VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Dec 16 2020 - 01:57:17 CST

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/