Skip to main content

Accelerating Genetic Sequence Alignment using CUDA compatible multi core GPU

This was my final year Research & Development individual project and From this research work I was used the massively parallel architecture of GPU as a parallel computing solution, for the improvement of one of the computationally intensive general purpose applications. With that concept I was able to improve dynamic programming based Global genetic Sequence Alignment algorithm with efficient use of heterogeneous memory hierarchy of GPU & CPU. For this research work, CUDA was used because it provides a parallel programming model and an instruction set architecture for Nvidia GPU with an extension of C language.

With this work we use two levels of implementations for Needleman-Wunsch Global sequence alignment algorithm. First implementation was based on  global memory of GPU and the other one is based on the fast, on-chip, Shared memory of GPU. Use of shared memory improved the performance of the implementation with the blocking strategy for the Needleman-Wunsch algorithm.

Read More:

Abstract About this project

More about this research from hipc 2010 conference

Comments

Post a Comment

Popular posts from this blog

How to install IBM WebSphere MQ on Ubuntu (Linux)

Following are the steps to install IBM WebSphere MQ version 8 on Ubuntu 14.04. 1) Create a user account with name "mqm" in Ubuntu. This should basically create a user called "mqm" and usergroup called "mqm" 2) Login to "mqm" user account and proceed with next steps 3) Increase the open file limit for the user "mqm" to "10240" or higher value. For this open "/etc/security/limits.conf" file and set the values as bellow. mqm       hard  nofile     10240 mqm       soft   nofile     10240 4) Increase the number of processes allowed for the user "mqm" to "4096" or higher value. For this open "/etc/security/limits.conf" file and set the values as bellow. You will need to edit this file as a sudo user. mqm       hard  nproc      4096 mqm       soft   nproc      4096 5) Install "RPM" on Ubuntu if you already don't have it. sudo apt-get install rpm ...
1 comment
Read more

Beautiful Trincomalee : One of the stunning places to visit in Sri-Lanka

Recently my self and few of my friends traveled to the ancient city of Trncomalee which is situated in eastern province and lies on the east cost of the little island. In ancient times it was identified as Gokanna and it was one of the major see ports in the international trading history of Sri Lanka. The city is home to the famous ancient Koneswaram Temple and it is said that this is the capital city of king Ravana . This was my first travel to this ancient city and I would say that, it is one of the best places to visit in Sri Lanka. There are lot of places to visit there including Konesvaram Temple, Dutch Fort, Nilaveli Beach, Marble Beach and Pigeon Island . Nilaveli beach is considered to be one of the best beaches in Sri Lanka and Knee deep shallow seas spreads out hundreds of meters towards the sea. That provides ideal and pure conditions for sun bathing. Some of the pictures taken(by me and my friends) trough out the tour is listed bellow as a evidence to the stunning...
2 comments
Read more

How to use Dynamic Registry Keys with WSO2 ESB Mediators

From this post I will going to briefly introduce about one of the new features provided by WSO2 ESB . Earlier WSO2 ESB supported static registry keys where users can select a key for the mediator as a static value. But from ESB 4.0.0 users can use dynamic registry keys where users can define XPath expression to evaluate the registry key in run time. For an example let's consider XSLT mediator. With earlier static registry key based method user have to define only single XSLT file for transformation. With the use of dynamic registry key, user will be able to use XPath expressions to dynamically generate the registry key, based on the message context. So with that user can have multiple XSLT files and based on the evaluated key mediator will be able to select the required XSLT file in run time. Following is a sample usage of static and dynamic registry keys and user can use both of them according to situation.   Static Registry Key – define the exact path to find the xslt fil...
6 comments
Read more