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

[Dr Dan Swan]

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