Welcome!

Linux Containers Authors: Anders Wallgren, Liz McMillan, Pete Waterhouse, Pat Romanski, Blue Box Blog

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
SYS-CON Events announced today that Alert Logic, Inc., the leading provider of Security-as-a-Service solutions for the cloud, will exhibit at SYS-CON's 18th International Cloud Expo®, which will take place on June 7-9, 2016, at the Javits Center in New York City, NY. Alert Logic, Inc., provides Security-as-a-Service for on-premises, cloud, and hybrid infrastructures, delivering deep security insight and continuous protection for customers at a lower cost than traditional security solutions. Ful...
SYS-CON Events announced today that Interoute, owner-operator of one of Europe's largest networks and a global cloud services platform, has been named “Bronze Sponsor” of SYS-CON's 18th Cloud Expo, which will take place on June 7-9, 2015 at the Javits Center in New York, New York. Interoute is the owner-operator of one of Europe's largest networks and a global cloud services platform which encompasses 12 data centers, 14 virtual data centers and 31 colocation centers, with connections to 195 ad...
Companies can harness IoT and predictive analytics to sustain business continuity; predict and manage site performance during emergencies; minimize expensive reactive maintenance; and forecast equipment and maintenance budgets and expenditures. Providing cost-effective, uninterrupted service is challenging, particularly for organizations with geographically dispersed operations.
SYS-CON Events announced today that Avere Systems, a leading provider of enterprise storage for the hybrid cloud, will exhibit at SYS-CON's 18th International Cloud Expo®, which will take place on June 7-9, 2016, at the Javits Center in New York City, NY. Avere delivers a more modern architectural approach to storage that doesn’t require the overprovisioning of storage capacity to achieve performance, overspending on expensive storage media for inactive data or the overbuilding of data centers ...
SYS-CON Events announced today that Commvault, a global leader in enterprise data protection and information management, has been named “Bronze Sponsor” of SYS-CON's 18th International Cloud Expo, which will take place on June 7–9, 2016, at the Javits Center in New York City, NY, and the 19th International Cloud Expo, which will take place on November 1–3, 2016, at the Santa Clara Convention Center in Santa Clara, CA. Commvault is a leading provider of data protection and information management...
SYS-CON Events announced today that VAI, a leading ERP software provider, will exhibit at SYS-CON's 18th International Cloud Expo®, which will take place on June 7-9, 2016, at the Javits Center in New York City, NY. VAI (Vormittag Associates, Inc.) is a leading independent mid-market ERP software developer renowned for its flexible solutions and ability to automate critical business functions for the distribution, manufacturing, specialty retail and service sectors. An IBM Premier Business Part...
With an estimated 50 billion devices connected to the Internet by 2020, several industries will begin to expand their capabilities for retaining end point data at the edge to better utilize the range of data types and sheer volume of M2M data generated by the Internet of Things. In his session at @ThingsExpo, Don DeLoach, CEO and President of Infobright, will discuss the infrastructures businesses will need to implement to handle this explosion of data by providing specific use cases for filte...
Cognitive Computing is becoming the foundation for a new generation of solutions that have the potential to transform business. Unlike traditional approaches to building solutions, a cognitive computing approach allows the data to help determine the way applications are designed. This contrasts with conventional software development that begins with defining logic based on the current way a business operates. In her session at 18th Cloud Expo, Judith S. Hurwitz, President and CEO of Hurwitz & ...
Fortunately, meaningful and tangible business cases for IoT are plentiful in a broad array of industries and vertical markets. These range from simple warranty cost reduction for capital intensive assets, to minimizing downtime for vital business tools, to creating feedback loops improving product design, to improving and enhancing enterprise customer experiences. All of these business cases, which will be briefly explored in this session, hinge on cost effectively extracting relevant data from ...
SYS-CON Events announced today that Pythian, a global IT services company specializing in helping companies adopt disruptive technologies to optimize revenue-generating systems, has been named “Bronze Sponsor” of SYS-CON's 18th Cloud Expo, which will take place on June 7-9, 2015 at the Javits Center in New York, New York. Founded in 1997, Pythian is a global IT services company that helps companies compete by adopting disruptive technologies such as cloud, Big Data, advanced analytics, and DevO...
As enterprises work to take advantage of Big Data technologies, they frequently become distracted by product-level decisions. In most new Big Data builds this approach is completely counter-productive: it presupposes tools that may not be a fit for development teams, forces IT to take on the burden of evaluating and maintaining unfamiliar technology, and represents a major up-front expense. In his session at @BigDataExpo at @ThingsExpo, Andrew Warfield, CTO and Co-Founder of Coho Data, will dis...
With the Apple Watch making its way onto wrists all over the world, it’s only a matter of time before it becomes a staple in the workplace. In fact, Forrester reported that 68 percent of technology and business decision-makers characterize wearables as a top priority for 2015. Recognizing their business value early on, FinancialForce.com was the first to bring ERP to wearables, helping streamline communication across front and back office functions. In his session at @ThingsExpo, Kevin Roberts...
SYS-CON Events announced today that iDevices®, the preeminent brand in the connected home industry, will exhibit at SYS-CON's 18th International Cloud Expo®, which will take place on June 7-9, 2016, at the Javits Center in New York City, NY. iDevices, the preeminent brand in the connected home industry, has a growing line of HomeKit-enabled products available at the largest retailers worldwide. Through the “Designed with iDevices” co-development program and its custom-built IoT Cloud Infrastruc...
Eighty percent of a data scientist’s time is spent gathering and cleaning up data, and 80% of all data is unstructured and almost never analyzed. Cognitive computing, in combination with Big Data, is changing the equation by creating data reservoirs and using natural language processing to enable analysis of unstructured data sources. This is impacting every aspect of the analytics profession from how data is mined (and by whom) to how it is delivered. This is not some futuristic vision: it's ha...
Silver Spring Networks, Inc. (NYSE: SSNI) extended its Internet of Things technology platform with performance enhancements to Gen5 – its fifth generation critical infrastructure networking platform. Already delivering nearly 23 million devices on five continents as one of the leading networking providers in the market, Silver Spring announced it is doubling the maximum speed of its Gen5 network to up to 2.4 Mbps, increasing computational performance by 10x, supporting simultaneous mesh communic...
The cloud promises new levels of agility and cost-savings for Big Data, data warehousing and analytics. But it’s challenging to understand all the options – from IaaS and PaaS to newer services like HaaS (Hadoop as a Service) and BDaaS (Big Data as a Service). In her session at @BigDataExpo at @ThingsExpo, Hannah Smalltree, a director at Cazena, will provide an educational overview of emerging “as-a-service” options for Big Data in the cloud. This is critical background for IT and data profes...
SYS-CON Events announced today that Men & Mice, the leading global provider of DNS, DHCP and IP address management overlay solutions, will exhibit at SYS-CON's 18th International Cloud Expo®, which will take place on June 7-9, 2016, at the Javits Center in New York City, NY. The Men & Mice Suite overlay solution is already known for its powerful application in heterogeneous operating environments, enabling enterprises to scale without fuss. Building on a solid range of diverse platform support,...
One of the bewildering things about DevOps is integrating the massive toolchain including the dozens of new tools that seem to crop up every year. Part of DevOps is Continuous Delivery and having a complex toolchain can add additional integration and setup to your developer environment. In his session at @DevOpsSummit at 18th Cloud Expo, Miko Matsumura, Chief Marketing Officer of Gradle Inc., will discuss which tools to use in a developer stack, how to provision the toolchain to minimize onboa...
SYS-CON Events announced today that Fusion, a leading provider of cloud services, will exhibit at SYS-CON's 18th International Cloud Expo®, which will take place on June 7-9, 2016, at the Javits Center in New York City, NY. Fusion, a leading provider of integrated cloud solutions to small, medium and large businesses, is the industry's single source for the cloud. Fusion's advanced, proprietary cloud service platform enables the integration of leading edge solutions in the cloud, including clou...
Most people haven’t heard the word, “gamification,” even though they probably, and perhaps unwittingly, participate in it every day. Gamification is “the process of adding games or game-like elements to something (as a task) so as to encourage participation.” Further, gamification is about bringing game mechanics – rules, constructs, processes, and methods – into the real world in an effort to engage people. In his session at @ThingsExpo, Robert Endo, owner and engagement manager of Intrepid D...