xace crash

Ed Griffiths edgrif at sanger.ac.uk
Tue Jan 23 11:06:43 EST 2001


Keith,

> Stack overflow: pid 6745, proc xace, addr 0x11dffffb0, pc 0x1201afa1c
> Segmentation fault (core dumped)
> 
> This happens even if I try running 'unlimit' first.  We do have 2 Gb
> memory on this machine, so memory shouldn't really be a problem.  Is there
> some upper limit of objects that can be 'expanded' from a collapsed branch
> in this manner?  The same display will let me expand the 24,000 or so
> Protein sequences without crashing.

Running unlimit will not necessarily give you unlimited stack space, all unix
users have a "hard" limit for each of the process resources such as "core",
"data", "stack" etc. If you use unlimit, the resource will only be allowed to
use up to this hard limit.

e.g. on my DEC:

griffin[edgrif]59: ulimit -s             # current stack limit
2048
griffin[edgrif]60: ulimit -Hs            # hard stack limit
32768
griffin[edgrif]63: unlimit               # unlimit stack
griffin[edgrif]64: ulimit -s             # new stack limit
32768

Although I used unlimit, my stack is still limited to the level set by the hard
level. You need to check what this is for your system, note that only root can
change hard limits.

You have a large number of objects so running out of stack space is a
possibility.

Let us know what you find.

cheers Ed

 ------------------------------------------------------------------------
| Ed Griffiths, Acedb development, Informatics Group,                    |
|               The Sanger Centre, Wellcome Trust Genome Campus,         |
|               Hinxton, Cambridge CB10 1SA, UK                          |
|                                                                        |
| email: edgrif at sanger.ac.uk  Tel: +44-1223-494780  Fax: +44-1223-494919 |
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