<div dir="ltr">Hi Tom and Greg, <div><br></div><div>Thanks for double checking this.</div><div>I can confirm that the solution works on our centos 8 smoothly.</div><div><br></div><div>Best, </div><div>Zhe</div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Jul 6, 2021 at 8:58 PM Greg Couch <<a href="mailto:gregc@cgl.ucsf.edu">gregc@cgl.ucsf.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<p>I see the bug now. On CentOS 8, there should not be a
libOSMesa.so in the ChimeraX/lib directory. Please remove it so
ChimeraX finds the system version:</p>
<p> sudo rm -rf
/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-packages/osmesa<br>
</p>
<p>I will change the daily build so it is not there. <br>
</p>
<p> -- Greg</p>
<div>On 7/6/2021 12:38 PM, Tom Goddard
wrote:<br>
</div>
<blockquote type="cite">
Hi Zhe,
<div><br>
</div>
<div> Thanks for debugging this. So it appears the
libOSMesa.so.8.0.0 included in ChimeraX dues use libLLVM-10.so.1
that your system does not have. The libOSMesa library is only
used for a very obscure ChimeraX capability, offscreen rendering
when Chimera is started with the "--offscreen" flag usually for
servers creating images. Do you need that?</div>
<div><br>
</div>
<div> I am surprised that the ChimeraX installation
would fail due to the missing dependency. Can you send your
install command and the output of how it fails just to me and
Greg Couch instead of the list.</div>
<div><br>
</div>
<div> I don't think we will include libLLVM in ChimeraX
-- it is large and as I said this is a very rarely used ChimeraX
feature. But we do want it not to break the installation.</div>
<div><br>
</div>
<div><span style="white-space:pre-wrap"> </span>Tom</div>
<div><br>
<div><br>
<blockquote type="cite">
<div>On Jul 6, 2021, at 11:38 AM, Zhe Wang via
ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank">chimerax-users@cgl.ucsf.edu</a>>
wrote:</div>
<br>
<div>
<div dir="ltr">
<blockquote type="cite">
<pre><span style="font-family:Arial,Helvetica,sans-serif">Hi Greg, </span>
</pre>
</blockquote>
<div dir="ltr">
<div><br>
</div>
<div>Thank you for your reply.</div>
<div>I do have the libOSMesa.so exist in our
/usr/lib64/ directory. But it seems not the one
ChimeraX is trying to import.</div>
<div>The ldd result show as the following:</div>
<div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:Monaco;color:rgb(248,255,252);background-color:rgba(0,0,0,0.9)"><span style="font-variant-ligatures:no-common-ligatures">ldd
./libexec/UCSF-ChimeraX/lib/python3.8/site-packages/osmesa/libOSMesa.so.8.0.0</span></div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:Monaco;color:rgb(248,255,252);background-color:rgba(0,0,0,0.9)"><span style="font-variant-ligatures:no-common-ligatures">./libexec/UCSF-ChimeraX/lib/python3.8/site-packages/osmesa/libOSMesa.so.8.0.0:
/lib64/libm.so.6: version `GLIBC_2.29' not found
(required by
./libexec/UCSF-ChimeraX/lib/python3.8/site-packages/osmesa/libOSMesa.so.8.0.0)</span></div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:Monaco;color:rgb(248,255,252);background-color:rgba(0,0,0,0.9)"><span style="font-variant-ligatures:no-common-ligatures"><span style="white-space:pre-wrap"> </span>linux-vdso.so.1
(0x00007ffe625ef000)</span></div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:Monaco;color:rgb(248,255,252);background-color:rgba(0,0,0,0.9)"><span style="font-variant-ligatures:no-common-ligatures"><span style="white-space:pre-wrap"> </span>libz.so.1
=> /lib64/libz.so.1 (0x00007fbcc8d47000)</span></div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:Monaco;color:rgb(248,255,252);background-color:rgba(0,0,0,0.9)"><span style="font-variant-ligatures:no-common-ligatures"><span style="white-space:pre-wrap"> </span>libpthread.so.0
=> /lib64/libpthread.so.0
(0x00007fbcc8b27000)</span></div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:Monaco;color:rgb(248,255,252);background-color:rgba(0,0,0,0.9)"><span style="font-variant-ligatures:no-common-ligatures"><span style="white-space:pre-wrap"> </span>libdl.so.2
=> /lib64/libdl.so.2 (0x00007fbcc8923000)</span></div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:Monaco;color:rgb(248,255,252);background-color:rgba(0,0,0,0.9)"><span style="font-variant-ligatures:no-common-ligatures"><span style="white-space:pre-wrap"> </span>libLLVM-10.so.1
=> not found</span></div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:Monaco;color:rgb(248,255,252);background-color:rgba(0,0,0,0.9)"><span style="font-variant-ligatures:no-common-ligatures"><span style="white-space:pre-wrap"> </span>libstdc++.so.6
=> /lib64/libstdc++.so.6 (0x00007fbcc858e000)</span></div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:Monaco;color:rgb(248,255,252);background-color:rgba(0,0,0,0.9)"><span style="font-variant-ligatures:no-common-ligatures"><span style="white-space:pre-wrap"> </span>libm.so.6
=> /lib64/libm.so.6 (0x00007fbcc820c000)</span></div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:Monaco;color:rgb(248,255,252);background-color:rgba(0,0,0,0.9)"><span style="font-variant-ligatures:no-common-ligatures"><span style="white-space:pre-wrap"> </span>libc.so.6
=> /lib64/libc.so.6 (0x00007fbcc7e4a000)</span></div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:Monaco;color:rgb(248,255,252);background-color:rgba(0,0,0,0.9)"><span style="font-variant-ligatures:no-common-ligatures"><span style="white-space:pre-wrap"> </span>libgcc_s.so.1
=> /lib64/libgcc_s.so.1 (0x00007fbcc7c32000)</span></div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:Monaco;color:rgb(248,255,252);background-color:rgba(0,0,0,0.9)"><span style="font-variant-ligatures:no-common-ligatures"><span style="white-space:pre-wrap"> </span>/lib64/ld-linux-x86-64.so.2
(0x00007fbcc97eb000)</span></div>
</div>
<div>On our centos 8 VM, it shows as:</div>
<div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:Monaco;color:rgb(248,255,252);background-color:rgba(0,0,0,0.9)"><span style="font-variant-ligatures:no-common-ligatures"><span style="white-space:pre-wrap"> </span>linux-vdso.so.1
=><span>
</span>(0x00007ffebc3c3000)</span></div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:Monaco;color:rgb(248,255,252);background-color:rgba(0,0,0,0.9)"><span style="font-variant-ligatures:no-common-ligatures"><span style="white-space:pre-wrap"> </span>libz.so.1
=> /lib64/libz.so.1 (0x00007f2fcf0c3000)</span></div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:Monaco;color:rgb(248,255,252);background-color:rgba(0,0,0,0.9)"><span style="font-variant-ligatures:no-common-ligatures"><span style="white-space:pre-wrap"> </span>libpthread.so.0
=> /lib64/libpthread.so.0
(0x00007f2fceea6000)</span></div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:Monaco;color:rgb(248,255,252);background-color:rgba(0,0,0,0.9)"><span style="font-variant-ligatures:no-common-ligatures"><span style="white-space:pre-wrap"> </span>libdl.so.2
=> /lib64/libdl.so.2 (0x00007f2fceca2000)</span></div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:Monaco;color:rgb(248,255,252);background-color:rgba(0,0,0,0.9)"><span style="font-variant-ligatures:no-common-ligatures"><span style="white-space:pre-wrap"> </span><a href="http://libllvm-3.9-mesa.so/" target="_blank">libLLVM-3.9-mesa.so</a>
=> /lib64/<a href="http://libllvm-3.9-mesa.so/" target="_blank">libLLVM-3.9-mesa.so</a>
(0x00007f2fccd71000)</span></div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:Monaco;color:rgb(248,255,252);background-color:rgba(0,0,0,0.9)"><span style="font-variant-ligatures:no-common-ligatures"><span style="white-space:pre-wrap"> </span>libstdc++.so.6
=> /lib64/libstdc++.so.6 (0x00007f2fcca68000)</span></div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:Monaco;color:rgb(248,255,252);background-color:rgba(0,0,0,0.9)"><span style="font-variant-ligatures:no-common-ligatures"><span style="white-space:pre-wrap"> </span>libm.so.6
=> /lib64/libm.so.6 (0x00007f2fcc766000)</span></div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:Monaco;color:rgb(248,255,252);background-color:rgba(0,0,0,0.9)"><span style="font-variant-ligatures:no-common-ligatures"><span style="white-space:pre-wrap"> </span>libc.so.6
=> /lib64/libc.so.6 (0x00007f2fcc3a3000)</span></div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:Monaco;color:rgb(248,255,252);background-color:rgba(0,0,0,0.9)"><span style="font-variant-ligatures:no-common-ligatures"><span style="white-space:pre-wrap"> </span>libgcc_s.so.1
=> /lib64/libgcc_s.so.1 (0x00007f2fcc18c000)</span></div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:Monaco;color:rgb(248,255,252);background-color:rgba(0,0,0,0.9)"><span style="font-variant-ligatures:no-common-ligatures"><span style="white-space:pre-wrap"> </span>/lib64/ld-linux-x86-64.so.2
(0x000055f2cf96c000)</span></div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:Monaco;color:rgb(248,255,252);background-color:rgba(0,0,0,0.9)"><span style="font-variant-ligatures:no-common-ligatures"><span style="white-space:pre-wrap"> </span>librt.so.1
=> /lib64/../lib64/librt.so.1
(0x00007f2fcbf84000)</span></div>
</div>
<div><br>
</div>
<div>So I feel like the ChimeraX mesa is
imported but not the system one. </div>
<div><br>
</div>
<div>Best, </div>
<div>Zhe</div>
</div>
</div>
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</blockquote>
</div>
<br>
</div>
</blockquote>
</div>
</blockquote></div>