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.

Comments

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 ...

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...

Creating a Simple Axis Service(.aar file) and Deploy it in WSO2 Application Server

In this post I am explaining how to Create a Simple Axis Service(.aar file) and Deploy it in WSO2 Application Server using a simple sample. And also at the end I am describing how to do the same thing with creation of a Jar Service. Lets assume "sample-home" as our parent directory and inside that we can create following folder structure. With this folder structure we can include our external libraries (jar files) inside lib folder and the "services.xml" file inside "META-INF" folder. Following is the sample services.xml definition which I used with this sample creation. < service name = "HelloService" > < Description > This is a sample service to explain simple aar service </ Description > < messageReceivers > < messageReceiver mep = "http://www.w3.org/2006/01/wsdl/in-out" class = "org.apache.axis2.rpc.receivers.RPCMessageReceiver" /> </ messageReceivers > < parame...

Ranga Siriwardena's Blog

Search This Blog