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

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@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 => /lib64/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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