VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jan 07 2020 - 15:21:49 CST

Hi,
  If installed correctly, VMD should find "menu main on" in its default
startup files. If you had/have an empty .vmdrc file, that would supercede
the default one, and could cause the behavior you describe below.
In any case, if things are working okay, it may be best to leave well enough
alone then. :-)

Best regards,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jan 07, 2020 at 09:19:04PM +0000, Chang, Christopher wrote:
> Thanks John. One of our local users monitors this list and helped me through it, so I got it up and running. Mostly it was some problems with path settings in vmd.sh, it seemed like there was not a single set of paths for $defaultvmddir, $vmdbasename, $TCL_LIBRARY, and $MASTERVMDDIR that would work correctly as written. (It's also possible I didn't execute an installation step I should have). The only other was that "menu main" doesn't default to "on", so I had to make that change in .vmdrc. Once I figured out the required setting, the expected interface came up no problems.
>
> FWIW,
>
> [cchang_at_el2 bin]$ diff vmd.sh vmd.sh.good
> 4,5c4,5
> < #defaultvmddir=/usr/local/lib/vmd
> < #vmdbasename=vmd
> ---
> > defaultvmddir=$VMDDIR
> > vmdbasename=vmd
> 34,35c34,35
> < VMDDIR=${VMDDIR-${defaultvmddir}}
> < export VMDDIR
> ---
> > #VMDDIR=${VMDDIR-${defaultvmddir}}
> > #export VMDDIR
> 90c90
> < TCL_LIBRARY="${VMDDIR}/scripts/tcl"
> ---
> > TCL_LIBRARY="${VMDDIR}/lib/scripts/tcl8"
> 298c298
> < elif [ -x "${VMDDIR}/${vmdbasename}_LINUXAMD64" ]
> ---
> > elif [ -x "${VMDDIR}/LINUXAMD64/${vmdbasename}_LINUXAMD64" ]
> 502c502
> < exec $vmdprefixcmd "$MASTERVMDDIR/$execname" "$@"
> ---
> > exec $vmdprefixcmd "$MASTERVMDDIR/LINUXAMD64/$execname" "$@"
>
> Thanks,
> Chris
>
> -----Original Message-----
> From: John Stone <johns_at_ks.uiuc.edu>
> Sent: Tuesday, January 7, 2020 1:51 PM
> To: Chang, Christopher <Christopher.Chang_at_nrel.gov>
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: VMD 1.9.3 Linux installation
>
> Hi,
> I think that something went wrong when you installed VMD into your local directory structure. VMD normally finds the OptiXShaders.ptx file within vmd/shaders/OptiXShaders.ptx (where the "vmd" directory is the top level directory that you installed into). You didn't indicate what steps you followed for installation, but if you can share the precise steps you took, it should be easy to resolve.
>
> Best regards,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Sat, Dec 14, 2019 at 12:27:05AM +0000, Chang, Christopher wrote:
> > Hi,
> >
> >
> >
> > When attempting to install the prebuilt binary, I unpack the tarball,
> > edit VMDDIR and TCL_LIBRARY settings in bin/vmd.sh. I can get a dispdev
> > text session without problem, but when trying to run with a graphical
> > interface I get
> >
> >
> >
> > [cchang_at_ed1 ~]$ vglrun vmd
> >
> > /projects/besqis/Packages/vmd-1.9.3/LINUXAMD64/vmd_LINUXAMD64:
> > /lib64/libGL.so.1: no version information available (required by
> > /projects/besqis/Packages/vmd-1.9.3/LINUXAMD64/vmd_LINUXAMD64)
> >
> > Info) VMD for LINUXAMD64, version 1.9.3 (November 30, 2016)
> >
> > 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, 36 CPUs detected.
> >
> > Info) CPU features: SSE2 AVX AVX2 FMA KNL:AVX-512F+CD+ER+PF
> >
> > Info) Free system memory: 636GB (84%)
> >
> > Info) Creating CUDA device pool and initializing hardware...
> >
> > Info) Detected 1 available CUDA accelerator:
> >
> > Info) [0] Quadro GV100 80 SM_7.0 @ 1.63 GHz, 32GB 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 GV100/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) X-Windows ClientMessage-based Spaceball device available.
> >
> > Info) Detected 1 available TachyonL/OptiX ray tracing accelerator
> >
> > Info) Compiling 1 OptiX shaders on 1 target GPU...
> >
> > ERROR) OptiXRenderer) ERROR: File not found (Details: Function "RTresult
> > _rtProgramCreateFromPTXFile(RTcontext, const char*, const char*,
> > RTprogram_api**)" caught exception:
> > /projects/besqis/Packages/vmd-1.9.3/shaders/OptiXShaders.ptx)
> > (OptiXRenderer.C:3898
> >
> > ...
> >
> >
> >
> > What needs to be set so that this file is found?
> >
> >
> >
> > Thanks; Chris
> >
> >
> >
> > Christopher Chang, Ph.D.
> >
> > Computational Scientist
> >
> > National Renewable Energy Laboratory
> >
> > 15013 Denver West Parkway, MS ESIF301
> >
> > Golden, CO 80401
> >
> >
>
> --
> 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/