[Dock-fans] cygwin: aborted (core dumped)

Philip Crawford p.crawford at unsw.edu.au
Sun Mar 18 14:29:04 PST 2007

Hi. On Cygwin, the limit, ulimit etc commands have no effect.  Things like
stacksize need to be set at compile (link) time. (I found out this with my
brother's help way back.)
If you have access to Visual Studio 6 (or later, probably) there is a
program with that called EDITBIN.EXE which can modify these parameters after
compile time.
It is also possible to pass link parameters to gcc, at least for stacksize,
which was what I needed to increase. But that was a stackdump, so your
requirements may be different.


Philip Crawford B Comp Sc, MIEEE
Medicine Computer Support Unit
The University of NSW, Sydney, NSW, 2052
Phone: +61-2-9385 2564
Fax: +61-2-9385 1258
Email: p.crawford at unsw.edu.au


From: dock-fans-bounces at docking.org [mailto:dock-fans-bounces at docking.org]
On Behalf Of Steven Finckbeiner
Sent: Sunday, 18 March 2007 11:05 AM
To: dock-fans at docking.org
Subject: [Dock-fans] cygwin: aborted (core dumped)

I'm trying to dock folate into DHFR.  
My box is as small as the binding site.
When I run DOCK in cygwin, I get this:

Initializing Library File Routines . . .
Initializing Orienting Routines . . .
Initializing Grid Score Routines . . .
   Reading the energy grid from smallbox.nrg
Error: memory exhausted!
   For Unix platforms increase the datasize, stacksize, and
   memoryuse using the limit, ulimit, or unlimit commands.
Aborted (core dumped)

I have the full install of cygwin and I can't find any of these commands.
When I ran showbox I didn't add any extra space.  I can't make it any
smaller.  Any ideas?

"It is nice to think that there are so many unsolved puzzles ahead for
biology, although I wonder whether we will ever find enough graduate
students."   Lewis Thomas

Steve Finckbeiner 
Roswell Park Cancer Institute 
Elm and Carlton Streets 
Buffalo, NY 14263-0001 
(716)845-5818 office
(716)697-5650 cell


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