[Bioperl-l] Blast : Bus Error
taerwin at tpg.com.au
Mon Jul 25 19:30:05 EDT 2005
I don't think it would be the linux installation as this would be set up
on different partitions. It could be faulty memory you can test it with:
The only other thing that I can think of is are you using the right
binary? (Did you download a linux binary?)
On Thu, 2005-07-21 at 11:58 +0200, Ferdinand Marlétaz wrote:
> 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
> 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 ?
> 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
> > 1024D/C2E163CB F4C4 A41A 665B 448A 3FA9 6AEA 12E3 39DA C2E1 63CB
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