ChimeraX bug report submission

[Greg Couch]

The following bug report has been submitted:
Platform:        Linux-4.15.0-55-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 0.91 (2019-07-25)
Description
Tried opening 3j3q with daily build.  Had the same problem with default version of system version of mesa 19.0.1.  This is with the latest development build, 19.2.

Log:
UCSF ChimeraX version: 0.91 (2019-07-25)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 3j3q

3j3q title:  
Atomic-level structure of the entire HIV-1 capsid [more info...]  
  
Chain information for 3j3q #1  
---  
Chain | Description  
0 1 10 11 12 13 14 15 16 17 18 19 1A 1B 1C 1D 1E 1F 1G 1H 1I 1J 1K 1L 1M 1N 1O
1P 1Q 1R 1S 1T 1U 1V 1W 1X 1Y 1Z 1a 1b 1c 1d 1e 1f 1g 1h 1i 1j 1k 1l 1m 1n 1o
1p 1q 1r 1s 1t 1u 1v 1w 1x 1y 1z 2 20 21 22 23 24 25 26 27 28 29 2A 2B 2C 2D
2E 2F 2G 2H 2I 2J 2K 2L 2M 2N 2O 2P 2Q 2R 2S 2T 2U 2V 2W 2X 2Y 2Z 2a 2b 2c 2d
2e 2f 2g 2h 2i 2j 2k 2l 2m 2n 2o 2p 2q 2r 2s 2t 2u 2v 2w 2x 2y 2z 3 30 31 32
33 34 35 36 37 38 39 3A 3B 3C 3D 3E 3F 3G 3H 3I 3J 3K 3L 3M 3N 3O 3P 3Q 3R 3S
3T 3U 3V 3W 3X 3Y 3Z 3a 3b 3c 3d 3e 3f 3g 3h 3i 3j 3k 3l 3m 3n 3o 3p 3q 3r 3s
3t 3u 3v 3w 3x 3y 3z 4 40 41 42 43 44 45 46 47 48 49 4A 4B 4C 4D 4E 4F 4G 4H
4I 4J 4K 4L 4M 4N 4O 4P 4Q 4R 4S 4T 4U 4V 4W 4X 4Y 4Z 4a 4b 4c 4d 4e 4f 4g 4h
4i 4j 4k 4l 4m 4n 4o 4p 4q 4r 4s 4t 4u 4v 4w 4x 4y 4z 5 50 51 52 53 54 55 56
57 58 59 5A 5B 5C 5D 5E 5F 5G 5H 5I 5J 5K 5L 5M 5N 5O 5P 5Q 5R 5S 5T 5U 5V 5W
5X 5Y 5Z 5a 5b 5c 5d 5e 5f 5g 5h 5i 5j 5k 5l 5m 5n 5o 5p 5q 5r 5s 5t 5u 5v 5w
5x 5y 5z 6 60 61 62 63 64 65 66 67 68 69 6A 6B 6C 6D 6E 6F 6G 6H 6I 6J 6K 6L
6M 6N 6O 6P 6Q 6R 6S 6T 6U 6V 6W 6X 6Y 6Z 6a 6b 6c 6d 6e 6f 6g 6h 6i 6j 6k 6l
6m 6n 6o 6p 6q 6r 6s 6t 6u 6v 6w 6x 6y 6z 7 70 71 72 73 74 75 76 77 78 79 7A
7B 7C 7D 7E 7F 7G 7H 7I 7J 7K 7L 7M 7N 7O 7P 7Q 7R 7S 7T 7U 7V 7W 7X 7Y 7Z 7a
7b 7c 7d 7e 7f 7g 7h 7i 7j 7k 7l 7m 7n 7o 7p 7q 7r 7s 7t 7u 7v 7w 7x 7y 7z 8
80 81 82 83 84 85 86 87 88 89 8A 8B 8C 8D 8E 8F 8G 8H 8I 8J 8K 8L 8M 8N 8O 8P
8Q 8R 8S 8T 8U 8V 8W 8X 8Y 8Z 8a 8b 8c 8d 8e 8f 8g 8h 8i 8j 8k 8l 8m 8n 8o 8p
8q 8r 8s 8t 8u 8v 8w 8x 8y 8z 9 90 91 92 93 94 95 96 97 98 99 9A 9B 9C 9D 9E
9F 9G 9H 9I 9J 9K 9L 9M 9N 9O 9P 9Q 9R 9S 9T 9U 9V 9W 9X 9Y 9Z 9a 9b 9c 9d 9e
9f 9g 9h 9i 9j 9k 9l 9m 9n 9o 9p 9q 9r 9s 9t 9u 9v 9w 9x 9y 9z A B C D E F G H
I J K L M N O P Q R S T U V W X Y Z a a0 a1 a2 a3 a4 a5 a6 a7 a8 a9 aA aB aC
aD aE aF aG aH aI aJ aK aL aM aN aO aP aQ aR aS aT aU aV aW aX aY aZ aa ab ac
ad ae af ag ah ai aj ak al am an ao ap aq ar as at au av aw ax ay az b b0 b1
b2 b3 b4 b5 b6 b7 b8 b9 bA bB bC bD bE bF bG bH bI bJ bK bL bM bN bO bP bQ bR
bS bT bU bV bW bX bY bZ ba bb bc bd be bf bg bh bi bj bk bl bm bn bo bp bq br
bs bt bu bv bw bx by bz c c0 c1 c2 c3 c4 c5 c6 c7 c8 c9 cA cB cC cD cE cF cG
cH cI cJ cK cL cM cN cO cP cQ cR cS cT cU cV cW cX cY cZ ca cb cc cd ce cf cg
ch ci cj ck cl cm cn co cp cq cr cs ct cu cv cw cx cy cz d d0 d1 d2 d3 d4 d5
d6 d7 d8 d9 dA dB dC dD dE dF dG dH dI dJ dK dL dM dN dO dP dQ dR dS dT dU dV
dW dX dY dZ da db dc dd de df dg dh di dj dk dl dm dn do dp dq dr ds dt du dv
dw dx dy dz e e0 e1 e2 e3 e4 e5 e6 e7 e8 e9 eA eB eC eD eE eF eG eH eI eJ eK
eL eM eN eO eP eQ eR eS eT eU eV eW eX eY eZ ea eb ec ed ee ef eg eh ei ej ek
el em en eo ep eq er es et eu ev ew ex ey ez f f0 f1 f2 f3 f4 f5 f6 f7 f8 f9
fA fB fC fD fE fF fG fH fI fJ fK fL fM fN fO fP fQ fR fS fT fU fV fW fX fY fZ
fa fb fc fd fe ff fg fh fi fj fk fl fm fn fo fp fq fr fs ft fu fv fw fx fy fz
g g0 g1 g2 g3 g4 g5 g6 g7 g8 g9 gA gB gC gD gE gF gG gH gI gJ gK gL gM gN gO
gP gQ gR gS gT gU gV gW gX gY gZ ga gb gc gd ge gf gg gh gi gj gk gl gm gn go
gp gq gr gs gt gu gv gw gx gy gz h h0 h1 h2 h3 h4 h5 h6 h7 h8 h9 hA hB hC hD
hE hF hG hH hI hJ hK hL hM hN hO hP hQ hR hS hT hU hV hW hX hY hZ ha hb hc hd
he hf hg hh hi hj hk hl hm hn ho hp hq hr hs ht hu hv hw hx hy hz i i0 i1 i2
i3 i4 i5 i6 i7 i8 i9 iA iB iC iD iE iF iG iH iI iJ iK iL iM iN iO iP iQ iR iS
iT iU iV iW iX iY iZ ia ib ic id ie if ig ih ii ij ik il im in io ip iq ir is
it iu iv iw ix iy iz j j0 j1 j2 j3 j4 j5 j6 j7 j8 j9 jA jB jC jD jE jF jG jH
jI jJ jK jL jM jN jO jP jQ jR jS jT jU jV jW jX jY jZ ja jb jc jd je jf jg jh
ji jj jk jl jm jn jo jp jq jr js jt ju jv jw jx jy jz k k0 k1 k2 k3 k4 k5 k6
k7 k8 k9 kA kB kC kD kE kF kG kH kI kJ kK kL kM kN kO kP kQ kR kS kT kU kV kW
kX kY kZ ka kb kc kd ke kf kg kh ki kj kk kl km kn ko kp kq kr ks kt ku kv kw
kx ky kz l l0 l1 l2 l3 l4 l5 l6 l7 l8 l9 lA lB lC lD lE lF lG lH lI lJ lK lL
lM lN lO lP lQ lR la lb lc ld le lf lg lh li lj lk ll lm ln lo lp lq lr ls lt
lu lv lw lx ly lz m n o p q r s t u v w x y z | capsid protein  
  
  
An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.  
  
Traceback (most recent call last):  
File "/home/chimera/chimerax_daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 72, in draw_new_frame  
view.draw(check_for_changes = False)  
File "/home/chimera/chimerax_daily/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 164, in draw  
self._draw_scene(camera, drawings)  
File "/home/chimera/chimerax_daily/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 222, in _draw_scene  
r.multishadow.set_multishadow_view(cp)  
File "/home/chimera/chimerax_daily/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 1504, in set_multishadow_view  
GL.glBindBuffer(GL.GL_UNIFORM_BUFFER, self._multishadow_matrix_buffer())  
File "/home/chimera/chimerax_daily/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 1561, in
_multishadow_matrix_buffer  
GL.glBufferData(GL.GL_UNIFORM_BUFFER, nbytes, pyopengl_null(),
GL.GL_DYNAMIC_DRAW)  
File "src/latebind.pyx", line 44, in OpenGL_accelerate.latebind.Curry.__call__  
File "/home/chimera/chimerax_daily/lib/python3.7/site-
packages/PyOpenGL-3.1.3b2-py3.7.egg/OpenGL/GL/VERSION/GL_1_5.py", line 89, in
glBufferData  
return baseOperation( target, size, data, usage )  
File "src/latebind.pyx", line 32, in
OpenGL_accelerate.latebind.LateBind.__call__  
File "src/wrapper.pyx", line 318, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src/wrapper.pyx", line 311, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src/errorchecker.pyx", line 53, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1285,  
description = b'out of memory',  
baseOperation = glBufferData,  
pyArgs = (  
GL_UNIFORM_BUFFER,  
2147483520,  
c_void_p(None),  
GL_DYNAMIC_DRAW,  
),  
cArgs = (  
GL_UNIFORM_BUFFER,  
2147483520,  
c_void_p(None),  
GL_DYNAMIC_DRAW,  
),  
cArguments = (  
GL_UNIFORM_BUFFER,  
2147483520,  
c_void_p(None),  
GL_DYNAMIC_DRAW,  
)  
)  
  
Traceback (most recent call last):  
File "/home/chimera/chimerax_daily/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/chimera/chimerax_daily/lib/python3.7/site-
packages/chimerax/core/filehistory.py", line 71, in <lambda>  
t.add_handler('frame drawn', lambda *args, s=self: s.capture_thumbnails_cb())  
File "/home/chimera/chimerax_daily/lib/python3.7/site-
packages/chimerax/core/filehistory.py", line 83, in capture_thumbnails_cb  
fs.capture_image(models, ses)  
File "/home/chimera/chimerax_daily/lib/python3.7/site-
packages/chimerax/core/filehistory.py", line 162, in capture_image  
self.image = models_image(session, models, size)  
File "/home/chimera/chimerax_daily/lib/python3.7/site-
packages/chimerax/core/filehistory.py", line 219, in models_image  
image = v.image(width, height, camera = c, drawings = models)  
File "/home/chimera/chimerax_daily/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 433, in image  
self.draw(c, drawings, swap_buffers = False)  
File "/home/chimera/chimerax_daily/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 164, in draw  
self._draw_scene(camera, drawings)  
File "/home/chimera/chimerax_daily/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 222, in _draw_scene  
r.multishadow.set_multishadow_view(cp)  
File "/home/chimera/chimerax_daily/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 1505, in set_multishadow_view  
GL.glBufferSubData(GL.GL_UNIFORM_BUFFER, offset, mm.nbytes, mm)  
File "src/latebind.pyx", line 44, in OpenGL_accelerate.latebind.Curry.__call__  
File "/home/chimera/chimerax_daily/lib/python3.7/site-
packages/PyOpenGL-3.1.3b2-py3.7.egg/OpenGL/GL/VERSION/GL_1_5.py", line 125, in
glBufferSubData  
return baseOperation( target, offset, size, data )  
File "src/latebind.pyx", line 32, in
OpenGL_accelerate.latebind.LateBind.__call__  
File "src/wrapper.pyx", line 318, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src/wrapper.pyx", line 311, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src/errorchecker.pyx", line 53, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1281,  
description = b'invalid value',  
baseOperation = glBufferSubData,  
pyArgs = (  
GL_UNIFORM_BUFFER,  
0,  
1024,  
array([[[ 1.57212635e-04, -9.86955820e-06, 1.38882344e-04,  
0.00000000e+00],  
[ 0.00000000e+00, 1.5...,  
),  
cArgs = (  
GL_UNIFORM_BUFFER,  
0,  
1024,  
array([[[ 1.57212635e-04, -9.86955820e-06, 1.38882344e-04,  
0.00000000e+00],  
[ 0.00000000e+00, 1.5...,  
),  
cArguments = (  
GL_UNIFORM_BUFFER,  
0,  
1024,  
array([[[ 1.57212635e-04, -9.86955820e-06, 1.38882344e-04,  
0.00000000e+00],  
[ 0.00000000e+00, 1.5...,  
)  
)  
  
Error processing trigger "frame drawn": GLError(  
err = 1281,  
description = b'invalid value',  
baseOperation = glBufferSubData,  
pyArgs = (  
GL_UNIFORM_BUFFER,  
0,  
1024,  
array([[[ 1.57212635e-04, -9.86955820e-06, 1.38882344e-04,  
0.00000000e+00],  
[ 0.00000000e+00, 1.5...,  
),  
cArgs = (  
GL_UNIFORM_BUFFER,  
0,  
1024,  
array([[[ 1.57212635e-04, -9.86955820e-06, 1.38882344e-04,  
0.00000000e+00],  
[ 0.00000000e+00, 1.5...,  
),  
cArguments = (  
GL_UNIFORM_BUFFER,  
0,  
1024,  
array([[[ 1.57212635e-04, -9.86955820e-06, 1.38882344e-04,  
0.00000000e+00],  
[ 0.00000000e+00, 1.5...,  
)  
):  
OpenGL.error.GLError: GLError(  
err = 1281,  
description = b'invalid value',  
baseOperation = glBufferSubData,  
pyArgs = (  
GL_UNIFORM_BUFFER,  
0,  
1024,  
array([[[ 1.57212635e-04, -9.86955820e-06, 1.38882344e-04,  
0.00000000e+00],  
[ 0.00000000e+00, 1.5...,  
),  
cArgs = (  
GL_UNIFORM_BUFFER,  
0,  
1024,  
array([[[ 1.57212635e-04, -9.86955820e-06, 1.38882344e-04,  
0.00000000e+00],  
[ 0.00000000e+00, 1.5...,  
),  
cArguments = (  
GL_UNIFORM_BUFFER,  
0,  
1024,  
array([[[ 1.57212635e-04, -9.86955820e-06, 1.38882344e-04,  
0.00000000e+00],  
[ 0.00000000e+00, 1.5...,  
)  
)  
  
File "src/errorchecker.pyx", line 53, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  




OpenGL version: 4.5 (Core Profile) Mesa 19.2.0-devel (git-9d2aa67 2019-07-25 bionic-oibaf-ppa)
OpenGL renderer: AMD TAHITI (DRM 2.50.0, 4.15.0-55-generic, LLVM 8.0.1)
OpenGL vendor: X.Org

[Greg Couch]

Adding a print of the number of bytes requested gives 2147483520 which is 64 * 33554430 (i.e., max_multishadows) which is the same as GL.GL_MAX_UNIFORM_BLOCK_SIZE. This is in core/opengl.py/Multishadow._multishadow_matrix_buffer. In the terminal window the error is:

radeon: Failed to allocate a buffer:
radeon:    size      : 2147483648 bytes
radeon:    alignment : 4096 bytes
radeon:    domains   : 4
radeon:    flags     : 4

Changing max_multishadows() to set the maximum from GL.GL_MAX_UNIFORM_BLOCK_SIZE // 64 to GL.GL_MAX_UNIFORM_BLOCK_SIZE // 128 works. GL.GL_MAX_UNIFORM_BLOCK_SIZE // 64 -1 doesn't.

[Greg Couch]

Fixed by limiting the maximum number of multishadows. Since that will limit the amount of uniform memory needed for the shader.