Dutch HPC Cloud Running at Full Throttle

By Jose Luis Vazquez-Poletti

October 19, 2011

Last October a special event took place at Amsterdam’s Science Park. After 2 years of hard work, the first user-friendly HPC cloud infrastructure in Europe is working at full throttle. The collaboration between the supercomputer center, SARA, and grid computing project, BiG Grid, lie behind this epic milestone.

The result of this collaboration is a HPC Cloud infrastructure with usability for the scientific community and performance in mind. On one hand, scientists can use a computer environment that is virtually identical to the environment they are used to. On the other, they get access to self-service and dynamically scalable high performance computing resources, which can be configured with a high level of detail.

What’s under the hood of the HPC Cloud system? Basically 608 cores and 4.75TB RAM distributed in 19 physical nodes with 32 Intel 2.13 GHz CPU cores and 256 GB RAM each. Also, each node has a 10 TB “local disk”.

Virtualization is done with KVM. The latest version of OpenNebula, considered a de facto standard in virtual infrastructure managers, was chosen to be the engine inside SARA’s HPC Cloud. In fact, the developers of OpenNebula were contacted during the first steps of the setup in order to discuss how to get the most of OpenNebula and make the final infrastructure address the challenging needs of the HPC community. Moreover, from the beginning they involved the users in the testing of the platform, resulting in an active contribution to the OpenNebula ecosystem.

The platform has attracted scientists from a wide range of fields such as Bioinformatics, Ecology, Geography or Computer Science. A number of the users presented on the 4th of October in Amsterdam  at the HPC Cloud day. Among these, there are some key applications I found interesting for this article.

The first one is from the University of Amsterdam’s Microarray Department/Integrative Bioinformatics Unit (MAD/IBU). Their research ranges from seed breeding to DNA damage but always facing gene transcription across the entire genome. Comparing strings in such big databases is a challenging task where a huge computational power becomes vital.

The Biomedical Imaging Group Rotterdam (BIGR) from Erasmus MC works in two main research lines. The first one is population imaging by developing robust, accurate and fully automated tools that allow to understand diseases from brain changes.  The second is about providing earlier and more accurate diagnosis through computer assisted tools.

The Netherlands Institute of Ecology (NIOO-KNAW) work at genome level and they don’t hesitate to use tools pertaining to the computing portal paradigm to perform basic research. In fact, they made some of these tools (Galaxy and Cloudman) to be available in the HPC Cloud environment. This way, the platform is not only useful for their analysis of high-throughput community sequencing data, but also for other research groups that will benefit of the ported tools.

The Koninklijke Bibliotheek (Royal Library) works in what is named humanities computing and I have to say that their use of HPC Cloud was a surprise for me. Basically the objective is to offer everyone access through Internet to everything published in and about the Netherlands between 1618 and 1995. Optical Character Recognition in nowadays documents is relatively easy to perform but the task gets complicated when working on very old books due to calligraphy and damage. However, they expect to digitalize 10% of these publications by 2013.

Considering the actual economic crisis, the Rotterdam School of Management of Erasmus University focuses on Finance and, in particular, liquidity or how to quickly trade large volume with low costs. The World market is the one establishing the ceiling of the amount data that needs to be processed. Their framework deals with more than 400 exchanges worldwide, 45 million different instruments, 350 data fields of historical data starting in 1996.

These are only some examples but again, remember that the HPC Cloud infrastructure was built having users in mind. A user that already knows what they want, and has an existing environment, can rebuilt that in the HPC cloud in an afternoon. In this context, 90-minute courses are taught to get users up and running, ready to deploy large clusters in the infrastructure. The result is that projects to port software to this infrastructure usually take only days instead of months or years.

The only drawback (for me) is that the platform funded by a national project so it can only accommodate Dutch researchers and their affiliations. However, SARA doesn’t close any doors for foreigners in the future, when the funding may change. And several dutch researchers participate in international projects, allowing access to the infrastructure to international project members.

I would like to express all my gratitude to the HPC Cloud project leader Drs. Floris Sluiter from SARA, who very kindly provided me the information needed for writing this article.

Links of Note

The presentations of the HPC Cloud Day on 4th October in Amsterdam:

program and presentations:

http://www.sara.nl/news/Festive-launch-of-new-hpc-cloud-infrastructure

Video recordings: http://ftp.sara.nl/pub/cave/outgoing/clouddag/

SARA is a national supercomputing center, originally founded by the University of Amsterdam, the Vrije University and the stichting Mathematisch Centrum (now Centrum Wiskunde & Informatica). Forty years have passed since its first commitment of processing data coming from the three founders and now it’s providing HPC services at a national level.

BiG Grid is a project led by NCF, Nikhef and NBIC that aims to set up the national grid infrastructure for scientific research.

About the Author

Dr. Jose Luis Vazquez-Poletti is Assistant Professor in Computer Architecture at Complutense University of Madrid (Spain), and a Cloud Computing Researcher at the Distributed Systems Architecture Research Group (http://dsa-research.org/).

He is (and has been) directly involved in EU funded projects, such as EGEE (Grid Computing) and 4CaaSt (PaaS Cloud), as well as many Spanish national initiatives.

From 2005 to 2009 his research focused in application porting onto Grid Computing infrastructures, activity that let him be “where the real action was”. These applications pertained to a wide range of areas, from Fusion Physics to Bioinformatics. During this period he achieved the abilities needed for profiling applications and making them benefit of distributed computing infrastructures. Additionally, he shared these abilities in many training events organized within the EGEE Project and similar initiatives.

Since 2010 his research interests lie in different aspects of Cloud Computing, but always having real life applications in mind, specially those pertaining to the High Performance Computing domain.

Website: http://dsa-research.org/jlvazquez/
Linkedin: http://es.linkedin.com/in/jlvazquezpoletti/

Subscribe to HPCwire's Weekly Update!

Be the most informed person in the room! Stay ahead of the tech trends with industry updates delivered to you every week!

Nvidia’s New Blackwell GPU Can Train AI Models with Trillions of Parameters

March 18, 2024

Nvidia's latest and fastest GPU, code-named Blackwell, is here and will underpin the company's AI plans this year. The chip offers performance improvements from its predecessors, including the red-hot H100 and A100 GPUs. Read more…

Nvidia Showcases Quantum Cloud, Expanding Quantum Portfolio at GTC24

March 18, 2024

Nvidia’s barrage of quantum news at GTC24 this week includes new products, signature collaborations, and a new Nvidia Quantum Cloud for quantum developers. While Nvidia may not spring to mind when thinking of the quant Read more…

2024 Winter Classic: Meet the HPE Mentors

March 18, 2024

The latest installment of the 2024 Winter Classic Studio Update Show features our interview with the HPE mentor team who introduced our student teams to the joys (and potential sorrows) of the HPL (LINPACK) and accompany Read more…

Houston We Have a Solution: Addressing the HPC and Tech Talent Gap

March 15, 2024

Generations of Houstonian teachers, counselors, and parents have either worked in the aerospace industry or know people who do - the prospect of entering the field was normalized for boys in 1969 when the Apollo 11 missi Read more…

Apple Buys DarwinAI Deepening its AI Push According to Report

March 14, 2024

Apple has purchased Canadian AI startup DarwinAI according to a Bloomberg report today. Apparently the deal was done early this year but still hasn’t been publicly announced according to the report. Apple is preparing Read more…

Survey of Rapid Training Methods for Neural Networks

March 14, 2024

Artificial neural networks are computing systems with interconnected layers that process and learn from data. During training, neural networks utilize optimization algorithms to iteratively refine their parameters until Read more…

Nvidia’s New Blackwell GPU Can Train AI Models with Trillions of Parameters

March 18, 2024

Nvidia's latest and fastest GPU, code-named Blackwell, is here and will underpin the company's AI plans this year. The chip offers performance improvements from Read more…

Nvidia Showcases Quantum Cloud, Expanding Quantum Portfolio at GTC24

March 18, 2024

Nvidia’s barrage of quantum news at GTC24 this week includes new products, signature collaborations, and a new Nvidia Quantum Cloud for quantum developers. Wh Read more…

Houston We Have a Solution: Addressing the HPC and Tech Talent Gap

March 15, 2024

Generations of Houstonian teachers, counselors, and parents have either worked in the aerospace industry or know people who do - the prospect of entering the fi Read more…

Survey of Rapid Training Methods for Neural Networks

March 14, 2024

Artificial neural networks are computing systems with interconnected layers that process and learn from data. During training, neural networks utilize optimizat Read more…

PASQAL Issues Roadmap to 10,000 Qubits in 2026 and Fault Tolerance in 2028

March 13, 2024

Paris-based PASQAL, a developer of neutral atom-based quantum computers, yesterday issued a roadmap for delivering systems with 10,000 physical qubits in 2026 a Read more…

India Is an AI Powerhouse Waiting to Happen, but Challenges Await

March 12, 2024

The Indian government is pushing full speed ahead to make the country an attractive technology base, especially in the hot fields of AI and semiconductors, but Read more…

Charles Tahan Exits National Quantum Coordination Office

March 12, 2024

(March 1, 2024) My first official day at the White House Office of Science and Technology Policy (OSTP) was June 15, 2020, during the depths of the COVID-19 loc Read more…

AI Bias In the Spotlight On International Women’s Day

March 11, 2024

What impact does AI bias have on women and girls? What can people do to increase female participation in the AI field? These are some of the questions the tech Read more…

Alibaba Shuts Down its Quantum Computing Effort

November 30, 2023

In case you missed it, China’s e-commerce giant Alibaba has shut down its quantum computing research effort. It’s not entirely clear what drove the change. Read more…

Nvidia H100: Are 550,000 GPUs Enough for This Year?

August 17, 2023

The GPU Squeeze continues to place a premium on Nvidia H100 GPUs. In a recent Financial Times article, Nvidia reports that it expects to ship 550,000 of its lat Read more…

Analyst Panel Says Take the Quantum Computing Plunge Now…

November 27, 2023

Should you start exploring quantum computing? Yes, said a panel of analysts convened at Tabor Communications HPC and AI on Wall Street conference earlier this y Read more…

DoD Takes a Long View of Quantum Computing

December 19, 2023

Given the large sums tied to expensive weapon systems – think $100-million-plus per F-35 fighter – it’s easy to forget the U.S. Department of Defense is a Read more…

Shutterstock 1285747942

AMD’s Horsepower-packed MI300X GPU Beats Nvidia’s Upcoming H200

December 7, 2023

AMD and Nvidia are locked in an AI performance battle – much like the gaming GPU performance clash the companies have waged for decades. AMD has claimed it Read more…

Synopsys Eats Ansys: Does HPC Get Indigestion?

February 8, 2024

Recently, it was announced that Synopsys is buying HPC tool developer Ansys. Started in Pittsburgh, Pa., in 1970 as Swanson Analysis Systems, Inc. (SASI) by John Swanson (and eventually renamed), Ansys serves the CAE (Computer Aided Engineering)/multiphysics engineering simulation market. Read more…

Intel’s Server and PC Chip Development Will Blur After 2025

January 15, 2024

Intel's dealing with much more than chip rivals breathing down its neck; it is simultaneously integrating a bevy of new technologies such as chiplets, artificia Read more…

Baidu Exits Quantum, Closely Following Alibaba’s Earlier Move

January 5, 2024

Reuters reported this week that Baidu, China’s giant e-commerce and services provider, is exiting the quantum computing development arena. Reuters reported � Read more…

Leading Solution Providers

Contributors

Choosing the Right GPU for LLM Inference and Training

December 11, 2023

Accelerating the training and inference processes of deep learning models is crucial for unleashing their true potential and NVIDIA GPUs have emerged as a game- Read more…

Training of 1-Trillion Parameter Scientific AI Begins

November 13, 2023

A US national lab has started training a massive AI brain that could ultimately become the must-have computing resource for scientific researchers. Argonne N Read more…

Shutterstock 1179408610

Google Addresses the Mysteries of Its Hypercomputer 

December 28, 2023

When Google launched its Hypercomputer earlier this month (December 2023), the first reaction was, "Say what?" It turns out that the Hypercomputer is Google's t Read more…

Comparing NVIDIA A100 and NVIDIA L40S: Which GPU is Ideal for AI and Graphics-Intensive Workloads?

October 30, 2023

With long lead times for the NVIDIA H100 and A100 GPUs, many organizations are looking at the new NVIDIA L40S GPU, which it’s a new GPU optimized for AI and g Read more…

AMD MI3000A

How AMD May Get Across the CUDA Moat

October 5, 2023

When discussing GenAI, the term "GPU" almost always enters the conversation and the topic often moves toward performance and access. Interestingly, the word "GPU" is assumed to mean "Nvidia" products. (As an aside, the popular Nvidia hardware used in GenAI are not technically... Read more…

Shutterstock 1606064203

Meta’s Zuckerberg Puts Its AI Future in the Hands of 600,000 GPUs

January 25, 2024

In under two minutes, Meta's CEO, Mark Zuckerberg, laid out the company's AI plans, which included a plan to build an artificial intelligence system with the eq Read more…

Google Introduces ‘Hypercomputer’ to Its AI Infrastructure

December 11, 2023

Google ran out of monikers to describe its new AI system released on December 7. Supercomputer perhaps wasn't an apt description, so it settled on Hypercomputer Read more…

China Is All In on a RISC-V Future

January 8, 2024

The state of RISC-V in China was discussed in a recent report released by the Jamestown Foundation, a Washington, D.C.-based think tank. The report, entitled "E Read more…

  • arrow
  • Click Here for More Headlines
  • arrow
HPCwire