Welcome!

Linux Containers Authors: XebiaLabs Blog, Pat Romanski, Cloud Best Practices Network, Elizabeth White, Yeshim Deniz

Related Topics: Linux Containers

Linux Containers: Article

Case Study: Biocomputing Solutions Using Linux Networx Cluster System

Tulane University is home to the Center for Computational Science (CCS), a unique facility

Tulane University is home to the Center for Computational Science (CCS), a unique facility designed to provide computational resources for research projects across many disciplines. The Center provides an infrastructure for investigators interested in computational science to exchange ideas, produce research, and establish new collaborations.

The Challenge
One of these collaborative efforts involves a team of researchers performing computational simulations of multi-scale models in biological systems. This research is funded through individual research grants from the National Institute of Health (NIH), National Science Foundation (NSF), and National Aeronautics and Space Administration (NASA), as well as a Center grant from the NIH entitled "Biocomputing: Integrating Molecular/Organ-Level Function."

"Since computationally demanding simulations of 3D models of bioelectric phenomena, fluid-structure interactions, and molecular dynamics simulation are important to these research projects, it was important for the CCS to obtain a scalable high-performance computing system that could be easily shared among several different research groups," said Dr. Donald Gaver, director of the CCS.

For example, Dr. Natalia Trayanova, professor of biomedical engineering, studies cardiac defibrillation - the application of a strong electric shock to the heart to restore cardiac rhythm and prevent sudden cardiac death. Despite the critical role that defibrillation therapy plays in saving human life, it is only known what happens on the surface of the heart during these electric shocks. By using computer models, Dr. Trayanova is able to produce a 3D simulation of a heart to better understand what happens during a shock within the cardiac walls. This improved understanding is expected to lead to new advancements and optimization of the clinical procedure of cardiac defibrillation.

"Computer models and 3D simulations are imperative to my research to better understand how electric shock affects the heart," said Dr. Trayanova. "Therefore, it is crucial that the computing system we use be capable of handling compute-intensive workloads and simulations."

Tulane's existing biomedical server was a shared memory machine, but the cost of upgrading and maintaining the system was already quite costly - Tulane knew expanding this existing system would be too expensive.

"To achieve successful, accurate results in a timely manner for our researchers' projects, we needed a computing system that was fast, reliable, but affordable," said Rene Salmon, senior systems analyst for CCS. "Since the outcome of so many projects would depend on the reliability and ease-of-use of the system, we had to seriously consider what type of computing system would benefit our users the most."

Investigating Linux Clusters
Tulane started looking for computing alternatives that could fit within their budget and provide the speed and reliability that was crucial for ensuring successful research results. After investigating several alternatives, Tulane became increasingly interested in Linux clusters. This distributed computing platform seemed to provide the price/performance ratio Tulane was interested in achieving. However, the researchers at the CCS were worried about the difficulty of migrating to a Linux cluster.

"With a Linux cluster we could afford many more CPUs, which allowed us to run much larger simulations and get faster results at a fraction of the cost," said Salmon. "However, we were concerned about what would be involved in migrating our codes to a new system. Luckily, our researches were willing to adapt their codes to run on a Linux cluster."

The scalability of Linux clusters was another attractive feature for Tulane. As researchers received more grant money from various sources, they could add more compute nodes to the cluster and increase its computing power.

"The great thing about the scalability of Linux clusters is that it allows our researchers to pool their resources so they can have access to more CPUs and computing power," said Salmon.

Managing the Linux Cluster
Since the Linux cluster would be running multiple programs for different users, it was imperative that the computing system Tulane chose be easy to use and manage. Tulane was drawn to the comprehensive management tools offered by Linux Networx, especially the Icebox management appliance and LinuxBIOS.

"Since we knew the cluster would be running multiple programs for several projects simultaneously, how we would manage the cluster became a big concern," said Salmon. "After looking at Linux Networx's management tools, we were very impressed with the capabilities of Icebox. The serial terminal server and a remote-controlled power distribution were also critical for ensuring a productive, scalable system."

Linux Networx's expertise with LinuxBIOS, an open source BIOS alternative, was another management feature that interested Tulane. LinuxBIOS performs the same basic functions as commercial BIOS only 10-20 times faster. LinuxBIOS initializes the hardware, checks for valid memory, and begins loading the operating system in about three seconds. Most commercial BIOS require about 30-60 seconds to perform the same tasks. In addition, LinuxBIOS can be configured and accessed from within the Linux operating system. This means changes to the BIOS can be made remotely to a single node or to all the nodes in a cluster system.

"LinuxBIOS was important to us for scalability reasons. We really liked the fact that we could make changes to the BIOS on the entire cluster from Linux with just a few commands," said Salmon.

With expertise in LinuxBIOS, comprehensive management tools, and powerful computing architecture, Linux Networx became Tulane's choice for their first cluster implementation.

"We wanted a Linux cluster vendor that could provide us with an easy-to-manage cluster that could scale and grow easily. Linux Networx did this for us," said Salmon.

Implementing a Linux Networx Cluster System
Starting with a 20-processor Evolocity system, Tulane researchers quickly noticed the benefits of Linux Networx cluster technology and have scaled up their cluster four times as additional grant money has been received. Their Evolocity cluster now totals over 80 AMD Opteron processors.

"The scalability of the Evolocity cluster has proved to be an essential feature as we've quadrupled the cluster's power since we first installed it," said Salmon. "Scaling the cluster has also been a fairly easy process as programs and codes were easily migrated."

Results
Tulane researchers quickly noticed the benefits and potential of Linux cluster technology. In the past, researchers were limited to running small simulations, now they can run much larger, complex simulations than was possible before.

"Running large, detailed simulations is essential to our research efforts as it allows us to better understand biomedical functions," said Dr. Trayanova. "Additionally, a quick turnaround time for running simulations is essential as there are several research groups that need time on the cluster to complete their simulations."

Most important, with the power and capabilities of the Linux Networx system, Tulane researchers can improve the quality of their research and achieve much more focused and valid results than they were able to accomplish previously.

"By completing these jobs in a timely manner, researchers can get results faster, which helps advance the entire mission of the biocomputing program and allows us to do better research," said Dr. Trayanova.

More Stories By Mark R. Hinkle

Mark Hinkle is the Senior Director, Open Soure Solutions at Citrix. He also is along-time open source expert and advocate. He is a co-founder of both the Open Source Management Consortium and the Desktop Linux Consortium. He has served as Editor-in-Chief for both LinuxWorld Magazine and Enterprise Open Source Magazine. Hinkle is also the author of the book, "Windows to Linux Business Desktop Migration" (Thomson, 2006). His blog on open source, technology, and new media can be found at http://www.socializedsoftware.com.

Comments (2) View Comments

Share your thoughts on this story.

Add your comment
You must be signed in to add a comment. Sign-in | Register

In accordance with our Comment Policy, we encourage comments that are on topic, relevant and to-the-point. We will remove comments that include profanity, personal attacks, racial slurs, threats of violence, or other inappropriate material that violates our Terms and Conditions, and will block users who make repeated violations. We ask all readers to expect diversity of opinion and to treat one another with dignity and respect.


Most Recent Comments
ITSG News Desk 11/07/05 11:13:54 AM EST

Tulane University is home to the Center for Computational Science (CCS), a unique facility designed to provide computational resources for research projects across many disciplines. The Center provides an infrastructure for investigators interested in computational science to exchange ideas, produce research, and establish new collaborations.

LinuxWorld News Desk 11/07/05 11:00:56 AM EST

Tulane University is home to the Center for Computational Science (CCS), a unique facility designed to provide computational resources for research projects across many disciplines. The Center provides an infrastructure for investigators interested in computational science to exchange ideas, produce research, and establish new collaborations.

@ThingsExpo Stories
China Unicom exhibit at the 19th International Cloud Expo, which took place at the Santa Clara Convention Center in Santa Clara, CA, in November 2016. China United Network Communications Group Co. Ltd ("China Unicom") was officially established in 2009 on the basis of the merger of former China Netcom and former China Unicom. China Unicom mainly operates a full range of telecommunications services including mobile broadband (GSM, WCDMA, LTE FDD, TD-LTE), fixed-line broadband, ICT, data communica...
For basic one-to-one voice or video calling solutions, WebRTC has proven to be a very powerful technology. Although WebRTC’s core functionality is to provide secure, real-time p2p media streaming, leveraging native platform features and server-side components brings up new communication capabilities for web and native mobile applications, allowing for advanced multi-user use cases such as video broadcasting, conferencing, and media recording.
SYS-CON Events announced today that delaPlex will exhibit at SYS-CON's @CloudExpo, which will take place on June 6-8, 2017, at the Javits Center in New York City, NY. delaPlex pioneered Software Development as a Service (SDaaS), which provides scalable resources to build, test, and deploy software. It’s a fast and more reliable way to develop a new product or expand your in-house team.
The explosion of new web/cloud/IoT-based applications and the data they generate are transforming our world right before our eyes. In this rush to adopt these new technologies, organizations are often ignoring fundamental questions concerning who owns the data and failing to ask for permission to conduct invasive surveillance of their customers. Organizations that are not transparent about how their systems gather data telemetry without offering shared data ownership risk product rejection, regu...
SYS-CON Events announced today that CA Technologies has been named "Platinum Sponsor" of SYS-CON's 20th International Cloud Expo®, which will take place on June 6-8, 2017, at the Javits Center in New York City, New York, and 21st International Cloud Expo, which will take place in November in Silicon Valley, California.
WebRTC is about the data channel as much as about video and audio conferencing. However, basically all commercial WebRTC applications have been built with a focus on audio and video. The handling of “data” has been limited to text chat and file download – all other data sharing seems to end with screensharing. What is holding back a more intensive use of peer-to-peer data? In her session at @ThingsExpo, Dr Silvia Pfeiffer, WebRTC Applications Team Lead at National ICT Australia, looked at differ...
With major technology companies and startups seriously embracing IoT strategies, now is the perfect time to attend @ThingsExpo 2016 in New York. Learn what is going on, contribute to the discussions, and ensure that your enterprise is as "IoT-Ready" as it can be! Internet of @ThingsExpo, taking place June 6-8, 2017, at the Javits Center in New York City, New York, is co-located with 20th Cloud Expo and will feature technical sessions from a rock star conference faculty and the leading industry p...
The Internet of Things can drive efficiency for airlines and airports. In their session at @ThingsExpo, Shyam Varan Nath, Principal Architect with GE, and Sudip Majumder, senior director of development at Oracle, discussed the technical details of the connected airline baggage and related social media solutions. These IoT applications will enhance travelers' journey experience and drive efficiency for the airlines and the airports.
In his keynote at @ThingsExpo, Chris Matthieu, Director of IoT Engineering at Citrix and co-founder and CTO of Octoblu, focused on building an IoT platform and company. He provided a behind-the-scenes look at Octoblu’s platform, business, and pivots along the way (including the Citrix acquisition of Octoblu).
SYS-CON Events announced today that Technologic Systems Inc., an embedded systems solutions company, will exhibit at SYS-CON's @ThingsExpo, which will take place on June 6-8, 2017, at the Javits Center in New York City, NY. Technologic Systems is an embedded systems company with headquarters in Fountain Hills, Arizona. They have been in business for 32 years, helping more than 8,000 OEM customers and building over a hundred COTS products that have never been discontinued. Technologic Systems’ pr...
In his keynote at @ThingsExpo, Chris Matthieu, Director of IoT Engineering at Citrix and co-founder and CTO of Octoblu, focused on building an IoT platform and company. He provided a behind-the-scenes look at Octoblu’s platform, business, and pivots along the way (including the Citrix acquisition of Octoblu).
A strange thing is happening along the way to the Internet of Things, namely far too many devices to work with and manage. It has become clear that we'll need much higher efficiency user experiences that can allow us to more easily and scalably work with the thousands of devices that will soon be in each of our lives. Enter the conversational interface revolution, combining bots we can literally talk with, gesture to, and even direct with our thoughts, with embedded artificial intelligence, whic...
SYS-CON Events announced today that CA Technologies has been named “Platinum Sponsor” of SYS-CON's 20th International Cloud Expo®, which will take place on June 6-8, 2017, at the Javits Center in New York City, NY, and the 21st International Cloud Expo®, which will take place October 31-November 2, 2017, at the Santa Clara Convention Center in Santa Clara, CA. CA Technologies helps customers succeed in a future where every business – from apparel to energy – is being rewritten by software. From ...
With 10 simultaneous tracks, keynotes, general sessions and targeted breakout classes, Cloud Expo and @ThingsExpo are two of the most important technology events of the year. Since its launch over eight years ago, Cloud Expo and @ThingsExpo have presented a rock star faculty as well as showcased hundreds of sponsors and exhibitors! In this blog post, I provide 7 tips on how, as part of our world-class faculty, you can deliver one of the most popular sessions at our events. But before reading the...
The best way to leverage your Cloud Expo presence as a sponsor and exhibitor is to plan your news announcements around our events. The press covering Cloud Expo and @ThingsExpo will have access to these releases and will amplify your news announcements. More than two dozen Cloud companies either set deals at our shows or have announced their mergers and acquisitions at Cloud Expo. Product announcements during our show provide your company with the most reach through our targeted audiences.
In his session at @ThingsExpo, Steve Wilkes, CTO and founder of Striim, will delve into four enterprise-scale, business-critical case studies where streaming analytics serves as the key to enabling real-time data integration and right-time insights in hybrid cloud, IoT, and fog computing environments. As part of this discussion, he will also present a demo based on its partnership with Fujitsu, highlighting their technologies in a healthcare IoT use-case. The demo showcases the tracking of patie...
20th Cloud Expo, taking place June 6-8, 2017, at the Javits Center in New York City, NY, will feature technical sessions from a rock star conference faculty and the leading industry players in the world. Cloud computing is now being embraced by a majority of enterprises of all sizes. Yesterday's debate about public vs. private has transformed into the reality of hybrid cloud: a recent survey shows that 74% of enterprises have a hybrid cloud strategy.
With major technology companies and startups seriously embracing Cloud strategies, now is the perfect time to attend @CloudExpo | @ThingsExpo, June 6-8, 2017, at the Javits Center in New York City, NY and October 31 - November 2, 2017, Santa Clara Convention Center, CA. Learn what is going on, contribute to the discussions, and ensure that your enterprise is on the right path to Digital Transformation.
Have you ever noticed how some IT people seem to lead successful, rewarding, and satisfying lives and careers, while others struggle? IT author and speaker Don Crawley uncovered the five principles that successful IT people use to build satisfying lives and careers and he shares them in this fast-paced, thought-provoking webinar. You'll learn the importance of striking a balance with technical skills and people skills, challenge your pre-existing ideas about IT customer service, and gain new in...
Bert Loomis was a visionary. This general session will highlight how Bert Loomis and people like him inspire us to build great things with small inventions. In their general session at 19th Cloud Expo, Harold Hannon, Architect at IBM Bluemix, and Michael O'Neill, Strategic Business Development at Nvidia, discussed the accelerating pace of AI development and how IBM Cloud and NVIDIA are partnering to bring AI capabilities to "every day," on-demand. They also reviewed two "free infrastructure" pr...