VMD-L Mailing List

From: Jim Parker (jimparker96313_at_gmail.com)
Date: Thu Aug 21 2014 - 16:26:37 CDT

Ok,
  found my error.
I should not use the option "SHARED"

To re-iterate for other users, from the configure script:
# SHARED - compile a shared library instead of a standalone executable

will generate a file vmd.so vice vmd_<arch>
the .so file can presumably be linked to another application, but doesn't
work on its own, nor will the alias 'vmd' execute it.

Thanks for helping me troubleshoot this.

Cheers,
--Jim

On Thu, Aug 21, 2014 at 3:25 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> 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.
>
> Cheers,
> John
>
> On Thu, Aug 21, 2014 at 03:22:06PM -0500, Jim Parker wrote:
> > John,
> > 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
> > directory
> > Make sure /myhome/tmp/bin/vmd-src is in your path.
> > VMD installation complete.A Enjoy!
> > A
> > The executable fails with
> > A
> > rlwrap: Command not found.
> > /myhome/tmp/lib/vmd-src/vmd_LINUXAMD64: Command not found.
> > A
> > 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.
> > A
> > 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
> > A
> > Then I try,
> > ./configureA LINUXAMD64 IMD SILENT TCL PTHREADSA SHARED NETCDF
> > make veryclean
> > make
> > make install
> > A
> > where I'm stuck.A No vmd_LINUXAMD64 is built.
> > A
> > 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
> > A
> > [1]http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/22467.html
> > A
> > Cheers,
> > --Jim
> > A
> > A
> > On Wed, Aug 20, 2014 at 4:27 PM, John Stone <[2]johns_at_ks.uiuc.edu>
> wrote:
> >
> > Hi,
> > 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.
> >
> > Cheers,
> > A John Stone
> > A [3]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
> > expect
> > >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
> > in
> > >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
> > <[1][4]jimparker96313_at_gmail.com>
> > >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
> > the
> > >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
> > would
> > >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
> > NETCDF
> > >A A A LP64
> > >
> > >A A A But the compilation fails with: undefined references to
> > libtachyon.so...
> > >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
> > Also,
> > >A A A added SHARED since LINUX uses shared libraries
> > >A A A With those changes, the code compiles without errors (only
> > warnings
> > >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:[5]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
> > [6]http://www.ks.uiuc.edu/~johns/A A A A A A Phone:
> [7]217-244-3349
> > [8]http://www.ks.uiuc.edu/Research/vmd/
> >
> > References
> >
> > 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/
>