[chimerax-users] using chimerx on unix

[Dvora Shait]

Thank you so much Greg
Barak, Nir, we are now in a process of building slurm scheduler on Almalinux 8, Danny suggested to install chimeraX there as soon as it is ready

BR
Dvory

From: Greg Couch <gregc at cgl.ucsf.edu>
Sent: Sunday, December 11, 2022 9:20 PM
To: Dvora Shait <dvory at tauex.tau.ac.il>; Barak Yariv <barakyariv at gmail.com>
Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>; Danny Shaked <danny at shaked.tau.ac.il>; Nir Ben-Tal <bental at tauex.tau.ac.il>
Subject: Re: [chimerax-users] using chimerx on unix


As you noticed on the ChimeraX download page, there is no CentOS 7 version of ChimeraX 1.5.  CentOS 7 is not supported by Qt 6, so we only have CentOS/RHEL/Rocky/AlmaLinux 8 and 9 rpms.

Running a newer version of Linux via singularity on CentOS 7 does not work because singularity uses the base OS kernel, and CentOS 7's 3.10 kernel is too old for Qt 6.  See the discussion at https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-June/003870.html.  I think you might like the singularity script in that discussion better.  If you follow the discussion, there are a couple of workarounds: (1) update the CentOS 7 kernel via the elrepo-kernel repo, or (2) remove the .note.ABI-tag section from ChimeraX's copy of libQt6Core.so.6.  (1) should always work, (2) appears to work in practice.  Both are considered unsupported.  And don't forget to install the appropriate graphics driver in the singularity kernel (potentially non-trivial).

The best solution is to update your system from CentOS 7 to a current version of Linux.

    -- Greg
On 12/10/2022 11:39 PM, Dvora Shait via ChimeraX-users wrote:
Thank you Tom,

I was trying to install chimeraX 1.5 on linux.
We have centos 7, and I downloaded ChimeraX-1.5.tar.gz from https://www.cgl.ucsf.edu/chimerax/download.html
However, apparently it contains binaries and not source code.
The binaries did not work in our centos 7.9 (glibc)
So I tried to use singularity – I installed ubuntu 22.04, and tried there the deb file: ucsf-chimerax_1.5ubuntu22.04_amd64.deb
However, got the pyqt6 error
I tried to download to the singularity image the binaries from ChimeraX-1.5.tar.gz, and got the same error

The singularity file I have built is attached
I activated it within command

  1.  singularity build --sandbox /powerapps/singularity/images/chimara/ChimeraX1.5.img chimerax.build
While putting the binaries in a directory I transferred to the image

  1.  singularity shell --writable /powerapps/singularity/images/chimara/ChimeraX1.5.img

And then within singularity:

Singularity> echo $PATH
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
Singularity> export PATH=/chimerax-1.5/bin:$PATH
Singularity> echo $LD_LIBRARY_PATH
/chimerax-1.5/lib:/.singularity.d/libs
Singularity> ls /chimerax-1.5/lib/libQt6Core.so.6
/chimerax-1.5/lib/libQt6Core.so.6
Singularity>


Singularity> ChimeraX
NOTE: Traceback (most recent call last):
  File "/chimerax-1.5/lib/python3.9/runpy.py", line 197, in
_run_module_as_main
    return _run_code(code, main_globals, None,
  File "/chimerax-1.5/lib/python3.9/runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "/chimerax-1.5/lib/python3.9/site-packages/chimerax/core/__main__.py",
line 1035, in <module>
    exit_code = init(sys.argv)
  File "/chimerax-1.5/lib/python3.9/site-packages/chimerax/core/__main__.py",
line 579, in init
    from chimerax.ui import initialize_qt
  File "/chimerax-1.5/lib/python3.9/site-packages/chimerax/ui/__init__.py",
line 21, in <module>
    from .gui import MainToolWindow, initialize_qt, menu_capitalize
  File "/chimerax-1.5/lib/python3.9/site-packages/chimerax/ui/gui.py", line
29, in <module>
    from Qt.QtWidgets import QApplication
  File "/chimerax-1.5/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


BUG: ImportError: libQt6Core.so.6: cannot open shared object file: No such file or
directory

File "/chimerax-1.5/lib/python3.9/site-packages/Qt/__init__.py", line 64, in
from PyQt6.QtCore import PYQT_VERSION_STR as PYQT6_VERSION

_See log for complete Python traceback._


Singularity>


Singularity> python
Python 3.9.11 (main, Nov 28 2022, 23:56:15)
[GCC 8.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import PyQt6
>>> import PyQt6.QtCore
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: libQt6Core.so.6: cannot open shared object file: No such file or directory
>>>

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