VMD-L Mailing List

From: Edgar Galicia (galicia.andres_at_gmail.com)
Date: Tue Mar 04 2025 - 05:00:36 CST

Dear Diego,

I tried what you suggested and some other things by looking on old post. This is what I learned:

Runing vmd-1.9.4a57/surf gives segmentation fault
Runing vmd-2/surf gives segmentation fault but explicitly says: ERROR Cannot read SURF output file: /tmp/vmdsurf.u80530.339.in <https://urldefense.com/v3/__http://vmdsurf.u80530.339.in/__;!!DZ3fjg!4hl6ueh_DpgPuASRJu1_sgXUojfhTrSXJdfiHqZsBdv7qI_kB4QvjB4OHpC3DMj8neSwlIBgMPeC9wIExYvpLR38vA$ >.tri

Then it occurred what if running vmd as sudo. While running vmd-1.9.4a57 still gives segmentation error, vmd2 is able to render the SURF representation. I have vmd installed in a local folder. But before it used to work, now it seems not. I also tried changing VMDTMPDIR to my working folder and still the same issue. Only works as sudo. Maybe this hints what could be wrong, but at least I’m happy that vmd2 is able to manage, although I cannot load my .vmdrc as sudo.

Best,
Edgar




> El 03.03.2025, a las 18:25, Diego Gomes <diego.enry_at_gmail.com> escribió:
>
> 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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto:dgomes_at_auburn.edu>
> <vmddebian.def><writeSurfInput.tcl>