From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Aug 27 2013 - 15:08:59 CDT

Rich,
  You're reading the right docs, but clearly I need to update
the text to be more user friendly than it is currently.
I'll see if I can get some time to do some documentation updates
(both these and various others) as I get ready for the next VMD release.

Cheers,
  John

On Tue, Aug 27, 2013 at 07:49:26PM +0000, Cook, Rich wrote:
> Thanks!
> In my own defense, I'm just following the instructions I found here:
> http://www.ks.uiuc.edu/Research/vmd/doxygen/compiling.html
>
> Is there a better document somewhere that actually says how to compile VMD from source in a way that works? I get the feeling I'm looking at the wrong thing. I just googled "how to build VMD" and ended up there.
> I appreciate the help
>
> -- Rich
>
>
> On Aug 27, 2013, at 12:20 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> wrote:
>
> > rich,
> >
> > it looks like you forgot to compile (make) before installing (make
> > install). for a number of reasons, the build procedure of VMD does not
> > always follow the typical conventions. it also looks as if you are
> > missing several of the configured add-on packages (stride, surf,
> > tachyon).
> >
> > axel.
> >
> > On Tue, Aug 27, 2013 at 8:31 PM, Cook, Rich <cook47_at_llnl.gov> wrote:
> >> Hmm, still failing. Here is what happens now:
> >>
> >> -----------------------------------------------------------------------
> >> mkdir -p //usr/local/tools/vmd-1.9.1
> >> + mkdir -p //usr/local/bin
> >> + tar -xzf /tmp/dpkg-mkdeb.X4xSdbFVeA/src/vmd-1.9.1.src.tar.gz
> >> + pushd plugins
> >> /tmp/dpkg-mkdeb.X4xSdbFVeA/src/plugins /tmp/dpkg-mkdeb.X4xSdbFVeA/src
> >> + make LINUXAMD64
> >> -------------- blah blah blah -- looking good??? then: --------------------------------
> >> Copying phylotree 1.2 files to
> >> //usr/local/tools/vmd-1.9.1/plugins/LINUXAMD64/tcl/phylotree1.2
> >> Copying psipred 1.1 files to //usr/local/tools/vmd-1.9.1/plugins/noarch/tcl/psipred1.1
> >> Copying seqdata 1.1 files to //usr/local/tools/vmd-1.9.1/plugins/noarch/tcl/seqdata1.1
> >> Copying seqedit 1.1 files to //usr/local/tools/vmd-1.9.1/plugins/noarch/tcl/seqedit1.1
> >> Copying stamp 1.2 files to
> >> //usr/local/tools/vmd-1.9.1/plugins/LINUXAMD64/tcl/stamp1.2
> >> + popd
> >> /tmp/dpkg-mkdeb.X4xSdbFVeA/src
> >> + pushd vmd-1.9.1
> >> /tmp/dpkg-mkdeb.X4xSdbFVeA/src/vmd-1.9.1 /tmp/dpkg-mkdeb.X4xSdbFVeA/src
> >> + export VMDINSTALLBINDIR=//usr/local/tools/vmd-1.9.1/bin
> >> + VMDINSTALLBINDIR=//usr/local/tools/vmd-1.9.1/bin
> >> + export VMDINSTALLLIBRARYDIR=//usr/local/tools/vmd-1.9.1
> >> + VMDINSTALLLIBRARYDIR=//usr/local/tools/vmd-1.9.1
> >> + ln -s //usr/local/tools/vmd-1.9.1/plugins
> >> + make linux.cuda64.opengl
> >> ./configure LINUXAMD64 OPENGL FLTK TK IMD VRPN SILENT LIBSBALL XINPUT TCL PTHREADS ACTC LIBTACHYON NETCDF PYTHON NUMPY CUDA
> >> + cd src
> >> + make install
> >> cp: cannot stat `../LINUXAMD64/vmd_LINUXAMD64': No such file or directory
> >> cp: cannot stat `../lib/stride/stride_LINUXAMD64': No such file or directory
> >> cp: cannot stat `../lib/surf/surf_LINUXAMD64': No such file or directory
> >> cp: cannot stat `../lib/tachyon/tachyon_LINUXAMD64': No such file or directory
> >> tar: plugins: Cannot open: File exists
> >> tar: Exiting with failure status due to previous errors
> >> Make sure //usr/local/tools/vmd-1.9.1/bin/vmd is in your path.
> >> VMD installation complete. Enjoy!
> >> -----------------------------------------------------------------------
> >> Maybe I'm not making the right symlink?
> >> -- Rich
> >>
> >> On Aug 27, 2013, at 8:29 AM, John Stone <johns_at_ks.uiuc.edu>
> >> wrote:
> >>
> >>> Richard,
> >>> You need to make a symlink from your PLUGINDIR location, into
> >>> vmd/plugins, if that wasn't where you had set PLUGINDIR to point to already.
> >>> That should cure that problem.
> >>>
> >>> Cheers,
> >>> John
> >>>
> >>>
> >>> On Tue, Aug 27, 2013 at 01:15:07AM +0000, Cook, Rich wrote:
> >>>> Hi, I am trying to build VMD from source.
> >>>> I'm following the instructions (I think) from
> >>>> http://www.ks.uiuc.edu/Research/vmd/doxygen/compiling.html#compiling
> >>>> Here is what I do, and what happens. I'd appreciate some guidance...
> >>>> tar -xzf $SRC_DIR/vmd-${_vers}.src.tar.gz
> >>>> # http://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/compiling.html
> >>>> pushd plugins
> >>>> make LINUXAMD64
> >>>> export PLUGINDIR=$1${prefix}/plugins
> >>>> make distrib # <----------- SUCCEEDS
> >>>> popd
> >>>> # http://www.ks.uiuc.edu/Research/vmd/doxygen/compiling.html#compiling
> >>>> pushd vmd-${_vers}
> >>>> export VMDINSTALLBINDIR=$1${prefix}/bin
> >>>> export VMDINSTALLLIBRARYDIR=$1${prefix}
> >>>> make linux.cuda64.opengl
> >>>> At this point, I get this:
> >>>> + make linux.cuda64.opengl
> >>>> ./configure LINUXAMD64 OPENGL FLTK TK IMD VRPN SILENT LIBSBALL XINPUT TCL
> >>>> PTHREADS ACTC LIBTACHYON NETCDF PYTHON NUMPY CUDA
> >>>> Halting configuration until VMD plugins are built.
> >>>> VMD plugin directory not found.
> >>>> Please compile the VMD plugins and do 'make distrib' to copy them
> >>>> into a 'plugins' directory linked or located in this directory.
> >>>> Be sure your PLUGINDIR environment variable is set before running
> >>>> 'make distrib' in the plugin build area.
> >>>> What gives? I have set PLUGINDIR as you can see in the commands above,
> >>>> but it is being ignored.
> >>>> Thanks for any help...
> >>>> --
> >>>> *Richard Cook
> >>>> * Lawrence Livermore National Laboratory
> >>>> Bldg-453 Rm-4024, Mail Stop L-557
> >>>> 7000 East Avenue, Livermore, CA, 94550, USA
> >>>> TEL (office) (925) 423-9605
> >>>> TEL (fax) (925) 423-6961
> >>>> ---
> >>>> Information Management & Graphics Grp., Services & Development Div.,
> >>>> Integrated Computing & Communications Dept.
> >>>> (opinions expressed herein are mine and not those of LLNL)
> >>>
> >>> --
> >>> 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/
> >>
> >> --
> >> ???Richard Cook
> >> ??? Lawrence Livermore National Laboratory
> >> Bldg-453 Rm-4024, Mail Stop L-557
> >> 7000 East Avenue, Livermore, CA, 94550, USA
> >> ??? (office) (925) 423-9605
> >> ??? (fax) (925) 423-6961
> >> ---
> >> Information Management & Graphics Grp., Services & Development Div., Integrated Computing & Communications Dept.
> >> (opinions expressed herein are mine and not those of LLNL)
> >>
> >>
> >>
> >>
> >
> >
> >
> > --
> > Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> > International Centre for Theoretical Physics, Trieste. Italy.
>
> --
> ???Richard Cook
> ??? Lawrence Livermore National Laboratory
> Bldg-453 Rm-4024, Mail Stop L-557
> 7000 East Avenue, Livermore, CA, 94550, USA
> ??? (office) (925) 423-9605
> ??? (fax) (925) 423-6961
> ---
> Information Management & Graphics Grp., Services & Development Div., Integrated Computing & Communications Dept.
> (opinions expressed herein are mine and not those of LLNL)
>
>
>

-- 
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/