[chimerax-users] using chimerx on unix

[Greg Couch]

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