VMD-L Mailing List

From: Cook, Rich (cook47_at_llnl.gov)
Date: Tue Aug 27 2013 - 13:31:05 CDT

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)