VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sat Mar 06 2021 - 15:26:51 CST

Rene,
  Looks like your Tk build needs -lfontconfig added to the link line...

Best,
  John

On Sat, Mar 06, 2021 at 10:21:00PM +0100, René Hafner TUK wrote:
> Hi John,
>
> thanks info about the update of the colvars. I wil try that once I
> fixed the compilation issue.
>
> Though I get 2 steps further when adding
>
> "-lfltk - lX11 -lXext -lXrender -lXft"
>
> Now I get:
>
> /lib/../lib64/libtk8.5.so: undefined reference to symbol 'FcUtf8ToUcs4'
>
> //usr/lib64/libfontconfig.so.1: error adding symbols: DSO missing from
> command line
>
> Any hints what the issue is here?
>
> Kind regards
>
> René
>
> On 3/6/2021 7:37 PM, John Stone wrote:
>
> Hi René,
> FYI, for your benefit, I synced up the VMD tree with the latest
> colvars git master last night.
>
> Regarding your linkage problem:
> It appears that your FLTK builds are compiled with the use of some
> X11 extension functions. To ensure they are correctly resolved at
> link time, you'll need to make sure that you're adding libXext to the
> link flags. You can either edit the configure script to add that for
> the FLTK section, or you can edit the generated Makefile and add it
> manually in the linkage list that follows fltk for your build, e.g.:
> .. -ltk8.6 -ltcl8.6 -lz -lmolfile_plugin -lfltk -lX11 -lXext -lm -ldl ...
>
> Make sure you place -lXext after -lX11.
> I should warn you that depending on how you've compiled FLTK, you may
> need to make further changes, to add linkage of libXrender libXft, and/or
> other libraries. They would all amount to the same sort of changes,
> adding -lXrender -lXft etc, to configure or the generated Makefile.
>
> One of the complexities of using GUI toolkits like FLTK and Tk is
> that they themselves have additional dependencies that change with
> version and/or build configuration, and their dependencies must
> also be completely satisfied at link time when you use them with VMD.
>
> Best regards,
> John Stone
> [1]vmd_at_ks.uiuc.edu
>
> On Sat, Mar 06, 2021 at 05:14:12PM +0100, René Hafner TUK wrote:
>
> Hi Giacomo,
>
> I got LEPTON working but the not VMD GUI compilation.
>
> * I forgot to include lepton into VMDs "./configure TK TCL ...
> LEPTON" - though this part is resolved now
>
> I can successfully compile without FLTK but not with FLTK.
>
>
>
> Here is the error log after
>
> `./configure LINUXAMD64 OPENGL FLTK TK TCL PTHREADS COLVARS LEPTON
>
> cd src
>
> make
>
> ....compiliing stuff....
>
> Linking vmd_LINUXAMD64 ...
> Stride.o: In function `ss_from_stride(DrawMolecule*)':
> Stride.C:(.text+0x35f): warning: the use of `tempnam' is dangerous, better
> use `mkstemp'
> /usr/bin/ld: ../lib/fltk/LINUXAMD64/libfltk.a(Fl_Double_Window.o):
> undefined reference to symbol 'XdbeAllocateBackBufferName'
> //usr/lib64/libXext.so.6: error adding symbols: DSO missing from command
> line
> collect2: error: ld returned 1 exit status
> make: *** [vmd_LINUXAMD64] Error 1
>
> `
>
> I tried multiple version of FLTK by now:
>
> * 1.0.11
>
> *1.3.4-2
>
> * 1.3.5
>
> and installed them as describe in VMDSourceDIR/lib/fltk/README.
>
> the error still persists.
>
> Which version are you and it does working with in general?
>
> Kind regards
>
> René
>
> On 3/5/2021 6:46 PM, Giacomo Fiorin wrote:
>
> Hi René, those should be enough. I just tested that the patches do work
> with the latest CVS snapshots of the VMD and plugins repositories, both
> of which you can download at:
> [1][2]https://www.ks.uiuc.edu/Research/vmd/doxygen/cvsget.html
> (In the process, I also updated the patch files to track the latest
> snapshots, thus silencing warnings about the offsets having changed).
> When everything goes correctly you should see the following line printed
> when you first initialize Colvars (either from the command line or the
> Dashboard):
> colvars: This version was built with the C++11 standard or higher.
> There isn't a similar message for Lepton (other than a customFunction
> variable just working), but I presume that you applied both patches in
> the same way.
> As for the Dashboard, I strongly recommend updating its version either
> before or after compilation (it is only Tcl/Tk code so it doesn't
> need compilation). The version of the Dashboard that the VMD repository
> currently contains is buggy.
> Can you do the following?
> 1) Specify what error message you got telling you that Lepton isn't
> enabled.
> 2) Check that you can successfully build VMD and plugins without any
> patches; if anything went wrong there, the VMD team may also help.
> Giacomo
> On Thu, Mar 4, 2021 at 3:36 PM René Hafner TUK
> [3]<[2]hamburge_at_physik.uni-kl.de> wrote:
>
> Dear VMD developers,
>
> I would like to able to have my colvar files using "customFunction"
> being parsed by VMD colvars cv_dashboard.
>
> I succesfully compiled VMD 1.9.4. alpha51 using the provided
>
> + source code on the website
>
> + plugins
>
> + lepton files from
> [3][4]https://github.com/openmm/openmm/tree/master/libraries/lepton
>
> +patches for c++11 and lepton from
> [4][5]https://github.com/giacomofiorin/vmd-patches
>
> As far as I understood only lepton support (which requires C++11 for
> VMD, therefore the patches) was missing to support this feature.
>
> What am I missing here?
>
> Kind regards
>
> René
>
> --
> --
> Dipl.-Phys. René Hafner
> TU Kaiserslautern
> Germany
>
> --
> --
> Dipl.-Phys. René Hafner
> TU Kaiserslautern
> Germany
>
> References
>
> Visible links
> 1. [6]https://www.ks.uiuc.edu/Research/vmd/doxygen/cvsget.html
> 2. [7]mailto:hamburge_at_physik.uni-kl.de
> 3. [8]https://urldefense.com/v3/__https://github.com/openmm/openmm/tree/master/libraries/lepton__;!!DZ3fjg!qZVLzfQlbkaM4vcGDznkmngKT53QGhjghQ5MwpFCsMyhvXSok4eQTirXp7zbwVFieg$
> 4. [9]https://urldefense.com/v3/__https://github.com/giacomofiorin/vmd-patches__;!!DZ3fjg!qZVLzfQlbkaM4vcGDznkmngKT53QGhjghQ5MwpFCsMyhvXSok4eQTirXp7wypfAkUg$
>
>
> --
> --
> Dipl.-Phys. René Hafner
> TU Kaiserslautern
> Germany
>
> References
>
> Visible links
> 1. mailto:vmd_at_ks.uiuc.edu
> 2. https://www.ks.uiuc.edu/Research/vmd/doxygen/cvsget.html
> 3. mailto:[2]hamburge_at_physik.uni-kl.de
> 4. https://urldefense.com/v3/__https://github.com/openmm/openmm/tree/master/libraries/lepton__;!!DZ3fjg!sdVGylMd7Uo8B24R3CtpNfmITZp-SamrD_j3ACun8UAs11BBfWfFSD4h2pn-ARyu$
> 5. https://urldefense.com/v3/__https://github.com/giacomofiorin/vmd-patches__;!!DZ3fjg!sdVGylMd7Uo8B24R3CtpNfmITZp-SamrD_j3ACun8UAs11BBfWfFSD4h2v_eAkgK$
> 6. https://www.ks.uiuc.edu/Research/vmd/doxygen/cvsget.html
> 7. mailto:hamburge_at_physik.uni-kl.de
> 8. https://urldefense.com/v3/__https://github.com/openmm/openmm/tree/master/libraries/lepton__;!!DZ3fjg!qZVLzfQlbkaM4vcGDznkmngKT53QGhjghQ5MwpFCsMyhvXSok4eQTirXp7zbwVFieg$
> 9. https://urldefense.com/v3/__https://github.com/giacomofiorin/vmd-patches__;!!DZ3fjg!qZVLzfQlbkaM4vcGDznkmngKT53QGhjghQ5MwpFCsMyhvXSok4eQTirXp7wypfAkUg$ 

-- 
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/