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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Received on Thu Mar 18 2010 - 16:30:02 PDT
