From: Cook, Rich (cook47_at_llnl.gov)
Date: Tue Aug 27 2013 - 15:29:47 CDT

That would be great!
I've gotten some feedback that the python interface is not going be very useful, so I will abdicate my compilation efforts on 1.9.1 until it gets easier or there is more value in it. I used to have this working, but lost my notes on the subject.
Thanks for suffering through with me.
-- Rich

On Aug 27, 2013, at 1:08 PM, John Stone <johns_at_ks.uiuc.edu>
 wrote:

> 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/

-- 
âœRichard 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)