time to science, time to results: accelerating research with aws - aws symposium 2014 - washington...
DESCRIPTION
This session demonstrates how the Cloud can accelerate breakthroughs in scientific research by providing on-demand access to powerful computing. The Session will feature scientific researchers making use of the Cloud to increase speed to results.TRANSCRIPT
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
Accelerating Research with AWS
Steve [email protected]
Jamie [email protected]
Angel [email protected]
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
Why?• “Work hard, have fun, make history”• Accelerate the pace of scientific discovery
What?• Motivations, Theory, and Practice
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
AWS Research Grants• Apply for credits to teach advanced courses,
tackle research endeavors, and explore new projects
• Bootstrap projects that previously would have required expensive up-front and ongoing investments in infrastructure
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
:
http://aws.amazon.com/solutions/case-studies/university-of-california-berkeley-amp-lab-carat-project/
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
Some more examples• MIT, Mark Pearrow, McGovern Institute
– Genetic and computational analysis, electrophysiological recordings, and non-invasive brain imaging
• University of Illinois Urbana-Champaign, Indranil Gupta, Computer Science
– Research issues in loosely federated clouds
• Singapore Management University, Ming Jiang – New techniques in malware analysis
• Technion, Israel Institute of Technology, Alex Zlotnik
– Systems for efficient execution of scientific workloads
• University of Maryland, Michael Schatz, Center for Bioinformatics and Computational Biology
– Assembly of large genomes using cloud computing
• ETH Zurich, Till Quack, Computer Vision Lab – Large scale annotation of photo collections
• University of Pennsylvania, Zachary Ives, Computer and Information Science Department
– Orchestra, collaborative data sharing system on the cloud
• Monash University, Blair Bethwaite, eScience and Grid Engineering Laboratory
– Mixing grids and clouds for high throughput science
• Harvard University, Vinothan N. Manoharan, SEAS, Department of Physics
– Exploring the physics of self-organization with digital holographic microscopy
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
Take home messageAWS Research Grants are a great way to bootstrap a project, or experiment on AWS
http://aws.amazon.com/grants
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
Scientific Computing Initiatives
Y0L0!
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
UCSF, UCSC, UCB
BGI
University of Cape Town
UT/MD Anderso
n
Seven Bridges Genomic
s
Caltech
Monash Universi
ty
Sanger Institut
eWellcome Trust
Fred Hutchinson
Cancer Research Center &
Sage Bionetworkks
BroadInstitute
OICR
U. Chicago
Plus hundreds of other sites around the world forCo-Is and ColleaguesCancer
Research UK
OHSU
RIKENIndian
Society of Human
Genetics
Global Alliance for Genomics & Health
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
1+ Million Cancer Genome Data
Warehouse
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
Enable collaboration• Easily and securely share data and
applications across institutions• Publish preconfigured resources
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
Data to the compute
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
Compute to the data
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
Download and Copy
S3Amazon RDS
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
Amazon RDS
Access in the Cloud
S3
RDS
RDS
RDS
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
Compute in the Cloud
S3
Amazon RDS
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
Baylor College of MedicineA platform built by Baylor College of Medicine Human Genome Sequencing Center and DNANexus using the Mercury Pipeline for the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium
Supports 300+ researchers around the world
Analyzed the genomes of over 14,000 individuals, encompassing 3,751 whole genomes and 10,940 whole exomes (~1PB of data)
Used 3.3 million core hours over 4 weeks to complete the job 5.7x faster than what could have been accomplished on-premise
The outcomes?
1. Easier collaboration
2. Faster time to science
3. Cost-effective: On-premise was prohibitively expensive
4. No longer constrained by on-premise capacity
5. Scientists focusing on Science as opposed to infrastructure
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
• A centralized repository of public datasets
• Seamless integration with cloud based applications
• No charge to the community• Tell us what else you’d like for us to
host …
AWS Public Data Sets1000 Genomes Project
Ensembl, GenBank, UniGene, PubChem
NASA NEX: Earth science data sets
The Cannabis Sativa Genome
US Census Data: US demographic data from 1980, 1990, and 2000 US Censuses
Freebase Data Dump: A data dump of all the current facts and assertions in the Freebase system, an open database covering millions of topics
Google Books n-grams
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
Technical computing: Why AWS?
The IT infrastructure needed for technical computing is:
Large, complex, expensive
Poorly utilized due to project cycles
Rapidly obsolete due to technology advances
Big simulations can require days or weeks per iteration
“Time in the queue” is a growing problem in larger firms
Result? Engineering innovation is slowed
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
Big JOB to do …
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
… with little resources to do it.
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
Use a large shared resource …
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
?
… but there is a queue.
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
The hidden cost of queues
• HPC users seek fastest possible time-to-results and must compete for scarce cluster resources
• IT support team seeks highest possibility utilization of expensive cluster resources
• Result:
• The job queue becomes the buffer for managing IT capacity
• Time needed to complete simulations is too long and hard to predict
?
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
Properly size your clusters …
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
… from small …
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
… to large …
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
… and lots of them!
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
Computational compound analysisSolar panel material Estimated serial computation time 264 years
156,314 core cluster across 8 regions1.21 petaFLOPS (Rpeak)
Simulated 205,000 materials18 hours for $33,000 16¢ per molecule
http://news.cnet.com/8301-1001_3-57611919-92/supercomputing-simulation-employs-156000-amazon-processor-cores/
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
Time: +00h
<10 cores
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
Time: +24h>1500 cores
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
Time: +72h
<10 cores
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
AWS value for HPC• Security: Deploy applications and store data in a secure, highly
configurable VPC environment
• Agility: Deploy the right infrastructure for each technical computing job, at the right time
• Scalability: Add and subtract servers in minutes to optimize time-to-results
• Cost Savings: Pay only for what you use, don’t pay for idle or outdated servers
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
Experimentoften
Fail quickly,at low cost
MoreInnovation
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
HPC Partners and Apps
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
Kyushu UniversitySupport seasonal demand for engineering and science computational resources.
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
Downstream Analysis
Compute Analytics ToolsDatabasesStorage
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
Questions
?
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
http://aws.amazon.com/solutions/case-studies/baylor/
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
Elastic Map Reduce
S3 Amazon EMRVery high,non-blocking,
parallel bandwidth
2. Start a cluster(Hadoop, SGE, custom)1. Put data in S3
3. Get the results
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
Easily scale to more computational nodes
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
Use Spot instances to save $$$
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
Amazon EC2
AWS Government, Education, and Nonprofits Symposium Washington, DC | June 24, 2014 - June 26, 2014
Launch in VPC for secure computing