Hello,

I am trying to install ChimeraX in an apptainer (singularity) container.  I am able to load molecules but running into two issues.

  1. I get a lot of python tracebacks (see below). I have also installed ChimeraX directly on the same machine from the RPM and do not see these error messages.
  2. Rendering is very slow, so I don't think it is using the graphics card.  The direct installation is similarly slow, but I have installed VMD on the same system and I can tell that it is using the graphics card, both from the log and the speed.

Please let me know if you have any suggestions to address either of these issues.

This is the command that I am using to launch ChimeraX

apptainer exec --bind /tmp/.X11-unix,/storage/storage1 --env DISPLAY=$DISPLAY --nv chimerax-rocky9.sif chimerax​

This is the definition file for the container.

BootStrap: docker​
From: rockylinux/rockylinux:9.4

%labels
    Maintainer Tyler Luchko
    Version 1.0

%help
    This is a Rocky Linux 9 container for ChimeraX 1.8

%setup
    # These are only required if running on the HPC.
    #mkdir -p ${APPTAINER_ROOTFS}/tmp
    mkdir -p ${APPTAINER_ROOTFS}/scratch

%post
    echo "Installing packages into the Rocky Linux 9 container"
    dnf -y install yum-utils
    dnf -y config-manager --set-enabled crb
    dnf -y install epel-release
    dnf -y install mesa-dri-drivers glx-utils
    dnf -y install /tmp/ucsf-chimerax-1.8-1.el9.x86_64.rpm
    dnf clean all

%environment
    export PATH=/usr/bin:/usr/sbin:/bin:/sbin
    export SHELL=/bin/bash
    export LANG=en_US.UTF-8

Sample error output is below.

Thank you,

Tyler

NOTE: available bundle cache has not been initialized yet
NOTE: Traceback (most recent call last):  
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 571, in start_tool  
    ti = api._api_caller.start_tool(api, session, self, tool_info)  
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1286, in start_tool  
    return cls._get_func(api, "start_tool")(session, ti.name)  
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/log/__init__.py", line 50, in start_tool  
    return cmd.get_singleton(session, create=True)  
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/log/cmd.py", line 30, in get_singleton  
    return tools.get_singleton(session, Log, 'Log', create=create)  
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/tools.py", line 216, in get_singleton  
    tinst = tool_class(session, tool_name, **kw)  
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/log/tool.py", line 161, in __init__  
    from chimerax.ui.widgets import ChimeraXHtmlView  
ImportError: cannot import name 'ChimeraXHtmlView' from 'chimerax.ui.widgets'
(/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/ui/widgets/__init__.py)  
 
During handling of the above exception, another exception occurred:  
 
Traceback (most recent call last):  
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/tools.py", line 418, in start_tools  
    bi.start_tool(session, tool_name)  
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 578, in start_tool  
    raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Log in
bundle ChimeraX-Log:  
cannot import name 'ChimeraXHtmlView' from 'chimerax.ui.widgets'
(/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/ui/widgets/__init__.py)  
 

BUG: Tool "Log" failed to start:  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Log in
bundle ChimeraX-Log:  
cannot import name 'ChimeraXHtmlView' from 'chimerax.ui.widgets'
(/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/ui/widgets/__init__.py)  
 
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 578, in start_tool  
raise ToolshedError(  
 
_See log for complete Python traceback._  
 

NOTE: UCSF ChimeraX version: 1.8 (2024-06-10)
NOTE: © 2016-2024 Regents of the University of California.  All rights reserved.
NOTE: [How to cite UCSF ChimeraX](cxcmd:help help:credits.html)  

NOTE: Traceback (most recent call last):  
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
    return self._func(self._name, data)  
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/bug_reporter/crash_report.py", line 138, in
_delayed_register_log_recorder  
    _register_log_recorder(session)  
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/bug_reporter/crash_report.py", line 172, in
_register_log_recorder  
    log.record_to_file(log_file)  
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/log/tool.py", line 410, in record_to_file  
    self._log_to_file(self.page_source)  
                      ^^^^^^^^^^^^^^^^  
AttributeError: 'Log' object has no attribute 'page_source'  
 

BUG: Error processing trigger "new frame":  
AttributeError: 'Log' object has no attribute 'page_source'  
 
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/log/tool.py", line 410, in record_to_file  
self._log_to_file(self.page_source)  
^^^^^^^^^^^^^^^^  
 
_See log for complete Python traceback._  


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