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Fragmentation Fault

Chia Hung chia at borcim.wustl.edu
Thu Feb 26 03:40:34 EST 2004

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

    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!!


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


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