Building a Bioinformatics Supercomputing Cluster
Our local cluster is able to search an up-to-date database with fewer concurrent users and better overall throughput times than is the NCBI Web site. Simple wall-clock time trials were performed using our cluster and the NCBI Web site. We used eight simple queries consisting of protein and DNA sequences. A timer was started after submitting a query from the Web site and stopped once the results were displayed in the browser window. Trials on the NCBI Web site were performed at various times throughout the span of two weeks. All eight trials were averaged and compared to the cluster's times. The purpose of timing the query from the point of submission until the results are displayed was to observe times that an actual user would incur. On average, the cluster took less time to complete a query.
Resources for this article: /article/8140.
Josh Stroschein (email@example.com) currently is pursuing his undergraduate degree in Computer Science and Criminal Justice. Josh is working on the cluster project through a grant at USD. He also works for Walton Internet Solutions, based in Vermillion, SD.
Doug Jennewein (firstname.lastname@example.org) is a research analyst in Computer Science, and he has been with the USD since 1998. He received his Masters degree in Computer Science from USD in 2004. Doug's main research interest is high performance computing.
Joe Reynoldson (email@example.com) is the research computing manager/instructor for the Computer Science Department, and he has been with USD since 1994. He received his Masters degree in Computer Science from USD in 1997. Joe teaches topics in Perl, systems management and Web development.
|HPC Cluster Grant Accepting Applications!||Jan 28, 2015|
|Sharing Admin Privileges for Many Hosts Securely||Jan 28, 2015|
|Red Hat Enterprise Linux 7.1 beta available on IBM Power Platform||Jan 23, 2015|
|Designing with Linux||Jan 22, 2015|
|Wondershaper—QOS in a Pinch||Jan 21, 2015|
|Ideal Backups with zbackup||Jan 19, 2015|
- Sharing Admin Privileges for Many Hosts Securely
- HPC Cluster Grant Accepting Applications!
- Red Hat Enterprise Linux 7.1 beta available on IBM Power Platform
- Designing with Linux
- Internet of Things Blows Away CES, and it May Be Hunting for YOU Next
- Ideal Backups with zbackup
- Wondershaper—QOS in a Pinch
- diff -u: What's New in Kernel Development
- Hats Off to Mozilla
- Slow System? iotop Is Your Friend