Hi Tom and Greg,

Thank you very much for your help.

It works now. I tried out the lines you have shown. It did work. I can produce the image I need.

To see what was the problem, I test line by line in this script (https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html). The problem came from "rc("preset apply publication 1")".

Here I post the debugging backtrace information I got. It seems related to the swrast rendering lib.

Though my problem solved, it will be good to know the reason of this too.

Thank you again for your informative help.

Best,

Zhe

(gdb) bt

#0 aa_general_rgba_line (ctx=0x9db160, v0=0x7fffeab809c8, v1=0x7fffeab80bb0) at swrast/s_aalinetemp.h:208

#1 0x00007fffecafd9b9 in _swsetup_edge_render_line_tri (ctx=0x9db160, ef=0x14d4060 '\001' <repeats 50 times>, "@\001", e0=5, e1=6, e2=30, v0=0x7fffeab809c8, v1=0x7fffeab80bb0, v2=0x7fffeab83970) at swrast_setup/ss_triangle.c:80

#2 0x00007fffecaffa7f in _swsetup_render_tri (render=0x7fffecafd8c0 <_swsetup_edge_render_line_tri>, facing=1, e2=30, e1=6, e0=5, ctx=0x9db160) at swrast_setup/ss_triangle.c:165

#3 triangle_twoside_unfilled_rgba (ctx=0x9db160, e0=5, e1=6, e2=30) at swrast_setup/ss_tritmp.h:181

#4 0x00007fffeca82feb in _tnl_render_triangles_elts (ctx=0x9db160, start=0, count=150, flags=<optimized out>) at tnl/t_vb_rendertmp.h:175

#5 0x00007fffeca83f65 in run_render (ctx=0x9db160, stage=<optimized out>) at tnl/t_vb_render.c:320

#6 0x00007fffeca78ccd in _tnl_run_pipeline (ctx=0x9db160) at tnl/t_pipeline.c:158

#7 0x00007fffeca7ae0c in _tnl_draw_prims (ctx=ctx@entry=0x9db160, arrays=arrays@entry=0xa2ab20, prim=prim@entry=0x7fffffffb5d0, nr_prims=nr_prims@entry=1, ib=ib@entry=0x7fffffffb5e0, min_index=<optimized out>, max_index=49) at tnl/t_draw.c:445

#8 0x00007fffeca7b125 in _tnl_vbo_draw_prims (ctx=0x9db160, arrays=0xa2ab20, prim=0x7fffffffb5d0, nr_prims=1, ib=0x7fffffffb5e0, index_bounds_valid=<optimized out>, min_index=0, max_index=49) at tnl/t_draw.c:375

#9 0x00007fffeca6da4e in vbo_validated_drawrangeelements (indices=0x0, type=5125, count=150, end=4294967295, start=4294967295, index_bounds_valid=0 '\000', mode=4, ctx=0x9db160) at vbo/vbo_exec_array.c:661

#10 vbo_exec_DrawElements (mode=4, count=150, type=5125, indices=0x0) at vbo/vbo_exec_array.c:755

#11 0x00007fffeb8221d9 in molecule::ObjectInstances::drawPushMatrix(chimera::LensViewer const*, molecule::ObjectInstances::DrawType) () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_molecule.so

#12 0x00007fffeb822253 in molecule::ObjectInstances::drawOpaque(chimera::LensViewer const*) () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_molecule.so

#13 0x00007fffeb823f84 in molecule::Shapes::drawOpaque(chimera::LensViewer const*) () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_molecule.so

#14 0x00007fffeb84fb76 in molecule::MoleculeLensModel::draw(chimera::LensViewer const*, chimera::LensViewer::DrawPass) const () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_molecule.so

#15 0x00007fffee09e3f9 in chimera::LensModel::xformDraw(chimera::LensViewer const*, chimera::LensViewer::DrawPass) const () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_chimera.so

#16 0x00007fffee09a8f4 in chimera::Lens::draw(chimera::LensViewer const*, chimera::LensViewer::DrawPass, int const*) () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_chimera.so

#17 0x00007fffee0a6e09 in chimera::LensViewer::drawSilhouette(chimera::Array<int, 4ul> const&, chimera::LensViewer::DrawPass, __gnu_cxx::__normal_iterator<chimera::ScreenBox*, std::vector<chimera::ScreenBox, std::allocator<chimera::ScreenBox> > >, __gnu_cxx::__normal_iterator<chimera::ScreenBox*, std::vector<chimera::ScreenBox, std::allocator<chimera::ScreenBox> > >) const () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_chimera.so

#18 0x00007fffee0a8b69 in chimera::LensViewer::drawScreenBoxes(chimera::Array<int, 4ul> const&, __gnu_cxx::__normal_iterator<chimera::ScreenBox*, std::vector<chimera::ScreenBox, std::allocator<chimera::ScreenBox> > >, __gnu_cxx::__normal_iterator<chimera::ScreenBox*, std::vector<chimera::ScreenBox, std::allocator<chimera::ScreenBox> > >) const () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_chimera.so

#19 0x00007fffee0a8e9d in chimera::LensViewer::draw() const () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_chimera.so

#20 0x00007fffee0ab551 in chimera::LensViewer::pilImages(int, int, char const*, int, bool) const () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_chimera.so

#21 0x00007fffee0dc98c in LensViewer_pilImages () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_chimera.so

#22 0x00000000004ad05f in do_call (nk=<optimized out>, na=<optimized out>, pp_stack=0x7fffffffc150, func=<optimized out>) at Python/ceval.c:4571

#23 call_function (oparg=<optimized out>, pp_stack=0x7fffffffc150) at Python/ceval.c:4379

#24 PyEval_EvalFrameEx (f=f@entry=0x296b7d0, throwflag=throwflag@entry=0) at Python/ceval.c:2994

#25 0x00000000004af3b0 in PyEval_EvalCodeEx (co=<optimized out>, globals=<optimized out>, locals=locals@entry=0x0, args=<optimized out>, argcount=argcount@entry=1, kws=kws@entry=0x1de02d8, kwcount=10, defs=0x7fffe69c57b8, defcount=19, closure=0x0) at Python/ceval.c:3589

#26 0x00000000004ac4fc in fast_function (nk=<optimized out>, na=1, n=<optimized out>, pp_stack=0x7fffffffc390, func=<optimized out>) at Python/ceval.c:4452

#27 call_function (oparg=<optimized out>, pp_stack=0x7fffffffc390) at Python/ceval.c:4377

#28 PyEval_EvalFrameEx (f=f@entry=0x1de0090, throwflag=throwflag@entry=0) at Python/ceval.c:2994

#29 0x00000000004af3b0 in PyEval_EvalCodeEx (co=<optimized out>, globals=<optimized out>, locals=locals@entry=0x0, args=args@entry=0x7ffff7f8a068, argcount=<optimized out>, kws=kws@entry=0x7fffe70e7968, kwcount=kwcount@entry=1, defs=defs@entry=0x7fff975f1458, defcount=defcount@entry=11, closure=0x0)

at Python/ceval.c:3589

#30 0x000000000051e205 in function_call (func=0x7fff96df7b90, arg=0x7ffff7f8a050, kw=0x7fffe6d94280) at Objects/funcobject.c:523

#31 0x0000000000425bb3 in PyObject_Call (func=func@entry=0x7fff96df7b90, arg=arg@entry=0x7ffff7f8a050, kw=kw@entry=0x7fffe6d94280) at Objects/abstract.c:2547

#32 0x00000000004a9158 in ext_do_call (nk=<optimized out>, na=<optimized out>, flags=<optimized out>, pp_stack=0x7fffffffc6a0, func=0x7fff96df7b90) at Python/ceval.c:4671

#33 PyEval_EvalFrameEx (f=f@entry=0x1f9acc0, throwflag=throwflag@entry=0) at Python/ceval.c:3033

#34 0x00000000004af3b0 in PyEval_EvalCodeEx (co=<optimized out>, globals=<optimized out>, locals=locals@entry=0x0, args=<optimized out>, argcount=argcount@entry=2, kws=kws@entry=0x16dad00, kwcount=0, defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:3589

#35 0x00000000004ac4fc in fast_function (nk=<optimized out>, na=2, n=<optimized out>, pp_stack=0x7fffffffc8d0, func=<optimized out>) at Python/ceval.c:4452

#36 call_function (oparg=<optimized out>, pp_stack=0x7fffffffc8d0) at Python/ceval.c:4377

#37 PyEval_EvalFrameEx (f=f@entry=0x16daae0, throwflag=throwflag@entry=0) at Python/ceval.c:2994

#38 0x00000000004af3b0 in PyEval_EvalCodeEx (co=<optimized out>, globals=<optimized out>, locals=locals@entry=0x0, args=args@entry=0x7fffe715bf68, argcount=<optimized out>, kws=kws@entry=0x7ffff7f8a068, kwcount=kwcount@entry=0, defs=defs@entry=0x7fff96dcb2a8, defcount=defcount@entry=1, closure=0x0)

at Python/ceval.c:3589

#39 0x000000000051e205 in function_call (func=0x7fff96b5fed8, arg=0x7fffe715bf50, kw=0x7fffe710fb40) at Objects/funcobject.c:523

#40 0x0000000000425bb3 in PyObject_Call (func=func@entry=0x7fff96b5fed8, arg=arg@entry=0x7fffe715bf50, kw=kw@entry=0x7fffe710fb40) at Objects/abstract.c:2547

#41 0x00000000004a9158 in ext_do_call (nk=<optimized out>, na=<optimized out>, flags=<optimized out>, pp_stack=0x7fffffffcbe0, func=0x7fff96b5fed8) at Python/ceval.c:4671

#42 PyEval_EvalFrameEx (f=f@entry=0x7fffe6d58960, throwflag=throwflag@entry=0) at Python/ceval.c:3033

#43 0x00000000004af3b0 in PyEval_EvalCodeEx (co=<optimized out>, globals=<optimized out>, locals=locals@entry=0x0, args=<optimized out>, argcount=argcount@entry=1, kws=kws@entry=0x7fffe70a5560, kwcount=0, defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:3589

#44 0x00000000004ac4fc in fast_function (nk=<optimized out>, na=1, n=<optimized out>, pp_stack=0x7fffffffce10, func=<optimized out>) at Python/ceval.c:4452

#45 call_function (oparg=<optimized out>, pp_stack=0x7fffffffce10) at Python/ceval.c:4377

#46 PyEval_EvalFrameEx (f=f@entry=0x7fffe70a53d0, throwflag=throwflag@entry=0) at Python/ceval.c:2994

#47 0x00000000004af3b0 in PyEval_EvalCodeEx (co=co@entry=0x7fffe714d7b0, globals=globals@entry=0x7fffe710f168, locals=locals@entry=0x7fffe710f168, args=args@entry=0x0, argcount=argcount@entry=0, kws=kws@entry=0x0, kwcount=kwcount@entry=0, defs=defs@entry=0x0, defcount=defcount@entry=0,

closure=closure@entry=0x0) at Python/ceval.c:3589

#48 0x00000000004af4f2 in PyEval_EvalCode (co=co@entry=0x7fffe714d7b0, globals=globals@entry=0x7fffe710f168, locals=locals@entry=0x7fffe710f168) at Python/ceval.c:669

#49 0x00000000004c41cc in PyImport_ExecCodeModuleEx (name=name@entry=0x7ffff04947fc "chimeraOpenSandbox", co=co@entry=0x7fffe714d7b0, pathname=pathname@entry=0x13a2a40 "test.pyc") at Python/import.c:731

#50 0x00000000004c452e in load_source_module (name=0x7ffff04947fc "chimeraOpenSandbox", pathname=0x13a2a40 "test.pyc", fp=fp@entry=0x1292be0) at Python/import.c:1121

#51 0x00000000004c48d7 in imp_load_source (self=<optimized out>, args=<optimized out>) at Python/import.c:3163

#52 0x00000000004acb39 in call_function (oparg=<optimized out>, pp_stack=0x7fffffffd200) at Python/ceval.c:4357

#53 PyEval_EvalFrameEx (f=f@entry=0x13b0860, throwflag=throwflag@entry=0) at Python/ceval.c:2994

#54 0x00000000004af3b0 in PyEval_EvalCodeEx (co=<optimized out>, globals=<optimized out>, locals=locals@entry=0x0, args=args@entry=0x7fff97626668, argcount=<optimized out>, kws=kws@entry=0x7ffff7f8a068, kwcount=kwcount@entry=0, defs=defs@entry=0x7fffee43a1a8, defcount=defcount@entry=1, closure=0x0)

at Python/ceval.c:3589

#55 0x000000000051e205 in function_call (func=0x7fffee4469b0, arg=0x7fff97626650, kw=0x7fffe71495c8) at Objects/funcobject.c:523

#56 0x0000000000425bb3 in PyObject_Call (func=func@entry=0x7fffee4469b0, arg=arg@entry=0x7fff97626650, kw=kw@entry=0x7fffe71495c8) at Objects/abstract.c:2547

#57 0x00000000004a9158 in ext_do_call (nk=<optimized out>, na=<optimized out>, flags=<optimized out>, pp_stack=0x7fffffffd510, func=0x7fffee4469b0) at Python/ceval.c:4671

#58 PyEval_EvalFrameEx (f=f@entry=0x139e490, throwflag=throwflag@entry=0) at Python/ceval.c:3033

#59 0x00000000004af3b0 in PyEval_EvalCodeEx (co=<optimized out>, globals=<optimized out>, locals=locals@entry=0x0, args=<optimized out>, argcount=argcount@entry=2, kws=kws@entry=0x897058, kwcount=1, defs=0x7fffee436068, defcount=12, closure=0x0) at Python/ceval.c:3589

#60 0x00000000004ac4fc in fast_function (nk=<optimized out>, na=2, n=<optimized out>, pp_stack=0x7fffffffd740, func=<optimized out>) at Python/ceval.c:4452

#61 call_function (oparg=<optimized out>, pp_stack=0x7fffffffd740) at Python/ceval.c:4377

#62 PyEval_EvalFrameEx (f=f@entry=0x896c20, throwflag=throwflag@entry=0) at Python/ceval.c:2994

#63 0x00000000004af3b0 in PyEval_EvalCodeEx (co=<optimized out>, globals=<optimized out>, locals=locals@entry=0x0, args=<optimized out>, argcount=argcount@entry=1, kws=kws@entry=0x7ffff7f1fac0, kwcount=0, defs=0x7ffff7ef0f80, defcount=16, closure=0x0) at Python/ceval.c:3589

#64 0x00000000004ac4fc in fast_function (nk=<optimized out>, na=1, n=<optimized out>, pp_stack=0x7fffffffd980, func=<optimized out>) at Python/ceval.c:4452

#65 call_function (oparg=<optimized out>, pp_stack=0x7fffffffd980) at Python/ceval.c:4377

#66 PyEval_EvalFrameEx (f=f@entry=0x7ffff7f1f938, throwflag=throwflag@entry=0) at Python/ceval.c:2994

#67 0x00000000004af3b0 in PyEval_EvalCodeEx (co=co@entry=0x7ffff7f9d230, globals=globals@entry=0x7ffff7f5f168, locals=locals@entry=0x7ffff7f5f168, args=args@entry=0x0, argcount=argcount@entry=0, kws=kws@entry=0x0, kwcount=kwcount@entry=0, defs=defs@entry=0x0, defcount=defcount@entry=0,

---Type <return> to continue, or q <return> to quit---

On Wed, Aug 1, 2018 at 10:56 PM Greg Couch <gregc@cgl.ucsf.edu> wrote:

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

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

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

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 disconnected additional 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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