[chimerax-users] Question about libLLVM

[Tom Goddard]

Hi Zhe,

  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.

	Tom


> On Jul 7, 2021, at 3:06 AM, Zhe Wang via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Tom and Greg, 
> 
> Thanks for double checking this.
> I can confirm that the solution works on our centos 8 smoothly.
> 
> Best, 
> Zhe
> 
> 
> On Tue, Jul 6, 2021 at 8:58 PM Greg Couch <gregc at cgl.ucsf.edu <mailto:gregc at cgl.ucsf.edu>> wrote:
> 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:
> 
>     sudo rm -rf /usr/libexec/UCSF-ChimeraX/lib/python3.8/site-packages/osmesa
> 
> I will change the daily build so it is not there.  
> 
>     -- Greg
> 
> On 7/6/2021 12:38 PM, Tom Goddard wrote:
>> Hi Zhe,
>> 
>>   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?
>> 
>>   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.
>> 
>>   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.
>> 
>> 	Tom
>> 
>> 
>>> On Jul 6, 2021, at 11:38 AM, Zhe Wang via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>> wrote:
>>> 
>>>> Hi Greg, 
>>> 
>>> Thank you for your reply.
>>> I do have the libOSMesa.so exist in our /usr/lib64/ directory. But it seems not the one ChimeraX is trying to import.
>>> The ldd result show as the following:
>>> ldd ./libexec/UCSF-ChimeraX/lib/python3.8/site-packages/osmesa/libOSMesa.so.8.0.0
>>> ./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)
>>> 	linux-vdso.so.1 (0x00007ffe625ef000)
>>> 	libz.so.1 => /lib64/libz.so.1 (0x00007fbcc8d47000)
>>> 	libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fbcc8b27000)
>>> 	libdl.so.2 => /lib64/libdl.so.2 (0x00007fbcc8923000)
>>> 	libLLVM-10.so.1 => not found
>>> 	libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007fbcc858e000)
>>> 	libm.so.6 => /lib64/libm.so.6 (0x00007fbcc820c000)
>>> 	libc.so.6 => /lib64/libc.so.6 (0x00007fbcc7e4a000)
>>> 	libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007fbcc7c32000)
>>> 	/lib64/ld-linux-x86-64.so.2 (0x00007fbcc97eb000)
>>> On our centos 8 VM, it shows as:
>>> 	linux-vdso.so.1 =>  (0x00007ffebc3c3000)
>>> 	libz.so.1 => /lib64/libz.so.1 (0x00007f2fcf0c3000)
>>> 	libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f2fceea6000)
>>> 	libdl.so.2 => /lib64/libdl.so.2 (0x00007f2fceca2000)
>>> 	libLLVM-3.9-mesa.so <http://libllvm-3.9-mesa.so/> => /lib64/libLLVM-3.9-mesa.so <http://libllvm-3.9-mesa.so/>(0x00007f2fccd71000)
>>> 	libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007f2fcca68000)
>>> 	libm.so.6 => /lib64/libm.so.6 (0x00007f2fcc766000)
>>> 	libc.so.6 => /lib64/libc.so.6 (0x00007f2fcc3a3000)
>>> 	libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f2fcc18c000)
>>> 	/lib64/ld-linux-x86-64.so.2 (0x000055f2cf96c000)
>>> 	librt.so.1 => /lib64/../lib64/librt.so.1 (0x00007f2fcbf84000)
>>> 
>>> So I feel like the ChimeraX mesa is imported but not the system one. 
>>> 
>>> Best, 
>>> Zhe
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>> 
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