[Chimera-users] Installing Chimera and ChimeraX on a CentOS box without root

Healey, Joe J.R.J.Healey at warwick.ac.uk
Tue Jun 20 00:30:02 PDT 2017


Hi Tom,


Ah ok, I understand, thanks for the reply. I didn't realise it was going to be quite so complicated!


My mac can't really handle the structures I'm trying to model, as it only has integrated graphics. But, perhaps I can use this to convince the Uni to buy me a more capable machine! ;)


Thanks again,


Joe



Joe Healey


M.Sc. B.Sc. (Hons) MSRB
PhD Student
MOAC CDT, Senate House
University of Warwick
Coventry
CV47AL
Mob: +44 (0) 7536 042620  |  Email: J.R.J.Healey at warwick.ac.uk

Jointly working in:
Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/> (WMS Microbiology and Infection Unit)
and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry)

Twitter: @JRJHealey<https://twitter.com/JRJHealey>  |  Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738
________________________________
From: Tom Goddard <goddard at sonic.net>
Sent: 19 June 2017 18:38:49
To: Healey, Joe
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Installing Chimera and ChimeraX on a CentOS box without root

Hi Joe,

  Chimera and ChimeraX are best run on your laptop and desktop.  Trying to get it to run on a Linux server with remote display is asking for failure.  But if you still want to pursue that here is what your errors mean.  The first error starting Chimera 1.11 means that there inconsistent versions of OpenGL on the server — two different OpenGL libraries.  Only a system administrator can fix this, usually by installing a new graphics driver which will hopefully remove any old ones it finds.  For ChimeraX, as it says on our download page "It does not run on RHEL/CentOS 7 as is…”  and on our download it suggests speculative and difficult steps if you are not accustomed to installing software on Linux.  By far the best option is to find a machine capable of running Chimera/ChimeraX rather than trying to prod a totally unsuitable machine into running them.

Tom


On Jun 19, 2017, at 4:49 AM, Healey, Joe <J.R.J.Healey at warwick.ac.uk<mailto:J.R.J.Healey at warwick.ac.uk>> wrote:

Hi Chimera team,

I need to install chimera and chimeraX on a server with a GPU which I now have access to assist in visualising larger structures, but I don't have any root privileges.


After the first pass installing both, Chimera 1.11 gives me this warning/error when attempting to run:

"OpenGL misconfiguration detected. /usr/lib/libGL.so.1 differs from /usr/X11R6/lib/libGL.so.1"

And when I close this dialogue box, I get this:

"Error of failed request:  BadValue (integer parameter out of range for operation)
  Major opcode of failed request:  149 (GLX)
  Minor opcode of failed request:  3 (X_GLXCreateContext)
  Value in failed request:  0x0
  Serial number of failed request:  717
  Current serial number in output stream:  718
libxcb: WARNING! Program tries to lock an already locked connection,
        which indicates a programming error.
        There will be no further warnings about this issue."

-----------

And when running ChimeraX for the first time, I get this:

"
ChimeraX: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by ChimeraX)
ChimeraX: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /cold/chem/msrnbi/bin/chimerax/bin/../lib/libpython3.6m.so.1.0)
ChimeraX: /lib64/libc.so.6: version `GLIBC_2.17' not found (required by /cold/chem/msrnbi/bin/chimerax/bin/../lib/libpython3.6m.so.1.0)
"


Evidently I need 2 different versions of GLIBC for ChimeraX, but assuming I can install these concurrently without root access, how would I go about telling ChimeraX where to look for the libraries?



Any advice/documentation you have to get the programs working would be much appreciated.


Joe Healey


M.Sc. B.Sc. (Hons) MSRB
PhD Student
MOAC CDT, Senate House
University of Warwick
Coventry
CV47AL
Mob: +44 (0) 7536 042620  |  Email: J.R.J.Healey at warwick.ac.uk<mailto:J.R.J.Healey at warwick.ac.uk>

Jointly working in:
Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/> (WMS Microbiology and Infection Unit)
and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry)

Twitter: @JRJHealey<https://twitter.com/JRJHealey>  |  Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738<http://orcid.org/0000-0002-9569-6738>
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