[Bio-Linux] Use of the Bio-Linux list

[Tim Booth]

Hi John,

The Bio-Linux list is for open discussion of Bio-Linux related issues.
While the list has been quiet of late and most people send requests like
this directly to the helpdesk, there is no reason not to put technical
questions, comments, tips etc. over the Bio-Linux list.  

If you don't want to get these messages then you are probably better off
being unsubscribed from this list and just staying on our
'envgen-announce' list which only carries announcement postings from the
NEBC.  Let me know if you would rather do that.

In this case, I've continued the e-mails with Jarrod via the helpdesk as
they are getting quite involved and are probably not of interest to most
people.

Cheers,

TIM

On Mon, 2007-06-11 at 15:20 +0100, John Newbury wrote:
> Do I really need to get this, and previous, messages?
> 
> John Newbury 
> 
> > -----Original Message-----
> > From: bio-linux-bounces at envgen.nerc-oxford.ac.uk 
> > [mailto:bio-linux-bounces at envgen.nerc-oxford.ac.uk] On Behalf 
> > Of Jarrod Hadfield
> > Sent: 11 June 2007 15:21
> > To: Bio-Linux help and discussion
> > Subject: Re: [Bio-Linux] biolinux wont boot
> > 
> > Hi Tim,
> > 
> > Sorry to bother you again.  For files in many directories I 
> > was getting the error "cannot stat"  and the final message on 
> > finishing was "tar: Error exit delayed from previous errors". 
> >  I'm guessing these files may be unbackupable?
> > 
> > Cheers,
> > 
> > Jarrod
> > On 11 Jun 2007, at 10:36, Tim Booth wrote:
> > 
> > > Hi Jarrod,
> > >
> > > The error "unable to read inode block" suggests to me that 
> > your disk 
> > > is failing.  The only other reason for getting a serious error like 
> > > this out of the blue would be if the machine had lost power 
> > suddenly, 
> > > but unless you know that has happened it is likely that you 
> > are going 
> > > to need to replace the drive.
> > >
> > > The first thing to do is to boot from a recovery CD and 
> > take a look.  
> > > I generally use Knoppix (knopper.net).  You'll need to download and 
> > > burn a CD image.
> > >
> > > The second thing is to see what data you can access from 
> > the recovery 
> > > CD and tar it up to somewhere safe like a network share or 
> > removable 
> > > disk.
> > >
> > > Then see which partition or partitions cannot be mounted 
> > via Knoppix.
> > > Once you have got any data you need off the good 
> > partitions, you can 
> > > try running fsck on the problem partitions.  Fsck may fail, 
> > or it may 
> > > fix things completely, or it may work but you will still 
> > have problems 
> > > reading the disk.  If things are fixed completely you 
> > should be able 
> > > to reboot back into Bio-Linux, but remember that your disk 
> > may still 
> > > be on the verge of packing in.
> > >
> > > If Knoppix can't fix the disk you will have to get a 
> > replacement disk 
> > > from Dell and recover from the disaster recovery partition on the 
> > > second hard drive.  We'll cross that bridge when we come to it.
> > >
> > > If you need and help with the above then give me a call on 
> > 018656 281 
> > > 975.
> > >
> > > I'll copy this mail thread into the helpdesk system to keep 
> > track of 
> > > it.
> > >
> > > Cheers,
> > >
> > > TIM
> > >
> > > On Mon, 2007-06-11 at 10:18 +0100, Jarrod Hadfield wrote:
> > >> Hi,
> > >>
> > >> I've jsut got back from holiday, to find I ca no longer 
> > log onto my 
> > >> biolinux machine.  I get the message 'fsck died with exit status 4"
> > >> I get prompted for the root password for maintenance, but 
> > get no joy 
> > >> = "unable to read inode block".  As far as I'm aware, the 
> > only thing 
> > >> that happened since I've been away, is that soemone tried to drag 
> > >> some stuff off onto a USB  stick.  Could this be the cause of the 
> > >> problem.
> > >>
> > >> Cheers,
> > >>
> > >> Jarrod
> > >>
> > >>
> > >>
> > >> _______________________________________________
> > >> Bio-Linux mailing list
> > >> Bio-Linux at envgen.nox.ac.uk
> > >> http://envgen.nox.ac.uk/mailman/listinfo/bio-linux
> > > --
> > > Tim Booth <tbooth at ceh.ac.uk>
> > > NERC Environmental Bioinformatics Centre at CEH Oxford
> > > +44 1865 281 975
> > >
> > >
> > > _______________________________________________
> > > Bio-Linux mailing list
> > > Bio-Linux at envgen.nox.ac.uk
> > > http://envgen.nox.ac.uk/mailman/listinfo/bio-linux
> > >
> > 
> > 
> > _______________________________________________
> > Bio-Linux mailing list
> > Bio-Linux at envgen.nox.ac.uk
> > http://envgen.nox.ac.uk/mailman/listinfo/bio-linux
> > 
> 
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at envgen.nox.ac.uk
> http://envgen.nox.ac.uk/mailman/listinfo/bio-linux
-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 
at CEH Oxford
+44 1865 281 975