<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Zhe,<div class=""><br class=""></div><div class=""> Glad to hear that deleting the OSMesa included in ChimeraX makes the --offscreen option work for generating images for EMDB. Greg has fixed the CentOS 8 ChimeraX build so it does not include OSMesa and just uses the system version so you will not need to delete it in future releases.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jul 7, 2021, at 3:06 AM, Zhe Wang via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi Tom and Greg, <div class=""><br class=""></div><div class="">Thanks for double checking this.</div><div class="">I can confirm that the solution works on our centos 8 smoothly.</div><div class=""><br class=""></div><div class="">Best, </div><div class="">Zhe</div><div class=""><br class=""></div></div><br class=""><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" class="">gregc@cgl.ucsf.edu</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div class=""><p class="">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 class=""> sudo rm -rf
/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-packages/osmesa<br class="">
</p><p class="">I will change the daily build so it is not there. <br class="">
</p><p class=""> -- Greg</p>
<div class="">On 7/6/2021 12:38 PM, Tom Goddard
wrote:<br class="">
</div>
<blockquote type="cite" class="">
Hi Zhe,
<div class=""><br class="">
</div>
<div class=""> 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 class=""><br class="">
</div>
<div class=""> 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 class=""><br class="">
</div>
<div class=""> 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 class=""><br class="">
</div>
<div class=""><span style="white-space:pre-wrap" class=""> </span>Tom</div>
<div class=""><br class="">
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On Jul 6, 2021, at 11:38 AM, Zhe Wang via
ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank" class="">chimerax-users@cgl.ucsf.edu</a>>
wrote:</div>
<br class="">
<div class="">
<div dir="ltr" class="">
<blockquote type="cite" class="">
<pre class=""><span style="font-family:Arial,Helvetica,sans-serif" class="">Hi Greg, </span>
</pre>
</blockquote>
<div dir="ltr" class="">
<div class=""><br class="">
</div>
<div class="">Thank you for your reply.</div>
<div class="">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 class="">The ldd result show as the following:</div>
<div class="">
<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)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">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)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">./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)" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span style="white-space:pre-wrap" class=""> </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)" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span style="white-space:pre-wrap" class=""> </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)" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span style="white-space:pre-wrap" class=""> </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)" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span style="white-space:pre-wrap" class=""> </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)" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span style="white-space:pre-wrap" class=""> </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)" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span style="white-space:pre-wrap" class=""> </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)" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span style="white-space:pre-wrap" class=""> </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)" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span style="white-space:pre-wrap" class=""> </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)" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span style="white-space:pre-wrap" class=""> </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)" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span style="white-space:pre-wrap" class=""> </span>/lib64/ld-linux-x86-64.so.2
(0x00007fbcc97eb000)</span></div>
</div>
<div class="">On our centos 8 VM, it shows as:</div>
<div class="">
<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)" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span style="white-space:pre-wrap" class=""> </span>linux-vdso.so.1
=><span class="">
</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)" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span style="white-space:pre-wrap" class=""> </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)" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span style="white-space:pre-wrap" class=""> </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)" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span style="white-space:pre-wrap" class=""> </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)" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span style="white-space:pre-wrap" class=""> </span><a href="http://libllvm-3.9-mesa.so/" target="_blank" class="">libLLVM-3.9-mesa.so</a>
=> /lib64/<a href="http://libllvm-3.9-mesa.so/" target="_blank" class="">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)" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span style="white-space:pre-wrap" class=""> </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)" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span style="white-space:pre-wrap" class=""> </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)" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span style="white-space:pre-wrap" class=""> </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)" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span style="white-space:pre-wrap" class=""> </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)" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span style="white-space:pre-wrap" class=""> </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)" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span style="white-space:pre-wrap" class=""> </span>librt.so.1
=> /lib64/../lib64/librt.so.1
(0x00007f2fcbf84000)</span></div>
</div>
<div class=""><br class="">
</div>
<div class="">So I feel like the ChimeraX mesa is
imported but not the system one. </div>
<div class=""><br class="">
</div>
<div class="">Best, </div>
<div class="">Zhe</div>
</div>
</div>
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</blockquote>
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</blockquote>
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</blockquote></div>
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