[Bio-Linux] Re: (no subject) (Siddharth Ray)

[Siddharth Ray]

Hello Dr. Swan,
I now understand the need for Dell machines. The main part is the X-windows
configuration which needs very specific system information. Anyways, I feel
that two changes can be incorporated to make biolinux highly portable:
1. Machine independence - I think the X-windows can be configured on the fly.
2. Hard drives -  The main problem I think is; when cloning was done the
computer already had 2 hard drives and earlier Windows XP was installed, I
think may be for that reason its showing the cylinder overlapping problem. Some
changes should be made so that the kernel properly mounts all the hard drives.
I know giving ideas is easy and implementing it is twice as tough but I think
its doable. Anyways I also plan to work on kernel level programming and might
be able to help in some aspects.

Thanks,
Siddharth Ray















On Mon, 24 Feb 2003 10:42:28 +0000, Dr Dan Swan wrote:

> On Sat, 2003-02-22 at 12:01, bio-linux-request at bioinf.ceh.ac.uk wrote:
> 
> Hi Siddharth,
> 
> > I am facing the following problems :
> > 
> > 1.)  I used fdisk on /dev/hda and got the following:
> >      (This machine happens to be a Dell cloned with biolinux)
> > The number of cylinders for this disk is set to 9726.
> > There is nothing wrong with that, but this is larger than 1024,
> > and could in certain setups cause problems with:
> 
> I have to say I'm rather confused about what is going on here.  The 1024
> cylinder limitation is a rather historic point in Linux these days. Ever
> since LILO supported Logical Block Addressing, this has been somewhat of
> a non-issue.  Some people still like to keep the boot partition under
> 1024 cylinders but there is no need to do this.
> 
> > 1) software that runs at boot time (e.g., old versions of LILO)
> 
> If this is a Bio-Linux clone - why is it running LILO?  We have chosen
> the far more flexible GRUB bootloader for Bio-Linux.  Have you changed
> this on your clone?
> 
> > 2) booting and partitioning software from other OSs
> > (e.g., DOS FDISK, OS/2 FDISK)
> 
> Bio-Linux was not developed with the intention of having dual boot
> systems.  It is meant to be a dedicated Linux workstation and we
> recommend that if people wish to run additional OS's should use VMWARE
> within Bio-Linux.  
> 
> > For /dev/hdb it is showing 16127 unallocated sectors (using v of fdisk)
> > p shows /dev/hdb1  start->1 End->9725 Blocks->78116031 Id->7
> > System->HPFS/NTFS
> 
> None of the Bio-Linux clones have a /dev/hdb as far as I know.  Have you
> attempted to add and configure a second hard drive on your Bio-Linux
> clone?  I assume you have - are you working with OS/2 (from the HPFS
> clue)
> 
> > Another error message which was generated was that:
> > The cylinders are overlapping...
> 
> Is this on /dev/hda? or /dev/hdb?  To be honest Linux doesn't actually
> actually have an alignment requirement for cylinders, and its more
> likely an error from over fussy partioning software. NT can handle
> non-aligned partions as well.  The only OS I can think of that really
> doesn't like it is DOS - hence DOS based partition tools can be very
> particular.
> 
> > The cylinder size is set at the time of loading linux. However, is there any
> > specific reason for setting the cylinder size to 9726. I think the default
is
> > 1024 and at least it can be a multiple of that. I know a couple of systems
> > having cylinder size other than 1024 but the main thing that worries me is
the
> > cylinder overlapping and stuff. Another thing which I wanted to point to is
> > that the machine which was cloned had 2 hard disks, but the 2nd hard disk
was
> > never mounted. Hence, if the linux system is being loaded via CD etc then it
> > should acknowledge the 2nd hard disk.
> 
> I see.  Have you added a second hard drive to a Linux machine before? 
> Until you tell Linux it its there, it may autodetect its presence but it
> will never be utilised.  The Bio-Linux v1.0 clones have a single hard
> drive.
> 
> > 2.) Is it that biolinux can only be installed on a Dell machine. Is it
company
> > specific because to my knowledge I have never heard of any OS to be company
> > specific unless their architecture is drastically different. I am new to
this
> > lab and the notion that people are having is that only Dell machines can be
> > cloned. 
> 
> No that's not strictly true, but it certainly helps.  Do you know how
> Bio-Linux is made and installed?  It's not a standard Linux
> distribution, its a system image - therefore its preconfigured to
> certain aspects of the Dell hardware its developed on - especially the
> video cards/NICs.  If you attempt to install it on other hardware we
> cannot make any guarantees that it will work.  We have managed to put it
> onto Dell Laptops which only required X to be configured.
> 
> Hope this helps,
> 
> Dan
> 
> -- 
> Dr Dan Swan - Bio-Linux Developer
> EGTDC, CEH, Mansfield Road, Oxford, OX1 3SR
> Tel: 01865 281 630 Fax: 01865 281 696
> http://envgen.nox.ac.uk/ | dswan at ceh.ac.uk
> 
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> 

"Keep me away from the wisdom which does not cry, the philosophy which does not laugh and the greatness which does not bow before children."
- Kahlil Gibran

MS, Department of Computer Sc. & Engg,
Pond Lab, State College,
PA - 16802, USA.