[chimerax-users] Question about libLLVM

[Greg Couch]

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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