VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Aug 21 2014 - 15:25:42 CDT
The install error you saw is looking for the Tachyon binary, which
would normally be included irrespective of whether LIBTACHYON is used.
You can safely ignore that error if you're not using Tachyon.
The real issue is that the installation directory didn't seem to
have the vmd_LINUXAMD64 binary, which means that either you got the
install paths mixed up in the configure script, or it didn't get copied
in during the in make and subsequent install phases. Check to see if it
at least got compiled or not.
On Thu, Aug 21, 2014 at 03:22:06PM -0500, Jim Parker wrote:
> A Thanks for the quick reply.A I tried eliminating LIBTACHYON, but I
> must be missing something because I get the same final response
> $ make install
> cp: cannot stat a**../lib/tachyon/tachyon_LINUXAMD64a**: No such file or
> Make sure /myhome/tmp/bin/vmd-src is in your path.
> VMD installation complete.A Enjoy!
> The executable fails with
> rlwrap: Command not found.
> /myhome/tmp/lib/vmd-src/vmd_LINUXAMD64: Command not found.
> There is no vmd_LINUXAMD64 file.
> Looking at the Makefile, an attempt will be made
> toA copyA lib/tachyon/tachyon_LINUXAMD64 regardless of the LIBTACHYON
> setting, so that error should be fine.A i.e., the Makefile attempted to
> create the file, but since it didn't exist, it just continued after
> printing a warning.
> However, I'm not sure where/when vmd_LINUXAMD64A should beA built.A
> I build the external programs Stride and Surf, copy to lib directory of
> the vmd build
> The plugins compile and I use
> make distrib
> to populate the plugins directory of the vmd build
> Then I try,
> ./configureA LINUXAMD64 IMD SILENT TCL PTHREADSA SHARED NETCDF
> make veryclean
> make install
> where I'm stuck.A No vmd_LINUXAMD64 is built.
> I found some archived mailing list items that indicated I may need to make
> a symlink from the plugins build directory to vmd/plugins, but the details
> were not clear.A However, currently using
> PLUGINDIR=/myhome/tmp/vmd/plugins whiich is the build directory
> On Wed, Aug 20, 2014 at 4:27 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
> A If you're compiling a text-mode VMD build, you would want your
> options to look more or less as you have them, but if you want to be
> able to use the built-in Tachyon, you'll need to compile it from source.
> If not, you can just delete the build option "LIBTACHYON" and that'll
> let you get past that.
> A John Stone
> A vmd_at_ks.uiuc.edu
> On Wed, Aug 20, 2014 at 04:17:16PM -0500, Jim Parker wrote:
> >A A Oops, fat fingered the <Send> button.
> >A A A continuing.
> >A A inspecting the lib/stride lib/surf and lib/tachyon folders, the
> only file
> >A A is a README file in each.
> >A A the folder /myhome/tmp/lib/vmd-src
> >A A contains a file vmd.so and none of the *_LINUXAMD64 files I would
> >A A to see.
> >A A I tried following the Makefile dependencies to understand how
> these 3
> >A A files were created, but as far as I can see they are just defined
> >A A VMD_OTHER_EXE and that handle is not used elsewhere.
> >A A Any help would be appreciated.
> >A A Cheers,
> >A A --Jim Parker
> >A A Department of Physics and Astronomy
> >A A The University of Texas at San Antonio
> >A A On Wed, Aug 20, 2014 at 4:09 PM, Jim Parker
> >A A wrote:
> >A A A Hello,
> >A A A AA I am attempting to compile a text-only (no OpenGL) version
> of VMD for
> >A A A use on an HPC cluster.AA Basically, I have many TCL scripts
> that work
> >A A A with atomselect methods and would like to have it available to
> >A A A compute nodes (which don't have OpenGL capability).
> >A A A I was hoping someone could recommend a set of options that
> >A A A generate a text only mode for a LINUXAMD64 computer.
> >A A A I saw that there are options provided for aix5&6.text compile
> modes, so
> >A A A I tried those same options with LINUXAMD64
> >A A A i.e. ./configure LINUXAMD64 IMD SILENT TCL PTHREADS LIBTACHYON
> >A A A LP64
> >A A A But the compilation fails with: undefined references to
> >A A A Examining these options, I omitted LP64, since it is not
> listed for any
> >A A A of the other LINUX modes and I assumed it was aix-specific.AA
> >A A A added SHARED since LINUX uses shared libraries
> >A A A With those changes, the code compiles without errors (only
> >A A A about unused variables), and I get
> >A A A No resource compiler required on this platform.
> >A A A which I understand indicates the compilation completed.
> >A A A However, make install gives the response
> >A A A cp: cannot stat a**./lib/stride/stride_LINUXAMD64a**: No such
> file or
> >A A A directory
> >A A A cp: cannot stat a**../lib/surf/surf_LINUXAMD64a**: No such
> file or
> >A A A directory
> >A A A cp: cannot stat a**../lib/tachyon/tachyon_LINUXAMD64a**: No
> such file or
> >A A A directory
> >A A A Make sure /home/surfer/tmp/bin/vmd-src is in your path.
> >A A A VMD installation complete.AA Enjoy!
> >A A A the resulting binary does not execute
> >A A A rlwrap: Command not found.
> >A A A /myhome/tmp/lib/vmd-src/vmd_LINUX: Command not found.
> >A A A And inspecting the lib/stride lib/surf and lib/tachyon
> folders, the only
> >A A A file is a README file in each.
> >A A A the folder /myhome/tmp/lib/vmd-src
> >A A A contains a file vmd.so and none of the *_LINUXAMD64
> > References
> >A A Visible links
> >A A 1. mailto:jimparker96313_at_gmail.com
> 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/A A A A A A Phone: 217-244-3349
> Visible links
> 1. http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/22467.html
> 2. mailto:johns_at_ks.uiuc.edu
> 3. mailto:vmd_at_ks.uiuc.edu
> 4. mailto:jimparker96313_at_gmail.com
> 5. mailto:jimparker96313_at_gmail.com
> 6. http://www.ks.uiuc.edu/~johns/
> 7. tel:217-244-3349
> 8. http://www.ks.uiuc.edu/Research/vmd/
-- 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/