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

Steven Finckbeiner sfinck187 at yahoo.com
Sun Mar 18 14:43:02 PST 2007


Phil: Thanks for the suggestion.  
Do you mean at the time I compile cygwin or DOCK?  
Where do I change the settings at compile?  Steve


----- Forwarded Message ----
From: Philip Crawford <p.crawford at unsw.edu.au>
To: Steven Finckbeiner <sfinck187 at yahoo.com>; dock-fans at docking.org
Sent: Sunday, March 18, 2007 6:29:04 PM
Subject: RE: [Dock-fans] cygwin: aborted (core dumped)



 
DIV {
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Steve,

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.

 

Cheers,

Phil


_____________________________________________

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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