[Chimera-users] Error from running headless Chimera

[Greg Couch]

Works for me :-)

I just tried the headless version of Chimera on CentOS 7.5.   I didn't 
use a script, but did the following commands:

     open 6c7m
     windowsize 512 512
     surf
     copy file test.png
     stop

And it created the image file and exited without a problem.

So it is unclear what the problem is.  You'll need to run gdb to find 
out where the segmentation fault occured.  Create a debugging version of 
the chimera program script, and change the 'exec $python' at the end to 
'gdb $python', run it, and then in gdb, 'run $CHIMERA/share/__main__.py 
chimera_surface.py'.  When chimera segmentation faults, type 'bt' to get 
a backtrace and send it to me.

FYI, the headless version of Chimera comes with libOSMesa, so you don't 
need to install it.  But it shouldn't cause problems if you did.  The 
libOSMesa distributed with chimera is ancient, version 7.6.1. So, if the 
backtrace shows that the bug is in libOSMesa, there's a good chance that 
if you replace chimera's libOSMesa.so with the system version, it will work.

     Good luck,

     Greg


On 08/01/2018 03:57 AM, Zhe Wang wrote:
> Hi,
>
> I am trying to using headless Chimera on RedHat linux server 7.3 to 
> produce some images.
> But I end up with a segmentation fault. Does anyone have an idea how 
> it comes to this?
> The headless chimera is from 
> https://www.cgl.ucsf.edu/chimera/download.html (64-bit daily build).
> The test code was taken without changes from 
> https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html.
> Any ideas will be appreciated.
>
> Best,
> Zhe
>
> PS: OSMesa 11.2.2 has been installed.
>
>
> Executing chimera_surface.py...
>
> Processing 6c7m.pdb
>
> Opening 6c7m.pdb...
>
> #0, chain A: kemp eliminase KE07
>
>
> 6c7m.pdb opened
>
> Center of rotation: 0.867528 -1.77985 11.157
>
> /software/chimera_headless/bin/mscalc 1.400000 2.000000 1
>
>
> MSMSLIB 1.3 started on ebi-cli-002.ebi.ac.uk 
> <http://ebi-cli-002.ebi.ac.uk>
>
> Copyright M.F. Sanner (March 2000)
>
> Compilation flags
>
>
>
> Surface 6c7m.pdb, category main, probe radius 1.4, vertex density 2
>
> 12 connected surface components
>
> Total solvent excluded surface area = 10612
>
> component areas = 10035.4, 126.971, 97.9893, 90.9594, 38.157, 36.4953, 
> 34.1487, 33.7557, 32.681, 30.3253, 29.9037, 25.222
>
> Total solvent accessible surface area = 11324.6
>
> component areas = 11265.5, 25.8506, 19.8737, 10.3135, 0.685134, 
> 0.778238, 0.522429, 0.365982, 0.314644, 0.177358, 0.178001, 0.00214196
>
>
> Surface 6c7m.pdb, category main has 12 components
>
> /software/chimera_headless/bin/mscalc 1.400000 10.000000 1
>
>
> MSMSLIB 1.3 started on ebi-cli-002.ebi.ac.uk 
> <http://ebi-cli-002.ebi.ac.uk>
>
> Copyright M.F. Sanner (March 2000)
>
> Compilation flags
>
> RESTART FROM TRI: 1
>
> radius of atom 5 goes from 1.880000 to 1.980000
>
> radius of atom 6 goes from 1.880000 to 1.980000
>
> radius of atom 1569 goes from 1.420000 to 1.520000
>
> Partial mode
>
>
> /software/chimera_headless/bin/mscalc 1.400000 10.000000 0
>
>
> MSMSLIB 1.3 started on ebi-cli-002.ebi.ac.uk 
> <http://ebi-cli-002.ebi.ac.uk>
>
> Copyright M.F. Sanner (March 2000)
>
> Compilation flags
>
> RESTART FROM TRI: 1
>
> radius of atom 5 goes from 1.880000 to 1.980000
>
> radius of atom 6 goes from 1.880000 to 1.980000
>
> radius of atom 1569 goes from 1.420000 to 1.520000
>
> Partial mode
>
>
> Calculation of some surface components failed.
>
>
> A single component of the surface was calculated correctly - the 
> failure occurred for disconnectedadditional components such as inside 
> bubbles.If the desired surface is already shown, there is no need for 
> concern.However, if it is not shown, see below for possible fixes.
>
>
> Surface calculation frequently fails for large, multi-chain 
> structures. The calculation may be successful if the chains are 
> treated individually, by using the "split" command before generating a 
> surface.If splitting is not desired or the structure is already a 
> single chain, changing molecular surface parameters in the Selection 
> Inspector or (before surface creation) the New Surfaces category of 
> Preferences may allow the calculation to succeed. More details are 
> given at
>
>
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html
>
>
> Surface 6c7m.pdb, category main, probe radius 1.4, vertex density 10
>
> 1 connected surface components
>
> Total solvent excluded surface area = 10036.7
>
> Total solvent accessible surface area = 11266.5
>
>
> Surface 6c7m.pdb, category main has 1 components
>
> Rendering high resolution image...
>
> Segmentation fault
>
>
>
>
>
>
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