[Bio-linux-dev] [Fwd: Re: NuGO Desktop]

[Tim Booth]

Hi Tony,

Yes, we did run into this problem, I think.  Stewart thought he'd solved
it by modifying the shutdown part of the Casper scripts to force a sync.
His notes say:

---
Orginator: BT
Date reported: 10 Dec 2008
Issue: USB stick problem on reboot seems like the disk failed to sync
before it was ejected. 

Suggested fix if any: The script /etc/init.d/casper controls the
shutdown and call on /sbin/casper-snapshot to sync disks. This is
supposed to work for USB stick as well as DVD but it might need to be
forced to sync.
Fix implemented: Edited the /etc/init.d/casper file within the squash
fs. In the subroutine do_stop created a condition that checks for the
word "persistent" in /proc/cmdline which can be used to differentiate
between usb and dvd. If system is running off usb the shutdown steps do
a sync before allow ubuntu to complete the shutdown and NO MESSAGE is
printed. With the DVD version it runs as before printing a message to
remove the disk and close the tray before pressing enter. Tested and
fixed.
Fix implemented by: SH
---

I remember at the time we reckoned the problem was that the live system
printed a message saying "please remove the disk" before completing the
shutdown.  This is fine for read-only media but any read-write volumes
were left still mounted and if you just pulled the stick out you left it
corrupted.  The solution was to ignore the message and finish shutting
down with the stick still plugged in.  Stewart's tweak makes this happen
automatically.

It's possible that Stewart missed something, but we've had few reports
of problems since his fix.  We tell people not to do important work on
the live systems - it's so easy just to knock the thing and make it stop
working and this leads to corruption of the FS.  There is no automated
fsck at boot, but so far manual fsck has been enough to get things
working again in all problem cases I've seen.

Cheers,

TIM

On Mon, 2009-09-14 at 13:31 +0100, Tony Travis wrote:
> Hello, Bio-Linux developers.
> 
> Here's and update on our NBX-stick project...
> 
> Have you had any feedback from Bio-Linux 5.0 users about problems with 
> persistent sessions corrupting your ext2 "casper-rw" partition?
> 
> It seems to work fine for 5-6 reboots, but then crashes badly :-(
> 
> Using fsck shows "casper-rw" corruption after only one reboot from a 
> persistent session. I'll test this by sacrificing my own NEBC USB-stick, 
> and report back if I have the same problems. However, I got exactly the 
> same problem on my 8GB Kingston DataTraveller, and I've low-level 
> formatted the NBX-sticks using the Alcor_MP (Mass Production) tool to 
> verify that there are no new (post manuf.) bad-blocks on the sticks but 
> I still get corruption. Linux "badblocks -swp 1" didn't find any bad 
> blocks on out NBX-stick, and neither did "mkfs -c ..."
> 
> Bye,
> 
>    Tony.
> email message attachment
> > -------- Forwarded Message --------
> > From: Tony Travis <a.travis at abdn.ac.uk>
> > Reply-To: Travis, Tony <a.travis at abdn.ac.uk>
> > To: John Charly (BIGCAT) <Charly.John at BIGCAT.unimaas.nl>
> > Cc: nbx-dev at googlegroups.com <nbx-dev at googlegroups.com>
> > Subject: Re: NuGO Desktop
> > Date: Mon, 14 Sep 2009 13:20:12 +0100
> > 
> > John Charly (BIGCAT) wrote:
> > > Hi Tony, I tried the the latest .iso for NuGO Linux from the NBX1. I
> > > got a crash report for the package biolinux-artemis. Here I attached
> > > the screenshot.
> > 
> > Hello, Charly.
> > 
> > OK, I know about that - It's a Bio-Linux problem that I'll have to fix.
> > 
> > Thanks for trying out the iso!
> > 
> > I'm still undecided about how best to format the USB sticks. The
> > 'official' Ubuntu "usb-creator" has been back-ported to Hardy, and that
> > is what I used to test NBX-sticks from the latest NuGO-Linux iso.
> > 
> > The difference to the NEBC "bio-linux-usb-maker" is that "usb-creator"
> > does NOT make a partition for an ext2 "casper-rw" filesytem. It uses a
> > container file in the FAT32 partition to create an ext3 (journaling)
> > filesystem. This seems a lot more robust, but there is a fix for
> > "casper" that me and Philip de Groot tried out in Italy that might fix
> > the problems with the ext2 "casper-rw" filesystem if we use 8.04.3 as
> > the basis for remastering the Ubuntu CD instead of 8.04.1, which NEBC
> > used: The 8.04.1 version is *known* to have problems with persistence!
> > 
> > I'll keep you posted, but please try running the "usb-creator" on the
> > NuGO-Linux DVD. You will need to create a symbolic link on the 'live'
> > user's Desktop to do this:
> > 
> >    ln -s /dev/sdb1 cdrom.iso
> > 
> > Then, specify this as the iso 'image' because "usb-creator" doesn't
> > detect that it's running from the DVD for some reason. You run the
> > official Ubuntu "usb-creator" from:
> > 
> >    System/Administration/Create a USB startup disk
> > 
> > Any feedback would be very useful!
> > 
> > Thanks,
> > 
> >    Tony.
> > --
> > Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition
> > and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
> > tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk
> > mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk/~ajt
> > 
> email message attachment
> > -------- Forwarded Message --------
> > From: John Charly (BIGCAT) <Charly.John at BIGCAT.unimaas.nl>
> > To: Travis, Tony <a.travis at abdn.ac.uk>
> > Subject: NuGO Desktop
> > Date: Mon, 14 Sep 2009 13:00:23 +0100
> > 
> > Hi Tony,
> >              I tried the the latest .iso for NuGO Linux from the NBX1. I got a crash report for the package biolinux-artemis. Here I attached the screenshot.
> > 
> > Thanks,
> > 
> > Charly
-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 
at CEH Oxford
+44 1865 281 975