Welcome!

Linux Containers Authors: Liz McMillan, Yeshim Deniz, Elizabeth White, Pat Romanski, Zakia Bouachraoui

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.

IoT & Smart Cities Stories
CloudEXPO New York 2018, colocated with DXWorldEXPO New York 2018 will be held November 11-13, 2018, in New York City and will bring together Cloud Computing, FinTech and Blockchain, Digital Transformation, Big Data, Internet of Things, DevOps, AI, Machine Learning and WebRTC to one location.
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.
Machine Learning helps make complex systems more efficient. By applying advanced Machine Learning techniques such as Cognitive Fingerprinting, wind project operators can utilize these tools to learn from collected data, detect regular patterns, and optimize their own operations. In his session at 18th Cloud Expo, Stuart Gillen, Director of Business Development at SparkCognition, discussed how research has demonstrated the value of Machine Learning in delivering next generation analytics to impr...
The challenges of aggregating data from consumer-oriented devices, such as wearable technologies and smart thermostats, are fairly well-understood. However, there are a new set of challenges for IoT devices that generate megabytes or gigabytes of data per second. Certainly, the infrastructure will have to change, as those volumes of data will likely overwhelm the available bandwidth for aggregating the data into a central repository. Ochandarena discusses a whole new way to think about your next...
The hierarchical architecture that distributes "compute" within the network specially at the edge can enable new services by harnessing emerging technologies. But Edge-Compute comes at increased cost that needs to be managed and potentially augmented by creative architecture solutions as there will always a catching-up with the capacity demands. Processing power in smartphones has enhanced YoY and there is increasingly spare compute capacity that can be potentially pooled. Uber has successfully ...
Chris Matthieu is the President & CEO of Computes, inc. He brings 30 years of experience in development and launches of disruptive technologies to create new market opportunities as well as enhance enterprise product portfolios with emerging technologies. His most recent venture was Octoblu, a cross-protocol Internet of Things (IoT) mesh network platform, acquired by Citrix. Prior to co-founding Octoblu, Chris was founder of Nodester, an open-source Node.JS PaaS which was acquired by AppFog and ...
The deluge of IoT sensor data collected from connected devices and the powerful AI required to make that data actionable are giving rise to a hybrid ecosystem in which cloud, on-prem and edge processes become interweaved. Attendees will learn how emerging composable infrastructure solutions deliver the adaptive architecture needed to manage this new data reality. Machine learning algorithms can better anticipate data storms and automate resources to support surges, including fully scalable GPU-c...
Predicting the future has never been more challenging - not because of the lack of data but because of the flood of ungoverned and risk laden information. Microsoft states that 2.5 exabytes of data are created every day. Expectations and reliance on data are being pushed to the limits, as demands around hybrid options continue to grow.
JETRO showcased Japan Digital Transformation Pavilion at SYS-CON's 21st International Cloud Expo® at the Santa Clara Convention Center in Santa Clara, CA. The Japan External Trade Organization (JETRO) is a non-profit organization that provides business support services to companies expanding to Japan. With the support of JETRO's dedicated staff, clients can incorporate their business; receive visa, immigration, and HR support; find dedicated office space; identify local government subsidies; get...
With 10 simultaneous tracks, keynotes, general sessions and targeted breakout classes, @CloudEXPO and DXWorldEXPO are two of the most important technology events of the year. Since its launch over eight years ago, @CloudEXPO and DXWorldEXPO have presented a rock star faculty as well as showcased hundreds of sponsors and exhibitors! In this blog post, we 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...