Subject: Re: CCL:Running Autodock3 under linux2

From: "Garrett M. Morris" <[email-masked]>
Date: Wed, 10 Oct 2001 15:36:30 -0700

There appears to be a great need for this nugget of information:  to
remove the limit on the stack size in Linux, type this simple command
at your prompt:

% limit stacksize unlimited

Even better, add this line to your .login/.cshrc/.profile:

limit stacksize unlimited

This command will work on Linux, UNIX and Mac OS X (the "X" is
pronounced "ten").  AutoDock will run on Mac OS X, by the way.

This should permit your system to run AutoDock, assuming you have
enough RAM.  (You can check if an executable is too big by using the
"size" command, e.g. "size autodock3". If you don't have enough RAM,
recompile the AutoGrid and AutoDock programs after you have reduced
MAX_GRID_PTS to 32 in "constants.h" - this will reduce the number of
points you can use in your grid maps.  It might be also be worth
investing in more RAM.)

Happy docking,

 :)

Garrett

On Wed, 10 Oct 2001, C. Michael McCallum wrote:

> * [email-masked] ([email-masked]) [011009 10:56]: 
> > Hi David, 
> It seems to be a general problem for linux users. 
> > Actually the problem is with smaller stack size in linux.So set
> > the stack size
> > to a larger size.
> > type in the shell:
> > ulimit -s 66666
> > the value is essentially any thing you like ( i.e of the order of 60 MB here)
> > Thr default for linux is 8MB. Keep increasing the stack size till it does not 
> > give core dump.
> > It should help..
> > 
> > Chinmoy Ranjan,
> 
> Chinmoy, this is a great general tip!  But does anyone know how to set the
> corresponding ulimit using csh or tcsh?  The default for linux is indeed set
> at 8M;  How can a csh or tcsh user set it higher (or unlimited)?  Is there a
> system-wide setting for this?  Anyone?
> 
> Cheers,
> 
> Mike McCallum
> 
> -- 
> C. Michael McCallum         |  "That may be one tough nut to crack,
> Associate Professor         |        but I am one determined
> Chemistry, UOP              |             little squirrel"
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> 
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> 

Best wishes,

Garrett

___
Dr Garrett M. Morris, MA, DPhil
The Scripps Research Institute,       tel: (858) 784-2292
Dept. Molecular Biology,  MB-5,       fax: (858) 784-2860
10550  North Torrey Pines Road,       email: [email-masked]
La Jolla,  CA 92037-1000,  USA.       www.scripps.edu/pub/olson-web/gmm