[chimerax-users] Version 1.4 for CentOS 7?

[Greg Couch]

Yes, the singularity container will not work unless the CentOS 7 kernel 
is updated.  I don't understand why the runtime loader fails to load the 
Qt shared library, but that is the symptom.

     -- Greg

On 6/17/2022 10:14 AM, Tru Huynh via ChimeraX-users wrote:
> Hello Greg,
>
> Thanks for sharing the singularity recipe!
>
> The only issue I have, is that the container will not run on our regular kernel
> as you mentionned below (1) although the error message is misleading!
>
> [tru at sillage ~]$ singularity run /home/tru/singularity.d/containers/r8-chimerax-pristine-2022-06-17-1833.sif --nogui
> Traceback (most recent call last):
>    File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/toolshed/info.py", line 490, in get_module
>      m = importlib.import_module(self.package_name)
>    File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/importlib/__init__.py", line 127, in import_module
>      return _bootstrap._gcd_import(name[level:], package, level)
>    File "<frozen importlib._bootstrap>", line 1030, in _gcd_import
>    File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
>    File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked
>    File "<frozen importlib._bootstrap>", line 680, in _load_unlocked
>    File "<frozen importlib._bootstrap_external>", line 850, in exec_module
>    File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
>    File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/save_command/__init__.py", line 101, in <module>
>      from .options import SaveModelOptionWidget
>    File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/save_command/options.py", line 14, in <module>
>      from Qt.QtWidgets import QFrame, QHBoxLayout, QLabel
>    File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/Qt/__init__.py", line 64, in <module>
>      from PyQt6.QtCore import PYQT_VERSION_STR as PYQT6_VERSION
> ImportError: libQt6Core.so.6: cannot open shared object file: No such file or directory
>
> During handling of the above exception, another exception occurred:
>
> Traceback (most recent call last):
>    File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/toolshed/info.py", line 375, in init_manager
>      api = self._get_api(session.logger)
>    File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/toolshed/info.py", line 509, in _get_api
>      m = self.get_module()
>    File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/toolshed/info.py", line 492, in get_module
>      raise ToolshedError("Error importing bundle %s's module: %s" % (self.name, str(e)))
> chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-SaveCommand's module: libQt6Core.so.6: cannot open shared object file: No such file or directory
>
> Bundle 'ChimeraX-SaveCommand' custom initialization failed
> UCSF ChimeraX version: 1.4 (2022-06-03)
> © 2016-2022 Regents of the University of California.  All rights reserved.
> cmd>
>
> There is a "hack" mentionned in the apptainer mailing list
> https://groups.google.com/a/apptainer.org/g/discuss/c/qhP4eJrtelk/m/7pGjIDTmAgAJ
> pointing to https://github.com/dnschneid/crouton/wiki/Fix-error-while-loading-shared-libraries:-libQt5Core.so.5
> ```
> strip --remove-section=.note.ABI-tag /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt6/Qt6/lib/libQt6Core.so.6
> ```
> for the el8 rpm, which makes chimerax 1.4 starting fine on 3.10.0-1160.66.1.el7.x86_64 :D
>
> so adding to you recipe:
> ```
> yum -y install binutils && strip --remove-section=.note.ABI-tag /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt6/Qt6/lib/libQt6Core.so.6
> ```
> seems to yield a workable solution!
>
> [tru at sillage ~]$ singularity run /home/tru/singularity.d/containers/r8-chimerax-2022-06-17-1750.sif --nogui
> WARNING: CPU random generator seem to be failing, disabling hardware random number generation
> WARNING: RDRND generated: 0xffffffff 0xffffffff 0xffffffff 0xffffffff
> UCSF ChimeraX version: 1.4 (2022-06-03)
> © 2016-2022 Regents of the University of California.  All rights reserved.
> cmd>
>
> ymmv, I have only done minimal testing.
>
> Best regards
>
> Tru
>
> On Thu, Jun 16, 2022 at 10:41:46AM -0700, Greg Couch via ChimeraX-users wrote:
>>     I'm adding this for completeness, but this is not a practical solution:
>>
>>     There is a way of getting ChimeraX 1.4 to run on CentOS 7 that we do NOT
>>     support.  There are two steps required: (1) you have to update the kernel
>>     to a newer version.  That can be done with the elrepo-kernel repository.
>>     And (2) you need a newer versions of various system libraries.  That can
>>     be done with by using a CentOS/RHEL 8 or 9 singularity container that has
>>     the same graphics driver as the CentOS 7 system and has the corresponding
>>     ChimeraX rpm installed.
>>
>>     So, unless it is your personal computer, that you could update to
>>     CentOS/RHEL 8 or 9 anyway, it is extremely unlikely that the system
>>     administrators will be willing to change to an unsupported kernel.  But
>>     just in case, an example singularity definition file is attached.  I was
>>     testing in a virtual machine using VMware Workstation, which is why the
>>     VMware graphics driver is installed.  Once you have the singularity
>>     container, I'd recommend making a chimerax alias.  For example:
>>
>>         alias chimerax="singularity run /PATH/chimerax.el8.sil"
>>
>>     So there you have it.  It is technically possible,  And don't forgot to
>>     regularly regenerate the singularity container to pick up security fixes.
>>
> ...
>