VMD-L Mailing List

From: Edgar Galicia (galicia.andres_at_gmail.com)
Date: Fri Feb 28 2025 - 15:25:06 CST

Dear vmd community,

I'm having an issue using the graphical representation Surf. It used to
work before in Ubuntu 22.04 but since I changed to Debian 12 I get a
segmentation fault error. Even rendering tested scripts Surf fails. I tried
in my MBA m2 with sequoia and it works. Would you have an idea of the issue?

These are my specs and error details:

Description: Debian GNU/Linux 12 (bookworm)
Release: 12
Codename: bookworm
arch: x86_64

Info) Finished with coordinate file
/pool/edgargalicia/GROMACS/KLNT/NO_ANGLE/LEO/solv2_center.gro.
0
Reading 1422 atoms..done
Probe radius = 3.400
Constructing solvent-accessible surface ..
Segmentation fault
Info) This surface is made with SURF from UNC-Chapel Hill. The reference
is:
Info) A. Varshney, F. P. Brooks, W. V. Wright, Linearly Scalable Computation
Info) of Smooth Molecular Surfaces, IEEE Comp. Graphics and Applications,
Info) v. 14 (1994) pp. 19-25.
Info) Reading Surf geometry output file...
Info) Read Surf output file, processing geometry...
Info) Done.
prueba.dat
Info) Rendering current scene to 'prueba.dat' ...
Info) Tachyon file generation finished
Info) Executing post-render cmd
''/home/edgargalicia/local/vmd/lib/tachyon_LINUXAMD64' -aasamples 12
prueba.dat -format TARGA -res 1280 720 -o prueba.dat.tga' ...
Tachyon Parallel/Multiprocessor Ray Tracer Version 0.99.1
Copyright 1994-2014, John E. Stone <john.stone_at_gmail.com>
------------------------------------------------------------
Scene Parsing Time: 0.1229 seconds
Scene contains 26167 objects.
Preprocessing Time: 0.0075 seconds
Rendering Progress: 100% complete
  Ray Tracing Time: 1.7258 seconds
    Image I/O Time: 0.2083 seconds
Info) Rendering complete.
Info) VMD for LINUXAMD64, version 1.9.4a57 (April 27, 2022)
Info) Exiting normally.

It seems that Surf runs but at some point it crashes. QuickSurf makes no
issues, but Surf does.

Best,
Edgar