From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Aug 27 2013 - 14:20:24 CDT

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.