing structure ...
> > > > > > > > > > > Info) Atoms: 327
> > > > > > > > > > > Info) Bonds: 337
> > > > > > > > > > > Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
> > > > > > > > > > > Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
> > > > > > > > > > > Info) Residues: 46
> > > > > > > > > > > Info) Waters: 0
> > > > > > > > > > > Info) Segments: 1
> > > > > > > > > > > Info) Fragments: 1 Protein: 1 Nucleic: 0
> > > > > > > > > > > Info) Finished with coordinate file 1crn.
> > > > > > > > > > > Info) In any publication of scientific results based in part or
> > > > > > > > > > > Info) completely on the use of the program STRIDE, please reference:
> > > > > > > > > > > Info) Frishman,D & Argos,P. (1995) Knowledge-based secondary structure
> > > > > > > > > > > Info) assignment. Proteins: structure, function and genetics, 23, 566-579.
> > > > > > > > > > > ERROR) STRIDE binary "C:\Program Files\VMD\stride_WIN64.exe" cannot be run; check permissions.
> > > > > > > > > > > ERROR) Call to Stride program failed.
> > > > > > > > > > > CUDA Thrust sort_by_key() failed: C:/Users/johns/Desktop/build/vmd/src/CUDASort.cu line 190
> > > > > > > > > > > dev_radix_sort_by_key() failed: C:/Users/johns/Desktop/build/vmd/src/CUDASpatialSearch.cu line 259
> > > > > > > > > > >
> > > > > > > > > > > On Tue, Dec 15, 2020 at 03:03:03PM -0600, John Stone wrote:
> > > > > > > > > > > > Stefan,
> > > > > > > > > > > > Can you tell me exactly what GPU hardware (and driver versions)
> > > > > > > > > > > > are in this machine?
> > > > > > > > > > > >
> > > > > > > > > > > > Are the QuickSurf errors you're getting repeatable? Can you make it
> > > > > > > > > > > > happen reliably? I'd love to have any/all test cases that can trigger
> > > > > > > > > > > > the 'CUDA Thrust sort_by_key()' failure that you posted.
> > > > > > > > > > > >
> > > > > > > > > > > > I believe I know what the issue is with Surf, that's another installer
> > > > > > > > > > > > packaging problem I have to resolve. It looks like I'll be making a
> > > > > > > > > > > > V3 later tonight. This is very good progress though for first contact
> > > > > > > > > > > > with real users. I'll send another note when I've got a V3 build ready.
> > > > > > > > > > > >
> > > > > > > > > > > > Best,
> > > > > > > > > > > > John
> > > > > > > > > > > >
> > > > > > > > > > > > On Tue, Dec 15, 2020 at 08:24:22PM +0100, Stefan Boresch wrote:
> > > > > > > > > > > > >
> > > > > > > > > > > > > John,
> > > > > > > > > > > > >
> > > > > > > > > > > > > thank you again. I just installed V2. The OspRay issue
> > > > > > > > > > > > > is still there, but the workaround with the environment variable works.
> > > > > > > > > > > > >
> > > > > > > > > > > > > [Could the OspRay error indicate that (in the library) some CPU
> > > > > > > > > > > > > instructions are used, which for some reason this particular CPU
> > > > > > > > > > > > > doesn't suppport (Intel(R) Core(TM) i7-1065G7 CPU)?]
> > > > > > > > > > > > >
> > > > > > > > > > > > > The Optix shader works (as does Quicksurf (which spits out some CUDA
> > > > > > > > > > > > > warnings), so I actually assume that NVIDIA/CUDA *does* work, contrary
> > > > > > > > > > > > > to the startup message.
> > > > > > > > > > > > >
> > > > > > > > > > > > > For the record, quicksurf gives me the following:
> > > > > > > > > > > > >
> > > > > > > > > > > > > CUDA Thrust sort_by_key() failed: C:/Users/johns/Desktop/build/vmd/src/CUDASort.cu line 190
> > > > > > > > > > > > > dev_radix_sort_by_key() failed: C:/Users/johns/Desktop/build/vmd/src/CUDASpatialSearch.cu line 259
> > > > > > > > > > > > >
> > > > > > > > > > > > > (But I believe I have seen this warning on Linux platforms, too..)
> > > > > > > > > > > > >
> > > > > > > > > > > > > What is new is that SURF doesn't work, the error is:
> > > > > > > > > > > > >
> > > > > > > > > > > > > ERROR) Cannot read SURF output file: C:\Users\stefa\AppData\Local\Temp\vmdsurf.u0.41.in.tri
> > > > > > > > > > > > >
> > > > > > > > > > > > > The directory exists, and I (user = stefa) can write/read from it, so this
> > > > > > > > > > > > > looks a bit strange.
> > > > > > > > > > > > >
> > > > > > > > > > > > > I cannot thank you enough for your efforts and persistence!
> > > > > > > > > > > > >
> > > > > > > > > > > > > Best regards,
> > > > > > > > > > > > > Stefan
> > > > > > > > > > > > >
> > > > > > > > > > > > > On Tue, Dec 15, 2020 at 12:06:50PM -0600, John Stone wrote:
> > > > > > > > > > > > > > Hi guys,
> > > > > > > > > > > > > > I've assembled a new 64-bit Windows installer that corrects
> > > > > > > > > > > > > > two of the prior issues you reported, and I've posted it with a
> > > > > > > > > > > > > > newer "V2" suffix:
> > > > > > > > > > > > > > http://www.ks.uiuc.edu/Research/vmd/alpha/
> > > > > > > > > > > > > >
> > > > > > > > > > > > > > The new test build corrects the two issues below:
> > > > > > > > > > > > > > 1) VMD plugin loading and startup scripts are up-to-date
> > > > > > > > > > > > > > 2) default vmd.rc file no longer has a stray debug/testing command in it
> > > > > > > > > > > > > >
> > > > > > > > > > > > > > The mismatched installation target directory in the installer GUI
> > > > > > > > > > > > > > remains for the time being.
> > > > > > > > > > > > > >
> > > > > > > > > > > > > > Stefan: I discussed the OSPRay startup issue with the OSPRay developers
> > > > > > > > > > > > > > and I will try and add some workaround code in VMD to make it
> > > > > > > > > > > > > > continue startup even in the case that OSPRay modules fail to load.
> > > > > > > > > > > > > >
> > > > > > > > > > > > > > Jerome: The behavior of file/path names with internationalized strings
> > > > > > > > > > > > > > data will need to be dealt with in a future build.
> > > > > > > > > > > > > >
> > > > > > > > > > > > > > I noted that you're all getting bogus CUDA driver warnings on systems
> > > > > > > > > > > > > > that don't contain NVIDIA GPU hardware, so I'll have to revisit that
> > > > > > > > > > > > > > code as well.
> > > > > > > > > > > > > >
> > > > > > > > > > > > > > Barring further installer/packaging corrections further
> > > > > > > > > > > > > > improvements will have to come in a later alpha version
> > > > > > > > > > > > > > since they'll require code changes.
> > > > > > > > > > > > > >
> > > > > > > > > > > > > > Best regards,
> > > > > > > > > > > > > > John Stone
> > > > > > > > > > > > > > vmd_at_ks.uiuc.edu
> > > > > > > > > > > > > >
> > > > > > > > > > > > > > --
> > > > > > > > > > > > > > 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/
> > > > > > > > > > > > > >
> > > > > > > > > > > >
> > > > > > > > > > > > --
> > > > > > > > > > > > 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/
> > > > > > > > > >
> > > > > > > > > > --
> > > > > > > > > > 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/
> > > > > > > >
> > > > > > > > --
> > > > > > > > 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/
> > > > > >
> > > > > > --
> > > > > > 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/
> > > >
> > > > --
> > > > 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/
> >
> > --
> > 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/
-- 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/
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