Article View: bionet.software.acedb
Article #92Re: Fragmentation Fault
From: Ed Griffiths
Date: Thu, 26 Feb 2004 14:01
Date: Thu, 26 Feb 2004 14:01
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3235 bytes
Chia Hung, > 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!! what Nicolas said could well be the cause but there is one other thing you should check..... All users have a ".acedbrc" file in their home directory, this contains acedb preferences which you can edit via the "Preferences" window from the xace main window. there are some blixem options that you should check, in particular BLIXEM_SCOPE & BLIXEM_HOMOL_MAX. These control the number of matches passed from acedb to blixem and it may be that you have these set at a level that means blixem is being passed too many matches and then runs out of memory or there is some other problem because of the number of matches. Find the other persons .acedbrc and compare it to yours. cheers Ed -- ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif@sanger.ac.uk Tel: +44-1223-494780 Fax: +44-1223-494919 | ------------------------------------------------------------------------
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X-Google-Language: ENGLISH,ASCII-7-bit X-Google-Thread: f6d40,81aac0f3a2c3b4be X-Google-Attributes: gidf6d40,public X-Google-ArrivalTime: 2004-02-26 06:01:51 PST Path: arc1-ca.pugleaf.net!archiver1.google.com!news1.google.com!newsfeed.stanford.edu!bloom-beacon.mit.edu!rfcgr.mrc.ac.uk!hgmp.mrc.ac.uk!net.bio.net From: Ed Griffiths <edgrif@sanger.ac.uk> Newsgroups: bionet.software.acedb Subject: Re: Fragmentation Fault Date: 26 Feb 2004 14:01:49 -0000 Organization: Sanger Institute Lines: 36 Sender: mod-ace@rfcgr.mrc.ac.uk Approved: BIOSCI Approval Key <biosci-approval-key@net.bio.net> Message-ID: <c1ku84$5bu$1@helium.hgmp.mrc.ac.uk> References: <BC62363D.D327%chia@borcim.wustl.edu> NNTP-Posting-Host: mercury.hgmp.mrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Trace: helium.hgmp.mrc.ac.uk 1077804109 5505 193.62.192.80 (26 Feb 2004 14:01:49 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: Thu, 26 Feb 2004 14:01:49 +0000 (UTC) X-Original-To: bionet-software-acedb@net.bio.net User-Agent: Mozilla/5.0 (X11; U; OSF1 alpha; en-US; rv:1.4) Gecko/20030903 X-Accept-Language: en, en-us X-Auth: PGPMoose V1.1 PGP bionet.software.acedb iQCVAwUAQD38TKCIqsWvyF5FAQGtbgP/eMauPvhMCvEpOzG2E5zOPYlh9+r10QRu GFJl/prpvYsiFVy/te+WaPrQZDB1DDtDYaizl0M9Ox4QQo2TIKQkwgDt8msnl79c beOfptWSK3kSdoBrfc5tDj5MlcAn2HlZvJY46N/ri/YEHkCgeqR6yQ0dnsMfdYYD yzt282rLFbc= =w5uH