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<p>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.</p>
<p>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
<a class="moz-txt-link-freetext" href="https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-June/003870.html">https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-June/003870.html</a>.
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).<br>
</p>
<p>The best solution is to update your system from CentOS 7 to a
current version of Linux. <br>
</p>
<p> -- Greg<br>
</p>
<div class="moz-cite-prefix">On 12/10/2022 11:39 PM, Dvora Shait via
ChimeraX-users wrote:<br>
</div>
<blockquote type="cite"
cite="mid:AS8PR02MB6951E164E49E1AD2B22C38DFB81E9@AS8PR02MB6951.eurprd02.prod.outlook.com">
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<div class="WordSection1">
<p class="MsoNormal"><span style="color:#1F497D">Thank you Tom,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">I was trying to
install chimeraX 1.5 on linux.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">We have centos
7, and I downloaded ChimeraX-1.5.tar.gz from
<a href="https://www.cgl.ucsf.edu/chimerax/download.html"
moz-do-not-send="true" class="moz-txt-link-freetext">https://www.cgl.ucsf.edu/chimerax/download.html</a></span><span
style="color:#002060"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#002060">However,
apparently it contains binaries and not source code.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#002060">The binaries
did not work in our centos 7.9 (glibc)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#002060">So I tried to
use singularity – I installed ubuntu 22.04, and tried there
the deb file: ucsf-chimerax_1.5ubuntu22.04_amd64.deb<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">However, got
the pyqt6 error<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">I tried to
download to the singularity image the binaries from
ChimeraX-1.5.tar.gz, and got the same error<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">The singularity
file I have built is attached<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">I activated it
within command<o:p></o:p></span></p>
<ul style="margin-top:0cm" type="disc">
<li class="MsoListParagraph"
style="color:#1F497D;margin-left:0cm;mso-list:l0 level1
lfo1">
singularity build --sandbox
/powerapps/singularity/images/chimara/ChimeraX1.5.img
chimerax.build<o:p></o:p></li>
</ul>
<p class="MsoNormal"><span style="color:#1F497D">While putting
the binaries in a directory I transferred to the image<o:p></o:p></span></p>
<ul style="margin-top:0cm" type="disc">
<li class="MsoListParagraph"
style="color:#1F497D;margin-left:0cm;mso-list:l0 level1
lfo1">
singularity shell --writable
/powerapps/singularity/images/chimara/ChimeraX1.5.img<o:p></o:p></li>
</ul>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">And then within
singularity:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="color:#1F497D">Singularity></span></b><span
style="color:#1F497D"> echo $PATH<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin<o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="color:#1F497D">Singularity></span></b><span
style="color:#1F497D"> export PATH=/chimerax-1.5/bin:$PATH<o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="color:#1F497D">Singularity></span></b><span
style="color:#1F497D"> echo $LD_LIBRARY_PATH<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">/chimerax-1.5/lib:/.singularity.d/libs<o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="color:#1F497D">Singularity></span></b><span
style="color:#1F497D"> ls /chimerax-1.5/lib/libQt6Core.so.6<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">/chimerax-1.5/lib/libQt6Core.so.6<o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="color:#1F497D">Singularity><o:p></o:p></span></b></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="color:#1F497D">Singularity></span></b><span
style="color:#1F497D"> ChimeraX<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">NOTE: Traceback
(most recent call last):<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> File
"/chimerax-1.5/lib/python3.9/runpy.py", line 197, in<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">_run_module_as_main<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> return
_run_code(code, main_globals, None,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> File
"/chimerax-1.5/lib/python3.9/runpy.py", line 87, in
_run_code<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> exec(code,
run_globals)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> File
"/chimerax-1.5/lib/python3.9/site-packages/chimerax/core/__main__.py",<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">line 1035, in
<module><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> exit_code =
init(sys.argv)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> File
"/chimerax-1.5/lib/python3.9/site-packages/chimerax/core/__main__.py",<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">line 579, in
init<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> from
chimerax.ui import initialize_qt<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> File
"/chimerax-1.5/lib/python3.9/site-packages/chimerax/ui/__init__.py",<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">line 21, in
<module><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> from .gui
import MainToolWindow, initialize_qt, menu_capitalize<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> File
"/chimerax-1.5/lib/python3.9/site-packages/chimerax/ui/gui.py",
line<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">29, in
<module><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> from
Qt.QtWidgets import QApplication<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> File
"/chimerax-1.5/lib/python3.9/site-packages/Qt/__init__.py",
line 64, in<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><module><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:red"> <span
style="background:yellow;mso-highlight:yellow">from
PyQt6.QtCore import PYQT_VERSION_STR as PYQT6_VERSION</span><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">ImportError:
libQt6Core.so.6: cannot open shared object file: No such
file or<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">directory<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">BUG:
ImportError: libQt6Core.so.6: cannot open shared object
file: No such file or<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">directory<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">File
"/chimerax-1.5/lib/python3.9/site-packages/Qt/__init__.py",
line 64, in<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">from
PyQt6.QtCore import PYQT_VERSION_STR as PYQT6_VERSION<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">_See log for
complete Python traceback._<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="color:#1F497D">Singularity><o:p></o:p></span></b></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="color:#1F497D">Singularity>
</span></b><span style="color:#1F497D">python<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Python 3.9.11
(main, Nov 28 2022, 23:56:15)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">[GCC 8.3.0] on
linux<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Type "help",
"copyright", "credits" or "license" for more information.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">>>>
import PyQt6<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">>>>
import PyQt6.QtCore<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Traceback (most
recent call last):<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> File
"<stdin>", line 1, in <module><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">ImportError:
libQt6Core.so.6: cannot open shared object file: No such
file or directory<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">>>><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
</div>
</blockquote>
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