VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Sep 13 2017 - 15:51:42 CDT

Francesco,
  The only suggestion I have presently is to dig a bit for that
error and see if you can find the cause. My guess is that the Python
Tkinter module has dependencies on that xcb_wait_for_reply64, but the
particular shared library in your path is missing that. There are
others with similar errors arising in other contexts on stackexchange here:
  https://unix.stackexchange.com/questions/316787/problem-with-libx11-so-6-undefined-symbol-xcb-wait-for-reply64

Hopefully that gets you headed in the right direction, but I personally
don't know anything about the "RCM" thing that you're describing.

Best regards,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Sep 13, 2017 at 06:31:25PM +0200, Francesco Pietra wrote:
> Hi John:
>
> As to the second, harmless error, debian9 amd64, that I am using, is now
> "stable" but until very recently it was "testing". So, aging is very fast
> with these affairs.
>
> As to the first, offending error, the complete output from the GALILEO
> cluster at CINECA in Italy is:
>
> francesco_at_vaio64:~/servers/cineca/RCM_remote_visualization$
> ./RCM_linux_64bit
> Traceback (most recent call last):
> Â File "<string>", line 10, in <module>
> Â File
> "/home/vagrant/devel/RCM/multivnc/PyInstaller/PyInstaller-2.1/PyInstaller/loader/pyi_importers.py",
> line 270, in load_module
> Â File "/tmp/build/rcm_client_tk/out00-PYZ.pyz/Tkinter", line 39, in
> <module>
> Â File
> "/home/vagrant/devel/RCM/multivnc/PyInstaller/PyInstaller-2.1/PyInstaller/loader/pyi_importers.py",
> line 409, in load_module
> ImportError: /usr/lib/x86_64-linux-gnu/libX11.so.6: undefined symbol:
> xcb_poll_for_reply64
> francesco_at_vaio64:~/servers/cineca/RCM_remote_visualization$
>
> I am now in Austria with a VAIO laptop which I had never tried before for
> remote visualization. In Italy, my linux boxes with either Debian 9 or an
> older version of the OS, Debian8 amd64, had no problem with the same
> remote visualization and the same RCM script.
>
> I could provide as an attachment, if of interest, the RCM script that I
> use when trying to connect to the server.
>
> Thanks a lot
>
> francesco
>
> On Wed, Sep 13, 2017 at 6:02 PM, John Stone <[1]johns_at_ks.uiuc.edu> wrote:
>
> Hi,
>  The first error doesn't seem to be VMD related at all, right? It
> appears
> to be some python script you're using? You need to provide more
> information
> for help on that.
>
> The second message is a warning that arises because you're using an
> older
> version of libGL.so than I compiled VMD against. It's not a problem,
> but
> that's why you get the warning.
>
> Best,
> Â John Stone
> Â [2]vmd_at_ks.uiuc.edu
> On Wed, Sep 13, 2017 at 05:04:00PM +0200, Francesco Pietra wrote:
> >Â Â While attempting to create a virtual screen with a remote cluster
> run by
> >Â Â centOS, the error arose:
> >
> >Â Â Â /loader/pyi_importers.py", line 409, in load_module
> >Â Â Â ImportError: /usr/lib/x86_64-linux-gnu/libX11.so.6: undefined
> symbol:
> >Â Â Â xcb_poll_for_reply64
> >
> >Â Â I am at debian9 amd64, where I have now noticed that VMD
> complains
> >
> >Â Â Â opt/lib/vmd/vmd_LINUXAMD64:
> /usr/lib/x86_64-linux-gnu/libGL.so.1: no
> >Â Â Â version information available (required by
> /opt/lib/vmd/vmd_LINUXAMD64)
> >
> >Â Â while functioning correctly.
> >
> >Â Â Thanks for advice
> >
> >Â Â francesco pietra
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> [3]http://www.ks.uiuc.edu/~johns/Â Â Â Â Â Â Phone: [4]217-244-3349
> [5]http://www.ks.uiuc.edu/Research/vmd/
>
> References
>
> Visible links
> 1. mailto:johns_at_ks.uiuc.edu
> 2. mailto:vmd_at_ks.uiuc.edu
> 3. http://www.ks.uiuc.edu/~johns/
> 4. file:///tmp/tel:217-244-3349
> 5. 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/