VMD-L Mailing List

From: René Hafner TUK (hamburge_at_physik.uni-kl.de)
Date: Sat Mar 06 2021 - 15:21:00 CST

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
> 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]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
>> <[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]https://urldefense.com/v3/__https://github.com/openmm/openmm/tree/master/libraries/lepton__;!!DZ3fjg!oNbO5bmlGAeLGRdyfYUcTI1b_2weaWQ6AecWvBqXqRLXtNDkYdQxyiGhAZuCjSE-gA$
>>
>> +patches for c++11 and lepton from
>> [4]https://urldefense.com/v3/__https://github.com/giacomofiorin/vmd-patches__;!!DZ3fjg!oNbO5bmlGAeLGRdyfYUcTI1b_2weaWQ6AecWvBqXqRLXtNDkYdQxyiGhAZsXFUFCyw$
>>
>> 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. https://www.ks.uiuc.edu/Research/vmd/doxygen/cvsget.html
>> 2. mailto:hamburge_at_physik.uni-kl.de
>> 3. https://urldefense.com/v3/__https://github.com/openmm/openmm/tree/master/libraries/lepton__;!!DZ3fjg!qZVLzfQlbkaM4vcGDznkmngKT53QGhjghQ5MwpFCsMyhvXSok4eQTirXp7zbwVFieg$
>> 4. https://urldefense.com/v3/__https://github.com/giacomofiorin/vmd-patches__;!!DZ3fjg!qZVLzfQlbkaM4vcGDznkmngKT53QGhjghQ5MwpFCsMyhvXSok4eQTirXp7wypfAkUg$ 

-- 
--
Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany