Welcome!

Linux Containers Authors: Mehdi Daoudi, Yeshim Deniz, Pat Romanski, Liz McMillan, Elizabeth White

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
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...
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 SoftLayer, an IBM Company, has been named “Gold Sponsor” of SYS-CON's 18th Cloud Expo, which will take place on June 7-9, 2016, at the Javits Center in New York, New York. SoftLayer, an IBM Company, provides cloud infrastructure as a service from a growing number of data centers and network points of presence around the world. SoftLayer’s customers range from Web startups to global enterprises.
Multiple data types are pouring into IoT deployments. Data is coming in small packages as well as enormous files and data streams of many sizes. Widespread use of mobile devices adds to the total. In this power panel at @ThingsExpo, moderated by Conference Chair Roger Strukhoff, panelists will look at the tools and environments that are being put to use in IoT deployments, as well as the team skills a modern enterprise IT shop needs to keep things running, get a handle on all this data, and deli...
SYS-CON Events announced today that Grape Up will exhibit at SYS-CON's 21st International Cloud Expo®, which will take place on Oct. 31 – Nov 2, 2017, at the Santa Clara Convention Center in Santa Clara, CA. Grape Up is a software company specializing in cloud native application development and professional services related to Cloud Foundry PaaS. With five expert teams that operate in various sectors of the market across the U.S. and Europe, Grape Up works with a variety of customers from emergi...
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.
SYS-CON Events announced today that Super Micro Computer, Inc., a global leader in compute, storage and networking technologies, will exhibit at 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. Supermicro (NASDAQ: SMCI), the leading innovator in high-performance, high-efficiency server technology, is a premier provider of advanced server Building Block Solutions® for Data Center, Cloud Computing, Enterprise IT, Hadoop/...
Amazon has gradually rolled out parts of its IoT offerings in the last year, but these are just the tip of the iceberg. In addition to optimizing their back-end AWS offerings, Amazon is laying the ground work to be a major force in IoT – especially in the connected home and office. Amazon is extending its reach by building on its dominant Cloud IoT platform, its Dash Button strategy, recently announced Replenishment Services, the Echo/Alexa voice recognition control platform, the 6-7 strategic...
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...
Judith Hurwitz is president and CEO of Hurwitz & Associates, a Needham, Mass., research and consulting firm focused on emerging technology, including big data, cognitive computing and governance. She is co-author of the book Cognitive Computing and Big Data Analytics, published in 2015. Her Cloud Expo session, "What Is the Business Imperative for Cognitive Computing?" is scheduled for Wednesday, June 8, at 8:40 a.m. In it, she puts cognitive computing into perspective with its value to the busin...
SYS-CON Events announced today that Hitachi, the leading provider the Internet of Things and Digital Transformation, will exhibit at 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. Hitachi Data Systems, a wholly owned subsidiary of Hitachi, Ltd., offers an integrated portfolio of services and solutions that enable digital transformation through enhanced data management, governance, mobility and analytics. We help globa...
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 & ...
Financial Technology has become a topic of intense interest throughout the cloud developer and enterprise IT communities. Accordingly, attendees at the upcoming 20th Cloud Expo at the Javits Center in New York, June 6-8, 2017, will find fresh new content in a new track called FinTech.
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 20th Cloud Expo, which will take place on June 6-8, 2017 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 add...
The age of Digital Disruption is evolving into the next era – Digital Cohesion, an age in which applications securely self-assemble and deliver predictive services that continuously adapt to user behavior. Information from devices, sensors and applications around us will drive services seamlessly across mobile and fixed devices/infrastructure. This evolution is happening now in software defined services and secure networking. Four key drivers – Performance, Economics, Interoperability and Trust ...
Grape Up is a software company, specialized in cloud native application development and professional services related to Cloud Foundry PaaS. With five expert teams that operate in various sectors of the market across the USA and Europe, we work with a variety of customers from emerging startups to Fortune 1000 companies.
Cybersecurity is a critical component of software development in many industries including medical devices. However, code is not always written to be robust or secure from the unknown or the unexpected. This gap can make medical devices susceptible to cybersecurity attacks ranging from compromised personal health information to life-sustaining treatment. In his session at @ThingsExpo, Clark Fortney, Software Engineer at Battelle, will discuss how programming oversight using key methods can incre...
The Internet of Things is clearly many things: data collection and analytics, wearables, Smart Grids and Smart Cities, the Industrial Internet, and more. Cool platforms like Arduino, Raspberry Pi, Intel's Galileo and Edison, and a diverse world of sensors are making the IoT a great toy box for developers in all these areas. In this Power Panel at @ThingsExpo, moderated by Conference Chair Roger Strukhoff, panelists discussed what things are the most important, which will have the most profound e...
@ThingsExpo has been named the Most Influential ‘Smart Cities - IIoT' Account and @BigDataExpo has been named fourteenth by Right Relevance (RR), which provides curated information and intelligence on approximately 50,000 topics. In addition, Right Relevance provides an Insights offering that combines the above Topics and Influencers information with real time conversations to provide actionable intelligence with visualizations to enable decision making. The Insights service is applicable to eve...
SYS-CON Events announced today that Super Micro Computer, Inc., a global leader in compute, storage and networking technologies, will exhibit at 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. Supermicro (NASDAQ: SMCI), the leading innovator in high-performance, high-efficiency server technology, is a premier provider of advanced server Building Block Solutions® for Data Center, Cloud Computing, Enterprise IT, Hadoop/...