[chimerax-users] Version 1.4 for CentOS 7?

Tru Huynh tru at pasteur.fr
Fri Jun 17 12:34:39 PDT 2022 

the second part...
"strip --remove-section=.note.ABI-tag /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt6/Qt6/lib/libQt6Core.so.6"
make the container runable on the default kernel :D

ymmv

Tru
On Fri, Jun 17, 2022 at 11:30:54AM -0700, Greg Couch via ChimeraX-users wrote:
> 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://urldefense.com/v3/__https://groups.google.com/a/apptainer.org/g/discuss/c/qhP4eJrtelk/m/7pGjIDTmAgAJ__;!!JFdNOqOXpB6UZW0!-wwSx-GLADwP24bJXXb-wcg0CJ0WYV2FiC6r3xglMHwtz2Np2zrVewbxCc5w4g$
> >pointing to https://urldefense.com/v3/__https://github.com/dnschneid/crouton/wiki/Fix-error-while-loading-shared-libraries:-libQt5Core.so.5__;!!JFdNOqOXpB6UZW0!-wwSx-GLADwP24bJXXb-wcg0CJ0WYV2FiC6r3xglMHwtz2Np2zrVewZFSPLcFg$
> >```
> >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.
> >>
> >...
> >
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-- 
Tru Huynh (PhD) | mailto:tru at pasteur.fr | tel +33 1 45 68 87 37
https://research.pasteur.fr/en/team/structural-bioinformatics/
Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France

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