1. Pacific Rim Application and Grid Middleware Assembly (PRAGMA)1:
Philip Papadopoulos, Ph.D.
Chief Technology Officer, San Diego Supercomputer Center Research Scientist, Calit2
University of California San Diego
Structural characteristics of community of practices are redefined to a domain of knowledge, a notion of community, and a practice
 Community of Practice
- Domain of knowledge – creates common ground, inspires members to participate, guides their learning and gives meaning to their action
- Community – Notion of community creates social fabric for learning. Strong community fosters interactions / encourages willingness to share ideas
- Practice - while the domain provides the general area of interest for the community, the practice is the specific focus around which the community develops, shares and maintains its core of knowledge
The Pacific Rim Applications and Grid Middleware Assembly (PRAG­MA), established in 2002, is a robust, international network of research scientists from more than 30 institutions who address shared science and cyberin­frastructure challenges
PRAGMA pursues activities in four broad interdependent areas
Fostering international scientific expeditions by forging teams of domain scientists and cyberinfrastructure researchers who develop and test necessary information technologies to solve specific scientific questions and create usable, international-scale, cyber environments;
Developing and improving a grassroots, international cyberinfrastructure for testing, computer science insight and advancing scientific applications by sharing resources, expertise, and software;
Infusing new ideas by developing new researchers with experience in cross-border science and by continuing to engage strategic partners;
Building and enhancing the essential people-to-people trust and organization developed through regular face-to-face meetings—a core component of PRAGMA’s success.
This talk will provide an overview of PRAGMA and highlight its accomplishments in its twelve years since inception, and will focus two current the scientific “virtual” expeditions, one on predicting freshwater quality in lake, the other on biodiversity in extreme environments. The talk will give some lesson’s learned in creating a distributed yet coordinated network of researchers, give examples from PRAGMA and from another ecological network, the Global Lakes Ecological Observatory Network, and mention opportunity for active student engagement in these networks. One goal for the talk is to explore how PRAGMA might help stimulate a discussion around such a network in biodiversity work in Southeast Asia and beyond.
1 US Participation funded by NSF Award OCI

2. PRAGMA Members and Affiliates
Community of Practice Scientific Expeditions and Infrastructure Experiments for Pacific Rim Institutions and Researchers
PRAGMA
Members
and
Affiliates
Why Did we start PRAGMA?
- To realize a vision of technology working together
- Means people have to work together!
For individuals new to a PRAGMA workshop – welcome!
As science becomes more distributed and collaborative, there are small to medium sized groups, distributed, that want to work together. PRAGMA is about enabling this long tail of science, through scientific expeditions and infrastructure experiments.
We have always focused on the Pacific Rim. You can see the institutions involved. This includes the four new sites that were accepted as members at PRAGMA 24
Established in 2002

3. PRAGMA’s Expedition Model of Collaboration
Domain Scientists
Long-Term sustained effort to answer scientific question(s) through co-design
Technology developers
Lake Ecology: understand the processes that govern lake eutrophication
Challenge: model lakes (simulation) with large ranges of inputs to understand algal blooms and fresh-water quality
Biodiversity: understand how patterns of specifies diversity emerge and how they are sustained
Challenge: Make Lifemapper simulation cluster portable to allow greater use by collaborators with restricted data
PRAGMA Experimental Network Testbed (ENT): explore of software defined networking in international context
Challenge: understand and evaluate Software Defined Networking capabilitieis at international scale
Expeditions PA
Thoughts about collaboration
How do I know what to build if I’m not talking deeply with potential users?
How can I understand their pain points if I’m not willing to site down and listen?

4. It’s NOT the capacity of the network – It’s connectivity!
In general, data in the PRAGMA Context isn’t “big”
Biodiversity data sets are:
O(10s of GBs)
By Policy, may need to be kept “in place”
Difficult to integrate into a common spatial frames
Species observation data
Climate simulation output data
Land use data
Satellite observations
Lake ecology data sets are:
Real world sensor inputs
In-person observations (e.g. Lake Observer App on Play Store/App Store)
Simulation output from 1D model
 Data can be shared, but limited sharing is normal

5. Virtual images sharing
Building on the International Development of PRAGMA’s Multi-Cloud Testbed
Goal: a persistent cloud testbed for PRAGMA members to run experiments.
Raw
image
Universal
Clonezilla Live VM
Pragma_boot
Local
Virtual
Images
Repository
Tools:
CZISO - enables sharing virtual cluster images, leverages
UCSD’s unlimited Google storage
Clonezilla (NCHC, Taiwan) to convert images to different formats (raw, qcow, zvol)
Cloud Scheduler - enhanced interface to boot/manage virtual clusters
Cloud
Scheduler
NCHC
Taiwan
AIST
Japan
NAIST
UCSD
USA
Virtual images sharing
Needed
- Mention of how GRAPLEr Relates
- Mention of how this drives / uses technologies developed elsewhere in PRAGMA
- Mention of international sites / partners involved
Pragma_boot – deploys virtual cluster images across PRAGMA physical sites using local network configuration settings

6. Our Approach Use “Overlay” Networks to provide a trusted environment for focused sharing of resources

8. General Lake Model (GLM ) through GRAPLEr
GRAPLEr Web Service
Expose simple R desktop interface to users
Handle packaging of multiple simulations into Condor
job, compression, job submission, post-processing
receive
Web service
HTCondor
send
Internet
R, plus
GRAPLEr
library
IPOP
overlay
network UF VT …
GRAPLEr UW
Azure
PRAGMA
GRAPLEr: A Lake Ecology Distributed Collaborative Environment Integrating Overlay Networks, High-throughput Computing and Web Services, Subratie, K, Aditya, S, Figueiredo, RJ, Carey, C, Hanson, P

9. Impacts Branch of fresh-water ecology dramatically changed
From statistical analysis only to analysis + simulation
10K+ simulations (parameter sweep) for a 5 year analysis (accomplished overnight with HTCondor)
Capability being brought into the classroom by PI Cayelan Carey at Virginia Tech
Also experimenting in a hybrid networking space

10. Overlay and SDN Hybrid for Seamless High Performance Virtual Network
Kyuho Jeong (UF) Kohei Ichikawa (NAIST) Renato Figueiredo (UF)

11. IPOP Recap
(nested)
VM1
eth0
(nested)
VM2
eth0
IPOP
(nested)
VM3
eth0
(nested)
VM4
eth0
Create direct P2P virtual tunnel across multiple NAT/Firewall using ICE protocol
Each virtual tunnel is mapped to either MAC or IP address
Tap device to interface with O/S network stack
Packets are encapsulated by IP/UDP header.
Runs in application layer
N2N Encryption (DTLS – Datagram Transport Layer Sec)
IPOP
IPOP TAP
IPOP TAP
veth0
veth1
veth0 veth1
L2 Bridge
L2 Bridge
NAT
eth0
NAT
eth0
Host
Host
NAT
NAT
IPOP
Overlay

12. IPOP Deployment across InternetVM
container
container
container VM
container
container
container
Layer 2 Virtualization Network
Virtual layer
Physical layer
Amazon EC2
container
IPOP
container
IPOP
Open vSwitch
Compute instance (VM)
Open vSwitch
Compute instance (VM)
container
IPOP
Open vSwitch
Cloud Network (Layer 3)
Compute instance (VM)
Cloud
Network (Layer3)
IPOP
Public Internet
container
Open vSwitch
Google Compute Engine
Compute instance (VM)
Overlay Datapath
Compute instance (VM)
Compute instance (VM)
SDN Datapath
Cloud Network (Layer 3)
PRAGMA Cloud/Cloudlab

13. PRAGMA on the Web Home: http://www.pragma-grid.org
Github: