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June 23, 2008

Faster by a Dozen

Posted in: Open Source, Researches

While most of the people are happy enough with their brand new dual core Pentium notebooks, researchers of computational material are starving for more cores. Why ? Simply because such a fast computers by ordinary standard run their molecular dynamics simulation for at least 3 months (and that if the electricity does not cut off !). So how could they trick the situation ?

Here comes the theory of parallel computing. In plain word, the theory said that if you can run a computing job (J) in a certain time length (T) on a computer, then N computer would run the job in (T/N) time length. That’s the theory, however ;-)

In implementation, there are many technicals aspects that must be solved, mainly:

  • How could we divide the whole job into smaller tasks that can run simultaneously on separate computer, yet the computational result will be consistently correct.
  • How could we initiate the job in one computer, then distribute the tasks into many computers through the network ?
  • How could we collect the result from the tasks running all over the networks back to the initiating computer ?

Worry not, that questions have been solved for years. Many software platforms are available for parallel computing such as PVM (Parallel Virtual Machine) or MPI (Message Passing Interface), and for the better news, the frameworks are freely available as open source software. Thus the most expensive part is providing the hardware, i.e: a lot of computers connected by a fast network.

Thanks to the Insentive research program from the ministry of Research and Technology, Engineering Physics ITB has been granted to build a “High Performance Cluster Computing System”. The first design is a flexible clustering system, consisting of 6 computers, where each computer is a dual processors system, That’s why the system is called a “Dozen”.

So what is good about the Dozen ? Not much. It allows the computer nodes to have flexible topologies, i.e:

  • Dual bus topology
  • Tree topology

The idea came after a long experience with molecular dynamics simulation and process control optimization. The first problem requires many parallel algorithms, thus it is more adapt to run in dual bus topology. On the contrary, process control simulation does search and bound algorithm which is more efficiently run on tree topology.

The research is leadered by Dr. Hermawan K. Dipojono, and the team includes Dr. Estiyanti Ekawati, Dr. Brian Yuliarto, and Ir. Eko Mursito Budi, MT. Expect Emotions ;-)

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