From: Stefan Boresch (stefan_at_mdy.univie.ac.at)
Date: Wed Dec 16 2020 - 04:44:38 CST

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://www.microsoft.com/en-us/surface/devices/surface-book-3/tech-specs
> >
> > 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 ftp://ftp.rcsb.org/advisory.doc 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/