VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Aug 21 2014 - 16:33:47 CDT

Jim,
  Right. The SHARED option is used when VMD is compiled for use within
external Python modules and the like. You would not normally use that
flag when compiling the normal standalone VMD builds.

Cheers,
  John

On Thu, Aug 21, 2014 at 04:26:37PM -0500, Jim Parker wrote:
> Ok,A
> A found my error.A
> I should not use the option "SHARED"
>
> To re-iterate for other users, from the configure script:
> # SHAREDA A A A A A - 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 <[1]johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> A 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.A Check to see if
> it
> at least got compiled or not.
>
> Cheers,
> A John
>
> On Thu, Aug 21, 2014 at 03:22:06PM -0500, Jim Parker wrote:
> >A A John,
> >A A AA Thanks for the quick reply.AA I tried eliminating
> LIBTACHYON, but I
> >A A must be missing something because I get the same final response
> >
> >A A $ make install
> >
> >A A cp: cannot stat a**../lib/tachyon/tachyon_LINUXAMD64a**: No such
> file or
> >A A directory
> >A A Make sure /myhome/tmp/bin/vmd-src is in your path.
> >A A VMD installation complete.AA Enjoy!
> >A A A
> >A A The executable fails with
> >A A A
> >A A rlwrap: Command not found.
> >A A /myhome/tmp/lib/vmd-src/vmd_LINUXAMD64: Command not found.
> >A A A
> >A A There is no vmd_LINUXAMD64 file.
> >A A Looking at the Makefile, an attempt will be made
> >A A toA copyA lib/tachyon/tachyon_LINUXAMD64 regardless of the
> LIBTACHYON
> >A A setting, so that error should be fine.AA i.e., the Makefile
> attempted to
> >A A create the file, but since it didn't exist, it just continued
> after
> >A A printing a warning.
> >A A A
> >A A However, I'm not sure where/when vmd_LINUXAMD64A should beA
> built.A
> >A A I build the external programs Stride and Surf, copy to lib
> directory of
> >A A the vmd build
> >A A The plugins compile and I use
> >A A make distrib
> >A A to populate the plugins directory of the vmd build
> >A A A
> >A A Then I try,
> >A A ./configureAA LINUXAMD64 IMD SILENT TCL PTHREADSA SHARED NETCDF
> >A A make veryclean
> >A A make
> >A A make install
> >A A A
> >A A where I'm stuck.AA No vmd_LINUXAMD64 is built.
> >A A A
> >A A I found some archived mailing list items that indicated I may
> need to make
> >A A a symlink from the plugins build directory to vmd/plugins, but
> the details
> >A A were not clear.AA However, currently using
> >A A PLUGINDIR=/myhome/tmp/vmd/plugins whiich is the build directory
> >A A A
> >A A
> [1][2]http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/22467.html
> >A A A
> >A A Cheers,
> >A A --Jim
> >A A A
> >A A A
> >A A On Wed, Aug 20, 2014 at 4:27 PM, John Stone
> <[2][3]johns_at_ks.uiuc.edu> wrote:
> >
> >A A A Hi,
> >A A A AA If you're compiling a text-mode VMD build, you would want
> your
> >A A A options to look more or less as you have them, but if you want
> to be
> >A A A able to use the built-in Tachyon, you'll need to compile it
> from source.
> >A A A If not, you can just delete the build option "LIBTACHYON" and
> that'll
> >A A A let you get past that.
> >
> >A A A Cheers,
> >A A A AA John Stone
> >A A A AA [3][4]vmd_at_ks.uiuc.edu
> >A A A On Wed, Aug 20, 2014 at 04:17:16PM -0500, Jim Parker wrote:
> >A A A >AA AA Oops, fat fingered the <Send> button.
> >A A A >AA AA A continuing.
> >A A A >
> >A A A >AA AA inspecting the lib/stride lib/surf and lib/tachyon
> folders, the
> >A A A only file
> >A A A >AA AA is a README file in each.
> >A A A >AA AA the folder /myhome/tmp/lib/vmd-src
> >A A A >AA AA contains a file vmd.so and none of the *_LINUXAMD64
> files I would
> >A A A expect
> >A A A >AA AA to see.
> >A A A >
> >A A A >AA AA I tried following the Makefile dependencies to
> understand how
> >A A A these 3
> >A A A >AA AA files were created, but as far as I can see they are
> just defined
> >A A A in
> >A A A >AA AA VMD_OTHER_EXE and that handle is not used elsewhere.
> >A A A >
> >A A A >AA AA Any help would be appreciated.
> >A A A >
> >A A A >AA AA Cheers,
> >A A A >AA AA --Jim Parker
> >A A A >AA AA Department of Physics and Astronomy
> >A A A >AA AA The University of Texas at San Antonio
> >A A A >
> >A A A >AA AA On Wed, Aug 20, 2014 at 4:09 PM, Jim Parker
> >A A A <[1][4][5]jimparker96313_at_gmail.com>
> >A A A >AA AA wrote:
> >A A A >
> >A A A >AA AA AA Hello,
> >A A A >AA AA AA AAA I am attempting to compile a text-only (no
> OpenGL) version
> >A A A of VMD for
> >A A A >AA AA AA use on an HPC cluster.AAA Basically, I have many
> TCL scripts
> >A A A that work
> >A A A >AA AA AA with atomselect methods and would like to have it
> available to
> >A A A the
> >A A A >AA AA AA compute nodes (which don't have OpenGL
> capability).
> >A A A >
> >A A A >AA AA AA I was hoping someone could recommend a set of
> options that
> >A A A would
> >A A A >AA AA AA generate a text only mode for a LINUXAMD64
> computer.
> >A A A >AA AA AA I saw that there are options provided for
> aix5&6.text compile
> >A A A modes, so
> >A A A >AA AA AA I tried those same options with LINUXAMD64
> >A A A >AA AA AA i.e. ./configure LINUXAMD64 IMD SILENT TCL
> PTHREADS LIBTACHYON
> >A A A NETCDF
> >A A A >AA AA AA LP64
> >A A A >
> >A A A >AA AA AA But the compilation fails with: undefined
> references to
> >A A A libtachyon.so...
> >A A A >AA AA AA Examining these options, I omitted LP64, since it
> is not
> >A A A listed for any
> >A A A >AA AA AA of the other LINUX modes and I assumed it was
> aix-specific.AA
> >A A A Also,
> >A A A >AA AA AA added SHARED since LINUX uses shared libraries
> >A A A >AA AA AA With those changes, the code compiles without
> errors (only
> >A A A warnings
> >A A A >AA AA AA about unused variables), and I get
> >A A A >
> >A A A >AA AA AA No resource compiler required on this platform.
> >A A A >
> >A A A >AA AA AA which I understand indicates the compilation
> completed.
> >A A A >AA AA AA However, make install gives the response
> >A A A >AA AA AA cp: cannot stat
> a**./lib/stride/stride_LINUXAMD64a**: No such
> >A A A file or
> >A A A >AA AA AA directory
> >A A A >AA AA AA cp: cannot stat
> a**../lib/surf/surf_LINUXAMD64a**: No such
> >A A A file or
> >A A A >AA AA AA directory
> >A A A >AA AA AA cp: cannot stat
> a**../lib/tachyon/tachyon_LINUXAMD64a**: No
> >A A A such file or
> >A A A >AA AA AA directory
> >A A A >AA AA AA Make sure /home/surfer/tmp/bin/vmd-src is in your
> path.
> >A A A >AA AA AA VMD installation complete.AAA Enjoy!
> >A A A >
> >A A A >AA AA AA the resulting binary does not execute
> >A A A >AA AA AA rlwrap: Command not found.
> >A A A >AA AA AA /myhome/tmp/lib/vmd-src/vmd_LINUX: Command not
> found.
> >A A A >
> >A A A >AA AA AA And inspecting the lib/stride lib/surf and
> lib/tachyon
> >A A A folders, the only
> >A A A >AA AA AA file is a README file in each.
> >A A A >AA AA AA the folder /myhome/tmp/lib/vmd-src
> >A A A >AA AA AA contains a file vmd.so and none of the
> *_LINUXAMD64
> >A A A >
> >A A A > References
> >A A A >
> >A A A >AA AA Visible links
> >A A A >AA AA 1. mailto:[5][6]jimparker96313_at_gmail.com
> >A A A --
> >A A A NIH Center for Macromolecular Modeling and Bioinformatics
> >A A A Beckman Institute for Advanced Science and Technology
> >A A A University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> >A A A [6][7]http://www.ks.uiuc.edu/~johns/AA AA AA AA AA A
> Phone: [7]217-244-3349
> >A A A [8][8]http://www.ks.uiuc.edu/Research/vmd/
> >
> > References
> >
> >A A Visible links
> >A A 1.
> [9]http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/22467.html
> >A A 2. mailto:[10]johns_at_ks.uiuc.edu
> >A A 3. mailto:[11]vmd_at_ks.uiuc.edu
> >A A 4. mailto:[12]jimparker96313_at_gmail.com
> >A A 5. mailto:[13]jimparker96313_at_gmail.com
> >A A 6. [14]http://www.ks.uiuc.edu/~johns/
> >A A 7. tel:[15]217-244-3349
> >A A 8. [16]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
> [17]http://www.ks.uiuc.edu/~johns/A A A A A A Phone:
> [18]217-244-3349
> [19]http://www.ks.uiuc.edu/Research/vmd/
>
> References
>
> Visible links
> 1. mailto:johns_at_ks.uiuc.edu
> 2. http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/22467.html
> 3. mailto:johns_at_ks.uiuc.edu
> 4. mailto:vmd_at_ks.uiuc.edu
> 5. mailto:jimparker96313_at_gmail.com
> 6. mailto:jimparker96313_at_gmail.com
> 7. http://www.ks.uiuc.edu/~johns/A
> 8. http://www.ks.uiuc.edu/Research/vmd/
> 9. http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/22467.html
> 10. mailto:johns_at_ks.uiuc.edu
> 11. mailto:vmd_at_ks.uiuc.edu
> 12. mailto:jimparker96313_at_gmail.com
> 13. mailto:jimparker96313_at_gmail.com
> 14. http://www.ks.uiuc.edu/~johns/
> 15. tel:217-244-3349
> 16. http://www.ks.uiuc.edu/Research/vmd/
> 17. http://www.ks.uiuc.edu/~johns/
> 18. tel:217-244-3349
> 19. 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/