View source for Parallel I/O Implementation on the Multiple Sequence Alignment Software ClustalW-MPI

{{project info
|description=Parallel I/O Implementation on the Multiple Sequence Alignment Software ClustalW-MPI
<!--|research project=-->
|fields=Computational science; Bioinformatics
|financing=PRACE
|active=No
|start date=2012-08-01
|end date=2013-05-31
}}


This project aims for optimizing the ClustalW software, which is the multiple sequence alignment code. [[NSC]] participates in this project as the PRACE collaborator, with the aim of designing and implementing parallel I/O for sequence alignment softwares. 

This project is a user support task under PRACE 2IP WP7.1, whose project ID is 2010PA1155.

== Implementation ==
Implementation procedure is as follows.

* Analysis on Code Structure
* Design of parallel I/O interface for sequence alignment input
* Implementation to the ClustalW Software

The code basically adopts the master-slave structure, so that the deployment of parallel I/O which is the collective operation necessitates the change on the structure of the code. [[NSC]] designed and experimented the parallel I/O strategy for sequence alignment softwares, by adopting the sub-group communicator. [[NSC]] endeavoured to optimize I/O-related variables for the best performance of sequence data input, and applied the designed implementation to the ClustalW software.

== Results ==
The employed scheme provides up to 6.8 times speed-up for sequence data input in case of using 8192 cores under BlueGene/Q system. Experiments provide the guideline to set various parameters for best I/O performances. Details are to be accessible under [http://www.prace-ri.eu/IMG/pdf/wp71.pdf PRACE White Paper archive].


== Members ==
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