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@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/7pGjIDTm... pointing to https://github.com/dnschneid/crouton/wiki/Fix-error-while-loading-shared-lib... ``` 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@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.
... -- Tru Huynh (PhD) | mailto:tru@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