Hi
This is not a pymol problem per se, but I'm trying to figure out
whether the error below is hardware-related (video card) or
software-related (i.e., video driver/mesa/opengl libraries, etc.). If
I run pymol from the command line (loading one of the demo files,
pept.r3d), the pymol graphics and interface windows appear briefly and
then close almost immediately. At the command line, the result is:
$ pymol /usr/share/pymol/test/dat/pept.r3d
Detected OpenGL version 2.0 or greater. Shaders available.
Detected GLSL version 1.20.
Executive: object "pept" created.
python2.7: nv50_pc.h:351: nv_alloc_instruction: Assertion
`pc->num_instructions < 2048' failed.
/usr/bin/pymol: line 2: 5112 Aborted python2.7 -O
${PYMOL_PATH}/__init__.py -q $*
Also, pymol seems to function OK if I do not try to load a file, i.e.,
the UI opens correctly and I can close it gracefully. If I try to load
the demo file from the interface, it crashes with the above error.
Starting pymol with -h yields the following:
$ pymol -h
PyMOL(TM) Molecular Graphics System, Version 1.5.0.3.
Copyright (c) Schrodinger, LLC.
All Rights Reserved.
Created by Warren L. DeLano, Ph.D.
PyMOL is user-supported open-source software. Although some versions
are freely available, PyMOL is not in the public domain.
If PyMOL is helpful in your work or study, then please volunteer
support for our ongoing efforts to create open and affordable scientific
software by purchasing a PyMOL Maintenance and/or Support subscription.
More information can be found at "http://www.pymol.org";.
Enter "help" for a list of commands.
Enter "help <command-name>" for information on a specific command.
Hit ESC anytime to toggle between text and graphics.
Detected OpenGL version 2.0 or greater. Shaders available.
Detected GLSL version 1.20.
OpenGL graphics engine:
GL_VENDOR: nouveau
GL_RENDERER: Gallium 0.4 on NV96
GL_VERSION: 2.1 Mesa 8.0.2
Detected 16 CPU cores. Enabled multithreaded rendering.
PyMOL>quit
PyMOL: normal program termination.
Alternatively, I can successfully generate png output from a script
(provided I disable screen output), e.g.
$ cat makePNG.pml
center origin
zoom complete=0
draw 2400
png test.png, dpi=600
$ pymol /usr/share/pymol/test/dat/pept.r3d -c -d "@./makePNG.pml"
Executive: object "pept" created.
PyMOL>@./makePNG.pml
PyMOL>center origin
PyMOL>zoom complete=0
PyMOL>draw 2400
PyMOL>png test.png, dpi=600
Ray: render time: 0.08 sec. = 45537.9 frames/hour (0.08 sec. accum.).
ScenePNG: wrote 640x480 pixel image to file "test.png".
If I ssh (with X-forwarding) to a remote machine with the identical
pymol setup, the display works fine. I've searched for the above
nv_alloc_instruction error, and it crops up on bugs related to the
nouveau video driver
(https://bugs.freedesktop.org/show_bug.cgi?id=46597). However, both
the local and remote machine both use this same driver, and all
supporting libraries as well. I've rebuilt the driver on the local
machine and all its dependencies, mesa, opengl, etc., with no change
in the above result. I've been pulling my hair out over this, and
thought I'd ask here if anyone had any ideas. Thanks in advance.
Cheers //Rolf
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