[Bio-linux-dev] USB-stick checksum failures

[Tim Booth]

Hi Tony,

As you say, that's pretty clear cut, and it came as a big surprise to
me.  Like you, I assumed that all the files in the casper/ directory
were untouched and all writes went to casper-rw/ via the union FS.

But then looking at the Deb changelog for the Casper package it talks
about the casper-update-initramfs hook which does exactly this -
supports updated kernels and initramfs on USB media - and apparently
it's been in there since Jaunty which is forever!  So if your users ran
any kind of update on the USB stick the behaviour you saw is exactly as
expected.

So I guess the bug here is that the md5sums file isn't being updated.  I
could probably submit this as a simple bug report/patch to Ubuntu.  On
the other hand, I might well look into disabling this feature on the
Bio-Linux sticks, because it seems to me that even if the md5sums file
is fixed it's liable to cause more problems than it fixes modifying
these files.  What do you think?

Cheers,

TIM

On Sat, 2015-03-07 at 23:52 +0000, Tony Travis wrote:
> On 07/03/15 22:23, Tony Travis wrote:
> > [...]
> > Any idea why "initrd.lz" is being written to?
> 
> Hi, Tim.
> 
> I've compared the original and updated initrd.lz's:
> 
> > # extract original initrd.lz from original USB-stick
> > root at beluga:/media/ajt/bl-live-iso/casper#
> > cp -ai initrd.lz /var/tmp/original-initrd.lz
> > cd /var/tmp
> > mkdir original-
> > initrd
> > cd original-initrd
> > lzma -dc -S .lz ../original-initrd.lz | cpio -id
> >
> > # extract updated initrd.lz from updated USB-stick
> > root at beluga:/media/ajt/bl-live-iso/casper#
> > cp -ai initrd.lz /var/tmp
> > cd /var/tmp
> > mkdir updatedupdated-initrd
> > lzma -dc -S .lz ../updated-initrd.lz | cpio -id
> >
> > # compare contents of initrd's
> > root at beluga:/var/tmp# diff -r original-initrd updated-initrd
> > Binary files original-initrd/etc/console-setup/cached.kmap.gz and updated-initrd/etc/console-setup/cached.kmap.gz differ
> > diff -r original-initrd/etc/default/keyboard updated-initrd/etc/default/keyboard
> > 9c9
> > < XKBLAYOUT="gb"
> > ---
> > > XKBLAYOUT="us"
> > Only in original-initrd/etc/ld.so.conf.d: zz_i386-biarch-compat.conf
> > Only in original-initrd/etc/modprobe.d: dkms.conf
> > Binary files original-initrd/usr/lib/x86_64-linux-gnu/libdrm.so.2 and updated-initrd/usr/lib/x86_64-linux-gnu/libdrm.so.2 differ
> 
> The file is NOT being corrupted, but it is being updated by changes to
> the keyboard and kernel 'drm' (i.e. display) modules. This all seems
> quite normal, according to diferent hardware, and explains why the
> 'self-test' fails. On read-only media (e.g. DVD) these files would not
> be changed and the 'self-test' would not fail...
> 
> Bye,
> 
>   Tony.
> 
> --
> Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
> Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
> AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
> http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis
> 
> 
> The University of Aberdeen is a charity registered in Scotland, No SC013683.
> Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir. SC013683.
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-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
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