VMD-L Mailing List

From: René Hafner TUK (hamburge_at_physik.uni-kl.de)
Date: Sat Mar 06 2021 - 16:20:35 CST

Hi John,

    sorry that was a dumb question...

    I finally got it now! :)

    I furthermore had to add the following libraries to the link line

    *"**... *-lfltk -lX11*-lXext -lXrender -lXft -lfontconfig -lXcursor
    -lXfixes -lXinerama"
    *

    in order to make it work.

    Tomorrow I will try it with the latest version from VMD cvs to get
    the latest fixes for colvars_dashboard too.

    Thanks a lot for the support, also to you @Giacomo.

René

On 3/6/2021 10:26 PM, John Stone wrote:
> 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://urldefense.com/v3/__https://github.com/openmm/openmm/tree/master/libraries/lepton__;!!DZ3fjg!qV5u3ETwI3LvLSY59EF9T1ni9pWvl8Vi-ZyaYbOVPVkxPskrFYoJqC7L40V5OWU6QA$
>>
>> +patches for c++11 and lepton from
>> [4][5]https://urldefense.com/v3/__https://github.com/giacomofiorin/vmd-patches__;!!DZ3fjg!qV5u3ETwI3LvLSY59EF9T1ni9pWvl8Vi-ZyaYbOVPVkxPskrFYoJqC7L40Wd2Fkmtg$
>>
>> 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$ 

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