From: Cook, Rich (cook47_at_llnl.gov)
Date: Tue Aug 27 2013 - 14:49:26 CDT

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)