[Chimera-users] Error from running headless Chimera
Zhe Wang
anchorwz at googlemail.com
Fri Aug 3 03:48:36 PDT 2018
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
<https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/preset.html> 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 at entry=0x9db160,
arrays=arrays at entry=0xa2ab20, prim=prim at entry=0x7fffffffb5d0,
nr_prims=nr_prims at entry=1, ib=ib at 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 at entry=0x296b7d0, throwflag=throwflag at entry=0)
at Python/ceval.c:2994
#25 0x00000000004af3b0 in PyEval_EvalCodeEx (co=<optimized out>,
globals=<optimized out>, locals=locals at entry=0x0, args=<optimized out>,
argcount=argcount at entry=1, kws=kws at 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 at entry=0x1de0090, throwflag=throwflag at entry=0)
at Python/ceval.c:2994
#29 0x00000000004af3b0 in PyEval_EvalCodeEx (co=<optimized out>,
globals=<optimized out>, locals=locals at entry=0x0,
args=args at entry=0x7ffff7f8a068,
argcount=<optimized out>, kws=kws at entry=0x7fffe70e7968,
kwcount=kwcount at entry=1, defs=defs at entry=0x7fff975f1458,
defcount=defcount at 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 at entry=0x7fff96df7b90,
arg=arg at entry=0x7ffff7f8a050, kw=kw at 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 at entry=0x1f9acc0, throwflag=throwflag at entry=0)
at Python/ceval.c:3033
#34 0x00000000004af3b0 in PyEval_EvalCodeEx (co=<optimized out>,
globals=<optimized out>, locals=locals at entry=0x0, args=<optimized out>,
argcount=argcount at entry=2, kws=kws at 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 at entry=0x16daae0, throwflag=throwflag at entry=0)
at Python/ceval.c:2994
#38 0x00000000004af3b0 in PyEval_EvalCodeEx (co=<optimized out>,
globals=<optimized out>, locals=locals at entry=0x0,
args=args at entry=0x7fffe715bf68,
argcount=<optimized out>, kws=kws at entry=0x7ffff7f8a068,
kwcount=kwcount at entry=0, defs=defs at entry=0x7fff96dcb2a8,
defcount=defcount at 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 at entry=0x7fff96b5fed8,
arg=arg at entry=0x7fffe715bf50, kw=kw at 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 at entry=0x7fffe6d58960, throwflag=throwflag at entry=0)
at Python/ceval.c:3033
#43 0x00000000004af3b0 in PyEval_EvalCodeEx (co=<optimized out>,
globals=<optimized out>, locals=locals at entry=0x0, args=<optimized out>,
argcount=argcount at entry=1, kws=kws at 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 at entry=0x7fffe70a53d0, throwflag=throwflag at entry=0)
at Python/ceval.c:2994
#47 0x00000000004af3b0 in PyEval_EvalCodeEx (co=co at entry=0x7fffe714d7b0,
globals=globals at entry=0x7fffe710f168, locals=locals at entry=0x7fffe710f168,
args=args at entry=0x0, argcount=argcount at entry=0, kws=kws at entry=0x0,
kwcount=kwcount at entry=0, defs=defs at entry=0x0, defcount=defcount at entry=0,
closure=closure at entry=0x0) at Python/ceval.c:3589
#48 0x00000000004af4f2 in PyEval_EvalCode (co=co at entry=0x7fffe714d7b0,
globals=globals at entry=0x7fffe710f168, locals=locals at entry=0x7fffe710f168)
at Python/ceval.c:669
#49 0x00000000004c41cc in PyImport_ExecCodeModuleEx
(name=name at entry=0x7ffff04947fc
"chimeraOpenSandbox", co=co at entry=0x7fffe714d7b0,
pathname=pathname at entry=0x13a2a40
"test.pyc") at Python/import.c:731
#50 0x00000000004c452e in load_source_module (name=0x7ffff04947fc
"chimeraOpenSandbox", pathname=0x13a2a40 "test.pyc", fp=fp at 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 at entry=0x13b0860, throwflag=throwflag at entry=0)
at Python/ceval.c:2994
#54 0x00000000004af3b0 in PyEval_EvalCodeEx (co=<optimized out>,
globals=<optimized out>, locals=locals at entry=0x0,
args=args at entry=0x7fff97626668,
argcount=<optimized out>, kws=kws at entry=0x7ffff7f8a068,
kwcount=kwcount at entry=0, defs=defs at entry=0x7fffee43a1a8,
defcount=defcount at 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 at entry=0x7fffee4469b0,
arg=arg at entry=0x7fff97626650, kw=kw at 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 at entry=0x139e490, throwflag=throwflag at entry=0)
at Python/ceval.c:3033
#59 0x00000000004af3b0 in PyEval_EvalCodeEx (co=<optimized out>,
globals=<optimized out>, locals=locals at entry=0x0, args=<optimized out>,
argcount=argcount at entry=2, kws=kws at 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 at entry=0x896c20, throwflag=throwflag at entry=0) at
Python/ceval.c:2994
#63 0x00000000004af3b0 in PyEval_EvalCodeEx (co=<optimized out>,
globals=<optimized out>, locals=locals at entry=0x0, args=<optimized out>,
argcount=argcount at entry=1, kws=kws at 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 at entry=0x7ffff7f1f938, throwflag=throwflag at entry=0)
at Python/ceval.c:2994
#67 0x00000000004af3b0 in PyEval_EvalCodeEx (co=co at entry=0x7ffff7f9d230,
globals=globals at entry=0x7ffff7f5f168, locals=locals at entry=0x7ffff7f5f168,
args=args at entry=0x0, argcount=argcount at entry=0, kws=kws at entry=0x0,
kwcount=kwcount at entry=0, defs=defs at entry=0x0, defcount=defcount at entry=0,
---Type <return> to continue, or q <return> to quit---
On Wed, Aug 1, 2018 at 10:56 PM Greg Couch <gregc at 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
>
>
>
>
>
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
>
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