[Dock-fans] Fw: Re: Fw: Re: Fwd: Re: Ligand Docking with DOCK6

Scott Brozell sbrozell at scripps.edu
Thu Apr 17 23:59:47 PDT 2008


Hi,

On Thu, 17 Apr 2008, Francesco Pietra wrote:

> To add that the debian-list subscriber who yesterday replied about bad_alloc, asking how the program was compiled, is doubtful about the correctness of the compilation, though I said that tests and docking with smaller ligands are OK. His post today:
> 
> >> Do you build this program yourself from source?
> >
> >Yes (g77-3.4 g++ 4.1.2 lib2c0-dev) from the configure file provided by
> >developers. No errors in either the serial or parallel compilations
> >(openmpi). Also, there is a very long test for both the serial and
> >parallel execution. All passed with a few marginal warnings for
> >different precision on different machines. Finally, docking of a
> >slightly smaller ligands occurs with no errors.
> 
> I'd build with debug info and run it under gdb and/or valgrind.  Might
> tell you where it is messing up.
> ___________
> 
> Do you believe worth while to follow his advice? If so, any web indication where to learn about compiling "with debug info and run it under gdb and/or valgrind"
> 

I ran the continuous score tests through valgrind:
http://blur.compbio.ucsf.edu/pipermail/dock-fans/2008-April/001514.html

First priority is to investigate selected_spheres.sph.

Scott




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