[Dockdev] Fixing a crashing bug (too big memory to allocate)

#AMR ALI MOKHTAR ALHOSSARY# AMRA0001 at e.ntu.edu.sg
Sun Nov 2 20:07:07 PST 2014


Hi all,

I have fixed a bug, which faced me while using Dock 6.6 to evaluate PDBbind v. 2013 PDB collection (which contains 195 divergent protein ligand complexes).
The bug caused the application to crash when I try to dock complexes with big receptor sites/ligands. That is because the application used to allocate residual matrix with size [(num_spheres * num_centers)^2].
Above certain number of nodes (i.e. of spheres-centres combinations), that amount of memory cannot be allocated.

I fixed the bug by dynamically allocating the matrix as a shredded 2 dimensional array (an array of arrays) of size [(num_spheres * num_centers)] each.
This way, it is expected that the application would be able to allocate much bigger mounts of memory according to the system limits. For example, one of the instances I ran after the batch consumed 53 GegaBytes of memory safely.

Please tell me how to contribute the batched code because I tried to attach it but it was not accepted by the mail list application.

P.S. sorry for cross posting, but I noticed that dockdev<mailto:dockdev at mailman.docking.org> is almost dead a long time ago.
Sincerely

Amr


Best Regards,
Amr AL-HOSSARY

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Amr Ali AL-HOSSARY |   Ph.D. Student | International PhD program in Computational Biology and Bioinformatics | School of Computer Engineering |   Nanyang Technological University | Singapore (GMT+8) |  Email:  aalhossary at pmail.ntu.edu.sg<mailto:aalhossary at pmail.ntu.edu.sg>, amr_alhossary at hotmail.com<mailto:amr_alhossary at hotmail.com> |  Mobile: +65-94572816




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