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
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

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