[Bioperl-l] Blast : Bus Error

[Ferdinand Marlétaz]

Well, I excclude memory problems (2 GB RAM on these machines) and
Database SIze problems (The error happens both with large and little
like 50 Mo DB). On top of that, I've already perform on the two
computers identical blast searches and the other computer runs very
well...
I don't think about Hardware problems too because this bugging
computer have led similar searches in the past without problem... So,
something could happened in the configuration what makes the blast
process faulty !  I just know that somebody have try to install linux
on this computer and don't manage to finish this installation. Maybe a
source of my current problems ?

What do you all think about that ?

Thanks 

Ferdi


2005/7/21, Andreas Kahari <ak at ebi.ac.uk>:
> [not to the list]
> 
> Hi guys,
> 
> There could also be a problem with a faulty memory module...  If
> the error is not consistently reproducible, then this is one
> possible cause.
> 
> Running out of memory should not produce a Bus Error.  It might
> produce a Segmentation Fault if the program doesn't care that
> the memory allocation failed, but not a Bus Error (as far as I
> know, but I don't run OS X here).
> 
> A way to diagnose this is to run exactly the same set-up on two
> identical machines until one of them causes the error more than
> once.  If the other machine seems to run ok then it is very
> possible that there is a hardware fault on the first machine (or
> some important system configuration setting is different without
> you knowing it).
> 
> Regards,
> Andreas
> 
> On Thu, Jul 21, 2005 at 11:12:26AM +0200, Laurent DOUCHY wrote:
> > Hello,
> > This problem can happen for several reasons :
> > your ram is not sufficiant and /or  you are working against a db like
> > nt too big for the combination PPC/blast/db; First verify your ram
> > (500Mo are not enougth) , secondly try to work when you can on a part
> > of nt ; try to  check the blast optimised by the Bioteam...
> > Cordially
> >
> > LN
> >
> > 2005/7/21, Ferdinand Marlétaz <ferdinand.marletaz at gmail.com>:
> > > Hi,
> > >
> > > I know my current problem is only farly related with bioperl but maybe
> > > omebody would have already encountered it so, it can be tryed...
> > >
> > > I try to run blast (tblastx) on a G5 powermac computer (OS : OS 10.4
> > > Tiger but the same was happening with 10.3 Panther), it starts perfect
> > > normal but after sometimes, it stops and displays either 'bus error'
> > > or 'segmentation fault'... I'm quite surprised because I've never got
> > > this problem on a second identical G5 in my lab ? I've try to change
> > > blast version from 2.10 to 2.11... but it don't solved the problem.
> > > I verify that it's not related to my databases in reformating them
> > > from fasta...
> > >
> > > So, I don't see where the problem can come from ? Does anybody have
> > > encountered such problems or erros and have a solution or an idea
> > > because I'd like to avoid reinstalling the system on this machine
> > > cause loss of time...
> [cut]
> 
> --
> Andreas Kähäri
> 
> EMBL-EBI/ensembl
> www.ensembl.org
> 
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>