San Diego Supercomputer Center “Seeds” HPC Clouds

By Amit Chourasia, Jan Zverina, SDSC

June 18, 2014

All sectors of the high-performance computing community – academia, industry, and government – have long been in need of an infrastructure that allows researchers to easily share their findings with other scientists or organizations in an efficient and secure manner.

Sharing these results are of vital importance because they form the basis for validation and potential next steps in any research project, from cosmology to genome sequencing. Computational visualizations and simulations, for example, have become an indispensable resource across numerous science domains. But while quick and effective assessments of such data are necessary for efficient use of the computational resources involved, such an exercise can be challenging when a research team is large and/or geographically dispersed, or some members don’t have direct access to an HPC system.

Moreover, current methods for sharing and assessing results, can be labor-intensive and unsupported by useful tools and procedures. Typically, a research team must create their own scripts and ad hoc procedures just to move results from system to system or user to user. These efforts usually rely on email, ftp, or secure copy (scp) despite the ubiquity of more flexible web-based technologies, and do not fully take advantage of the interactive capabilities of today’s mobile devices.

In late 2012 the San Diego Supercomputer Center (SDSC) at the University of California, San Diego, was awarded a three-year, $810,000 grant from the National Science Foundation to develop a resource that lets researchers seamlessly share and stream scientific visualizations on a variety of platforms, including mobile devices. Called SeedMe for ‘Swiftly Encode, Explore, Disseminate My Experiments’, SDSC’s web-based architecture is designed to enable rapid sharing of content directly from applications running on HPC- or cloud-based resources.

This spring, a team of SDSC researchers developed a working implementation, which in addition to visualizations videos supports other content such as plots, files, and tickers – all of which are essential to scientific research. Easy-to-use programmatic and command line tools with documentation are available for end users to interact with SeedMe.org. A quick start guide, geared for HPC researchers, is also available.

“SeedMe now provides an essential yet missing component in current high-performance computing,” said Amit Chourasia, a senior visualization scientist at SDSC and principal investigator for the project. “We’re now inviting researchers from industry and academia and across numerous domains to take advantage of SeedMe’s easy-to-use functionality for sharing their results with peers or the public at large.”

“The current HPC infrastructure relies heavily on controlled access,” said Michael Norman, SDSC’s director and co-principal investigator for the project. “SeedMe provides secure input and public output complementing HPC resources without compromising their security model. We believe this project will have a transformative impact throughout numerous domains, as research has become increasingly collaborative, requiring better tools and resources that aid the sharing of information.”

seedme1

SeedMe User Interaction Sequence. Source, Amit Chourasia/SDSC

SeedMe is unique from other web-based interfaces in that it is completely focused on efficiently sharing scientific content. While SeedMe could be described in general terms as a DropBox for science, the computational research community requires several additional capabilities and integration tools.

“One such requirement is easy instrumentation of simulation codes, as well as support for instrumenting analysis routines from a variety of software tools,” said Chourasia. “That instrumentation may provide periodic tracking and monitoring by posting progress messages, job status, early data snippets, scripts, parameter files, and other reusable components. But no single web service or tool suite addresses the breadth of scientific computing challenges as effectively and easily as the SeedMe infrastructure.”

According to Chourasia, some of the most common complaints among researchers when needing to share results with colleagues include the fact that many simply cannot afford to spend time and valuable funding dollars to create their own system for sharing their results. “Many find that it is cumbersome or costly. They also don’t want to waste time searching email attachments, or constantly have to check files to monitor progress, or spend long hours encoding videos from a set of images to work on all devices.”

Toward that end, the objective of SeedMe is to foster rapid assessment, iteration, communication, and dissemination of research by making that research ubiquitously accessible on any device, including mobile ones, and on a near real-time basis. Results can be shared within private groups only or posted for public consumption, depending on user preferences.

“SeedMe aims to fill the automation and accessibility gap in computational research,” said Chourasia, noting that a core focus of the project is to promote accessibility of preliminary, ad hoc, and ephemeral content – all vital to efficient and successful research.

Visualization Speed-ups

Visualizations and simulations are an ever growing part of today’s scientific research. These state-of-the-art simulations are now creating visualization images at runtime using in-situ processing. Images or sequence of images can now be shared with others using SeedMe with simple asynchronous integration providing an easy monitoring and assessment mechanism for collaborators.

SeedMe also capitalizes on recent strides in video standardization across web-based communities, providing a significant speed-up in video encoding by using parallel-distributed processing, which is not possible on existing HPC platforms due to lack of state-of-the-art video compression tools on Linux-like operating systems.

seed3

Left: An image from a sequence of volume rendering of steam from volcano eruption simulation. A corresponding video created from the image sequence on left at desired frame rate provided by user. The videos are encoded at various resolutions (including native resolution) and are available for playback and download. Source Amit Chourasia / Darcy Ogden, UC San Diego

Right: An image from computation and visualization of Mandelbrot set. Here the computation and visualization are done in-situ and the images are uploaded to SeedMe asynchronously. Source: Brad Whitlock, Intelligent Light and Amit Chourasia, UC San Diego

“Our goal has been to convert a manual, serial, error-prone process into an automatic, easy-to-use streamlined, parallel and web accessible cyberinfrastructure, and at the same time create videos that are not only encoded at very high quality to mitigate compression artifacts for scientific content, but also make these easily downloadable for researchers” said Chourasia.

Early users are welcoming SeedMe. “It is so convenient to share research results with collaborators, compared with sending results through emails,” said Hao Xu, a post-doctoral researcher who has been running simulations about the evolution of galaxies on the Blue Waters supercomputer at National Center for Supercomputing Applications (NCSA).

“SeedMe provides convenient ways to organize results, which can be easily updated, making sure collaborators or new collaborators all see the most recent results,” said Xu, who has been working with SDSC Director Norman, an astrophysicist by training. “It also avoids the pain of finding figures and plots in emails, and is even proving to be a very useful resource during conference calls.”

Going forward, the SeedMe research team will explore the possibility of making the resource a platform for sharing reusable content. NCSA researcher Matthew Turk is currently investigating how best to share IPython Notebooks from yt software, which is used to analyze and visualize datasets from astrophysical simulations, nuclear engineering, and radio telescope data.

“By building in support to yt for uploading directly to SeedMe, we hope to enable faster, easier, and more seamless sharing of results for anyone using yt,” said Turk. “SeedMe also allows easy control over sharing permissions, while providing an easy-to-use interface for uploading images and data to a central location.”

Tutorials Planned

As an open, web-accessible and searchable research archive, SeedMe also is suitable for education and outreach programs. In addition to organizing tutorials, talks, and webinars to train new users and receive user feedback, the program will provide internships to high school and undergraduate students enabling them to learn about web technologies and the diverse range of research, while at the same time support monitoring of content on the project website.

Tutorials and workshops are already in the works, with presentations planned for XSEDE14 and SC14, as well as a webinar as part of SDSC’s Industry Partners program on July 24. Such sessions will show potential users how they can accomplish the following on personal computers and mobile devices directly from compute jobs.

  • Get fast feedback on compute jobs
  • Share that feedback rapidly with collaborators across the globe
  • Provide access to preliminary results to guide further job submission
  • Support discussion of feedback and results among collaborators.

Author Information

Amit Chourasia, 858 822-3656 or [email protected]

Jan Zverina, SDSC Communications, 858 534-5111 or [email protected]

Warren R. Froelich, SDSC Communications, 858 822-3622 or [email protected]

Complete details of the SeedMe project can be found at http://www.seedme.org/. The NSF award number for the SeedMe project is OCI-1235505. In addition to Chourasia and Norman, the SeedMe project team includes Mona Wong-Barnum, David Nadeau, and Andrew Ferbert, all with SDSC.

Subscribe to HPCwire's Weekly Update!

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

A Beginner’s Guide to the ASC19 Finals

April 22, 2019

Three thousand watts. That's how much power the competitors in the 2019 ASC Student Supercomputer Challenge here in Dalian, China, have to work with. Everybody would like more juice to run compute-intensive HPC simulatio Read more…

By Alex Woodie

Is Data Science the Fourth Pillar of the Scientific Method?

April 18, 2019

Nvidia CEO Jensen Huang revived a decade-old debate last month when he said that modern data science (AI plus HPC) has become the fourth pillar of the scientific method. While some disagree with the notion that statistic Read more…

By Alex Woodie

At ASF 2019: The Virtuous Circle of Big Data, AI and HPC

April 18, 2019

We've entered a new phase in IT -- in the world, really -- where the combination of big data, artificial intelligence, and high performance computing is pushing the bounds of what's possible in business and science, in w Read more…

By Alex Woodie with Doug Black and Tiffany Trader

HPE Extreme Performance Solutions

HPE and Intel® Omni-Path Architecture: How to Power a Cloud

Learn how HPE and Intel® Omni-Path Architecture provide critical infrastructure for leading Nordic HPC provider’s HPCFLOW cloud service.

powercloud_blog.jpgFor decades, HPE has been at the forefront of high-performance computing, and we’ve powered some of the fastest and most robust supercomputers in the world. Read more…

IBM Accelerated Insights

Bridging HPC and Cloud Native Development with Kubernetes

The HPC community has historically developed its own specialized software stack including schedulers, filesystems, developer tools, container technologies tuned for performance and large-scale on-premises deployments. Read more…

Google Open Sources TensorFlow Version of MorphNet DL Tool

April 18, 2019

Designing optimum deep neural networks remains a non-trivial exercise. “Given the large search space of possible architectures, designing a network from scratch for your specific application can be prohibitively expens Read more…

By John Russell

A Beginner’s Guide to the ASC19 Finals

April 22, 2019

Three thousand watts. That's how much power the competitors in the 2019 ASC Student Supercomputer Challenge here in Dalian, China, have to work with. Everybody Read more…

By Alex Woodie

At ASF 2019: The Virtuous Circle of Big Data, AI and HPC

April 18, 2019

We've entered a new phase in IT -- in the world, really -- where the combination of big data, artificial intelligence, and high performance computing is pushing Read more…

By Alex Woodie with Doug Black and Tiffany Trader

Interview with 2019 Person to Watch Michela Taufer

April 18, 2019

Today, as part of our ongoing HPCwire People to Watch focus series, we are highlighting our interview with 2019 Person to Watch Michela Taufer. Michela -- the Read more…

By HPCwire Editorial Team

Intel Gold U-Series SKUs Reveal Single Socket Intentions

April 18, 2019

Intel plans to jump into the single socket market with a portion of its just announced Cascade Lake microprocessor line according to one media report. This isn Read more…

By John Russell

BSC Researchers Shrink Floating Point Formats to Accelerate Deep Neural Network Training

April 15, 2019

Sometimes calculating solutions as precisely as a computer can wastes more CPU resources than is necessary. A case in point is with deep learning. In early stag Read more…

By Ken Strandberg

Intel Extends FPGA Ecosystem with 10nm Agilex

April 11, 2019

The insatiable appetite for higher throughput and lower latency – particularly where edge analytics and AI, network functions, or for a range of datacenter ac Read more…

By Doug Black

Nvidia Doubles Down on Medical AI

April 9, 2019

Nvidia is collaborating with medical groups to push GPU-powered AI tools into clinical settings, including radiology and drug discovery. The GPU leader said Monday it will collaborate with the American College of Radiology (ACR) to provide clinicians with its Clara AI tool kit. The partnership would allow radiologists to leverage AI techniques for diagnostic imaging using their own clinical data. Read more…

By George Leopold

Digging into MLPerf Benchmark Suite to Inform AI Infrastructure Decisions

April 9, 2019

With machine learning and deep learning storming into the datacenter, the new challenge is optimizing infrastructure choices to support diverse ML and DL workfl Read more…

By John Russell

The Case Against ‘The Case Against Quantum Computing’

January 9, 2019

It’s not easy to be a physicist. Richard Feynman (basically the Jimi Hendrix of physicists) once said: “The first principle is that you must not fool yourse Read more…

By Ben Criger

Why Nvidia Bought Mellanox: ‘Future Datacenters Will Be…Like High Performance Computers’

March 14, 2019

“Future datacenters of all kinds will be built like high performance computers,” said Nvidia CEO Jensen Huang during a phone briefing on Monday after Nvidia revealed scooping up the high performance networking company Mellanox for $6.9 billion. Read more…

By Tiffany Trader

ClusterVision in Bankruptcy, Fate Uncertain

February 13, 2019

ClusterVision, European HPC specialists that have built and installed over 20 Top500-ranked systems in their nearly 17-year history, appear to be in the midst o Read more…

By Tiffany Trader

Intel Reportedly in $6B Bid for Mellanox

January 30, 2019

The latest rumors and reports around an acquisition of Mellanox focus on Intel, which has reportedly offered a $6 billion bid for the high performance interconn Read more…

By Doug Black

It’s Official: Aurora on Track to Be First US Exascale Computer in 2021

March 18, 2019

The U.S. Department of Energy along with Intel and Cray confirmed today that an Intel/Cray supercomputer, "Aurora," capable of sustained performance of one exaf Read more…

By Tiffany Trader

Looking for Light Reading? NSF-backed ‘Comic Books’ Tackle Quantum Computing

January 28, 2019

Still baffled by quantum computing? How about turning to comic books (graphic novels for the well-read among you) for some clarity and a little humor on QC. The Read more…

By John Russell

IBM Quantum Update: Q System One Launch, New Collaborators, and QC Center Plans

January 10, 2019

IBM made three significant quantum computing announcements at CES this week. One was introduction of IBM Q System One; it’s really the integration of IBM’s Read more…

By John Russell

Deep500: ETH Researchers Introduce New Deep Learning Benchmark for HPC

February 5, 2019

ETH researchers have developed a new deep learning benchmarking environment – Deep500 – they say is “the first distributed and reproducible benchmarking s Read more…

By John Russell

Leading Solution Providers

SC 18 Virtual Booth Video Tour

Advania @ SC18 AMD @ SC18
ASRock Rack @ SC18
DDN Storage @ SC18
HPE @ SC18
IBM @ SC18
Lenovo @ SC18 Mellanox Technologies @ SC18
NVIDIA @ SC18
One Stop Systems @ SC18
Oracle @ SC18 Panasas @ SC18
Supermicro @ SC18 SUSE @ SC18 TYAN @ SC18
Verne Global @ SC18

IBM Bets $2B Seeking 1000X AI Hardware Performance Boost

February 7, 2019

For now, AI systems are mostly machine learning-based and “narrow” – powerful as they are by today's standards, they're limited to performing a few, narro Read more…

By Doug Black

The Deep500 – Researchers Tackle an HPC Benchmark for Deep Learning

January 7, 2019

How do you know if an HPC system, particularly a larger-scale system, is well-suited for deep learning workloads? Today, that’s not an easy question to answer Read more…

By John Russell

Arm Unveils Neoverse N1 Platform with up to 128-Cores

February 20, 2019

Following on its Neoverse roadmap announcement last October, Arm today revealed its next-gen Neoverse microarchitecture with compute and throughput-optimized si Read more…

By Tiffany Trader

Intel Launches Cascade Lake Xeons with Up to 56 Cores

April 2, 2019

At Intel's Data-Centric Innovation Day in San Francisco (April 2), the company unveiled its second-generation Xeon Scalable (Cascade Lake) family and debuted it Read more…

By Tiffany Trader

France to Deploy AI-Focused Supercomputer: Jean Zay

January 22, 2019

HPE announced today that it won the contract to build a supercomputer that will drive France’s AI and HPC efforts. The computer will be part of GENCI, the Fre Read more…

By Tiffany Trader

Oil and Gas Supercloud Clears Out Remaining Knights Landing Inventory: All 38,000 Wafers

March 13, 2019

The McCloud HPC service being built by Australia’s DownUnder GeoSolutions (DUG) outside Houston is set to become the largest oil and gas cloud in the world th Read more…

By Tiffany Trader

Intel Extends FPGA Ecosystem with 10nm Agilex

April 11, 2019

The insatiable appetite for higher throughput and lower latency – particularly where edge analytics and AI, network functions, or for a range of datacenter ac Read more…

By Doug Black

UC Berkeley Paper Heralds Rise of Serverless Computing in the Cloud – Do You Agree?

February 13, 2019

Almost exactly ten years to the day from publishing of their widely-read, seminal paper on cloud computing, UC Berkeley researchers have issued another ambitious examination of cloud computing - Cloud Programming Simplified: A Berkeley View on Serverless Computing. The new work heralds the rise of ‘serverless computing’ as the next dominant phase of cloud computing. Read more…

By John Russell

  • arrow
  • Click Here for More Headlines
  • arrow
Do NOT follow this link or you will be banned from the site!
Share This