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Docking (aISS), after Optimizing Final Configurations, get *** stack smashing detected ***: terminated #1152

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ericchenanpt opened this issue Jan 3, 2025 · 5 comments
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@ericchenanpt
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Describe the bug
After using the aISS submodule to dock two molecules, the genetic optimization algorithm will run, but as the Optimizing X best structures with gfn2 step, I receive the error:
*** stack smashing detected ***: terminated

To Reproduce
Steps to reproduce the behaviour:

  1. happens with input (include input files)

I tried with H2O and MeOH (as well as other molecules, but these were the smallest):

h2o.xyz:
h2o.xyz.txt

3

O            0.00723291871761        0.38078004550145        0.00000000000000
H           -0.77812249283762       -0.17570365630729       -0.00000000000000
H            0.77088956412001       -0.20507638919416       -0.00000000000000

meoh.xyz
meoh.xyz.txt

6

C           -0.36700780121479        0.01859276068171       -0.00227771469379
O            0.91309966541086       -0.49922598289838       -0.29646154488359
H           -0.54925566216741        0.04025699439432        1.07553909436486
H           -0.49443995477539        1.02327131513620       -0.41434530116864
H           -1.08695569033798       -0.64987854425628       -0.47019695206980
H            1.58455943308471        0.06698344694244        0.10774241845096
  1. start xtb with (all the options here)

xtb dock meoh.xyz h2o.xyz

  1. run xtb with your options and the --verbose flag

log.txt

  1. output showing the error
    error.txt

Expected behaviour
I expected to get the geometry output of optimized docking location

Additional context
I apologize if this issue isn't formatted correctly, I'm quite new to this. Thank you for taking a look!

@ericchenanpt ericchenanpt added the unconfirmed This report has not yet been confirmed by the developers label Jan 3, 2025
@foxtran
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foxtran commented Feb 1, 2025

@ericchenanpt, I could not reproduce your bug with current master branch with GFortran 11 (x86_64 Arch).

@marcelmbn
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@cplett Can you quickly look into this? If you can also not reproduce the behavior (like @foxtran, thanks for the comment), we can safely close.

@cplett
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cplett commented Feb 7, 2025

Hi,
I noticed in your log.txt file that you used conda to install xtb version 6.7.1. This version had a bug with the aISS docking tool, which could cause errors similar to the one you observed. The issue has been fixed with #1089 and the bleeding-edge version should work fine again. Alternatively, you can use previous xtb versions where this bug was also not present.

@marcelmbn
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@cplett Can you change the labels accordingly and/or close if the conda-forge installation is clearly the reason for this failure and is already solved now?

@ericchenanpt
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ericchenanpt commented Feb 7, 2025

I just tried the docking on 6.6.1, worked like a charm. @cplett was correct. I've closed this issue, and hopefully anyone else running into the same problem finds this thread!

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