labels don't work in headless mode

[Greg Couch]

labels don't work because they're are using the GUI to get the font information.

[goddard@…]

Please provide a traceback.  There is no label GUI in ChimeraX.

[Greg Couch]

Used switch.cxc from the G-Protein Switch Regions example on the image gallery, ​http://www.rbvi.ucsf.edu/chimerax/gallery.html and added another line at the end to save an image. Generated the backtrace with:

$ gdb chimerax-daily
(gdb) run --offscreen --exit switch.cxc

Which results in:

Program received signal SIGSEGV, Segmentation fault.
0x00007fffd4ee7353 in QGuiApplication::font() ()
   from /home/socr/a/chimera/chimerax_daily/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5Gui.so.5

And the C++ backtrace starts with:

#0  0x00007fffd4ee7353 in QGuiApplication::font() ()
   from /home/socr/a/chimera/chimerax_daily/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5Gui.so.5
#1  0x00007fffd4fc48dd in QFontDatabase::load(QFontPrivate const*, int) ()
   from /home/socr/a/chimera/chimerax_daily/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5Gui.so.5
#2  0x00007fffd4f9b71a in QFontPrivate::engineForScript(int) const ()
   from /home/socr/a/chimera/chimerax_daily/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5Gui.so.5
#3  0x00007fffd4fcc0f3 in QTextEngine::fontEngine(QScriptItem const&, QFixed*, QFixed*, QFixed*) const ()
   from /home/socr/a/chimera/chimerax_daily/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5Gui.so.5
#4  0x00007fffd4fcdb8e in QTextEngine::shapeText(int) const ()
   from /home/socr/a/chimera/chimerax_daily/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5Gui.so.5
#5  0x00007fffd4fcea6c in QTextEngine::shape(int) const ()
   from /home/socr/a/chimera/chimerax_daily/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5Gui.so.5
#6  0x00007fffd4fd51e8 in QTextEngine::boundingBox(int, int) const ()
   from /home/socr/a/chimera/chimerax_daily/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5Gui.so.5
#7  0x00007fffd4fb99f9 in QFontMetrics::boundingRect(QString const&) const ()
   from /home/socr/a/chimera/chimerax_daily/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5Gui.so.5
#8  0x00007fffd02ec232 in meth_QFontMetrics_boundingRect ()
   from /home/socr/a/chimera/chimerax_daily/lib/python3.7/site-packages/PyQt5/QtGui.so
#9  0x00007ffff7905263 in _PyMethodDef_RawFastCallKeywords (method=0x7fffd0613d60 <methods_QFontMetrics+64>, self=<optimized out>,
    args=0x2da83c0, nargs=1, kwnames=<optimized out>) at Objects/call.c:694

And running "chimerax-daily --offscreen --exit switch.cxc" directly gives:

Fatal Python error: Segmentation fault

Thread 0x00007fc953404700 (most recent call first):
  File "/home/socr/a/chimera/chimerax_daily/lib/python3.7/threading.py", line 300 in wait
  File "/home/socr/a/chimera/chimerax_daily/lib/python3.7/threading.py", line 552 in wait
  File "/home/socr/a/chimera/chimerax_daily/lib/python3.7/threading.py", line 1175 in run
  File "/home/socr/a/chimera/chimerax_daily/lib/python3.7/threading.py", line 926 in _bootstrap_inner
  File "/home/socr/a/chimera/chimerax_daily/lib/python3.7/threading.py", line 890 in _bootstrap

Current thread 0x00007fc97d311740 (most recent call first):
  File "/home/socr/a/chimera/chimerax_daily/lib/python3.7/site-packages/chimerax/graphics/drawing.py", line 2088 in text_image_rgba
  File "/home/socr/a/chimera/chimerax_daily/lib/python3.7/site-packages/chimerax/label/label2d.py", line 605 in _update_label_image
  File "/home/socr/a/chimera/chimerax_daily/lib/python3.7/site-packages/chimerax/label/label2d.py", line 591 in _update_graphics
  File "/home/socr/a/chimera/chimerax_daily/lib/python3.7/site-packages/chimerax/label/label2d.py", line 555 in draw
  File "/home/socr/a/chimera/chimerax_daily/lib/python3.7/site-packages/chimerax/graphics/drawing.py", line 1440 in _draw_multiple
  File "/home/socr/a/chimera/chimerax_daily/lib/python3.7/site-packages/chimerax/graphics/drawing.py", line 1478 in draw_overlays
  File "/home/socr/a/chimera/chimerax_daily/lib/python3.7/site-packages/chimerax/graphics/view.py", line 173 in draw
  File "/home/socr/a/chimera/chimerax_daily/lib/python3.7/site-packages/chimerax/graphics/view.py", line 457 in image
  File "/home/socr/a/chimera/chimerax_daily/lib/python3.7/site-packages/chimerax/image_formats/save.py", line 113 in save_image
  File "/home/socr/a/chimera/chimerax_daily/lib/python3.7/site-packages/chimerax/image_formats/__init__.py", line 24 in save
  File "/home/socr/a/chimera/chimerax_daily/lib/python3.7/site-packages/chimerax/save_command/cmd.py", line 73 in provider_save
  File "/home/socr/a/chimera/chimerax_daily/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2805 in run
  File "/home/socr/a/chimera/chimerax_daily/lib/python3.7/site-packages/chimerax/save_command/cmd.py", line 60 in cmd_save
  File "/home/socr/a/chimera/chimerax_daily/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2805 in run
  File "/home/socr/a/chimera/chimerax_daily/lib/python3.7/site-packages/chimerax/core/commands/run.py", line 31 in run
  File "/home/socr/a/chimera/chimerax_daily/lib/python3.7/site-packages/chimerax/core/scripting.py", line 139 in open_command_script
  File "/home/socr/a/chimera/chimerax_daily/lib/python3.7/site-packages/chimerax/core_formats/__init__.py", line 37 in open
  File "/home/socr/a/chimera/chimerax_daily/lib/python3.7/site-packages/chimerax/open_command/cmd.py", line 359 in collated_open
  File "/home/socr/a/chimera/chimerax_daily/lib/python3.7/site-packages/chimerax/open_command/cmd.py", line 146 in provider_open
  File "/home/socr/a/chimera/chimerax_daily/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2805 in run
  File "/home/socr/a/chimera/chimerax_daily/lib/python3.7/site-packages/chimerax/open_command/cmd.py", line 95 in cmd_open
  File "/home/socr/a/chimera/chimerax_daily/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2805 in run
  File "/home/socr/a/chimera/chimerax_daily/lib/python3.7/site-packages/chimerax/core/commands/run.py", line 31 in run
  File "/home/socr/a/chimera/chimerax_daily/lib/python3.7/site-packages/ChimeraX_main.py", line 748 in init
  File "/home/socr/a/chimera/chimerax_daily/lib/python3.7/site-packages/ChimeraX_main.py", line 897 in <module>
  File "/home/socr/a/chimera/chimerax_daily/lib/python3.7/runpy.py", line 85 in _run_code
  File "/home/socr/a/chimera/chimerax_daily/lib/python3.7/runpy.py", line 193 in _run_module_as_main
Segmentation fault

[Greg Couch]

G-Protein Switch Regions switch.cxc with "save switch.png" at end

[Greg Couch]

Actually version 1.1.dev202006180113

[Tom Goddard]

So QFontMetrics.boundingRect() crashes if it is not a Qt GUI application. Discussed here

​https://stackoverflow.com/questions/31732698/getting-font-metrics-without-gui-console-mode

Not clear there is any solution. Also not clear why Qt needs a GUI to measure font sizes. To make labels ChimeraX of course has to know font sizes.

[Tom Goddard]

Greg fixed this using Qt offscreen platform.

Begin forwarded message:

From: Greg Couch
Subject: Re: ChimeraX offscreen rendering
Date: July 9, 2020 at 6:22:59 PM PDT
To: Tom Goddard , Eric Pettersen
Cc: Scooter Morris , Chimera Staff

I had been looking into this and was able to get offscreen rendering of labels to work. It turned out to be fairly trivial. Qt has the concept of platform backends, eg., X11, and there happens to be an offscreen backend. Using the Qt offscreen backend when ChimeraX is in offscreen mode allows the QFont code to work. I've attached an offscreen rendering of Elaine's G-Protein Switch Regions image that was rendered completely offscreen on plato.

-- Greg