[chimerax-users] Question about libLLVM

[Zhe Wang]

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> 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> 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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