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Fragmentation Fault

Nicolas Thierry-Mieg Nicolas.Thierry-Mieg at imag.fr
Thu Feb 26 08:35:24 EST 2004


I think the question is "what are the specs of the machine on which 
acedb runs" more than the specs of your linux box (since it is only used 
as an xterm)

since everything works for one user on the same machine, I believe the 
problem might come from some stack size or other limit, set in your 
distant shell

eg, if your distant machine (the one running acedb) is a linux and you 
use bash on it, try the command
ulimit -a
you can try setting some values to unlimited (most probably the stack 
size: ulimit -s unlimited)

if your distant shell is tcsh, the command is limit, check your tcsh 
manpage for details

if it's some other shell I don't know, but there are generally analogues 
to these commands

Well, i'm no acedb guru so it could be anything else, in that case 
someone else can perhaps help you

hope this helps

Chia Hung wrote:
> Hi, AceDB gurus,
>     I am currently using AceDB v. 4.9h on a Dell dual Xeon processor (I
> Don't know the RAM size) running RedHat Linux 8 with Gnome window
> manager/desktop manager. Both AceDB program and the databases are located on
> a remote machine. I am using the Linux box pretty much as a terminal.
>     My database is a bacterial genome of ~ 5 megabases (class Sequence) with
> ~ 300 subsequences, ~ 2,000 Pep_homol and 38,000 protein objects. The
> Pep_homol (and protein objects) was generated from blastx of the bacterial
> genome against 8 other bacterial organisms.  I have been experiencing
> "Segmentation Fault" errors when I do Blixem to look at the blastx
> homologies. The error occurrences are somewhat irregular. Sometimes I can
> look at Blixem of twenty or more subsequences (opening and closing the
> window), but then sometimes the program will quit after a couple of Blixem
> events.
>     I have tried to leave the Blixem window open but that seemed to have
> made the problem worse. I also have tried logging to my account from other
> machines or logging in as other users, but the problem persisted. In
> addition, I have tried AceDB versions 4.9s, 4.9t, 4.9u, 4.9y and 4.9z. The
> problems were still there.
>     The weird thing is that one other person in the lab (whose account
> belongs to a different user group), had no problem at all. I have logged in
> as another user in that same group (but not the account of the person
> without any problem), but that did not help the situation.
>     I understand that "Segmentation Fault" is a hard problem to diagnose.
> Does anyone have any hints or insights as to why this is happening and /or
> how I might be able to alleviate the problem? Thanks for your help!!
>     Sincerely,
>     Chia
> _______________________________________________
> Chia Hung
> Postdoctoral Research Fellow
> Department of Molecular Microbiology
> Washington University School of Medicine
> 660 S. Euclid Ave., Box 8230
> St. Louis, MO  63110
> Tel: (314) 747-3627
> Fax: (314) 362-1232
> ---

Nicolas Thierry-Mieg
Laboratoire LSR-IMAG, BP 53, 38041 Grenoble Cedex 9, France
tel : (33/0)4-76-63-55-79, fax : (33/0)4-76-63-55-50

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