Babel on Extreme Systems

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Babel on Extreme Systems

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I realize OpenBabel is not designed for dealing with extreme systems, but I really appreciate offloading some of my work to it. I haven't written a minimal test case yet, so I can't submit a bug report just yet. Essentially I am using OBConversion to read protein complexes from PDB-like files with the standard PDB format in OpenBabel. The reason I say PDB-like is the files were generated by a homology modeling workflow and I noticed that what OpenBabel successfully read all had warnings about not strictly following the PDB standard. When I try loading the groEL complex, I am getting a stack overflow induced segmentation fault that Valgrind traces to line 733 of ketulize.cpp. I am on linux and I recently had another program that wouldn't even compile due to large static arrays.

Do you think I should try recompiling OpenBabel with -mcmodel=large? Any other suggestions? I can't really justify too much community service to my professor at this point in my PhD, so refactoring OpenBabel to use more heap allocations is not really an option. Eventually my system will be dealing with millions of OBMol objects managed by my code. Thank you so much for your help.

Nathan

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Re: Babel on Extreme Systems

Noel O'Boyle
Administrator
The kekulization code has been replaced in the development version
(available from Github). Note that there are also other changes so you
should do this with caution.

- Noel

On 29 June 2017 at 04:57, Nathan Jenkins via OpenBabel-discuss
<[hidden email]> wrote:

> I realize OpenBabel is not designed for dealing with extreme systems, but I
> really appreciate offloading some of my work to it. I haven't written a
> minimal test case yet, so I can't submit a bug report just yet. Essentially
> I am using OBConversion to read protein complexes from PDB-like files with
> the standard PDB format in OpenBabel. The reason I say PDB-like is the files
> were generated by a homology modeling workflow and I noticed that what
> OpenBabel successfully read all had warnings about not strictly following
> the PDB standard. When I try loading the groEL complex, I am getting a stack
> overflow induced segmentation fault that Valgrind traces to line 733 of
> ketulize.cpp. I am on linux and I recently had another program that wouldn't
> even compile due to large static arrays.
>
> Do you think I should try recompiling OpenBabel with -mcmodel=large? Any
> other suggestions? I can't really justify too much community service to my
> professor at this point in my PhD, so refactoring OpenBabel to use more heap
> allocations is not really an option. Eventually my system will be dealing
> with millions of OBMol objects managed by my code. Thank you so much for
> your help.
>
> Nathan
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> OpenBabel-discuss mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>

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