SBGrid ChimeraX 1.3 fails to start on Ubuntu 20.04

[d.e.richman@…]

The SBGrid ChimeraX 1.3 does not start on Ubuntu 20.04 failing to find libssl.so.10.

Begin forwarded message:

From: Dan Richman
Subject: Re: [ChimeraX] #6675: Problem after 'close' without 'vseries stop'
Date: May 5, 2022 at 12:09:34 PM PDT
To: Tom Goddard
Cc: "ChimeraX-bugs@…" <ChimeraX-bugs@…>

Hi Tom, pardon my delay. I included a bunch of information below about the errors if I install SBGrid's default ChimeraX (1.3).

Attempting to launch it the typical way in the sbgrid environment:

drichman@blackbird:~$ chimerax
The executable chimerax was not found.
The version of the application that contains chimerax may not be installed
or may not be configured in this shell.

Please check your version configuration in ~/.sbgrid.conf .

Email bugs@… for help or to report an error.

(There's no .sbgrid.conf)

The sbwhich command confirms it doesn't find the chimerax executable but does work otherwise, e.g.,

drichman@blackbird:~$ sbwhich chimerax
chimerax: Command not found.

drichman@blackbird:~$ sbwhich relion
/programs/x86_64-linux/relion/3.1.3_cu10.2/bin/relion

If I try its path directly, these are the errors:

drichman@blackbird:~$ /programs/x86_64-linux/chimerax/1.3/bin/chimerax
Traceback (most recent call last):

File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 197, in _run_module_as_main

return _run_code(code, main_globals, None,

File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 87, in _run_code

exec(code, run_globals)

File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 1018, in <module>

exit_code = init(sys.argv)

File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 425, in init

initialize_ssl_cert_dir()

File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/utils.py", line 72, in initialize_ssl_cert_dir

import ssl

File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/ssl.py", line 98, in <module>

import _ssl # if we can't import it, let the error propagate

ImportError: libssl.so.10: cannot open shared object file: No such file or directory

Or the bin.capsules version:

drichman@blackbird:~$ /programs/x86_64-linux/chimerax/1.3/bin.capsules/chimerax
The executable chimerax was not found.

The version of the application that contains chimerax may not be installed
or may not be configured in this shell.
Please check your version configuration in ~/.sbgrid.conf .

Email bugs@… for help or to report an error.

If I instead install chimerax@1.2.5-c8, it does launch, just giving these warnings:

drichman@blackbird:~$ chimerax
WARNING: Release of profile requested but WebEnginePage still not deleted. Expect troubles !
WARNING: Release of profile requested but WebEnginePage still not deleted. Expect troubles !
WARNING: Release of profile requested but WebEnginePage still not deleted. Expect troubles !

[Tom Goddard]

The solution is to install the Ubuntu 20.04 ChimeraX 1.3 available on the ChimeraX download web page.

Another route might be to find what package installs libssl.so.10 on your Ubuntu 20 system.

I will ask SBGrid how they handle different Linux distributions and report what they say here.

[Tom Goddard]

Asked SBGrid via web form ​https://sbgrid.org/about/contact/

I am curious how SBGrid handles different Linux distributions.  I develop ChimeraX and we have different distributions for CentOS 7, Ubuntu 20.04 and several others.  An SBGrid user Dan Richman at Johns Hopkins gets an error starting SBGrid ChimeraX 1.3 on Ubuntu 20.04 because it can't find the needed system libssl.so.10.  I guess SBGrid is providing a CentOS 7 ChimeraX that won't run on Ubuntu 20.  Does SBGrid have methods to tailor their distribution to specific Linux distributions?

Thanks!
   Tom