birgHPC: Instant Computing Cluster for Bioinformatics

[THChew]

birgHPC (Bioinformatic Research Group High Performance Computing) is a
free Linux Live CD distribution based on PelicanHPC and Debian Live.
It is developed by the Bioinformatics Research Group (BIRG), Faculty
of Biosciences and Bioengineering, Universiti Teknologi Malaysia.

The idea of creating birgHPC comes from the fact that most PCs in the
computer laboratories are under utilised. The students, for example,
only use the computer laboratories during the day but after office
hours and especially during holidays, these PCs are idle. These PCs
can provide valuable computing resources to researchers by simply
converting them into a high performance computing cluster.
Conventional cluster setup, however, is troublesome and lengthy,
involving manual software configurations and installations and not to
mention extra budget. birgHPC aims to simplify these by using Linux
Live CD technology, combining with automated configurations and built-
in software. The main feature of birgHPC is the ability to convert PCs
interconnected within the same private local area network (LAN) to a
high performance computing cluster, specifically for molecular
dynamics studies, using just one CD. Other features included in
birgHPC are the Ganglia cluster monitoring, the auto slots detection,
both OpenMPI and MPICH2 capabilities as well as tools for molecular
dynamics (GROMACS, Grace, DSSP, VMD and PyMol) and bioinformatics
(mpiBLAST and ClustalW-MPI).

Visit http://birg1.fbb.utm.my/birghpc (or http://www.birg1.bioscience.utm.my/birghpc
if you are inside UTM) for more information and downloads.

[Muhd Syazwan Md Khusaini]

can you host it anywhere else? or probably make a torrent?

thanks :)

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[TH Chew]

Thank you for your interest. Is the download speed slow?

Regards,
THChew

[najmi....@gmail.com]

Congrats!
Home-brewed LiveCD, yes?

On Wed, Feb 16, 2011 at 10:42 AM, THChew <teon...@gmail.com> wrote:

[najmi....@gmail.com]

Hi,

For me torrent is a good practice since the bandwidth is shared
through the other peers who are currently downloading/finished
downloading.

I guess UTM's internal speed is superb (at least for FSKSM, my faculty).

[TH Chew]

Hi Syazwan,

birgHPC now is hosted on Sourceforge. Please visit http://sourceforge.net/projects/birghpc/.

Thanks.

On Mon, Feb 21, 2011 at 8:45 AM, TH Chew <teon...@gmail.com> wrote:

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Regards,
THChew

[sharuzzaman]

Good idea on utilising the idle PC in lab.

But, with LiveCD, if you have 100 machine, you have to burn 100 CD if
you want to start all machine at the same time, or 1 CD and 100 times
walking around rebooting the PC with the LiveCD.

A better approach is to host the image in a server, and each PC in lab
will be booted with the image via netboot. You can use PXE that is
available in all recent generation computer to execute the netboot.

More info in this site, with links to external sites as well:
http://www.kegel.com/linux/pxe.html

Thanks.

> Visithttp://birg1.fbb.utm.my/birghpc(orhttp://www.birg1.bioscience.utm.my/birghpc

[TH Chew]

Hi,

birgHPC indeed is using the netboot approach. All you need is burning one copy of the birgHPC CD, boot the headnode and netboot the rest of the compute node.

Thanks.

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Regards,
THChew

[Sharuzzaman Ahmat Raslan]

cool.

interested to share your implementation method?

maybe in the upcoming MOSC 2011?

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Sharuzzaman Ahmat Raslan