Menu

#191 Pymol segfaults on pdb load if user is not in video group

v1.7.1.0
open
nobody
None
5
2017-07-18
2017-07-18
No

I have pymol 1.8.4.0 installed on gentoo linux. If my user account is not in the video group, booting pymol and loading a pdb gives the following:

libGL error: failed to open drm device: Permission denied
libGL error: failed to load driver: i965
 PyMOL(TM) Molecular Graphics System, Version 1.8.4.0.
 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 1.30.
 OpenGL graphics engine:
  GL_VENDOR:   VMware, Inc.
  GL_RENDERER: Gallium 0.4 on llvmpipe (LLVM 3.9, 256 bits)
  GL_VERSION:  3.0 Mesa 17.0.6
 Detected 4 CPU cores.  Enabled multithreaded rendering.
HEADER    LIPID BINDING PROTEIN                   30-JUN-04   1TW4
TITLE     CRYSTAL STRUCTURE OF CHICKEN LIVER BASIC FATTY ACID BINDING
TITLE    2 PROTEIN (BILE ACID BINDING PROTEIN) COMPLEXED WITH CHOLIC
TITLE    3 ACID
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: FATTY ACID-BINDING PROTEIN;
COMPND   3 CHAIN: A, B;
COMPND   4 SYNONYM: L-FABP, LIVER BASIC FABP, LB- FABP, BILE ACID-
COMPND   5 BINDING PROTEIN
 ObjectMolecule: Read secondary structure assignments.
 ObjectMolecule: Read crystal symmetry information.
 CmdLoad: "/home/work/Molecules/1TW4.pdb" loaded as "1TW4".
Segmentation fault

This is reproducable for other pdbs.

The libGL errors at the start are fine: pymol can't access /dev/dri/card0, so it complains. But it should not segfault when a file is loaded - it should throw an error, or exit a little more gracefully.

The segfault does not occur when the user is in the videos group (nor do the libGL errors, no surprise).

Discussion


Log in to post a comment.

Want the latest updates on software, tech news, and AI?
Get latest updates about software, tech news, and AI from SourceForge directly in your inbox once a month.