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<p class="MsoNormal"><span style="color:#1F497D">Hi Dvori/Danny,<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">When will you finish this and start ChimeraX’s installation?<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">Best,<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">Nir<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
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<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b>From:</b> Dvora Shait <br>
<b>Sent:</b> Monday, December 12, 2022 7:22 AM<br>
<b>To:</b> Greg Couch <gregc@cgl.ucsf.edu>; Barak Yariv <barakyariv@gmail.com><br>
<b>Cc:</b> ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>; Danny Shaked <danny@shaked.tau.ac.il>; Nir Ben-Tal <bental@tauex.tau.ac.il><br>
<b>Subject:</b> RE: [chimerax-users] using chimerx on unix<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">Thank you so much Greg<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">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<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">BR<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Dvory<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b>From:</b> Greg Couch <<a href="mailto:gregc@cgl.ucsf.edu">gregc@cgl.ucsf.edu</a>>
<br>
<b>Sent:</b> Sunday, December 11, 2022 9:20 PM<br>
<b>To:</b> Dvora Shait <<a href="mailto:dvory@tauex.tau.ac.il">dvory@tauex.tau.ac.il</a>>; Barak Yariv <<a href="mailto:barakyariv@gmail.com">barakyariv@gmail.com</a>><br>
<b>Cc:</b> ChimeraX Users Help <<a href="mailto:chimerax-users@cgl.ucsf.edu">chimerax-users@cgl.ucsf.edu</a>>; Danny Shaked <<a href="mailto:danny@shaked.tau.ac.il">danny@shaked.tau.ac.il</a>>; Nir Ben-Tal <<a href="mailto:bental@tauex.tau.ac.il">bental@tauex.tau.ac.il</a>><br>
<b>Subject:</b> Re: [chimerax-users] using chimerx on unix<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<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.<o:p></o:p></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 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).<o:p></o:p></p>
<p>The best solution is to update your system from CentOS 7 to a current version of Linux.
<o:p></o:p></p>
<p> -- Greg<o:p></o:p></p>
<div>
<p class="MsoNormal">On 12/10/2022 11:39 PM, Dvora Shait via ChimeraX-users wrote:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal"><span style="color:#1F497D">Thank you Tom,</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">I was trying to install chimeraX 1.5 on linux.</span><o:p></o:p></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">https://www.cgl.ucsf.edu/chimerax/download.html</a></span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#002060">However, apparently it contains binaries and not source code.</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#002060">The binaries did not work in our centos 7.9 (glibc)</span><o:p></o:p></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</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">However, got the pyqt6 error</span><o:p></o:p></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</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">The singularity file I have built is attached</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">I activated it within command</span><o:p></o:p></p>
<ol style="margin-top:0in" start="1" type="1">
<li class="MsoNormal" style="color:#1F497D;mso-list:l0 level1 lfo3">singularity build --sandbox /powerapps/singularity/images/chimara/ChimeraX1.5.img chimerax.build<o:p></o:p></li></ol>
<p class="MsoNormal"><span style="color:#1F497D">While putting the binaries in a directory I transferred to the image</span><o:p></o:p></p>
<ol style="margin-top:0in" start="2" type="1">
<li class="MsoNormal" style="color:#1F497D;mso-list:l0 level1 lfo3">singularity shell --writable /powerapps/singularity/images/chimara/ChimeraX1.5.img<o:p></o:p></li></ol>
<p class="MsoNormal"><span style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">And then within singularity:</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><b><span style="color:#1F497D">Singularity></span></b><span style="color:#1F497D"> echo $PATH</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin</span><o:p></o:p></p>
<p class="MsoNormal"><b><span style="color:#1F497D">Singularity></span></b><span style="color:#1F497D"> export PATH=/chimerax-1.5/bin:$PATH</span><o:p></o:p></p>
<p class="MsoNormal"><b><span style="color:#1F497D">Singularity></span></b><span style="color:#1F497D"> echo $LD_LIBRARY_PATH</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">/chimerax-1.5/lib:/.singularity.d/libs</span><o:p></o:p></p>
<p class="MsoNormal"><b><span style="color:#1F497D">Singularity></span></b><span style="color:#1F497D"> ls /chimerax-1.5/lib/libQt6Core.so.6</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">/chimerax-1.5/lib/libQt6Core.so.6</span><o:p></o:p></p>
<p class="MsoNormal"><b><span style="color:#1F497D">Singularity></span></b><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><b><span style="color:#1F497D">Singularity></span></b><span style="color:#1F497D"> ChimeraX</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">NOTE: Traceback (most recent call last):</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> File "/chimerax-1.5/lib/python3.9/runpy.py", line 197, in</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">_run_module_as_main</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> return _run_code(code, main_globals, None,</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> File "/chimerax-1.5/lib/python3.9/runpy.py", line 87, in _run_code</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> exec(code, run_globals)</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> File "/chimerax-1.5/lib/python3.9/site-packages/chimerax/core/__main__.py",</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">line 1035, in <module></span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> exit_code = init(sys.argv)</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> File "/chimerax-1.5/lib/python3.9/site-packages/chimerax/core/__main__.py",</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">line 579, in init</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> from chimerax.ui import initialize_qt</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> File "/chimerax-1.5/lib/python3.9/site-packages/chimerax/ui/__init__.py",</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">line 21, in <module></span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> from .gui import MainToolWindow, initialize_qt, menu_capitalize</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> File "/chimerax-1.5/lib/python3.9/site-packages/chimerax/ui/gui.py", line</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">29, in <module></span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> from Qt.QtWidgets import QApplication</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> File "/chimerax-1.5/lib/python3.9/site-packages/Qt/__init__.py", line 64, in</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"><module></span><o:p></o:p></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></span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">ImportError: libQt6Core.so.6: cannot open shared object file: No such file or</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">directory</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">BUG: ImportError: libQt6Core.so.6: cannot open shared object file: No such file or</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">directory</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">File "/chimerax-1.5/lib/python3.9/site-packages/Qt/__init__.py", line 64, in</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">from PyQt6.QtCore import PYQT_VERSION_STR as PYQT6_VERSION</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">_See log for complete Python traceback._</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><b><span style="color:#1F497D">Singularity></span></b><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><b><span style="color:#1F497D">Singularity> </span></b><span style="color:#1F497D">python</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">Python 3.9.11 (main, Nov 28 2022, 23:56:15)</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">[GCC 8.3.0] on linux</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">Type "help", "copyright", "credits" or "license" for more information.</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">>>> import PyQt6</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">>>> import PyQt6.QtCore</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">Traceback (most recent call last):</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> File "<stdin>", line 1, in <module></span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">ImportError: libQt6Core.so.6: cannot open shared object file: No such file or directory</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">>>> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> </span><o:p></o:p></p>
</blockquote>
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