ChimeraX startup crash on Ubuntu 16.04

[Luca.Jovine@…]

Hello, I’ve been trying to run ChimeraX on one of our machines (Ubuntu 16.04 OS, GeForce GTX 1080 Ti GPUs).
If I try launching the stable version (0.6) I get:


/usr/local/chimerax$ chimerax-0.6/bin/ChimeraX
WARNING: QOpenGLShader::compile(Vertex): failed
WARNING: QOpenGLShader::compile(Fragment): failed
WARNING: Could not link shader program:
 ""
Fatal Python error: Segmentation fault

Thread 0x00007f2f92259700 (most recent call first):
  File "/usr/local/ucsf_chimerax/chimerax-0.6/lib/python3.6/ssl.py", line 631 in read
  File "/usr/local/ucsf_chimerax/chimerax-0.6/lib/python3.6/ssl.py", line 871 in read
  File "/usr/local/ucsf_chimerax/chimerax-0.6/lib/python3.6/ssl.py", line 1009 in recv_into
  File "/usr/local/ucsf_chimerax/chimerax-0.6/lib/python3.6/socket.py", line 586 in readinto
  File "/usr/local/ucsf_chimerax/chimerax-0.6/lib/python3.6/http/client.py", line 258 in _read_status
  File "/usr/local/ucsf_chimerax/chimerax-0.6/lib/python3.6/http/client.py", line 297 in begin
  File "/usr/local/ucsf_chimerax/chimerax-0.6/lib/python3.6/http/client.py", line 1331 in getresponse
  File "/usr/local/ucsf_chimerax/chimerax-0.6/lib/python3.6/urllib/request.py", line 1321 in do_open
  File "/usr/local/ucsf_chimerax/chimerax-0.6/lib/python3.6/urllib/request.py", line 1361 in https_open
  File "/usr/local/ucsf_chimerax/chimerax-0.6/lib/python3.6/urllib/request.py", line 504 in _call_chain
  File "/usr/local/ucsf_chimerax/chimerax-0.6/lib/python3.6/urllib/request.py", line 544 in _open
  File "/usr/local/ucsf_chimerax/chimerax-0.6/lib/python3.6/urllib/request.py", line 526 in open
  File "/usr/local/ucsf_chimerax/chimerax-0.6/lib/python3.6/urllib/request.py", line 223 in urlopen
  File "/usr/local/ucsf_chimerax/chimerax-0.6/lib/python3.6/site-packages/chimerax/core/toolshed/available.py", line 30 in load
  File "/usr/local/ucsf_chimerax/chimerax-0.6/lib/python3.6/site-packages/chimerax/core/toolshed/__init__.py", line 385 in reload_available
  File "/usr/local/ucsf_chimerax/chimerax-0.6/lib/python3.6/threading.py", line 864 in run
  File "/usr/local/ucsf_chimerax/chimerax-0.6/lib/python3.6/threading.py", line 916 in _bootstrap_inner
  File "/usr/local/ucsf_chimerax/chimerax-0.6/lib/python3.6/threading.py", line 884 in _bootstrap

Current thread 0x00007f2fdd99a740 (most recent call first):
  File "/usr/local/ucsf_chimerax/chimerax-0.6/lib/python3.6/site-packages/chimerax/ui/gui.py", line 156 in build
  File "/usr/local/ucsf_chimerax/chimerax-0.6/lib/python3.6/site-packages/ChimeraX_main.py", line 565 in init
  File "/usr/local/ucsf_chimerax/chimerax-0.6/lib/python3.6/site-packages/ChimeraX_main.py", line 788 in <module>
  File "/usr/local/ucsf_chimerax/chimerax-0.6/lib/python3.6/runpy.py", line 85 in _run_code
  File "/usr/local/ucsf_chimerax/chimerax-0.6/lib/python3.6/runpy.py", line 193 in _run_module_as_main
[1:1:0100/000000.074235:ERROR:broker_posix.cc<http://broker_posix.cc>(41)] Invalid node channel message
Segmentation fault (core dumped)
/usr/local/chimerax$


whereas if I try the daily 0.7 version (from today):


/usr/local/chimerax$ chimerax-0.7/bin/ChimeraX
NOTE: Traceback (most recent call last):
  File "/usr/local/ucsf_chimerax/chimerax-0.7/lib/python3.6/runpy.py", line
193, in _run_module_as_main
    "__main__", mod_spec)
  File "/usr/local/ucsf_chimerax/chimerax-0.7/lib/python3.6/runpy.py", line
85, in _run_code
    exec(code, run_globals)
  File "/usr/local/ucsf_chimerax/chimerax-0.7/lib/python3.6/site-
packages/ChimeraX_main.py", line 783, in <module>
    exit_code = init(sys.argv)
  File "/usr/local/ucsf_chimerax/chimerax-0.7/lib/python3.6/site-
packages/ChimeraX_main.py", line 551, in init
    _xdg.install_if_needed(sess, localized_app_name)
AttributeError: module 'chimerax.core._xdg' has no attribute
'install_if_needed'


ERROR: AttributeError: module 'chimerax.core._xdg' has no attribute
'install_if_needed'

File "/usr/local/ucsf_chimerax/chimerax-0.7/lib/python3.6/site-
packages/ChimeraX_main.py", line 551, in init
_xdg.install_if_needed(sess, localized_app_name)

 _See log for complete Python traceback._

If you wish to report this error, send mail to [chimerax-
bugs@cgl.ucsf.edu<mailto:bugs@cgl.ucsf.edu>](mailto:chimerax-bugs@cgl.ucsf.edu) and describe what you
were doing and include a copy of the contents of the log. Don't include any
data you wish to remain private since a publicly viewable bug report will be
created.

/usr/local/chimerax$


…what I am doing wrong?

Thanks and best regards,

Luca

------------------------------------------------------------------------
Luca Jovine, Ph.D.
Professor of Structural Biology & EMBO Member
Karolinska Institutet
Department of Biosciences and Nutrition & Center for Innovative Medicine
Medicinaren 25 Neo
Blickagången 16, SE-141 83 Huddinge, Sweden
E-mail: luca.jovine@ki.se<mailto:luca.jovine@ki.se>
W3: http://jovinelab.org
------------------------------------------------------------------------

[Eric Pettersen]

From a follow-up ticket:

Hello again, I should add the the 0.6 error only happens over SSH (ssh -2 -Y -C), not if I launch the program from the machine itself. However the 0.7 issue is the same, regardless of whether I am on the actual machine or not.
Thanks,
Luca

[Greg Couch]

The bug in daily ("0.7") build has been fixed, so please retry the daily build.

[Luca.Jovine@…]

Thank you, indeed 0.7 works now (although still not via SSH)!
Best, Luca

[Greg Couch]

The ssh bug is typically caused by incompatible graphics drivers. If you copy libGL.so from the machine you are ssh'ing from to a new directory on the machine that you are ssh'ing to, and set the LD_LIBRARY_PATH environment variable to that directory, it might work :-)

[Luca.Jovine@…]

Thank you, the workaround works between linux machines - but unfortunately not on my laptop, which runs Mac OS. This has no libGL.so, but rather a shared library (/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib) that does not work when copied to the remote host.

[Greg Couch]

A similar fix should work for the Mac. Assuming the remote host is a Linux server, you "just" need to find the right libGL.so to use. I would expect that a libGL.so from a recent version of Mesa would work on the remote host, but I have not tried it myself. And if you can't get that to work, you'll need to use a remote display program, like one that implements the vnc protocol.

Good luck!

Greg

[Luca.Jovine@…]

Alright, will try! In any case, it’s not a big deal to just sFTP files to my laptop and open them locally with ChimeraX for Mac OS.
Thanks again,
Luca

[Greg Couch]

You're welcome.