VMD-L Mailing List

From: René Hafner TUK (hamburge_at_physik.uni-kl.de)
Date: Sat Mar 06 2021 - 10:14:12 CST

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:
> https://www.ks.uiuc.edu/Research/vmd/doxygen/cvsget.html
> <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
> <hamburge_at_physik.uni-kl.de <mailto: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
> https://urldefense.com/v3/__https://github.com/openmm/openmm/tree/master/libraries/lepton__;!!DZ3fjg!uOsuICSW4NO-G5FneWHO6wB8-CEyJ1a7jwU9ecu_LfUFJ_HuMmbS5cOafrnJGe6r6A$
> <https://urldefense.com/v3/__https://github.com/openmm/openmm/tree/master/libraries/lepton__;!!DZ3fjg!qZVLzfQlbkaM4vcGDznkmngKT53QGhjghQ5MwpFCsMyhvXSok4eQTirXp7zbwVFieg$>
>
> +patches for c++11 and lepton from
> https://urldefense.com/v3/__https://github.com/giacomofiorin/vmd-patches__;!!DZ3fjg!uOsuICSW4NO-G5FneWHO6wB8-CEyJ1a7jwU9ecu_LfUFJ_HuMmbS5cOafrnE3rjJUg$
> <https://urldefense.com/v3/__https://github.com/giacomofiorin/vmd-patches__;!!DZ3fjg!qZVLzfQlbkaM4vcGDznkmngKT53QGhjghQ5MwpFCsMyhvXSok4eQTirXp7wypfAkUg$>
>
>
>
> 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