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.

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