VMD-L Mailing List

From: Diego Gomes (diego.enry_at_gmail.com)
Date: Mon Mar 03 2025 - 11:25:53 CST

Hi Edgar, I'm running fine while using the official Debian 16 container
(apptainer/singularity definition attached).

Maybe running Surf interactively could produce a better error message to
help us trace what's wrong.

As input, Surf needs: index, radius, and x y z coordinates for the atoms to
compute the surface.
You may get them with the attached VMD script:
writeSurfInput.tcl (output: output.dat)

to run interactively do something similar to this:
~/software/vmd-1.9.4.58/lib/surf_LINUXAMD64 -W 1 -C output.dat
&>surf.vmd194.log
Outputs is: output.dat.tri (triangles 85Mb, ascii)

~/software/vmd-2.0/lib/surf_LINUXAMD64 -W 1 -C output.dat &>surf.vmd2.log
Outputs are: output.dat.tri (triangles 43Mb, binary), output.dat.idx
(indexes 2.4M, binary)

In case of failure send me the terminal output from surf (surf.vmd194.log
and/or surf.vmd2.log)

( FTR... for this system size, VMD 2.0a4 is 4x faster than VMD 1.9.4a58 )

Let me know about the results.

On Sat, Mar 1, 2025 at 2:24 PM Edgar Galicia <galicia.andres_at_gmail.com>
wrote:

> Dear Diego,
>
> I tried with vmd 2 as well and got the same error. I’m surprised that this
> same machine with Ubuntu didn’t have such issues. Perhaps I’m missing a
> library? Enclosed you will find my gro file.
>
> Best,
> Edgar
>
>
>
> El 01.03.2025, a las 04:33, Diego Gomes <diego.enry_at_gmail.com> escribió:
>
> Hi Edgar, can you share your GRO file? I'm willing to test it on various
> platforms.
>
> Try the VMD 2.0 alpha4? It has an updated version of SURF, built with a
> newer compiler and libraries.
>
> Be aware it's still an early alpha, crashes may occur.
> https://www.ks.uiuc.edu/Research/vmd/alpha/
>
> Friendly,
> Diego.
>
>
> On Fri, Feb 28, 2025 at 4:16 PM Edgar Galicia <galicia.andres_at_gmail.com>
> wrote:
>
>> 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
>>
>
>
> --
> Diego Enry B. Gomes, PhD
> Department of Physics at Auburn University &
> NIH Center for Macromolecular Modeling and Visualization
> Leach Science Center - Ste. 3182 - Auburn, AL
> dgomes_at_auburn.edu
>
>
> 

-- 
Diego Enry B. Gomes, PhD
Department of Physics at Auburn University &
NIH Center for Macromolecular Modeling and Visualization
Leach Science Center - Ste. 3182 - Auburn, AL
dgomes_at_auburn.edu