MSI
Minnesota Supercomputing Institute
Perspective: Starting out at MSI
CASC Spring Meeting
2015
© 2015 Regents of the University of Minnesota. All rights reserved.
Organization
Office of the Vice President for Research
Advanced Systems
Operations
- Common Services
- HPC Systems
- Storage Systems
- Hosted Services
Research & User
Services
-User Support Lead
-User Training
-Optimization &
Benchmarking
-HPC Research
-Communication
-Outreach
Application
Development
Research
Informatics
Support Systems
Administration
- Custom App
Dev
- System
Programming
-Informatics
education
-Informatics
research
-Informatics
services
-Life Science
Computing
- HR
- Policies & SOPs
-Budget &
purchasing
- Building &
facilities
- Grants manag.
- Project manag.
- Inventory
© 2015 Regents of the University of Minnesota. All rights reserved.
MSI Users by Discipline
© 2015 Regents of the University of Minnesota. All rights reserved.
Services
Batch HPC
Interactive
HPC
Web Portals &
Databases
Consulting
Data Storage
© 2015 Regents of the University of Minnesota. All rights reserved.
HPC Resources
•  Itasca
–  Cores: 8,744
–  Memory: 31.3 TB
–  Peak: 100 TF
•  Mesabi
–  Cores: 16,848
–  Memory: 67 TB
–  Accelerators: 80 K40
gpGPUs
–  Peak: 675 TF
•  Cascade
– 
– 
– 
– 
32 Tesla gpGPUs
8 Kepler gpGPUs
2 Intel Phi
192 CPU Cores
© 2015 Regents of the University of Minnesota. All rights reserved.
Interactive HPC
Environments
• 
• 
• 
• 
iSub:
NICE:
NX NoMachine
Citrix for Windows
•  Itasca
–  Cores: 8,744
–  Memory: 31.3 TB
–  Peak: 100 TF
•  Mesabi
–  Cores: 16,848
–  Memory: 67 TB
–  Accelerators: 80 K40
gpGPUs
–  Peak: 675 TF
•  Cascade
– 
– 
– 
– 
32 Tesla gpGPUs
8 Kepler gpGPUs
2 Intel Phi
192 CPU Cores
© 2015 Regents of the University of Minnesota. All rights reserved.
Storage
•  High Performance Storage
–  2.4 PB
–  25GB/s read/write
–  Available on HPC resources
•  Hadoop Cluster
–  39 compute nodes
–  14 TB Hadoop HDFS
•  Tier-2 Storage
– 
– 
– 
2.1 PB
Available via Amazon’s S3 interface
Available anywhere in the world
– 
– 
3.5 PB tape-based storage
offline storage
•  Archive Storage
© 2015 Regents of the University of Minnesota. All rights reserved.
MSI HighPerformance
Computing Clusters
s3.msi.umn.edu
Linux Home
Directories
High-Performance
Scratch
Interactive Systems
HighPerformance
Persistent
Storage
(PANFS)
Linux Home
Directories
Persistent
Storage
(Ceph)
s3.msi.umn.edu
Campus and
External Access
s3.msi.umn.edu
© 2015 Regents of the University of Minnesota. All rights reserved.
Consulting
• 
• 
• 
• 
24 -- Consulting Staff
17 -- Staff with advanced degrees
10 to 20 -- Workshops and Tutorials annually
46 -- Projects supported annually
© 2015 Regents of the University of Minnesota. All rights reserved.
Portals & Databases
Multiple “omics” platform
Emphasis on Mass Spectrometry based Proteomics
© 2015 Regents of the University of Minnesota. All rights reserved.
Portals & Databases
National Center for Food Protection and Defense
• 
• 
• 
NCFPD headquartered
at UMN
Vulnerability of the
Nation’s food supply
FIDES Dashboard
• 
• 
• 
Focused Integration of
Data for Early Signals
Maps shipments to US
from Exporting
countries
Wordpress-like
discussion panel
© 2015 Regents of the University of Minnesota. All rights reserved.
Challenge Analyzing Clinical Data
•  CLIA certification
–  Clinical Lab Improvement Amendments
–  Protocols cannot be changed without
revalidation
–  Solution: virtual machines
–  Implemented in Amazon and Private MSI
OpenStack Cluster
© 2015 Regents of the University of Minnesota. All rights reserved.
Old Workflow
New Workflow
UMGC
MSI
Data Release
Clinician’s Space
Analyze Data
(Variants/CNVs)
UMGC
MSI
Data Release
Analyze Data
(Variants/CNVs)
OpenStack
Clinician’s Space
Amazon
Launch time reduced from ~ 12 hrs to ~2 hrs
© 2015 Regents of the University of Minnesota. All rights reserved.
AgroInformatics:
An Integrated Informatics Initiative
MSI and CFANS (College of Food, Agricultural and Natural
Resource Sciences) are joining forces to launch
AgroInformatics.
Vision
Create (and purposefully populate) the informatics
platforms that integrate and synthesize data to form new
knowledge and innovative ideas for sustainable agricultural
productivity growth and flavorful nutritious food.
© 2015 Regents of the University of Minnesota. All rights reserved.
Perspective
Business Model, etc.
Library
Shareholder
Cost
Center
Industry
Collaboration
“Business models of HPC centres in higher education in
Europe” (2013) Eurich, Calleja, Boutellier. J. Comput higher Educ.
© 2015 Regents of the University of Minnesota. All rights reserved.
Perspectives
Business
Model
Advantages
Disadvantages
Library Model
•  Enables exploration of
unfunded ideas
•  Means to steer
research directions
•  Depends on commitment of Univ.
•  Everyone indirectly pays for HPC
Shareholder
Model
•  Fair, proportional
distribution of services
•  Priority rules can be
applied
•  Problems when shareholder
leaves consortium
•  Non-users are not encouraged to
experiment with HPC
From: “Business models of HPC centres in higher education in
Europe” (2013) Eurich, Calleja, Boutellier. J. Comput higher Educ.
© 2015 Regents of the University of Minnesota. All rights reserved.
Perspectives
Business
Model
Advantages
Disadvantages
Library Model
•  Enables exploration of
unfunded ideas
•  Means to steer
research directions
•  Depends on commitment of Univ.
•  Everyone indirectly pays for HPC
•  Challenges keeping customer
service Focus*
•  Challenges setting research
Priorities internally*
Shareholder
Model
•  Fair, proportional
distribution of services
•  Priority rules can be
applied
•  Problems when shareholder
leaves consortium
•  Non-users are not encouraged to
experiment with HPC
From: “Business models of HPC centres in higher education in Europe” (2013)
Eurich, Calleja, Boutellier. J. Comput higher Educ.
* Wilgenbusch added
© 2015 Regents of the University of Minnesota. All rights reserved.
Perspective
© 2015 Regents of the University of Minnesota. All rights reserved.
Perspective
© 2015 Regents of the University of Minnesota. All rights reserved.
Perspective
Thank You
February 2
March 3
© 2015 Regents of the University of Minnesota. All rights reserved.