Clemson NextNet
SDN Use Cases for
Life Sciences Research
Kuang-Ching “KC” Wang
Associate Professor
Clemson University
KC Wang
Clemson University
Sponsored by NSF grant OCI‐1245936
July 17 2013
1
Clemson NextNet: A NSF CC-NIE Project
Objectives:
•
Direct access to I2
100G Innovation
Platform
•
Science DMZ from
anywhere, w/o
manual plumbing
•
Campus production,
end-to-end support
•
Flexible, optimized
10~40G access to
resources on
campus and other
universities
•
Software defined
network (SDN)
KC Wang
Clemson University
July 17 2013
2
What is the Fuss About SDN?
Network
Researchers:
Traditional Network
SDN
Industry: Traditional Networking
Traditional Networking
Traditional network gettinging unmanageable
(not about bandwidth)!
VLAN 2
• IP address à Server ID
VLAN 3
– Each network device knows the complete L2/L3 network
• Legacy protocols converge slowly
VLAN 1
– Not keeping pace with network trends
• Virtual environments becoming unmanageable
– Maintaining server/network coherency very labor intensive
• Service provider networks grafted on
– No provision for provider-to-provider bridging
Traffic segregation methods were
introduced to help increase scale
– What about QoS and SLAs in a virtual environment?
Still no global controller; switches growing in complexity
6
KC Wang
Clemson University
We’re reaching the practical limits of cost and complexity
7
July 17 2013
3
What Do Our (Life Sciences) Folks Need?
Two Clemson life sciences
researchers in attendance today:
• Alex Feltus
– Associate Professor in
Genetics & Biochemistry
– Faculty Consultant in Clemson
University Genomics Institute
– Research: Rapid crop design with
massive gene interaction networks
…
Data
Store
N
Palmetto
HPC
Cluster
• David Kwartowitz
– Assistant Professor in
Bioengineering
– Research: Rapid processing stereo
laparoscopic data for real-time preand intra-surgery support
KC Wang
Clemson University
July 17 2013
Real-time medical imaging
4
The Feltus Lab Builds Massive Gene Interaction Networks Using RNA Expression Profiles From
Next-Generation Sequence (NGS) and Microarray Experiments.
Rice (Oryza sativa)
Goal: Rapidly design new
crop varieties for a specific
environment including “old”
environments with a
changed climate…
Personalized Agriculture
KC Wang
Clemson University
July 17 2013
5
Slide prepared by Alex Feltus
Massive amounts of DNA/RNA/Genetic Data in Databases
1.64 Quadrillion base pairs in 5 yrs!
KC Wang
Clemson University
July 17 2013
http://www.ncbi.nlm.nih.gov/Traces/sra/
6
Slide prepared by Alex Feltus
A
5.7G
5.7G
5.8G
5.8G
6.7G
6.7G
6.8G
6.8G
6.5G
6.5G
6.6G
6.6G
7.3G
7.3G
7.4G
7.4G
5.6G
5.6G
5.7G
5.7G
8.8G
8.8G
8.9G
8.9G
NGS Biomarker Example Datasets
RAW DATA (uncompressed)
Sample_Feltus1_L006_R1.cat.fastq
Sample_Feltus1_L006_R2.cat.fastq
Sample_Feltus1_L007_R1.cat.fastq
Sample_Feltus1_L007_R2.cat.fastq
Sample_Feltus2_L006_R1.cat.fastq
Sample_Feltus2_L006_R2.cat.fastq
Sample_Feltus2_L007_R1.cat.fastq
Sample_Feltus2_L007_R2.cat.fastq
Sample_Feltus3_L006_R1.cat.fastq
Sample_Feltus3_L006_R2.cat.fastq
Sample_Feltus3_L007_R1.cat.fastq
Sample_Feltus3_L007_R2.cat.fastq
Sample_Feltus4_L006_R1.cat.fastq
Sample_Feltus4_L006_R2.cat.fastq
Sample_Feltus4_L007_R1.cat.fastq
Sample_Feltus4_L007_R2.cat.fastq
Sample_Feltus5_L006_R1.cat.fastq
Sample_Feltus5_L006_R2.cat.fastq
Sample_Feltus5_L007_R1.cat.fastq
Sample_Feltus5_L007_R2.cat.fastq
Sample_Feltus6_L006_R1.cat.fastq
Sample_Feltus6_L006_R2.cat.fastq
Sample_Feltus6_L007_R1.cat.fastq
Sample_Feltus6_L007_R2.cat.fastq
KC Wang
Clemson University
2.4G
2.4G
2.7G
2.7G
2.6G
2.6G
3.0G
3.0G
2.2G
2.2G
2.9G
2.9G
PROCESSED DATA (compressed)
Sample_Feltus1_L007_R1.MERGED.BAM
Sample_Feltus1_L007_R1.MERGED.BAM
Sample_Feltus2_L006_R1.MERGED.BAM
Sample_Feltus2_L007_R1.MERGED.BAM
Sample_Feltus3_L006_R1.MERGED.BAM
Sample_Feltus3_L007_R1.MERGED.BAM
Sample_Feltus4_L006_R1.MERGED.BAM
Sample_Feltus4_L007_R1.MERGED.BAM
Sample_Feltus5_L006_R1.MERGED.BAM
Sample_Feltus5_L006_R1.MERGED.BAM
Sample_Feltus6_L006_R1.MERGED.BAM
Sample_Feltus6_L007_R1.MERGED.BAM
6 RNA Samples in Duplicate
163.6 GB (raw) + 31.8 GB (processed) =
195.4 GB of critical data files
(<6 hours to process on cluster)
Does not include: Intermediate processing files
Reference genome (0.72 GB)
July 17 2013
7
Slide prepared by Alex Feltus
The CUTTERS (Kwartowitz) lab is working to enable remote processing of stereo
laparoscopic data for real-time feedback with surgical robot systems
on partner sites (Vanderbilt, Mayo Clinic)
Mayo Clinic, MN
Vanderbilt, TN
KC Wang
Clemson University
July 17 2013
Palmetto
HPC
Clemson, SC Cluster
8
How Does It Work Today
Data
Center
Research
Network
Campus
Network
G
ISP 1
Internet
…
Campus
Network
R&E
net 1
ISP 2
Internet
Research
Network
…
Data
Center
Campus
Network
KC Wang
Clemson University
Data
Center
Research
Network
July 17 2013
R&E
net
Down the road
• compliances
• User-specific
privileges
• access control
9
What Are We Building NOW
CCNIE/Science DMZ- stage 1
I2 AL2S
10gig
10gig
~180 nodes
(Palmetto)
10 gig
Openflow control
traffic via current
production
network
10gig
100gig
10gig
10gig sr
S4810
Brocade MLX-e
(Palmetto)
Biotech
10gig sr
Current Production Network
Pica 8 3920
10 gig sr
10gig sr
Sirrine
Big Switch Controller
40 gig lr
10gig sr
ITC MRV
Optical MUX
10gig to 40
gig fanout
40 gig lr
Pica 8 3920
10gig sr
Dwdm
link
40 gig lr
10gig sr
Z9000
End Users
Riggs
Poole
10gig sr
40gig lr
Poole MRV
Optical Mux
s4810
40gig lr
10gig sr
Rhodes
10gig sr
s4810
End Users
10gig sr
McAdams
s4810
10gig sr
End Users
KC Wang
Clemson University
July 17 2013
10
Porting GENI Research Prototype to Production
SOS: Seamless Large Data Transport
SOS
Controller
SOS
agent
Steroid OpenFlow Service (SOS)
by Aaron Rosen and KC Wang
3.2
SOS
agent
3.1
SOS pipe
• Seamless TCP throughput upgrade,
e.g., 2.5 Mbps  120 Mbps
• Multipath support
TCP
• Automatic site agent detection
2
4.2
4.1
1
SOS-enabled
switch
SOS-enabled
switch
TCP
Perceived point-to-point or multi-point connection
SOS
SCinet
Upcoming demos of SOS:
SOS
Stanford
• NSF 12th GENI conference,
Kansas City, MO.
• Supercomputing 2011,
Seattle, WA.
KC Wang
Clemson University
GENI
core
SOS
UW-Madison
SOS
Clemson
July 17 2013
11
Condo of Condos:
Connecting Campus HPC with SDN
• NSF grant to expand Clemson’s condominium HPC
model to a national scale
KC Wang
Clemson University
July 17 2013
12
Significance of IT Support Team to Bootstrap
Researcher Use of HPC and SDN
Number of Users
New Palmetto Cluster Users
KC Wang
Clemson University
May 2010: Galen joins CITI and
begins recruiting & training
users
And to Create a Transformative University
• a unique coalition among academy, IT, and industrial partners
within and beyond Clemson.
IT partners
• University IT (condo of
condos …)
• Internet2
• ESNET
Academic partners
• Researchers
• Na onal labs
• SDN research
groups
CC-NIE & Research Center
IT
Research
Teaching
Government agencies
• GENI
• US Ignite
• DoD, DoT, DoE
• State DHHS
Industry partners
• Companies
• SDN R&D Labs
3
• Synergy with other university research centers: Cyberinstitute,
ICAR, and Watts Innovation Center
KC Wang
Clemson University
July 17 2013
14
Synergy with Cross-Communities Momentum
Research Communities
Companies
Universities
...
Open Source Communities
KC Wang
Clemson University
IT Communities
July 17 2013
15
FURTHER QUESTIONS
KWANG@CLEMSON.EDU
KC Wang
Clemson University
July 17 2013
16