Harvard/Yale meetup at MGHPCCby Maggie McFee - Nov. 13, 2019
While attending the PEARC conference, Maggie and Austin ran into some of our Yale Research Computing counterparts: Kaylea, Robert, and Ben. While there's an intense sports rivalry between the two schools, this wasn't the case with our RC departments. We really hit it off well and we talked about ... Read More
Convergent regulatory evolution & loss of flight in paleognathous birdsThe Evolution of Flightless Birds: Study explores the genetics behind how they developed
"Since Darwin’s era, scientists have wondered how flightless birds like emus, ostriches, kiwis, cassowaries, and others are related, and for decades the assumption was that they must all share a common ancestor who abandoned the skies for a more grounded life.
By the early ... Read More
FASRC Cluster Refresh 2019
As of the November 2019 rankings, Cannon has ranked #144 on the Top500 list!
For current cluster details, please see: https://www.rc.fas.harvard.edu/about/cluster-architecture/
For current partition configurations and changes, please see the Running Jobs page
The lease on the Odyssey compute cluster comes to an end this year, and a hardware refresh of the cluster will occur in September.
Current ... Read More
Deep learning of aftershock patterns following large earthquakes
Phoebe M. R. DeVries, Fernanda Viégas, Martin Wattenberg & Brendan J. Meade
"Aftershocks are a response to changes in stress generated by large earthquakes and represent the most common observations of the triggering of earthquakes. The maximum magnitude of aftershocks and their temporal decay are well described by empirical laws (such as Bath’s law and Omori’s ... Read More
Unraveling the Stellar Content of Young Clusters
"CfA astronomers Rafael Martinez-Galarz and Howard Smith and their two colleagues have developed a new statistical analysis technique to address the problem of confused SEDs in clustered environments. Using the highest spatial resolution images for each region, the team identifies the distinguishable stars (at least this many are in the cluster) and their emission at ... Read More
Revisiting the Six City Study
"Last June, eight new Harvard-affiliated researchers revisited the study, using new technologies and innovations in statistical analysis and examining Medicare data—the largest and most public dataset available documenting the health of U.S. citizens—thus presumably averting renewed charges of secret science (an issue raised anew by current EPA administrator Scott Pruitt). Their findings breathe new life ... Read More
Mapping Invisible Ocean Pollutants
Prof. Elsie Sunderland's lab seeks to build a picture of pollutants which threaten our oceans.
“People struggle with this idea that we could impact planetary level processes. But we do. There’s irrefutable
evidence on many, many scales that we’re changing the natural functioning of these ecosystems.”
Read more in Harvard Magazine's full story
Accelerating Viscoelastic Calculations
Read more about how Brendan Meade's group used machine learning and the Odyssey cluster
to accelerate large-scale viscoelastic calculations using neural net concepts at Harvard Magazine.
Earthquakes Around the World - Harvard Magazine
For a deeper dive, you'll find their paper describing the work at https://arxiv.org/abs/1701.08884
ABSTRACT: "One of the most significant challenges involved in efforts to understand ... Read More
Air Pollution and Mortality in the Medicare Population
ABSTRACT - We constructed an open cohort of all Medicare beneficiaries (60,925,443 persons) in the continental United States from the years 2000 through 2012, with 460,310,521 person-years of follow-up. Annual averages of fine particulate matter (particles with a mass median aerodynamic diameter of less than 2.5 μm ) and ozone were estimated according to the ... Read More
A Language Out of Nothing
Searching for the nature of speech, sign, and universal grammar
"Davidson’s work on sign languages spans the divide between applied and theoretical linguistics, contributing to both abstract debates about language in the mind and questions with immediate impacts on people’s lives. Harvard’s small but formidable linguistics department thrives on its interest in the union of theory ... Read More
Green Computing Today, Not TomorrowHarvard and FASRC believe in innovation and a sustainable energy footprint. From our green data center in Holyoke, MA to clean energy initiatives on campus, we are committed to improving the world around us.
MGHPCC is our green data center in Holyoke, MA which was purpose-built to achieve sustainable, clean energy and cooling. The new solar ... Read More
NESE: Large-Scale Extendable Storage
"As big data becomes a common analytical tool in fields from the sciences to the humanities, Harvard’s computer infrastructure experts are turning their attention to an increasingly pressing question: How do you manage it all?
In recent years, Harvard invested in the Odyssey computing cluster, whose 60,000 CPUs provide the sheer computing horsepower needed to crunch ... Read More
Teaching Computers to Identify Odors
"Using a machine-learning algorithm, Murthy and colleagues were able to “train” a computer to recognize the neural patterns associated with various scents, and to identify whether specific odors were present in a mix of smells. The study is described in a Sept. 1 paper in the journal Neuron." - Harvard Gazette
Read more at ... Read More
A Redox-flow Battery with an Alloxazine-based Organic Electrolyte
Odyssey helps researchers create the next generation of energy storage systems. Using organic electrolytes, a redox-flow battery offers many benefits and improvements over current energy storage schemes using more environmentally-friendly compounds.
Excerpt: Redox-flow batteries (RFBs) can store large amounts of electrical energy from variable sources, such as solar and wind. Recently, redox-active organic molecules in aqueous ... Read More
IARPA ADVANCED MACHINE LEARNING CHALLENGE
IARPA has awarded more than $28 million to Harvard’s John A. Paulson School of Engineering and Applied Sciences (SEAS), Center for Brain Science (CBS), and Department of Molecular and Cellular Biology for research into advanced neuroscience and machine learning.
Professors David Cox, Jeff Lichtman, Hanspeter Pfister, Haim Sompolinsky and Ryan Adams look to push the ... Read More
New Methods for Flu Tracking and PredictionStatistics Professor Samuel Kou and colleagues have created new tracking methods for influenza using data from across the Internet and the power of Odyssey.
"The approach, called ARGO, for AutoRegression with Google search data, combines Google data with historical records from the CDC and information on seasonality of the flu. It also accounts for changes in ... Read More
New Module Search ToolsThe RC/Informatics portal now has a new application for searching modules in the new module system.
This search tool includes all of the modules in the new module system, and provides key information, including application descriptions, how to load the module, and in many cases, build notes that help describe the difference between various builds.
A command ... Read More
Brain Genomics Superstruct Project
The goal of the Brain Genomics Superstruct Project (GSP) is to enable large-scale exploration of the links between brain function, behavior, and ultimately genetic variation. To provide the broader scientific community data to probe these associations, a repository of structural and functional magnetic resonance imaging (MRI) scans linked to genetic information was constructed from a ... Read More
Data & Software Carpentry workshop registrations now open!Registration is now open for both Software Carpentry - R (July 22 - 23) and Data Carpentry - Genomics (August 19 - 20). Please see the following pages for more information on the workshops and registration:
Software Carpentry - R: https://rc.fas.harvard.edu/software-carpentry-workshop-july-22-23/
Data Carpentry - Genomics: https://rc.fas.harvard.edu/data-carpentry-genomics-august-19-20/
We have received a few emails asking us about the difference between ... Read More
Odyssey Software Updates, June-2015Software updates and installs since May 1st:
NOTE: All software is installed under the Lmod module system on Odyssey. And please read our guidelines for software install requests.
Fast C++ matrix library with easy to use functions and syntax, deliberately similar to Matlab
Simulation tools to generate synthetic next-generation sequencing reads
Set of utilities that manipulate variant calls in ... Read More
Odyssey helps simulate conditions on Mars & beyond
Simulations using the Odyssey cluster played a key role in two new papers, one authored by Harvard Assistant Professor Robin Wordsworth and one by Prof. Wordsworth along with colleagues across the country, which concern planetary conditions on Mars and on tidally locked rocky planets.
The first, Atmospheric Heat Redistribution and Collapse on Tidally Locked Rocky Planets ... Read More
FAS Research Computing Implements Novel Big Data Storage SystemFOR IMMEDIATE RELEASE
CAMBRIDGE, M.A. - After years of careful research, scientists in the FAS Research Computing organization have noticed that a large proportion of the “big data” we generate as part of our research isn’t actually of all that much value.
Today we are announcing our new storage system called DevNull™. DevNull™ has been designed to ... Read More
Harvard’s Odyssey unlocks big data
Increasingly, big data is changing life’s game board.
As technology evolves and becomes further integrated into society, massive amounts of data are being collected and stored. From the app on your cellphone to the swipe of your credit card to the systems that monitor everyday activities, data is endlessly transmitted and interpreted. With supercomputers within easy ... Read More
Explosion of Research Data Drives “Tipping Point” for IT FacilitiesJames Cuff, Assistant Dean for Research Computing, sits down with Data Center Knowledge to discuss his upcoming keynote address at the 2015 Data Center World Global Conference. Cuff will talk about the current and future state of the data center in his address. “Data centers are the back bone of civilization,” Cuff said. “Basic science is ... Read More
Evolution in Action: Observing Yeast Over 500 GenerationsWhat does evolution look like? How much does genetic background influence evolution? Is evolutionary adaptability random or predictable? These are questions the Desai Lab has set out to answer. With a research focus on evolutionary dynamics, the Desai Lab observes evolution in action. To do this, the lab has designed experiments that allow them to quickly detect ... Read More
Research Computing Among Sponsors for Martin Karplus Celebration SymposiumHarvard FAS Research Computing (FASRC) has partnered with Dell to sponsor part of the Martin Karplus Celebration Symposium on October 1, 2014.
The Symposium is a one-day event celebrating the life and work of Martin Karplus, the Theodore William Richards Professor of Chemistry Emeritus at Harvard University. Karplus was one of three winners of the 2013 ... Read More
Simulations run on Odyssey lead to first realistic virtual universeAstronomers have created the first realistic virtual universe by running large-scale cosmological simulations on supercomputers. The project, known as Illustris, was led by Mark Vogelsberger of MIT and the Harvard-Smithsonian Center for Astrophysics. Illustris produced detailed galaxy simulations by using complex computer models that captured the physical components and processes of the universe from 12 ... Read More
Research Computing partner in Massachusetts Open Cloud projectHOLYOKE – Friday, April 25, 2014 – Governor Deval Patrick today announced a $3 million capital investment to launch the Massachusetts Open Cloud project, a university-industry collaboration designed to create a new public cloud computing infrastructure to spur big data innovation. Governor Patrick also announced the release of the 2014 Mass Big Data Report, which ... Read More
Research Computing Announces Internet2 HPC Advisory Group MembershipDENVER—April 7, 2014—Internet2 today announced at the 2014 Internet2 Global Summit the creation of the Internet2 Program Advisory Group for High Performance and Research Computing and the inaugural co-chairs and members.
"I'm excited to lead this important venture along with my colleague and friend Dave Lifka," said Jim Bottum, the Group’s Co-Chair and Clemson University’s Chief Information ... Read More
MGHPCC project team wins Harvard Green Carpet Award
The Harvard Office for Sustainability has awarded the Harvard project team for the Massachusetts Green High Performance Computing Center (MGHPCC) a Green Carpet Award. The award recognizes Sustainability Leaders at Harvard who exemplify innovation and creativity through the development and execution of campus sustainability plans that focus on the reduction of energy use, green house ... Read More
Research Computing powers computation behind BICEP2 discovery
Research Computing has provided computational support and infrastructure for the BICEP2 project. Research Computing provided the BICEP2 project with 400TB of storage space and access to more than 30,000 cores of compute.Research Computing also provided virtual machine support for BICEP2 websites and data. The project consumed 5.1 million CPU hours on Odyssey since 2010.
Of those ... Read More
NBA drafts Big Data
Harvard researchers have used Odyssey to dig deep into NBA player data, creating a new statistical framework for basketball analytics. The research, led by Kirk Goldsberry, Visiting Scholar at the Center for Geographic Analysis, Luke Bornn, Assistant Professor in the Department of Statistics, Dan Cervone, and Alex D’Amour both PhD students in the Department of ... Read More
Research Computing part of $5.3M NSF award for Advanced Cyberinfrastructure CAMBRIDGE, M.A. – The National Science Foundation has awarded a consortium of six universities a $5.3 million grant to support a national network of Advanced Cyberinfrastructure Research and Education Facilitators (ACI-REFs). Harvard University’s FAS Research Computing group is one of the collaborating institutions. The project, called Advanced Cyberinfrastructure - Research and Educational Facilitation: Campus-based Computational ... Read More
FAS Research Computing to join Gluster Community Board CAMBRIDGE, M.A. – FAS Research Computing (FASRC) has signed a letter of intent to join the Gluster Community Board, the leading community for open software-defined storage. James Cuff, Assistant Dean for Research Computing at Harvard University, will represent FASRC. The board is comprised of individuals and organization representatives committed to the success of the GlusterFS ... Read More
Altered diet can quickly change gut microbiome in humans Animal and plant-based foods have contrasting effects on the human gut microbiome. Credit: John Kaufmann, http://www.jek2004.com
Led by the Turnbaugh lab in the Center for Systems Biology at Harvard University, researchers have discovered that the microbes found in the human gut respond rapidly to a new diet. The researchers placed ten people on two defined ... Read More
The Clean Energy ProjectThe Clean Energy projects searches for next generation plastic solar cell materials using RC computational resources. The project, led by Professor Alán Aspuru-Guzik, has generated data about 2.3 million candidate compounds for organic electronic materials. To find out more about the project see here.
Migratory behavior of planetary systemsUsing Odyssey to run numerical integrations, research on how planetary systems evolve and migrate has provided new insights. The centuries old theory of orderly planetary system architectures is being challenged by new evidence that suggests many planetary systems underwent a period of upheaval during which giant planets “migrated” from where they formed. For a full ... Read More
The Equality of Opportunity ProjectHarvard economists measure the upward mobility of children in the bottom fifth of U.S. households using big data and Odyssey. The economists found that there is substantial variation in the U.S. in the prospects for escaping poverty and some of the strongest predictors of upward mobility are social capital and family structure. For more details ... Read More
Temperature extremes unprecedented in the past 600 yearsHarvard scientists use Odyssey to run climate models measuring the scale and frequency of recent warm temperature extremes. The results led to conclusive evidence that the summers of 2005, 2007, 2010 and 2011 in the high northern latitudes were warmer than those of all prior years back to 1400.
For the full paper see here.
MGHPCC Awarded LEED® Platinum Certification
The Massachusetts Green High Performance Computing Center (MGHPCC) has become the first university research data center to receive a LEED® Platinum certification, the highest green building ranking. The MGHPCC is also one of only 13 data centers in the country to receive a Platinum certification. Computing centers are typically large users of energy.
“As our name ... Read More
Research Computing Adds 28,000 Processors to Cluster With the opening of the Massachusetts Green High Performance Computing Center (MGHPCC) in November 2012, Research Computing began the build out of its new server infrastructure located in Holyoke, MA. The end result was a cluster 28,000 processors stronger bringing total compute to over 54,000 CPUs. While computing power went up, total energy consumption went down. The ... Read More
MGHPCC Open for BusinessState of the Art Data Center Will Keep Massachusetts at Forefront of Innovation Economy
HOLYOKE – Friday, November 16, 2012 – Governor Deval Patrick and Lieutenant Governor Timothy Murray joined university leaders and technology executives today to cut the ribbon on the Massachusetts Green High Performance Computing Center (MGHPCC). The new Center will keep Massachusetts at the ... Read More