Forget to mention that the whole MAXCHAR issue is internal to
antechamber (defined in antechamber/define.h).
--Eric
On Mar 18, 2010, at 4:27 PM, Eric Pettersen wrote:
> Hi all,
> I recently upgraded the version AmberTools that Chimera was using
> to 1.3 with all patches applied (please don't ask what version it
> was using before!). Compilation wasn't excessively difficult but I
> found I was getting random crashes with various charge calculations
> (e.g. bccharge() in antechamber/charge.c). Tracking down the cause
> was a headache. It turns out that string buffers used to compose
> commands to hand off to system() were only allocated as 256
> characters (MAXCHAR). Now, in Chimera on a mac, the Amber
> executables typically live in a directory like:
>
> /Users/pett/Applications/Chimera-daily-aqua.app/Contents/Resources/
> bin/amber11/bin
>
> and the input/output files are in temporary system folders like:
>
> /var/folders/VH/VHqktDJe2RWZSE+1YwqPE+++Hpc/-Tmp-/tmp4iniru
>
> So you can see how an executable, a couple of input files, and an
> output file could easily overflow 256 characters. When I recompiled
> with MAXCHAR set to 2048 all the mysterious crashes went away.
>
> I guess I'm proposing that either MAXCHAR be increased to at least
> 2K (most modern shells allocate 4K or more for commands) or that
> there be a separate macro (MAXCMD?) for strings that are supposed to
> be handed off to system().
>
> --Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
> http://www.cgl.ucsf.edu
>
>
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> AMBER-Developers.ambermd.org
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Received on Thu Mar 18 2010 - 17:00:02 PDT
