VMD-L Mailing List

From: Jim Parker (jimparker96313_at_gmail.com)
Date: Thu Aug 21 2014 - 15:22:06 CDT

 John,
  Thanks for the quick reply. I tried eliminating LIBTACHYON, but I must
be missing something because I get the same final response

$ make install

cp: cannot stat ‘../lib/tachyon/tachyon_LINUXAMD64’: No such file or
directory
Make sure /myhome/tmp/bin/vmd-src is in your path.
VMD installation complete. 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
to copy lib/tachyon/tachyon_LINUXAMD64 regardless of the LIBTACHYON
setting, so that error should be fine. 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_LINUXAMD64 should be built.
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,
./configure LINUXAMD64 IMD SILENT TCL PTHREADS SHARED NETCDF
make veryclean
make
make install

where I'm stuck. 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. However, currently using PLUGINDIR=/myhome/tmp/vmd/plugins
whiich is the build directory

http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/22467.html

Cheers,
--Jim

On Wed, Aug 20, 2014 at 4:27 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> 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.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Aug 20, 2014 at 04:17:16PM -0500, Jim Parker wrote:
> > Oops, fat fingered the <Send> button.
> > A continuing.
> >
> > inspecting the lib/stride lib/surf and lib/tachyon folders, the only
> file
> > is a README file in each.
> > the folder /myhome/tmp/lib/vmd-src
> > contains a file vmd.so and none of the *_LINUXAMD64 files I would
> expect
> > to see.
> >
> > I tried following the Makefile dependencies to understand how these 3
> > files were created, but as far as I can see they are just defined in
> > VMD_OTHER_EXE and that handle is not used elsewhere.
> >
> > Any help would be appreciated.
> >
> > Cheers,
> > --Jim Parker
> > Department of Physics and Astronomy
> > The University of Texas at San Antonio
> >
> > On Wed, Aug 20, 2014 at 4:09 PM, Jim Parker <[1]
> jimparker96313_at_gmail.com>
> > wrote:
> >
> > Hello,
> > A I am attempting to compile a text-only (no OpenGL) version of
> VMD for
> > use on an HPC cluster.A Basically, I have many TCL scripts that
> work
> > with atomselect methods and would like to have it available to the
> > compute nodes (which don't have OpenGL capability).
> >
> > I was hoping someone could recommend a set of options that would
> > generate a text only mode for a LINUXAMD64 computer.
> > I saw that there are options provided for aix5&6.text compile
> modes, so
> > I tried those same options with LINUXAMD64
> > i.e. ./configure LINUXAMD64 IMD SILENT TCL PTHREADS LIBTACHYON
> NETCDF
> > LP64
> >
> > But the compilation fails with: undefined references to
> libtachyon.so...
> > Examining these options, I omitted LP64, since it is not listed for
> any
> > of the other LINUX modes and I assumed it was aix-specific.A Also,
> > added SHARED since LINUX uses shared libraries
> > With those changes, the code compiles without errors (only warnings
> > about unused variables), and I get
> >
> > No resource compiler required on this platform.
> >
> > which I understand indicates the compilation completed.
> > However, make install gives the response
> > cp: cannot stat a**./lib/stride/stride_LINUXAMD64a**: No such file
> or
> > directory
> > cp: cannot stat a**../lib/surf/surf_LINUXAMD64a**: No such file or
> > directory
> > cp: cannot stat a**../lib/tachyon/tachyon_LINUXAMD64a**: No such
> file or
> > directory
> > Make sure /home/surfer/tmp/bin/vmd-src is in your path.
> > VMD installation complete.A Enjoy!
> >
> > the resulting binary does not execute
> > rlwrap: Command not found.
> > /myhome/tmp/lib/vmd-src/vmd_LINUX: Command not found.
> >
> > And inspecting the lib/stride lib/surf and lib/tachyon folders, the
> only
> > file is a README file in each.
> > the folder /myhome/tmp/lib/vmd-src
> > contains a file vmd.so and none of the *_LINUXAMD64
> >
> > References
> >
> > Visible links
> > 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/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>