2 0 1 8 C O L L A B O R AT I V E OV E R V I E W

P A C I F I C R I M A P P L I C AT I O N A N D G R I D M I D D L E WA R E A S S E M B LY

CONTENTS
3.

10.

INTRODUCTIONHIGHLIGHTS

34.

EDUCATION

GLEON Research and PRAGMA Lake Expedition
Virtual Biodiversity Expedition and Lifemapper
PRAGMA Experimental Network Testbed
Hybrid Overlay/SDN Virtual Network

PRAGMA Students

PRAGMA Cloud and Virtualization

MURPA/QURPAAI Bridging Cloud Infrastructure

AIST Internships

Towards Extending the PRAGMA Cloud toInclude an Open Data Platform

44.

Visualization Infrastructure and Activities

COMMUNITY

Web-Based Science and Engineering Platform
for Advanced Cyber-learning

52.
Building Community
CENTRA-PRAGMA
Collaborations

WORKSHOPS AND
WORKING GROUPS

56.

MEMBERS, PARTNERS
AND SPONSORS

22018 COLLABORATIVE OVERVIEWINTRODUCTION
The Pacific Rim Application and Grid Middleware Assembly, PRAGMA, is an open, grass-roots,
international organization that makes cyberinfrastructure accessible, easy to use, and useful for
long tail of science communities to advance their science. These communities, often internationalin composition, are addressing societally important problems and are frequently unable to access,fully utilize, or keep pace with rapidly evolving cyberinfrastructure (CI) technologies and approaches.
Through active participation and contributions of all members, PRAGMA focuses on how to makethese new and rapidly changing CI technologies usable by these communities of scientists, within atrusted envelope of shared, easy-to-use computer and data resources.
Since its inception in 2002, PRAGMA, through its workshops, projects, and students, acts as• A conduit of ideas among members, for example bypushing the envelope of AI research through the recent
deployment of the National Institute of Advanced Industrial Science and Technology’s (AIST) state-of-the-art AI
Bridging Cloud Infrastructure, and between members
and the broader community of CI researchers;• An enabler of multi-disciplinary, multi-institutional,
international collaborations, exemplified by our expeditions in water quality, biodiversity, and experimental
network research, resulting in new knowledge that often transforms fields of research;• An experimenter with new technologies and approaches, often on shared, jointly-constructed testbeds, such as
PRAGMA’s Experimental
Network Testbed (PRAGMA-ENT) and the PRAGMA cloud, for pre-production testing, measurement,
and research, in some cases leading to incorporationof approaches in national
infrastructure, e.g., NSF’s
production virtualization
resource Comet;• A producer and refiner of community software driven
by specific applications, but generalizable to others, forexample GRAPLEr, Lifemapper, and PRAGMA’s cluster
virtualization suite, including PRAGMA boot and Cloud
Scheduler GUI; and• A forum for students and researchers to build thetrusted people networks of inter-disciplinary scientists
for long-term successful collaborations and careers.
The PRAGMA organization actively marries applicationneeds with technology capabilities to advance scienceand infrastructure, both in short-term experiments andlong-term expeditions. It actively seeks and engages newparticipants, promotes opportunities for development ofstudents, and works to build and maintain increasing levels of trust among its community. It promotes collaborative and individual partner
accomplishments and, as
appropriate, migrates tools
experimented with (or developed by) PRAGMA tonational and international
infrastructures.

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THE PACIFIC RIM APPLICATIONS AND GRID MIDDLEWARE ASSEMBLY

The annual PRAGMA Collaborative Overview highlights accomplishments by PRAGMA
and its members. Collectively, this year’s accomplishments advance PRAGMA’s longterm goals of creating accessible, easy-to-use, and useful trusted computational anddata resource environments (envelopes) for long tail science communities. This year’s
PRAGMA Collaborative Overview highlights the following specific key accomplishments:
Lake Expedition: Researchers have used GRAPLEr, an
R-based open-source software, to gain new understanding of the impact of land use and climate change on water
quality and have improved the usability of GRAPLEr for
use in research and teaching in undergraduate and graduate classrooms. Furthermore, driven by the need for moreaccurate predictions of water quality, the multidisciplinarylake expedition team, through the Smart and Connected Reservoir project (which was motivated by technology advances achieved in PRAGMA projects), designed
and prototyped a sensor gateway that will securely relay
data from sensors in the field to data centers via hybrid
software defined networking (SDN) overlays. These sensor data are to be incorporated into modeling applications, such as PRAGMA’s GRAPLEr computing system, toachieve the goal of improving water quality forecasts.
Biodiversity Expedition: Understanding species distribution and conducting macroecological modeling for biogeographic and biodiversity analyses of plant and animal
species are challenges for biodiversity researchers andconservationists. Lifemapper is an open-source modelingenvironment that supports those needs. PRAGMA supported upgrades to streamline workflows in Lifemapper
and tune the software environment for optimal resource

allocation. Both advances extend the usefulness of thetool for researchers by allowing faster deployment of Lifemapper at new research sites, creating software thatcan run efficiently on a range of PRAGMA-member hardware for local researchers, and facilitating more rapid development of new workshop training modules.
PRAGMA Experimental Network Testbed (PRAGMA-ENT):PRAGMA-ENT offers researchers complete freedom to access network resources to develop, experiment with, andevaluate new ideas without concerns of interfering with aproduction network. This year’s efforts focused on developing an on-demand virtual local area network (VLAN)
service to deploy an international path between the U.S.
and Japan in an on-demand manner. In addition, researchers were able to evaluate their SDN monitoring tool in the
wide-area environment as well as evaluate SDN-IP approaches using the PRAGMA-ENT environment.
Hybrid Overlay/SDN Virtual Network: Anticipating scientists’ needs to securely connect sensors to data centers
and networks, this activity is exploring the use of SDN in
IoT/edge computing with hybrid solutions that utilize both
SDN switches and overlay networks to create software-defined virtual networks.

42018 COLLABORATIVE OVERVIEWCloud and Virtualization:
Virtualization has been an
approach to allow for a flexible configuration of PRAGMA testbed resources that
we refer to as the PRAGMA cloud. This year we 1)
enabled multi-site virtual clusters and integration with
PRAGMA-ENT, 2) experimented with GPUs and deeplearning applications, and 3) explored the use of containers and a container orchestration engine, in particular
Kubernetes, to allow for automating deployment, scaling,
and management of containerized applications. Our goal
is to provide an environment in the PRAGMA cloud where
we can explore the use and measure the performance ofcontainers for different applications.
AI Bridging Cloud Infrastructure: PRAGMA partner AIST
has deployed the AI Bridging Cloud Infrastructure (ABCI)
for the development and deployment of AI applications
for industry and society. This unique facility opened inAugust 2018, and its staff have begun working with key
users to facilitate their research and advance the usage of
ABCI. To promote the value of ABCI and push the envelope of AI research, ABCI leadership has built partnerships
with other groups, such as the Pacific Research Platform
led by researchers at UC San Diego and is working with
PRAGMA member the National Center for High-Performance Computing (NCHC) in Taiwan to help develop a
new AI-focused infrastructure at NCHC. The ABCI team isalso exploring how the PRAGMA community can build alarge-scale distributed AI research platform by connecting ABCI and AI supercomputers operated by the other
PRAGMA member institutions.
PRAGMA Data Infrastructure: Driven by specific needs
in diverse and societally important areas of biodiversity, food security, and air quality, as well as opportunities
provided by new data platforms such as the AI Bridging Cloud Infrastructure, PRAGMA is expanding its Cloud
Infrastructure to an international shared data platform.

Concretely, we have tests
planned to mirror iDigBio
biodiversity data at the NSF
Comet facility, to move datafrom UC San Diego to the
ABCI facility in Japan to support neuroscience research,and to integrate persistent identifiers (PIDs) with distributed data storage systems. Moreover, we are deploying
tools to display Tstat monitoring data, are able to assign
PIDs to dynamic data we work with, and have developed
expertise around data storage systems and managing
time series data.
Visualization: Harnessing the advent of large display
walls for immersive visualization and analytics, this collaborative effort builds on Scalable Amplified Group Environment 2 (SAGE2) collaborative environments to provide visual prototypes of complex workflows in multiple
areas, including eHealth and smart cities. Key technicaladvances include creating integrated data backends tomultiple visual displays and adding voice commands tofacilitate interaction with the data. This effort aims towork with diverse groups to diversify applications using
this technology.
Cyberlearning: EDISON, EDucation-research Integration
through Simulation On the Net, is the well-known e-science platform that is aimed at advancing learning throughsimulations. This year’s technical advancements include
implementing a new scientific workbench and new scientific workflows, which allow users to bring together various environments or modules. Its achievements have beenrecognized through the winning of the “Top 100 R&D for
the Outstanding Achievement in 2017” award.
Community Building: PRAGMA is open to all who arewilling to actively participate in PRAGMA activities, workshops, projects, experiments, and platforms. In addition,
to stay aware of a broader community and seek new challenges, we make concerted efforts to reach new communities of individuals and applications via the Southeast
5

THE PACIFIC RIM APPLICATIONS AND GRID MIDDLEWARE ASSEMBLY

member since inception, Karpjoo Jeong who hosted
PRAGMA 23 and helped start programs specificallytargeting PRAGMA students, Putchong Uthayopas,
who co-hosted PRAGMA 12 and PRAGMA 24, andwho joined PRAGMA very early, and Wing-KeungKwan, who hosted PRAGMA 20 and has been an
enthusiastic participant. Finally, we wish to thankTeri Simas for her efforts to help make PRAGMA thefamily it is today.

LOOKING FORWARD
Asia International Research and Training Program (SEAIP)
hosted by PRAGMA member NCHC in Taiwan, collocating
meetings with our workshops, such as meetings on AI infrastructure and research, and by PRAGMA members attending conferences in new areas.
Students: PRAGMA is committed to creating globally-minded problem solvers for 21st century challenges.
Students play a fundamental role in PRAGMA activities,
engaging in both research and professional skill development at workshops. Students are also provided opportunities to gain hands-on experience working on projects
and, in some cases, spending face-to-face time with researchers in a host lab. These have been mutually beneficial to the students and to PRAGMA. Some exchanges arehighlighted this year, one of which has led to preliminary
work on capturing time series data for measuring efficiency of virtualization approaches.

PRAGMA EVOLVESOver the last 16 years, PRAGMA leadership has evolved
gradually through rotation of members on the steeringcommittee. Accompanying this year’s selection of a newchair, we re-envisioned an organizational structure to more
broadly engage members of the steering committee and
PRAGMA. PRAGMA’s strong people network and clear,
flexible operating principles and procedures has enabled
a smooth transition of leadership to a new generation ofleaders around the Pacific Rim. These structural changes
are summarized in PRAGMA at-a-Glance. This year, we welcome five new members to the steering committee: Jason
Haga (AIST), Weicheng Huang (NCHC), Ruth Lee (KISTI),
Nurul Malim (USM), and Shava Smallen (UC San Diego). We
also would like to thank five individuals who have helped
shape PRAGMA: Philip Papadopoulos, former PRAGMA
Chair and a member since its inception, Whey-Fone Tsai, a

In the coming years, we will build on our current
activities and plans described in this Collaborative
Overview. PRAGMA’s success will be weighted by• New science from the expeditions and new insightsfrom our experimentation and measurements;• Use of tools and other PRAGMA products by the broader community and incorporation of some into national
and international infrastructures;• New collaborations generated by PRAGMA and newcommunities able to use these new cyberinfrastructuretechnologies;• Student opportunities for research and professional
development; and• Publications that share the results of our work with thebroader community.
PRAGMA’s future is bright thanks to its strong people-network, partners working together to make CI technologies useful to new scientific communities and theirchallenges, and its investment in people who will be future leaders in their fields.

REFERENCES
For more about PRAGMA, its past accomplishments, andsoftware, please see:Arzberger, P. (2017) A reflection on the origins, evolution,and future of PRAGMA. Concurrency Computat: Pract. Ex­
per. e4136. doi.org/10.1002/cpe.4136.
PRAGMA Collaborative Overview:www.pragma-grid.net/overview
PRAGMA Software: www.pragma-grid.net/products62018 COLLABORATIVE OVERVIEW

7
THE PACIFIC RIM APPLICATIONS AND GRID MIDDLEWARE ASSEMBLYAT A GLANCEPRAGMA was established in 2002 to enable the long tail of science through scientific expeditions
and infrastructure experimentation for Pacific Rim institutions and researchers.
Members: 27 Institutional Members. See Institutions andSponsors for a list of institutions and abbreviations usedin this Collaborative Overview.
Website: www.pragma-grid.net
Governance: Steering Committee and PRAGMA’s Operating Principles and Procedures
Steering Committee Co-Chairs: Shinji Shimojo (Osaka
University) and Shava Smallen (UC San Diego)
Chairs of other steering committee functional area roles:

Workshops of Participants: Workshops are held twice ayear to share progress and plan future activities. Open toall, workshops are hosted by PRAGMA members, often in
conjunction with other activities.
2018 WORKSHOPS• PRAGMA 34: May 9–12, 2018. Co-hosted by AIST and
Osaka University. Location in Akihabara, Tokyo, Japan.
Held in conjunction with the Workshop on High Performance Infrastructure for AI, in conjunction with the 3rd
annual CENTRA meeting.

• Workshop Engagement: Kohei Ichikawa (Nara Institute of Science and Technology, NAIST)• PRAGMA 35: October 3–6, 2018. Hosted by Universiti
Sains Malaysia, Penang, Malaysia and co-hosted by Malaysia Digital Economy Corporation. Held in conjunction with Big Data Week Asia (Kuala Lumpur) and the
Big Data Summit 2 (Penang).

• Communications: Heru Suhartanto (U Indonesia)

2019 WORKSHOPS• Mentoring: Jason Haga (National Institute of Advanced
Industrial Science and Technology, AIST)• PRAGMA 36: April 25–27, 2019. To be hosted by the
Korea Institute of Science and Technology Information(KISTI). Held in Jeju, Korea in conjunction with the 4th
annual CENTRA meeting (April 22–24, 2019).

• Membership: Fang-Pang Lin (National Center for
High-performance Computing, NCHC)

Collectively, the PRAGMA Steering Committee Co-Chairs
and the Functional Area Role Chairs constitute an executive committee of the steering committee.

• PRAGMA 37: September 11–13, 2019. To be hosted by
the UC San Diego, La Jolla, California, USA.

82018 COLLABORATIVE OVERVIEWPARTNERS• GLEON: The Global Lake Ecological Observatory Network’s mission is to understand, predict, and communicate the role and responses of lakes in a changing
global environment (gleon.org).

SCIENTIFIC EXPEDITIONS• LIMNOLOGY: Predicting lake eutrophication and training the next generation of lake scientists• BIODIVERSITY: Understanding biological adaptationin extreme environments• ENT: Developing an experimental network testbed forexperimenting with software-defined networks andmonitoring impacts of choices
WORKING GROUPS• RESOURCES: Making the distributed resources of
PRAGMA useful for diverse applications in projects like
PRAGMA Cloud Testbed, PRAGMA ENT, and Open Data
Platform• CENTRA: The long-term goal of the Collaborations to
Enable Transnational Cyberinfrastructure Applications
is to advance the scientific understanding of distributed, software-defined cyberinfrastructure. CENTRA
refers to a partnership and evolving framework forcollaborations among research centers, institutes, andlaboratories across the world. It engages junior researchers with software-defined infrastructure and initial collaborations in three application domains: environmental modeling, disaster management, as well as
smart and connected communities (www.globalcentra.
org).
• SEAIP: The Southeast Asia International Research
and Training Program is hosted annually by Taiwan’s
National Center for High-Performance Computing(NCHC). The program aims to promote collaborations
in cyberinfrastructure among researchers in Southeast
Asia and between researchers in Southeast Asia andtheir counterparts in other parts of the world (event.
nchc.org.tw/2018/seaip).

• TELESCIENCE: Making and improving access to or use of
remote equipment (e.g., tiled-display walls or sensors) inareas like environmental monitoring and traffic flow
• BIOSCIENCES: Creating stable infrastructure to perform computational genomics analyses with a focus
on rice breeding and integrating technologies to create
an infrastructure to advance the screening of potential
compounds to combat infectious diseases• CYBERLEARNING: Developing
simulation-basedlearning technology with current focus on EDISONSTUDENTSSPONSORS• PRAGMA STUDENTS: Stimulating international,
cross-disciplinary collaborations among students andjunior researchers

Multiple, often associated with members and fundedthrough many different national science foundations. See
Institutions and Sponsors for a list of this year’s sponsors
by institution.

9
THE PACIFIC RIM APPLICATIONS AND GRID MIDDLEWARE ASSEMBLY

102018 COLLABORATIVE OVERVIEWTHE GLEON RESEARCH AND PRAGMA LAKE
EXPEDITION (GRAPLE) COLLABORATION
Improving usability, securely integrating sensor data into modeling via sensor gateways, andadvancing understanding of water quality globally
The PRAGMA Lake Expedition is an interdisciplinary collaboration between computer scientists and lake modelers affiliated with The Global Lake Ecological Observatory
Network (GLEON). This collaborative effort is advancing
the current understanding of the effects of climate change
and eutrophication (i.e., increased nutrient pollution of nitrogen and phosphorus, leading to increased plant growth)on harmful algal blooms in lakes. The GRAPLE team is advancing state-of-the-art water quality prediction throughthe use of models. Its main software product is GRAPLEr,
an R-based open-source software that brings the powerof distributed computing to the fingertips of lake ecology
modelers (see graple.org).

platform in ecology undergraduate curricula at 12 universities showed that participation in our training activities
significantly increases students’ computational literacy(Farrell and Carey 2018).

Beyond the classroom, recent GRAPLEr applications
highlight how the distributed computing platform (spanning PRAGMA resources at the University of Florida(UF) and the Nara Institute of Science and Technology(NAIST) in Japan, as well as the San Diego Supercomputer Center’s dedicated XSEDE cluster, Comet) is enabling
new discoveries on how climate change can affect lakewater quality (Figure 1). Students and postdocs on thelake expedition team are using GRAPLEr to model nutriThe lake team (led by Cayelan Carey, Renato Figueireent dynamics of lakes with contrasting levels of initial wado, and Paul Hanson) has continued to make progress in
ter quality under a range of likely future climate warming
the development of
scenarios. Our temGRAPLEr, using it inperature warming
several teaching andsimulations reveal
research activities
substantial year-tothroughout the year.
year and amongDevelopment effortslake variability infocused on improvthe responses of difing the usability offerent water quality
GRAPLEr, particumetrics. While conlarly in regards tocentrations of total
the handling of user
nitrogen in the suraccounts and accessface waters (epilimFigure 1. As air temperatures increase (from 0 to 7°C, shown by the blue to red
control, to facilitatenion) consistently
scale), simulation modeling indicates that while epilimnetic (surface water) total
use of GRAPLEr by nitrogen concentrations will generally not change, phosphorus concentrations
decrease
under
instructors and stu- will increase, but only in lakes with initially low levels of nutrients. Lake Mendota
the highest warmdents in classes. As- (Madison, Wisconsin, USA) has high initial levels of nitrogen and phosphorus,
ing scenario for all
whereasLake
Sunapee(Sunapee,
New
Hampshire,
USA)
has
low
levelsofsessments of underlakes, regardless ofgraduate students nitrogen and phosphorus. These two lakes and GLEON sites provide exemplar
their initial water
contrasting conditions for testing warming scenarios using the GRAPLEr platusing the GRAPLEr
quality conditions,form (adapted from Farrell et al. 2018).

11
THE PACIFIC RIM APPLICATIONS AND GRID MIDDLEWARE ASSEMBLY

surface total phosphorus concentrations consistently increase, but only in lakes with good initial water qualitythat occurs with low phosphorus concentrations (Farrell
et al. 2018). These differential responses of nitrogen andphosphorus may promote greater harmful algal blooms
in lakes that previously had not exhibited degraded water
quality. Our observed differences in nitrogen and phosphorus concentrations in response to warming highlightthe power of GRAPLEr for capturing both intra- and inter-annual variability across a range of lakes, which inturn allows us to more effectively predict ecological responses to climate change and adaptively prioritize management efforts.
Through an NSF-supported Smart and Connected Communities (SCC) project called Smart and Connected Water Systems (see SmartReservoir.org) that emerged synergistically from a PRAGMA lake expedition collaboration,a main focus of activities in the past year has been on
the design and prototyping of “sensor gateways”—computers that run a full-fledged operating system, middleware, and applications, yet are small and robust enoughto be deployed in the field—that connect to the Internet(typically through cellular 4G/LTE links) and to sensors
on lakes/reservoirs. Sensor gateways run a full-fledged
Linux operating system and connect to a “trusted enve-

lope,” allowing significantly more flexibility and programmability compared to traditional approaches and providing a layer of access control and privacy through virtualprivate networking (VPN) techniques that prevent accessand eavesdropping from untrusted parties. The computerscience prototyping and deployment of sensor gateways
connected to IPOP, an open-source user-centric software
virtual network, within the SCC project directly resulted
from the PRAGMA lake expedition. The SCC project further expands and integrates the IPOP overlay networkwith modules to communicate with sensors attached toCampbell data-loggers, Git-based modules to manage
committing sensor data from the gateway to servers
within the VPN, management modules, and a workflowthat automates data curation and publication. The SCC
project’s aim is to create an end-to-end workflow for
ecological forecasting, where data from sensor gateways
seamlessly drive the execution of models in the cloud(through GRAPLEr), within the trust envelope of a distributed overlay VPN. PRAGMA, in turn, will benefit fromthis new application of PRAGMA technology, which feeds
back to the lake expedition’s next steps. Our next goals
within the PRAGMA lake expedition are to apply the lessons learned and new technology developed in the SCC
project to additional GLEON lake sites, and potentiallyother PRAGMA expeditions.

122018 COLLABORATIVE OVERVIEWPARTICIPANTS
Virginia Tech: Cayelan Carey, Kait Farrell, Nicole Ward,
Mary Lofton, Ryan McClure, Jon Doubek, Arianna Krinos;
University of Wisconsin: Paul Hanson; University of Flori­
da: Renato Figueiredo, Ken Subratie, Vahid Daneshmand;
National Institute of Science and Technology (NAISTPRAGMA Cloud resources added to GRAPLEr): Kohei
Ichikawa; UC San Diego (Collaborating on PRAGMA Cloud
addition): Shava Smallen

REFERENCES
Farrell, K. J. and Carey, C. C. 2018. Power, pitfalls, andpotential for integrating computational literacy into un­dergraduate ecology courses. Ecology and Evolution. In
press. DOI: 10.1002/ece3.4363.
Farrell, K. J., Carey, C. C., Krinos, A. I., Ward, N. K., Hanson,
P. C., Figueiredo, R. J., Daneshmand, V., and Subratie, K.
Increasing air temperatures differentially alter intra- andinter-annual nitrogen and phosphorus cycling in a eutro­
phic and an oligotrophic lake. Oral presentation, Ecologi­
cal Society of America, New Orleans, August 2018.
Subratie, K., Aditya, S., Mahesula, S., Figueiredo, R., Carey,
C. and Hanson, P. (2017). GRAPLEr: A distributed collab­
orative environment for lake ecosystem modeling that in­tegrates overlay networks, high-throughput computing,and Web services. Concurrency and Computation: Prac­tice and Experience, [online] 29(13), p.e4139. Available at:
dx.doi.org/10.1002/cpe.4139.

SOFTWARE
GRAPLEr. See graple.org to download and learn more
about the software.
PRAGMA IPOP overlay: ipop-project.org

SMART AND CONNECTED WATER SYSTEMSNSF 1737424 funded the Smart and Connected Water
Systems as part of its Smart and Connected Communities
program. The Smart and Connected Water Systems has
multiple aims, including creating an embedded networkof high-frequency water quality sensors, developing andevaluating a new model-data fusion, and working directlywith the community on models of trust and training materials. See smartreservoir.org for more information.

13
THE PACIFIC RIM APPLICATIONS AND GRID MIDDLEWARE ASSEMBLYVIRTUAL BIODIVERSITY EXPEDITION
AND LIFEMAPPER
Adapting Lifemapper software to varying installation environments, user backgrounds, data size, andcomputational complexity via upgrades, optimization tuning, and training workshops

Figure 2: Lifemapper workshop at NCHC, May 2018.

Lifemapper, an open-source modeling environment created at the University of Kansas, allows researchers to pursue species distribution and macroecological modelingfor biogeographic and biodiversity analyses of terrestrial
species. The Virtual Biodiversity Expedition (VBE) is utilizing unique Lifemapper installations for PRAGMA sites
using species occurrence data, specified by a researcher,and phylogenetic (evolutionary) data derived from DNA
sequencing studies to explain the ecological and evolutionary contributions to observed spatial patterns of species diversity.
PRAGMA work includes enabling Lifemapper to more efficiently utilize a range of available resources from small
virtual cluster installations for individual researchers to
the NSF XSEDE Comet supercomputer installation forhigh throughput projects. As part of this effort, code wasstreamlined and refactored to create more flexible workflows via Makeflow and Work Queue, a framework developed by Cooperative Computing Lab at The University ofNotre Dame. As part of a separate project, Lifemapper
also added a new meta-community phylogenetic analyses(MCPA) capability to link evolutionary speciation and geologic and graphic hypotheses to analyses of species distributions. We increased the utility of these MCPA results bycreating a new browser-based client for Lifemapper servers and output packages. The new client enables browsing through output packages created for multi-species
experiments and utilizes multiple linked views, including
a phylogenetic tree, a map, and scatterplots to visualize
different dimensions of the data simultaneously (Figure3). Selections in one visualization window trigger selections in the other windows. While this work was primarily

14
2018 COLLABORATIVE OVERVIEWFigure 3. Linked view of phylogenetic tree, map of highlighted species distributions, and variable correlations displayed in Lifemapper.

funded by other sources, the new client was built with theintention of facilitating user interaction, data exploration,and training in PRAGMA’s “Distributable Lifemapper” installations and workshops. In collaboration with CENTRA,
the new client is browser-based to enable easy porting toa SAGE2 (Scalable Amplified Group Environment). SAGE2
is a software and collaborative virtual environment thatallows local and remote participants to visualize data onlarge, high-resolution displays. It is increasingly available
at PRAGMA sites. While we are working towards a native
SAGE2 Lifemapper client, multiple users running Chromeor the standalone SAGE2 user interface client on their own
machines can currently interact with a Lifemapper client
running on a SAGE2 server.
The Lifemapper toolkit is designed to work with Rocksclusters using the Rocks roll packaging system, allowing
it to be deployed and run in different computational environments. Rolls contain RPM (Package Manager) format
packages that install and configure the Lifemapper software for either virtual or physical hardware. This spring, we
deployed Lifemapper at the National Center for High-performance Computing (NCHC), a member of National Applied Research Laboratory in Taiwan, with GBIF (Global
Biodiversity Information Facility)-provided species occurrences and high-resolution environmental data for Taiwan.
We developed new training materials, and in May 2018,
PRAGMA, CENTRA, and NCHC jointly sponsored a work1

shop for 30 students and researchers at NCHC (Figure 2)
with the new Lifemapper client where participants wereintroduced to using Lifemapper for predicting species
distributions, macroecological modeling, and biodiversity
analyses, highlighting phylogenetic tree integration. Participants have joined a Lifemapper user group mailing list
to share information and strategies for Lifemapper-enabled research.
Lifemapper software improvements over the last five
years have allowed researchers to consider increasing thescale of problems addressed. Deploying Lifemapper tohigh-end resources facilitates those studies. In particular,
Lifemapper is deployed in the USA using virtual clusters
on the XSEDE program’s Comet supercomputer resource,
enabling agile and rapid scaling to match computationalload. We populated and computed North American plant
distribution data (using data from iDigBio1) on this virtual
Comet cluster and also identified problems of scaling toavailable resources. With the computation and analysis of
distribution for all of North America plants, researchers canaddress major questions of ecological and evolutionary
importance with significant conservation implications. For
example, we can ask: Where are endemics, species uniqueto a certain area, located? And we can formulate important hypotheses based on biogeographic features and test
them. For example, does the Mississippi River represent a
major differences in phylogenetic diversity to the east andwww.idigbio.org
15

THE PACIFIC RIM APPLICATIONS AND GRID MIDDLEWARE ASSEMBLY

west of the river? In short, the resultant computation is a resource for researchers of North American plants, conservationists, as well as ecologists
from diverse disciplines.
We are currently focusing on optimizing available resources for the sizeand complexity of a dataset, and on enabling scientists to use their own
datasets. During the summer of 2018, we identified areas of improvement
for workflow optimizations that will lead to the higher throughput of Lifemapper analyses. A major goal is to redesign computational jobs in orderto streamline and simplify individual job submissions. In the process, wewill develop a more accurate picture of CPU and memory requirements forindividual job types so we can better allocate and use resources. Anotherexciting area of our current work is streamlining the data ingestion process,which will allow multiple users to work with multiple data packages while
maximizing resource utilization.

PARTICIPANTS
University of Kansas: James Beach, Aimee Stewart, C.J. Grady; UC San Diego:
Philip Papadopoulos, Nadya Williams; National Center for High-performance
Computing (NCHC): Fang-Pang Lin, Hsiu-Mei Chou, Jih-Sheng Chang

REFERENCES
Grady, C.J., Stewart, A.M (22 July 2018) Training in “Using DigitizedHer­barium Data in Research: Applications for Ecology, Phylogenetics, and Bio­
geography” [Workshop]. Held at Botany 2018, Rochester,MN, 20-26 July 2018. www.2018.botanyconference.org/engine/search/index.php?func=­detail&aid=55
Stewart, A.M, Grady, C.J. (4 May 2018) Lifemapper Workshop. Full day
workshop hosted by NCHC, Hsinchu, Taiwan.
Williams N., Stewart A., Papadopoulos P. Virtualizing Lifemapper software
infrastructure for biodiversity expedition. Concurrency Computat: Pract Ex­
per. 2017;e4137. https://doi.org/10.1002/cpe.4137

SOFTWARE
Lifemapper website lifemapper.org.
The core Lifemapper code is available at github.com/lifemapper.
Lifemapper software now includes tools for installing and configuring Lifemapper third party dependencies, configuring the Lifemapper installation
for local hardware, and bootstrapping the database with default or user data.
Lifemapper GitHub repositories github.com/pragmagrid/lifemapper-server
and github.com/pragmagrid/lifemapper-compute contain code for installation of the two primary components (server and compute) of Lifemapper;
these components may be installed on the same or separate Rocks clusters.

16
2018 COLLABORATIVE OVERVIEWPRAGMA EXPERIMENTAL NETWORKINGTESTBED (PRAGMA-ENT)
Extending PRAGMA ENT’s capabilities and using ENT
to evaluate new tools and approaches

The PRAGMA Experimental Network Testbed (PRAGMA-ENT) expedition has the goal of
constructing an international software-defined networking (SDN)/OpenFlow testbed foruse by PRAGMA researchers and collaborators. PRAGMA-ENT is breakable in the sensethat it offers complete freedom for researchers to access network resources to develop,
experiment with, and evaluate new ideas without concerns of interfering with a production
network. PRAGMA-ENT also provides networking support to the PRAGMA multi-cloud anduser-defined trust envelopes. This exposes SDN to the broader PRAGMA community andfacilitates the long tail of eScience by creating new collaborations and infrastructure among
institutions in the Pacific Rim area.
The PRAGMA-ENT team has been connecting resources in the United States (University of
Florida, UC San Diego and Indiana University); Japan (Nara Institute of Science and Technology (NAIST), National Institute of Information and Communications Technology (NICT),
Osaka University, National Institute of Advanced Industrial Science and Technology (AIST),
and National Institute of Informatics (NII)); Taiwan (National Applied Research Laboratories(NARLabs)); Thailand (Thammasat University), and Malaysia (MIMOS) (Figure 4). Since all
OpenFlow switches at each site are interconnected through dedicated virtual local area network (VLAN) links and overlay virtual links, PRAGMA users can develop their own controllers to manage the entire network testbed and/or perform or measure large-scale network
experiments. This year, researchers used PRAGMA-ENT to evaluate their SDN monitoring
tool in the wide-area environment (Watanakeesuntorn et al. 2017). Another researcher developed a hybrid overlay/SDN environment for IoT/edge computing (See Hybrid Overlay/
SDN virtual network section).
We are currently working to develop a Network Function Virtualization (NFV) testbed thatuses PRAGMA-ENT resources together with PRAGMA Cloud resources. We are trying to develop the environment so that researchers can conduct various experiments on NFV using
our globally distributed computing and networking resources. Some researchers currently
are evaluating SDN-IP using the environment (Aguirre et al 2018).
We have been also working to develop an on-demand VLAN service to deploy an international path between the U.S. and Japan in an on-demand manner. One of our international
paths, Science Information NETwork (SINET), provides network services interface (NSI) to
control international VLAN paths. Using the on-demand VLAN service will allow us to develop more dynamic and flexible environments for the experiments.
17
THE PACIFIC RIM APPLICATIONS AND GRID MIDDLEWARE ASSEMBLY

AIST
NICT
NII

JGN-X
RISE

SINET5NAIST
Osaka UInternet
Pacific
Wave

Indiana U

StarLight

UC
San Diego

FloridaLambdaRail
U Florida

TWAREN
Thammasat U

NAR
Labs

MIMOS

Figure 4: PRAGMA-ENT L2 Backbone. High-speed research networks (Florida Lambda Rail, Internet2, JGN-X,
SINET, TWAREN, PacificWave and StarLight) interconnect OpenFlow-enabled hardware switches in the United States (University of Florida, UC San Diego, and Indiana University), Japan (Nara Institute of Science andTechnology, National Institute of Information and Communications Technology, Osaka University, National
Institute of Advanced Industrial Science and Technology, and National Institute of Informatics), Taiwan(National Applied Research Laboratories), Thailand (Thammasat University), and Malaysia (MIMOS). The
solid and dashed lines indicate physical connections and virtual connections, respectively.

PARTICIPANTS
Nara Institute of Science and Technology (NAIST): Kohei Ichikawa, Wassapon Watanakeesuntorn, Pongsakorn U­chupala (now at Sony), Chawanat Nakasan (now at Kanazawa
Univ.), Che Huang (now at NTT); University of Florida: Matthew Collins, Kyuho Jeong,
Renato Figueiredo, Jose Fortes; National Institute of Information and Communication
Technology (NICT): Hiroaki Yamanaka, Jin Tanaka; UC San Diego: Nadya Williams,
Shava Smallen, Philip Papadopoulos; Osaka University: Juan Sebastian Aguirre,
Yoshiyuki Kido, Susumu Date, Yasuhiro Watashiba, Shinji Shimojo; National Insti­
tute of Advanced Industrial Science and Technology (AIST): Jason Haga, Ryosei
Takano, Yoshio Tanaka; National Institute of Informatics (NII): Atsuko Takefusa;
National Applied Research Laboratory (NARLabs) and the National Center for
High-performance Computing (NCHC): Li-Chi Ku, Fang­Pang Lin, Jen­Wei Hu,
Te­Lung Liu; Indiana University Bloomington: Quan (Gabriel) Zhou, Beth Plale,Jennifer Schopf; Internet2: John Hicks, Rick McMullen (now at Texas A&M);
Kasetsart University: Putchong Uthayopas; Thammasat University: Wanida
Putthividhya, Prapaporn Rattanatamrong; MIMOS: Luke Jing Yuan

REFERENCES
Aguirre, J. S., Ichikawa, K., Kido, Y., Date, S., Shimojo, S. (2018) Ap­
plication aware traffic engineering functionality for an SDN tran­sit
network. PRAGMA 34 workshop, May 2018.
Watanakeesuntorn, W., Uthayopas, P., Chantrapornchai, C., Ichikawa, K. (2017) Real-time monitoring and visualization software
for Open­Flow network. 15th International Conference on ICT
and Knowl­edge Engineering, November 2017.

18
2018 COLLABORATIVE OVERVIEWHYBRID OVERLAY/SDN
VIRTUAL NETWORKExtending SDN technologies to IoT devices via hybrid
software defined virtual networks
Software defined networking (SDN) is a mature technology widely used by network administrators in the datacenter. Its use within the datacenter and on backbone connections
across datacenters leverages the fact that a single or few administrative entities own thedata plane (switches, routers, links) and can manage it through a centralized control plane.
Leveraging SDN techniques to connect the multitude of IoT (Internet of Things) devices acrossthe Internet, such as those found in smart cities, health, or environmental applications, presents
a very different set of challenges; nonetheless, SDN exposes key primitives to packet handling,which provides a basis for software-defined edge networking.
We are investigating the use of SDN in IoT/edge computing with hybrid solutions that utilize both
SDN switches and overlay networks to create software-defined virtual networks. In our approach, asoftware-managed overlay network takes the responsibility of creating peer-to-peer virtual links, by
establishing tunnels across the public Internet—even when devices are in different network providers
and constrained by middleboxes, such as network address translators (NATs) and firewalls. The overlay network virtual links terminate in ports of SDN-controlled software switches, allowing packets sent/
received by IoT, edge, and cloud resources that reach a switch to be forwarded across the overlay to othernodes. The resulting virtualized overlay network can create a software abstraction of the layer 2 (physicaladdressing) network and, in doing so, simplify the complexities associated with the deployment of middlewareand applications across edge and cloud resources on the wider Internet. In addition, the overlay network allows
dynamic membership and grouping of resources and enforces authentication and privacy in communication,
addressing key management and security concerns.
This year, we have enhanced the IPOP overlay network to allow tunneling of traffic from/to SDN-programmed switch
ports across the Internet (Subratie et al 2018). In our approach, switches are software modules, and virtual links are overlay tunnels also implemented as software running on endpoints to encapsulate one protocol within another (Ethernet/IPover IP in our approach with IPOP tunnels). Together, the hybrid overlay/SDN approach is thus fully software-defined andcan be instantiated in a variety of resources: e.g., physical machines, virtual machines, or containers. As a next step, weare investigating the use of PRAGMA-ENT as a platform for evaluation of the hybrid approach, with software-based SDN
switches (Open vSwitch) at the edge and ENT hardware switches at the core.

PARTICIPANTS
Renato Figueiredo, Ken Subratie (University of Florida)

REFERENCES
Subratie, K., Figueiredo, R., “Towards Island Networks: SDN-enabled Virtual Private Networks with Peer-to-Peer Overlay Links for Edge Computing”, to appear, Proceedings of IDCS, Tokyo, Japan, 201819
THE PACIFIC RIM APPLICATIONS AND GRID MIDDLEWARE ASSEMBLYPRAGMA CLOUD AND VIRTUALIZATION
Enabling experiments on the PRAGMA Cloud testbed
The PRAGMA Cloud testbed provides a persistent setof resources for researchers to run their applications. To
reduce administrative overhead for participation in the
PRAGMA Cloud Testbed, we leverage existing virtualization technologies (e.g., Rocks, CloudStack, OpenNebula)at our partner sites. We have developed lightweight tools,
such as pragma_boot, which enables a virtual cluster (VC)
to be seamlessly booted at different PRAGMA partner sites
and automatically “fixes” the instantiated images to fit local site requirements (e.g., local IP addresses, DNS names,
number of compute nodes, and PRAGMA-ENT interfaces);cziso, which leverages Clonezilla to store virtual cluster images centrally in Google Drive in a universal format andthen converts to the locally supported image format (e.g.,
KVM+ZFS volume or KVM+QCOW2) at a partner site; and a
Cloud Scheduler GUI that enables users to schedule when
and where to execute their virtual clusters (Figure 5). The
PRAGMA Cloud Testbed currently has a total of more than
500 CPUs and ~1.5 TB of memory amongst five resources in Japan, Taiwan, and the United States. The PRAGMA
Cloud GUI is accessible from cloud.pragma-grid.net. Inter-

ested users should contact pragma-cloud-admin@googlegroups.com for an account.
Last year, a new version of Cloud Scheduler GUI was developed by undergraduate students Nannapas Banluesombatkul and Prapansak Kaewlamul, advised by Prapaporn Rattanatamrong, from Thammasat University. Since
then, we deployed it on our production server, configured it with current PRAGMA cloud resource details, anddemonstrated its capabilities during PRAGMA 33 in Brisbane, Australia. The students authored a paper that waspresented and published in the 21st International Computer Science and Engineering Conference in Bangkok,
Thailand in November 2017.
During January–February 2018, an undergraduate student
from Chungnam National University in South Korea, Eunjeong Jang, worked on the development of a prototype
administrative interface for the Cloud Scheduler GUI.
Other updates to the PRAGMA Cloud testbed are described in the following subsections.
Universal
Image

Raw Imageczis

Cloud Scheduler

NAIST

Japan

AIST

Japan
UC San Diego

USA

NCHC

TaiwanClonezilla

Local
VirtualCluster
Repository

Clonezilla Live VM PRAGMA_bootFigure 5: PRAGMA Cloud Testbed architecture.

20
2018 COLLABORATIVE OVERVIEWWORK WITH PRAGMA-ENT AND
MULTI-SITE VIRTUAL CLUSTERS
The pragma_boot tool enables a virtual cluster(VC) to be seamlessly booted at PRAGMA partner
sites and automatically “fixes” the existing VC images to fit local site requirements. This past year,
pragma_boot was enhanced to have the ability
to configure a PRAGMA-ENT interface on a user’s
virtual cluster.
Enabling a PRAGMA-ENT interface on a user’s VC
can be used to enable a VC’s access to a protected dataset or to create a multi-site VC. During
PRAGMA 33 in Brisbane, Australia, we demonstrated the capability of creating a multi-site VC
with one site at Indiana University (USA), another site at NAIST (Japan), and did a live boot ata third site at UC San Diego (USA) as shown in
Figure 6. This multi-site capability is also being
leveraged for the Network Function Virtualization(NFV) testbed described in the PRAGMA Experimental Network Testbed highlight.
To integrate this new multi-site capability to the
Cloud Scheduler GUI, we engaged two additional
undergraduate students from Thammasat University, Visaruth Punnium and Pasit Pongpojkasem
who were advised by Prapaporn Rattanatamrong.
The students added the ability to select two or
more sites for a single multi-site virtual cluster
reservation and also enabled advanced searchingcapabilities for a multi-site reservation (see Figure 7). The students presented the results of theirefforts in a poster during the PRAGMA 34 workshop in Tokyo, Japan.

IU (USA)public Rocks SGE

ent

ent

Frontend

privateNAIST(Japan)private Rocks SGE

Biolinux private
Computeent

ent
10.103.1.0/16$ pragma boot wa-dock
16 add-iface=openflow:
10.103.4.0/16

Compute10.103.2.0/16

publicent

DOCK
Frontend
private

UCSD(USA)
privateent

DOCKS
Compute10.103.4.0/16

Figure 6: Multi-site virtual cluster at three geographically distributed sites,
each configured with PRAGMA-ENT interfaces that enable a private network overlay amongst the resources.

Figure 7: Screenshot of the new multi-site advanced searching functionality in the PRAGMA Cloud Scheduler GUI. Multiple choices are shown for arequest of a total of 64 CPUs and 128 GB of memory—the users can selectthe best one that suits their requirements.

GPUs can offer improvements for machine learning applications involved with video and audio processing. To
facilitate a more rapid exploration of these technologies,
PRAGMA developed a new Rocks gpupt roll1 that enables GPUs to be allocated or passed through to virtual
machines. We installed eight Tesla and GeForce GTX typeGPUs on UC San Diego PRAGMA Cloud resources and allocated GPUs to two virtual clusters for two separate ex2

publicprivateEARLY EXPERIMENTATION WITHGPUS AND MACHINE LEARNING

1

Biolinux
Frontend

periments that were demonstrated during the PRAGMA 34
workshop in Tokyo, Japan. One virtual cluster was allocated to University of Florida for a deep learning experimentto find museum specimens that had been contaminatedwith mercury salts as part of the Integrated Digitized Biocollections (iDigBio) project2. A second virtual cluster was
allocated to a team from National Chiao Tung University(Taiwan) for a deep learning experiment to process trafficmonitoring images.

github.com/pragmagrid/gpupt
www.idigbio.org
21

THE PACIFIC RIM APPLICATIONS AND GRID MIDDLEWARE ASSEMBLYDEPLOYING CONTAINERS ON
PRAGMA CLOUD

App A

App B

Bins/Libs

Bins/Libs

App A

App A

App B

App B

Over the past few years, container-based virtualGuestBins/Libs
OS
Bins/Libs
Guest
OS
Bins/Libs
Bins/Libs
App A
App B
ization has matured and become pervasive as aHypervisor
Docker Engine
Guest
OS
Guest OS
Bins/Libs
Bins/Libs
lightweight method to package complex applicaHypervisor
Docker
HostOS
HostEngine
OStion environments and microservices. A container
Host OSHostOS
is a lightweight, stand-alone, executable packageServerServerthat includes binaries, libraries, runtime environServer
Server
Virtual Machine
Container
ment, and configuration to run applications (seeVirtual Machine
Container
Figure 8). Containers have much shorter startup Figure 8: The architecture of a container versus a virtual machine.
App A
App B
App A
App B
times of 1–2 minutes compared to virtual machines’
Bins/Libs
Bins/Libs
Bins/Libs
Bins/Libs
Physical or Virtual
15–30 minutes. While some PRAGMA applications Public IP
Docker Engine
Docker Engine
Physicalor Virtual
Public IP
Cluster ofMachines
Host OS
Host OS
Cluster of Machines(e.g., lake ecology) may benefit from being pack- App A
App BServerServerBins/Libs
aged in containers, it may not be appropriate for Bins/Libs
Docker Engine
PrivateNet
Net
Privatean application like Lifemapper, which has complex
Host OS
App A
App B
App A
App B
Serversoftware dependencies. We have provided an enBins/Libs
Bins/Libs
Bins/Libs
Bins/Libs
Built
with
Builtvia
viaRocks
RockswithDocker Engine
Docker Engine
vironment in the PRAGMA Cloud where we canKubernetes
MasterKubernetes
MasterKubernetes
Roll
Kubernetes
Roll
Host OS
Host OS
explore the use of containers and quantitatively
ServerServerassess usage of both technologies, containers, andKubernetes Nodes
Kubernetes Nodes
Figure 9: Kubernetes deployment on a standard Rocks virtual cluster.
full virtualization.
App A

App B

Bins/Libs

Bins/Libs

App A

App B

App A

App B

Bins/Libs

Bins/Libs

Bins/Libs

Bins/Libs

Docker Engine

Docker Engine

Host OS

Host OSServerServerDocker Engine
Host OSServerKubernetes is an open-source system for automating deployment, scaling, and management of containerized applications. During the PRAGMA 34 meeting wedemonstrated a new Kubernetes virtual cluster instancefor PRAGMA Cloud. To create the Kubernetes virtual cluster, a new Rocks roll1 was developed that enables easy deployment and configuration of Kubernetes on a standard
Rocks cluster (see Figure 9). Kubernetes requires a specific OS kernel version, so packaging it as a virtual cluster
1

App A

App B

App A

App B

Bins/Libs

Bins/Libs

Bins/Libs

Bins/Libs

Docker Engine

Docker Engine

Host OS

Host OSServerServerenables it to be run on any PRAGMA Cloud testbed site.
The Kubernetes virtual cluster image is based on Rocks 7,
which was released in December 2017.
Over the next year, we will leverage the Kubernetes
virtual cluster and use it to experiment withapplication containers. We believe Kubernetes will enable PRAGMA

github.com/rocksclusters/kubernetes

222018 COLLABORATIVE OVERVIEWto deploy new applications for users more quickly, andwe will investigate which services could be re-packaged
as Kubernetes applications. Containers will also facilitate
network performance monitoring on the PRAGMA Cloud
testbed as each deployed application container can inherit
a common instrumented container that will be built to include monitoring tools like Tstat. Kubernetes cluster federation is emerging now, and we plan to utilize this capability
with eduGAIN/OAuth2-based authentication and to investigate federation with other Kubernetes deployments,
such as UC San Diego’s Cognitive Hardware and Software
Ecosystem Community Infrastructure (CHASE-CI) and Pacific Research Platform (PRP) projects.

PARTICIPANTS

REFERENCES
Banluesombatkul, N., Kaewlamul, P., Rattanatamrong, P.
Williams, N., and Smallen, S. (2017) PRAGMA Cloud Scheduler: Improving usability of the PRAGMA Cloud testbed.
2017 21st International Computer Science and Engineering
Conference (ICSEC). IEEE, 2017.
Punnium, V., Pongpojkasem, P., Smallen, S., Williams, N.
and Rattanatamrong, P. (2018) Multi-site Cluster Reservation for PRAGMA cloud (Poster). PRAGMA 34, May 9–12,
2018, Tokyo, Japan.

SOFTWARE
PRAGMA’s software products discussed in this highlightare available at www.pragma-grid.net/products.

UC San Diego: Shava Smallen, Nadya Williams, Philip Papadopoulos; Thammasat University: Nannapas Banluesombatkul, Prapansak Kaewlamul, Visaruth Punnium, Pasit
Pongpojkasem, Prapaporn Rattanatamrong;
National Institute of Science and Technol­ogy: Kohei Ichikawa

23
THE PACIFIC RIM APPLICATIONS AND GRID MIDDLEWARE ASSEMBLY

AI BRIDGING CLOUD INFRASTRUCTURE (ABCI)
Deploying world-class infrastructure to push the envelope of artificial intelligence research

Figure 10. Fluorescent image of nuclear targeted neural activity sensors in the zebrafish brain. Activityof neurons that responded to low oxygen were identified. A particularly interesting subpopulation
responding to the low oxygen environment are highlighted in red. All neurons appear in green.

With the recent global interest in artificial intelligence(AI), The National Institute of Advanced Industrial Science and Technology (AIST) in Japan is positioning itself
to be one of the leaders in the development and deployment of AI applications for both industry and society. As
a community resource, ABCI1 will foster collaboration between academia, industry, and vendors of IT solutions.
Researchers will be able to leave the AI “fabrication” to
ABCI and focus on their research. AI technologies, especially machine/deep learning, are highly dependent on
calculations at scale using big datasets to train AI algorithms and improve their accuracy. In order to address
this computational challenge, AIST built ABCI, the world’s
first large-scale, open innovation platform for AI researchand development. ABCI consists of 1,088 computation1

nodes with 4,352 NVIDIA Tesla V100 GPUs, 2,176 Intel
Xeon Gold 6148 CPUs, Infiniband EDR, 476 TiB memory,
1.74 PB NVMe SSD, 22 PB large-capacity GPFS storage
system, and high-speed network connections, all housedin an ultra-green datacenter building. By commoditizing
and introducing supercomputer cooling technologies,
the expected average power usage effectiveness (PUE)over a year is less than 1.1. This infrastructure achieves
more than 550 petaflops (half-precision floating point)
and 37 petaflops (double-precision floating point) theoretical peak performance. ABCI is currently the fastest
computer in Japan and placed fifth on the global Top500
list as of June 2018, with a high performance Linpack(HPL) benchmark of 19.9 petaflops.

abci.ai242018 COLLABORATIVE OVERVIEWThis platform integrates high performance computing(HPC), big data, ultra-high bandwidth, and low latency
hardware in a modern design to enable better cooperation between HPC applications and machine learning,which will become a very important factor in the futureof AI. To facilitate academic AI research, we are connecting ABCI to a global, high-speed network research platform (the Pacific Research Platform2) to extend research
opportunities to a broad number of international institutions. One of the first grand challenge projects we aresupporting is mapping whole-brain-scale signal integration events in zebrafish (Figure 10) with researchers fromthe Salk Institute for Biological Studies and the Scripps
Institute of Oceanography in San Diego. This will open
the possibility of creating novel neural deep-learning architectures of the fish brain to be used in a wide variety
of application areas, including robotics, sensor design,and behavioral sciences.
ABCI started full-fledged operation in August 2018. AISTis creating an ABCI utilization service to provide learned
models, open data, and training data sets to its users forthe acceleration of joint academic-industry AI R&D. For
2

the PRAGMA community, this platform will be a valuable
resource to further AI research between our members.
Additionally, the community will gain informative “lessons learned” from operating such a platform and a reference architecture for PRAGMA members interested inestablishing data centers combining HPC and AI to drive
future innovations. Members from the National Centerfor High Performance Computing (NCHC) in Taiwan havealready exchanged information several times with AIST
as they move to build an AI-focused infrastructure. It is
expected that the PRAGMA community will build a largescale distributed AI research platform by connecting
ABCI with AI supercomputers operated by other PRAGMA member institutions.

PARTICIPANTS
National Institute of Advanced Industrial Science and Tech­
nology (AIST): Hirotaka Ogawa, Ryousei Takano, Satoshi
Sekiguchi, Yoshio Tanaka, Jason Haga; Salk Institute for Bi­
ological Studies: Gerald Pao, Scripps Institution for Ocean­ography: George Sugihara

prp.ucsd.edu

25
THE PACIFIC RIM APPLICATIONS AND GRID MIDDLEWARE ASSEMBLY

TOWARDS EXTENDING THE PRAGMA CLOUD TO
INCLUDE AN OPEN DATA PLATFORM
Integrating data servers from international partners to support a notion of FAIR data
Driven by the needs of key applications as well as thegrowing opportunities for artificial intelligence (AI) research infrastructure, PRAGMA has taken steps to extend its PRAGMA Cloud infrastructure to an international shared data platform. Additionally, guiding our initialsteps in this extension are the Force 11 FAIR (Findable,
Accessible, Interoperable, and Reusable) Principles, starting with persistent IDs, especially for data not necessarily
associated with publications. By expanding the PRAGMA
Cloud testbed to include an open data platform, we intend to boost the efficiency of data-driven research, facilitate novel AI research that utilizes computational resources within the PRAGMA network, and enable piloting
and testing of strategies for making early-life data FAIR.

MOTIVATION AND ACCOMPLISHMENTS
Two examples of our work illustrate and underpin boththe benefit and the need for the international data platform. First, PRAGMA’s virtual biodiversity expedition’sLifemapper system creates distribution maps and predictions using a wealth of existing species occurrence data,
combined with global climate, terrain, and land cover information. The NSF-funded, University of Florida-based
project iDigBio’s1 servers are a major source of species
occurrence data but are not designed to host Lifemapper
cluster-based simulations. To address this need, by theend of 2018, we will have deployed an iDigBio mirror at
UC San Diego, co-located to utilize the NSF-funded XSEDE
resource Comet, and we will have created a data platform
between U Florida and UC San Diego (via standard network paths to connect to UC San Diego’s DMZ). Regularperformance monitoring and synchronization of data will
give us insights on how performance varies over time and1make Lifemapper more efficient by having data co-locatedwith virtual cluster capabilities on Comet.
Second, through a partnership developed through the
PRAGMA community, Japan’s Artificial Intelligence
Bridging Cloud Infrastructure (ABCI) is initially available
for some U.S. researchers’ use. During summer 2018, we
explored a practical method of efficient transfer of data
across the Pacific from San Diego to Japan and are testing to gain insight on acceptable performance. The motivating research involves the use of novel neuromorphic
deep learning architectures running on GPU-enabled
nodes at ABCI, using light sheet microscopy imaging
data of zebrafish brain activity that scientists from the
Salk Institute in the U.S. have collected. The data and results need to be transferred efficiently and without error
and need to be stored at the destination (ABCI) in a manner that makes the data immediately usable by the GPUs
and deep learning architectures. (See AI Bridging Cloud
Infrastructure highlight for details of the science.)
To date, our study of data movement across internationalboundaries has been technical in nature and has focusedon the first step of making data FAIR, namely evaluating
how and when to assign globally unique, persistent IDs(PIDs) to data that is early in its lifecycle. Furthermore,
our efforts focus on data that needs sharing long before
it is associated with research publications, of which many
choices exist.
PRAGMA’s strategy for FAIR data evaluation in the PRAGMA
Cloud testbed draws on the Research Data Alliance (RDA)
discussions around constructing an international fabriccomposed of data objects, where all data objects are find-Integrated Digital Biocollections, https://www.idigbio.org/

26
2018 COLLABORATIVE OVERVIEW

able. This vision for FAIR data assigns PIDs (handles) to data
objects, with information about objects stored to a globally
available type registry. PRAGMA has pioneered the notionof PID Kernel Information (PID KI), which embeds a small
amount of metadata about a data object into the object’s
handle record. We have evaluated how and when to assign
PIDs to data through two project efforts that have significant societal benefit: Rice Galaxy and AirBox.
RICE GALAXY: Rice genomic researchers seek to improverice yields, thereby reducing world hunger, through research and access to tools and infrastructure. Rice molecular genetics, breeding, and diversity researchers haveadopted sequencing-based technologies and high-density genotyping chips for genome variation discovery(e.g., single nucleotide polymorphism (SNPs), indels,large structural variants) (Juanillas et al. 2018). Rice Galaxy adopted the Galaxy bioinformatics framework2 andbuilt federated Galaxy resources, with shared datasets,
software tools, and analysis workflows tailored to theneeds of rice genetic/genome/diversity researchers andbreeders. Pilot extension of Rice Galaxy to open sciencehas the goal of advancing the platform for open access,hence making Rice Galaxy consistent with the data access policy (CGIAR3) that guides the Rice Galaxy community and data sharing. The design employs a hands-off
technique (data provenance capture) to gather informa-tion about a researcher’s rice genomics analysis as theanalysis is running. Through this technique, acquired information is compiled with pre-analysis information thatis available at the beginning of the analysis workflow(Luo et al. 2018). Key metadata is stored to the PID as
PID Kernel Information (Luo Oct 2017, Luo Dec 2017). The
data management software services were ported in 2018
to virtual machines (VMs) running at the Advanced Science and Technology Institute (ASTI) in the Philippines
while using the NSF-funded RPID testbed (NSF 1659310)
for obtaining test IDs. The specially instrumented andconfigured Rice Galaxy VMs, developed by PRAGMA, arenow deployed at ASTI for beta testing.
AIRBOX: Air pollution is a major concern in modern life.
Fine grained particulate matter measuring less than 2.5
micrometers, i.e., PM2.5, is particularly harmful to health.
The Airbox project aims to put equipment and data sharing analysis tools in the hands of the public to monitor
air quality.
At the March 2017 PRAGMA 32 meeting in Gainsville
Florida, Indiana University, the University of Florida, andthe National Center for High-performance Computing(NCHC) defined a strategy for “chunking” sensor dataso that immutable chunks could be findable (Plale etal. 2018). The strategy was then implemented as a set

galaxyproject.org
a global research partnership for a food secure future dedicated to reducing poverty, enhancing food and nutrition
security, and improving natural resources, see www.cgiar.org

2

3

27
THE PACIFIC RIM APPLICATIONS AND GRID MIDDLEWARE ASSEMBLY

Instrumentation Data Storage

Site 1

Instrumentation Data Storage

Site 2Site...

Figure 11. Instrumented PRAGMA Cloud testbed using
containers that inherit a common TSTAT logging
container. Application and Tstat metrics get sent toredundant centralized instrumentation data storage.

Site...

Base Container

App1 Container

Base Container

App1 Container

FDT

Lifemapper

FDT

Lifemapper

TSTAT

TSTAT

TSTAT

TSTAT

Bins/libs

Bins/libs

Bins/libs
Site 3

Bins/libs
Site 4of type definitions that are stored to an instance of theData Type Registry that is managed by the NSF-funded
Robust Persistent Identification of Data (RPID) testbed(see Data subsection below). The PRAGMA AirBox project utilizes the services of the RPID testbed, including requesting test PIDs from the handle service, storing typedefinitions to the Data Type Registry, and experimenting
with PID Kernel Information representations.
The AirBox pilot has been used in a classroom training
exercise for student projects that are carried out using
cloud resources. Students analyze the AirBox sensor datathat is regularly published to the cloud. The data are accessed through Azure VMs that are configured with tools
for analyzing the sensor data. The purpose is to demonstrate that online courses can utilize cloud resources in
the classroom (Plale and Kouper 2017). The pilot utilizes
sensor data from the Airbox Project with permission from
NCHC in Hsinchu City, Taiwan.

FUTURE PLANS
Currently, in the PRAGMA Cloud, we are actively testing
the use of a Kubernetes virtual cluster to support application containers (see PRAGMA Cloud and Virtualization
highlight). We will use performance monitoring containers that will facilitate instrumentation of the PRAGMA
testbed (see Figure 11). The instrumented container willcontain monitoring tools like Tstat and data transfer tools
like FDT. The plan for the data platform consists of infrastructure monitoring, PID assignment, and data storage:

tstat.polito.it
Influx Data Company, www.influxdata.com
6
www.netsage.global

INFRASTRUCTURE MONITORING: Infrastructure monitoring will begin with existing tools, with selection approached from an application’s point of view of the infrastructure, an uncommon and novel perspective. Initial
work performed during Spring 2018 by a student from
Chungnam National University (South Korea) displayed
Tstat, TCP STatistical and Analysis Tool4, and data using the TICK stack (Telegraf, InfluxDB, Chronograf, andKapacitor)5. We also intend to leverage work from the
NetSage project6, whose service collects networking datafrom active and passive measurements (e.g., perfSONAR7, Tstat, SNMP), stores the data centrally, and visualizes it with Grafana8.
PID ASSIGNMENT: PID assignment leverages the
NSF-funded RPID testbed (see Data subsection below).
The RPID testbed services support assignment and resolution of temporary PIDs (handles). The ability to assign
temporary PIDs is critical for testing. RPID supports PID
Kernel Information profiles, which are exploratory extensions to handles that we continue to utilize to study connections between data objects generated during both
Rice Galaxy and Airbox projects.
DATA STORAGE: There are now multiple open source data
storage systems that are suitable for managing time series
data. PRAGMA partners at AIST, NCHC, and MIMOS are
beginning to develop expertise around the Ceph object
store9, which holds promise as a common distributed data
storage platform for the PRAGMA Cloud testbed data platform. Other storage servers are under discussion within
PRAGMA. Evaluation criteria for data storage include thewww.perfsonar.net
Grafana Labs
9
ceph.com

4

7

5

8

28
2018 COLLABORATIVE OVERVIEW

following: How well do PIDs map to identity/naming strategy used in the data storage system? Does the storage
system support multiple unique IDs? How are data objects
discoverable through unique IDs? How well do the systems
federate across administrative boundaries? How efficientis the system in moving large amounts of data in/out for
purposes of analysis? How well do the systems support
access control where data are restricted?

PARTICIPANTS
UC San Diego: Nadya Williams, Philip Papadopoulos, Shava Smallen; National Center for High-performance Com­puting (NCHC): Weicheng Huang, Steven Shiau, Ceasar
Sun, Hsiu-Mei Chou; Indiana University, Bloomington: BethPlale, Yu Luo; National Institute of Advanced Industrial Sci­
ence and Technology (AIST): Jason Haga, Ryosei Takano,
Yoshio Tanaka; Salk Institute for Biological Studies: Gerald
Pao, Chen-min Yeh, Eric Saberski; Rice Galaxy Project: In­
ternational Rice Research Institute (IRRI): Ramil Mauleon,
Venice Juanillas; Advanced Science and Technology Insti­
tute (ASTI): Jelina Tanya H. Tetangco; AIST: Jason Haga; In­diana University: Airbox Project: Academia Sinica: Ling-Jyh
Chen; NCHC: Hsiu-Mei Chou; Indiana University: Beth Plale;
TSTAT (Infrastructure Monitoring) Project: Chungnam; Na­tional University: Chungnam National University: Minsung
Joh, Minsun Lee

SOFTWARE
Tstat roll: github.com/pragmagrid/tstat
PRAGMA Data Service: github.com/Data-to-Insight-Center/RDA-PRAGMA-Data-Service

REFERENCESS
Juanillas, V. M., Dereeper, A., Beaume, N., Droc, G., Dizon,J., Mendoza, J. R., Perdon, J. P., Mansueto, L., Triplett,L., Lang, J., Zhou, G., Ratharanjan, K., Plale, B., Haga, J.,
Leach, J. E., Ruiz, M., Thomson, M., Alexandrov, N., Larmande, P., Kretzschmar, T., and Mauleon, R. P. (2018)
Rice Galaxy: an open resource for plant science, bioRxiv
358754. 2018. doi: doi.org/10.1101/358754.
Luo, Y., Zhou, Q., Ratharanjan, K., and Plale, B. (2018) Persistent IDs: Application to Workflow and Sensor Applications (poster). PRAGMA 34, Tokyo, Japan, May 9, 2018.
www.pragma-grid.net/images/pragma34/Luo.pdf

org/sites/default/files/RDA%20Plenary%20Yu%20.pdf
Luo, Y. (2017) Toward FAIR Open Science with PID Kernel Information: the RPID testbed. IEEE Workshop on Big
Data Metadata and Management BDMM’17 (invited talk).
Boston, MA, USA, Dec 2017.
Plale, B., Kouper, I., et al. (2017) SEADTrain data analysis:
Hands-on tutorial. Presentation materials. ESIP Summer
2017 meeting in Bloomington, IN, figshare.com/articles/
SEADTrain_Data_Analysis/6873800.
Plale, B. et al. (2018). Persistent IDs for AirBox Air Quality
Monitors (poster). Figshare. Presentation PRAGMA 32/CENTRA Mar 2017, doi.org/10.6084/m9.figshare.6875567.v2.

DATA
PRAGMA PID AIRBOX DATA: All devices operational as ofMay. The data is from 2 channels: i) MAPS channel – datafrom May 2017–Jan 2018 (9 months); size: ~500MB and ii)
Airbox-Copy channel—data from Sept 2017–Jan 2018 (5months); size: ~850MB. Total ~1.3GB Airbox data. github.
com/Data-to-Insight-Center/SEADTrain/tree/master/
data and github.com/Data-to-Insight-Center/SEADTrain/
wiki/SEADTrain-Data-Description.
The data used in this training exercise is made available through a collaboration of the Pacific Rim Applications and Grid Middleware Assembly (National
Science Foundation award #1234983), the Center of Excellence for Cyber Enablement of Applications (MOST
104-2923-E-492-002-MY3), and Academia Sinica (MOST
105-2221-E-001-016-MY3). Special thanks to Edimax Inc.
and the LASS community for their support, technical advice, and administrative assistance.
ROBUST PERSISTENT IDENTIFICATION OF DATA (RPID):The NSF-funded (#1659310) robust PID testbed, called
the RPID testbed (pronounced “rapid”), stimulates andenables evaluation of powerful new complementary outputs of the Research Data Alliance (RDA) in PID oriented
data management. See rpidproject.github.io/rpid. See
also Luo 2017.

Luo, Y. (2017) Towards FAIR Open Science with PID Kernel Information. Research Data Alliance Plenary 10, Montreal, Canada, Oct 2017. Retrieved from www.rd-alliance.
29
THE PACIFIC RIM APPLICATIONS AND GRID MIDDLEWARE ASSEMBLYVISUALIZATION INFRASTRUCTURE AND ACTIVITIES
Improving understanding through visualizing multiple integrated data sources
The use of large format tiled display walls for immersive
visualization and analytics continues to be an active areain PRAGMA and builds on strong ties with the Collaborations to Enable Transnational Cyberinfrastructure Applications (CENTRA) partnership and the University of
Hawaii, Manoa. The application areas have expanded beyond the disaster management platform developed using
SAGE2 (Scalable Amplified Group Environment 2), LAVA
(Laboratory for Advanced Visualization Applications) at
the University of Hawaii, Manoa, and EVL (Electronic Visualization Laboratory) at the University of Illinois, Chicago. One growing application area is in e-health, in which
a visualization workflow to provide decision support for
medical research projects in Thailand (MedThaiSAGE) is
being developed through a collaboration between the
National Institute of Advanced Industrial Science andTechnology (AIST) and Mahidol University. The idea isto enable practitioners and policy
makers to explore
a variety of different data in orderto make informed
decisions when

implementing future policies. With this goal in mind, a
prototype platform has been developed (see Figure 12)that links together different types of data in the backend
to provide various views of the data on the display wall.
A second application area is developing a visualization
tool for traffic monitoring in Taiwan using machine learning (Figure 13). This smart city application, in a collaboration between AIST and Taiwan’s National Chiao Tung University (NCTU), would enable urban planners to analyze
traffic patterns in drone and webcam videos when making
decisions. Thus, these applications serve as working prototypes of systems designed to support decision-making
capabilities for different domains in a shared collaborative environment. The future vision is to create an immersive platform that provides a visual “workflow” thatcan facilitate the understanding of data by decision-makers during both
non-critical andcritical situations.
These
applications can leverage the stable
PRAGMA com-

Figure 12. Image of the unified, single visualization interface of MedThaiSAGE. Multiple
types of data are visible at once and are linked together to propagate any changes inthe data as the user explores it. The application is designed to run natively in SAGE2
workspaces. This work is a collaboration between AIST and Mahidol University, withtechnical collaboration from the University of Hawaii.

30
2018 COLLABORATIVE OVERVIEWFigure 13. Screen shot of SAGE2 workspace of machine learning
application for traffic monitoring. Multiple camera locations can bevisualized and analyzed for the number of cars that pass a virtualgate set by the user.

pute infrastructure and are drivers for the Pan-Pacific
Visualization Alliance established within CENTRA.
At the PRAGMA 35 conference, a keynote presentation
was given in conjunction with the Big Data Summit 2
that focused on visualization applications for a variety
of domains. One highlight was illustrating how complex
workflows could be facilitated across multiple applications by linking the data passed between applications
and incorporating voice commands. This keynote wasan important outreach opportunity for extending PRAGMA’s goal of developing strong international collaborations and engaging new partners.

PARTICIPANTS
National Institute for Advanced Industrial Science andTechnology (AIST): Jason Haga; National Chiao Tung
University (NCTU): Jimmy Ching-Yu Liu (student),
Chih-Wei Yi; Mahidol University: Jarernsri Mitrpanont,
Jirayu Roungsuriyaviboon (student), Thada Sathapornwatanakul (student), Wudhichart Sawangphol; Universi­
ty of Hawaii, Manoa: Dylan Kobayashi (student)

31
THE PACIFIC RIM APPLICATIONS AND GRID MIDDLEWARE ASSEMBLYWEB-BASED SCIENCE AND ENGINEERING
PLATFORM FOR ADVANCED CYBER-LEARNING
Implementing new workbench and workflow environments in the EDISON platform
for computational science and engineering
EDISON, which stands foret cetera for developers of
EDucation-research Inteapps (which are simulagration through Simulation
tion software programs).
On the Net, is the wellThis tool enables users toknown e-Science platform
conduct their simulations
developed to meet the sciefficiently and lowers theentific computing needs
barriers to users with fewof domain scientists. The
er computational technolnumber of disciplines andogy skill, as in the case ofusers of EDISON have incomputational medicine
creased annually since its
users. Figure 14 shows anlaunch in 2011 and currentexample situation in which
Figure 14. EDISON’s Web-based scientific workbench.
ly there are eight academic
the workbench was useddisciplines and more thanto provide an advanced
ten thousand users of the platform each year. The viglecture environment for a Physiology course where theorous activity has been accelerated by the deployment
users (normally medical interns) were able to read docuand use of several new e-Science technologies, such as
ments of theory while simultaneously running simulationa scientific workbench and workflows. EDISON scientificapps to visualize and test the theories being learned. The
workbench is a user-friendly browser-based simulation
tutor and interns participating in the course reported thatrunning panel that contains the customized work areas ofusing the cyber-learning environments provided them
input, output, visualization, monitoring, job control, andmuch greater understanding of the subject.

Figure 15. An example of Web-based scientific workflow: Multiphysics simulation for a human heart.

32
2018 COLLABORATIVE OVERVIEWAnother important technical advancement
SOFTWARE
in 2017-2018 was the development and
EDISON portal: www.edison.re.kr/home. A
application of the scientific workflow tool.
Korean (full version) and English (partial
The EDISON portal provides a workflow exversion) are available.
ecution environment that can incorporate
Scientific Workbench: www.edison.re.kr/
scientific apps developed by various simuweb/portal/scienceappstore. Log-in withlation developers from different disciplines.
user ID and password are required for runThis means that the workflow tool conducts
ning simulation apps. Please contact Ruth
consecutive executions of multiple apps by
Lee (jsruthlee@kisti.re.kr) if interested inapplying various functions: serial, parallel,using the scientific workbench or scientificconditional, loop, format converting, and etworkflow applications.
cetera. This workflow tool can be appliedin college courses to integrate learning as
Scientific Workflow: www.edison.re.kr/
well as individual cyber-learning. Figure 15
web/portal/workflow-workbench. Log-in
shows the connection of six EDISON apps
with user ID and password are required forfor a multi-physical analysis of a humanrunning simulation apps.
heart as a workflow. After an actual application in a college lecture, it was demonstratREFERENCES
ed that by reflecting the clarity of the strucKim, N., On N. R., Lee, J. S., Nam, D., Cho,ture of the computation flow, the level ofK., Choe, K. T., and Yu, J. (2015). An emlearners’ understanding of the given probpirical analysis of the user acceptance oflem increased. In addition to this example, Figure 16. EDISON was acomputer simulations utilized for higher
there have been examples of other possible proud recipient of a 2017 National R&D Top 100 Outstandeducation in science and engineering, ICIC
application areas, such as automation of
ing Achievement Award.
Express Letters, Part B: Applications, 6 (4),presolving and post processes, optimal enpp. 1197–1203.
gineering design, percolation analysis, andmore. Therefore, it is highly anticipated that beginners in
Ma, J., Lee J. S., Cho, K., and Park, M. (2017). Design andengineering can be encouraged to understand their speimplementation of information management tools for the
cialties in a bigger picture of the analysis processes.
EDISON open platform. KSII Transactions on Internet andBy the virtue of the above efforts, the EDISON program
won a 2017 National Top 100 Outstanding Achievement
Award for R&D from Ministry of Science and ICT, Korea(Figure 16). Nowadays, STEAM (Science, Technology,
Engineering, Art, and Mathematics) education is increasingly emphasized throughout the world. To be fully successful in STEAM in K-12 and higher education, various
useful cyber-learning tools are now being developed andprovided. In response to this requirement, the EDISON
workbench and workflow tools will be applied to a variety of new science and engineering problems and upgraded with proper technologies as part of future efforts.

Information Systems, 11(2) pp. 1089–1104.
Park, S. R., Lee, J. S., and Cho, K. (2016). Effectivenessof online simulation-based e-learning for computational
science and engineering in higher education. Advanced
Science Letters, 22(9) pp. 2257–2261.
Ryu, H., Yu, J. L., Jin, D., Lee, J. H., Nam, D., Lee, J. S.,
Cho, K., Byun, H. J., and Byeon, O. (2014). EDISON science gateway: A cyber-environment for domain-neutralscientific computing, IEICE Transactions on Informationand Systems, E97-D(8), pp.1953–1964.

PARTICIPANTS
Korea Institute of Science and Technology Information(KISTI): Dr. Ruth Lee (PI), Dr. Junghun Shin (Team Leader), Dr. Jeonghyun Jerry Seo (Team Leader), Sunil Ahn(Team Leader), Namgyu Kim (Team Leader)

33
THE PACIFIC RIM APPLICATIONS AND GRID MIDDLEWARE ASSEMBLY

34
2018 COLLABORATIVE OVERVIEWSTUDENTS IN PRAGMA
Creating globally minded problem solvers for 21st century challenges
PRAGMA is committed to engaging new communities ofresearchers and building a broader scientific community.
To do this, we focus on two main efforts: One is to engage
students in PRAGMA activities and research; the other is
to work with communities of researchers to leverage theirinterests and broaden the impact of the work we do. Bothof these activities enrich PRAGMA by infusing ideas, questions, and energy into our workshops and our experiments
and encouraging development between workshops.
PRAGMA’s efforts to engage students are aimed at creating globally minded problem solvers for 21st century
challenges. In particular, we want to inspire students
to become research leaders who can function well in acollaborative, multidisciplinary, and multi-cultural world.
Our approach focuses on two strategies:• Enhancing professional experiences for and development of students at PRAGMA workshops and• Providing students with research experiences
throughout the PRAGMA network.
To these ends, we established the PRAGMA Student organization in 2012 and work with PRAGMA members toencourage student research mobility experiences throughprograms like the Queensland Research Projects Abroad(QURPA) and Monash Undergraduate Research Projects
Abroad (MUPRA) programs, Internships at AIST, and project-based research exchanges at member sites (for more
examples, see PRAGMA Students and PRAGMA Data Infrastructure highlights). This section describes these activities.

35
THE PACIFIC RIM APPLICATIONS AND GRID MIDDLEWARE ASSEMBLYPRAGMA STUDENTS
Building a future generation of international researchers

PRAGMA 35 student workshop participants and mentors, Penang, Malaysia October 3, 2018

PRAGMA Students, an organization formed in 2012, aims
to help students gain opportunities for professional experiences within PRAGMA’s trusted social and technicalnetworks. As a student organization inside PRAGMA, thegroup is led by a student committee and advised by senior
PRAGMA researchers.
To date, activities of PRAGMA Students have included organizing PRAGMA-affiliated student workshops and poster sessions as part of the biannual PRAGMA Workshops
and developing a unique model to provide multiple opportunities for students to participate in PRAGMA’s collaborative scientific research. PRAGMA provides a trusted network of people and opportunities in leadership that help
students gain valuable professional experience.
There are several advantages to joining PRAGMA Students and the PRAGMA community. These opportunities
include, but are not limited to, the following activities:
1. Participating in workshops and conferences in an international setting, which stimulates inspiration, information sharing, and collaboration;

2. Working with PRAGMA mentors and advisors onchallenging, state-of-the-art research projects, whichstrengthens research skills and ability for scientific exploration;
3. Visiting other PRAGMA sites as part of short-term residential research opportunities, which provide both scientific and cultural experiences.
For the May 2018 PRAGMA 34 workshop in Tokyo, Japan,
PRAGMA Students organized the poster session. Membersof the PRAGMA Students committee reviewed and selected posters from all workshop participants. Around 21 posters were carefully evaluated, and detailed review feedback
was provided to the submitters. Workshop participants
were asked to put stickers on their favorite posters, and anaward was presented to the top four posters that received
the most stickers from participants during the poster session. The poster winners came from Taiwan, the UnitedStates, Thailand, and Japan institutes. This activity also
took place at PRAGMA 35. (See Posters subsections forlists of Best Posters).

362018 COLLABORATIVE OVERVIEWIn addition, PRAGMA Students organized a lightning talksession for all PRAGMA participants that gave poster authors an opportunity to briefly talk about their researchin one-minute presentations. The session allowed participants to get feedback on their work while gaining valuable
presentation experience. Eighteen authors gave brief talks
about their respective research projects.
During the PRAGMA 35 workshop in Penang, Malaysia,
PRAGMA Students held a new session, Student Presentation Session, which gave an opportunity for students to
do a 15-minute presentation and receive feedback from
PRAGMA mentors. Nine students participated in this session. Additionally, prior to PRAGMA 35, on September 26,
2018, we held a webinar, led by Jason Haga (AIST), to help
students prepare for academic presentations.
For the PRAGMA 35 poster and lightning talk sessions, 25
posters were accepted and 23 poster authors gave 1-minlightning talks to introduce their posters. Best student poster recipients were from Malaysia and Indonesia institutes.
Outside of the workshop venue, some students in PRAGMA partook in short-term residential research opportunities. Wassapon Watanakeesuntorn, a master student fromthe Nara Institute of Science and Technology (NAIST),
was a visiting scholar from August to September 2018 at
The National Institute of Advanced Industrial Science andTechnology (AIST) in Tsukuba, Japan where he worked
on a project called “Novel Neuromorphic Deep Learning
Architectures from Empirical Dynamical Modeling of the
Zebrafish Brain.” As part of this project, PRAGMA aims tooptimize the code and use the AI Bridging Cloud Infrastructure (ABCI) data center to run the deep learning al-

gorithm on this project. This internship project is a collaboration project with UC San Diego. (See also AI Bridging
Cloud Infrastructure highlight.)
We would like to note that five members of the PRAGMA Student Steering Committee, Pongsakorn U-chupala (NAIST), Quan Zhou (Indiana University), Chawanat
Nakasan (NAIST), Che Huang (NAIST), and Giljae Lee (UFlorida) all received their PhDs during this year. Congratulations!

PRAGMA STUDENT STEERING COMMITTEE
Wassapon Watanakeesuntorn (NAIST), Can Wu (Chinese
Academy of Sciences), Chiao-Ning Chuang (National Chiao
Tung University)

STUDENT MENTORS (to October 2018)
Beth Plale (Indiana University), Karpjoo Jiang (Konkuk Uni­
versity, Korea) (through May 2018), Putchong Uthayopas(Kasetsart University). Note: Jason Haga has assumed re­sponsibility for the Mentoring Functional Area Role on theSteering Committee.

PRAGMA 34 BEST POSTERS
1st: Chiao-Ning Chuang, Chien-Heng Wu, Wen-Yi Chang,and Whey-Fone Tsai. National Chiao Tung University, Tai­wan. Implementation of Deep Learning Algorithm on
Personal Big Data Platform for Engineering Applications
2nd: Yu Luo, Quan Zhou, Kunalan Ratharanjan, Beth Plale,
Ramil Mauleon, Jason Haga, and Hsiu-Mei Chou. Indiana
University Bloomington, USA. Persistent IDs: Application
to Workflow and Sensor Applications

37
THE PACIFIC RIM APPLICATIONS AND GRID MIDDLEWARE ASSEMBLY

2nd: Muhammad Reza Aditya, Resskytha Permata Sari, Adri Nursimarsiyan,
and Nova Eka Diana. Universitas YARSI,
Indonesia. Mobile-based Augmented
Reality for Sundanese Alphabets Education
3rd: Andi Batari Ahmad and Nova Eka
Diana. Universitas YARSI, Indonesia.
Deep Learning Classification for Liver
Disease3rd: Suchanat Mangkhangjaroen. Thammasat University,
Thailand. ONE: Online Note Extraction to Music Cheat
Honorable Mention: Juan Sebastian Aguirre Zarraonandia. Osaka University, Japan. Application Aware
Traffic Engineering Functionality for an SDN Transit Network

Honorable Mention: Muhammad Jaziem Bin Mohamed Javeed, Aini Atirah
Binti Rozali, Siti Zuraidah Binti Mohamad
Zobir, Habibah Binti Abdul Wahab, andNurul Hashimah Ahamed Hassain Malim.
Universiti Sains Malaysia, Malaysia. Curating Target-Activity Information for NADI Compounds Based on CHEMBL
Using Similarity Searching and Pattern Matching

PRAGMA 35 BEST STUDENTPRESENTATIONS
1st: Chiao-Ning Chuang. National Chiao Tung
University, Taiwan. Image Restoration for CCTV
Images for Natural Disaster Management
2nd: Muhammad Jaziem bin Mohamed Javeed.
Universiti Sains Malaysia, Malaysia. LINGO Profiles
Fingerprint (LPFP) and Association Rule Mining(ARM) for Predicting Drug Target Interactions(DTIs)
3rd: Nuraisah. Universitas YARSI, Indonesia. Tuberculosis (TB) Disease Interactive Map in Jakarta
Capital Special Region

PRAGMA 35 BEST POSTERS
1st: Saravanan Sagadevan, Nurul Hashimah Ahamed
Hassain Malim, Nurul Izzati Ridzuwan, and Muhammad Baqir Hakim Mohammad Bashir. Universiti
Sains Malaysia, Malaysia. Criminality Linguistics
Detection on Social Networks Through Personality Traits

38
2018 COLLABORATIVE OVERVIEWMURPA/QURPA
Providing international research internships at the University of Queensland and Monash University

In today’s educational arena, universities must provide
students with opportunities to work and study abroad toprepare them for global citizenship and professional competence in a multi-cultural workplace. Numerous reports
have challenged universities to develop educational programs that provide an integrated academic basis for developing students’ cultural/global competencies.

allowing them to integrate into host research groups asteam members. Students have both a local mentor in Australia as well as one at the remote site and often serve
as a bridge between international research projects. In
2016/2017, four Monash students travelled to UC San Diego, the University of Auckland in New Zealand, the Max
Plank Institute in Germany, and AIST in Japan.

Since 2008, Monash University students have been travelling to international partners under the Monash Undergraduate Research Projects Abroad (MURPA) program andsince 2014 under the University of Queensland Research
Projects Abroad (QURPA) program. To date, 53 students
have participated in the programs and have travelled to
UC San Diego, the National Center for Supercomputing
Applications (NCSA) in Illinois, The Technion in Israel, theInstitute for Infocomm Research (I2R) in Singapore, theUniversity of Warwick in Coventry, England, and AIST in
Japan. Students are placed for a period of eight weeks,

Monash University Computer Science student MichaelFranklin travelled to the Institute for Advanced Industrial Science and Technology, in Tsukuba, Japan. He worked
with Dr. Jason Haga on immersive visualization for big datafor river disaster management. Michael’s project aimed to
expand an existing river disaster management virtual reality (VR) application, providing the ability to read live dataand perform data analysis to identify regions of interest.
Computer Science Honors student Jason Xu travelled to
the Max Planck Institute for Evolutionary Biology, in Germany. He worked with Professor Arne Traulsen and Dr.
39

THE PACIFIC RIM APPLICATIONS AND GRID MIDDLEWARE ASSEMBLY

Laura Hindersin studying evolutionary processes on networks. He showed, using large-scale simulations, that calculations in the limit of weak selection break down whenpopulations are embedded in a network structure. Jason’s
work was instrumental in formulating some of the researchquestions he’s now tackling with Dr. Julian Garcia, as partof his honors thesis.
Alexander Zenin from Monash travelled to UC San Diego
where he worked with Winston Armstrong at the San Diego Supercomputer Center. Alex is interested in cybersecurity, and he worked on a project identifying security
vulnerabilities in processes for storing, accessing, and processing sensitive medical data. He devised a workflow for
penetration tests assembling and using different tools toassess vulnerability.
Engineering and computer science student Laura Cummack travelled to the University of Auckland in New Zealand. She worked on the ICON bionic joint project, under
the supervision of Dr. Desney Greybe. The team Laura
worked on was tasked with developing joint sensing exoskeletons to support the motion of patients who needmovement and strength assistance. Laura worked in thepart of the project that models specific features of individual patients. She produced a tool for model generation using Python, based on legacy code. The process calibrates
the model to data specific to the user.

The view of a MURPA/QURPA seminar at the University of
Queensland. The presenter is Professor Taisuke Boku from the
University of Tsukuba, Japan.

virtual seminars given by world renowned experts. Theseseminars allow students to “meet” potential mentors andget information about potential projects. In 2018, the seminar series focused on presenters from the National Center
for Supercomputing Applications (NCSA) at the University
of Illinois in Urbana-Champaign, Illinois.
As done in the past, seminars were broadcast simultaneously to Monash University (in Melbourne) and the University of Queensland (in Brisbane), with audiences able toask questions from either venue. The seminar infrastructure supports a wide range of video conference technologies (both open source and commercial) and is displayedon a 20 MPixel OptiPortal.

Both the MURPA and QURPA programs include an advanced seminar scheme in which students can attend

402018 COLLABORATIVE OVERVIEWAIST INTERNSHIP PROGRAM
Providing information technology research opportunities and experiences with cultural context
With the increase in globalization of science and the abilityof information technologies to cross international boundaries, it is critical to provide information technology research
opportunities and experiences with cultural context. To
address this challenge, the National Institute of Advanced
Industrial Science and Technology (AIST) is leveraging its
past extensive experience with the Pacific Rim Experiences for Undergraduates (PRIME) program (see References) to create an international hub for computer science
research through visiting student internships designed tobroaden, strengthen, and maintain AIST’s presence on the
global research stage. Started in 2014, AIST has expanded its internship activity each year. In 2017, we hosted 14
internship students from France, Taiwan, USA, Thailand,and Australia. There was a total of seven publications fromthe internships, including two Best Paper awards at the2017 International Conference on Information Technology(InCIT 2017) in Bangkok and the 2018 Computer Games
Multimedia and Allied Technologies (CGAT) conference inSingapore, respectively. For 2018, we have continued ourinternships with 11 students. Our student research has covered a wide-range of topics, including immersive visualization, networking for the Internet of Things (IoT) era, artificial intelligence, gamification, and cyberinfrastructure.
Importantly, we are strategically aligning these student activities to both facilitate international collaborations andsupport interactions under different formal agreements,
such as memorandums of understanding (MoUs). For example, a recent MoU between AIST and Mahidol University,
combined with more than 24 student internships, helped
establish a new satellite laboratory, Mahidol AIST Research
Unit (MARU), on the Mahidol University campus.
Earlier in 2018, AIST completed a new five-year MoU withUC San Diego to develop collaborations using AIST’s AI
Bridging Cloud Infrastructure (ABCI) as the key infrastructure for researcher and student exchanges. One student
from the Nara Institute of Science and Technology (NAIST)
worked on building containers and deploying them on
ABCI for our zebrafish grand challenge project (see PRAG-41
THE PACIFIC RIM APPLICATIONS AND GRID MIDDLEWARE ASSEMBLY

AIST Internship students on final presentation day, 2017.

MA Data Infrastructure and AI Bridging Cloud Infrastructure highlights). We aretapping into the PRAGMA and CENTRA communities to find partners that areinterested in helping to advance research in this area through our research opportunities. For example, we recently hosted an intern from the National Chiao
Tong University, supported by the Center of Excellence Cyber-Enablement ofApplications (CECEA), who studied ways to improve real-world webcam images using a machine learning approach. The student, Chiao-Ning Chuang,
won a best poster award at PRAGMA 34 and a best student presentation
award at PRAGMA 35. We believe these activities are a critical step toward the goal of creating strong international collaborations. Moreover,these activities demonstrate AIST’s long-term commitment to enhancing global IT research and supporting PRAGMA’s strategy of providing students with research experiences throughout the PRAGMA
network in order to create globally minded problem solvers for21st century challenges.

PARTICIPANTS
AIST: Jason Haga, Ryousei Takano

REFERENCES
Haga J., Galvin J., Arzberger P., Wienhausen G. PRIME: A
Model of Experiential Learning within a Global ResearchCommunity. In Education in Action: Experiential Learning in Higher Education, editors Forbes D., Lin J., andLosh E. UCSD Sixth College. pp 297-306. June 2012.
Arzberger, P., Wienhausen, G., Abramson, D.,
Galvin, J., Date, S., Lin, F-P., Nan, K., Shimojo, S.
PRIME: An Integrated and Sustainable Undergraduate International Research Program. Ad­
vances in Engineering Education. 2010, 2(2).
PRIME Website: prime.ucsd.edu

422018 COLLABORATIVE OVERVIEW43
THE PACIFIC RIM APPLICATIONS AND GRID MIDDLEWARE ASSEMBLY

44
2018 COLLABORATIVE OVERVIEWBUILDING COMMUNITY: INFUSING IDEAS AND
BROADENING IMPACT
PRAGMA actively looks for opportunities to build and broaden its community, thus infusing ideas
into PRAGMA and broadening the impact of PRAGMA’s approach, accomplishments, and products.
To address PRAGMA’s goal of making cyberinfrastructure (CI) accessible, easy to use, and useful tocommunities, we continue to seek out new areas and develop new and existing communities. We do thisthrough workshops around our biannual PRAGMA workshop (see Workshops and Working Groups) as wellas through other mechanisms. Sometimes the effort to engage new participants focuses on geography andlocation, and sometimes it focuses on research topics. In this section, we highlight key activities during thelast year to engage more participants in PRAGMA and to disseminate results broadly.

REACHING A BROAD
AUDIENCE
Dissemination of Results
In addition to hosting face-to-facemeetings to engage new participants, we disseminate our practices, experiences, and results via
publications, presentations, and posters. Over the last six
years, PRAGMA collectively published approximately 100
articles, more than 40 of which involved students. In 2017,a special issue of Concurrency and Computation: Practiceand Experience (Plale and Chen, 2017) was released, withseven research papers and an overview. This special issue
resulted from the first International Clouds for Data Science (PRAGMA ICDS’15) conference, held in conjunction
with PRAGMA 29 in October 2015, at Universitas Indonesia. The papers in the special issue, and in general all of ourpublications, fall into three broad categories: research thattakes advantage of the research networks and connected
local clusters that connect the PRAGMA institutions; research inspired by the science expeditions defined as partof PRAGMA; and location-specific solutions that cameabout because of the long standing and nurturing collaborative community that PRAGMA has built and fosteredover a long period of time.

In addition, PRAGMA-developed
software is typically open source
and available on our website (seeSoftware). Over the last five years,
PRAGMA members have created,
improved, or added components
to 26 published software products
and services: seven to enable the
PRAGMA Multicloud (PRAGMA Cloud Scheduler, Cziso,
DynIP, PRAGMA Boot, PRAGMA Boot Google Drive Virtual Cluster, Vc-out-parser, Clonzilla, Tensorflow Rocks
Roll, Tstat Rocks Roll, Kubernetes Rocks Roll, Gpupt, andVirtual Cluster Image repository), one for the Lake Expedition (GRAPLEr), and one for the Virtual Biodiversity
Expedition (Lifemapper); three for PRAGMA-ENT (Opimon, Overseer, smoc); two SDN (IPOP, ViNe]; three fordata provenance (Rice Genomic PID Data Service, PRAGMA Data Repository, PROV-Scaffold); two in Biosciences (Hydra, Virtual Image Biolinux genomics tools); one
in Cyberlearning (EDISON), and one in Telescience (JFG
Haiku Hunt).
Finally, PRAGMA produces the PRAGMA Collaborative
Overview (PCO) on an annual basis, which highlights accomplishments across PRAGMA activities.

45
THE PACIFIC RIM APPLICATIONS AND GRID MIDDLEWARE ASSEMBLYSEAIP 2017 Meeting, National Chi Nan University, Nantou Taiwan

REFERENCES
Plale B. and Chen M., Eds. Pacific Rim Applications andGrid Middleware Assembly (PRAGMA) special issue on international clouds for data science, Concurrency and Computation: Practice and Experience, John Wiley and Sons,
Vol. 29, Issue 13, 2017. DOI: 10.1002/cpe.v29.13/issuetoc(onlinelibrary.wiley.com/doi/10.1002/cpe.v29.13/issuetoc).

SOFTWARE
See www.pragma-grid.net/products and individual sections in this year’s Collaborative Overview.
PRAGMA Collaborative Overview: www.pragma-grid.net/
overview

ENGAGING NEW SOUTHEAST ASIA
MEMBERSSoutheast Asia International Research and Training
Program (SEAIP) and PRAGMA Institute: Taichungand Nantou, December 4–8, 2017
The SEAIP’s ongoing series of workshops (see seaip.
narlabs.org.tw) are organized by the National Center for
High-performance Computing (NCHC) and are supportedby the National Applied Research Laboratories (NARlabs)
and the Ministry of Science and Technology in Taiwan.
SEAIP meetings have opened doors for collaborations between researchers in Southeast Asia and the rest of theworld and have formed the basis for growing PRAGMA
and CENTRA collaborations in Southeast Asia.

The theme of the 13th SEAIP workshop, held December
4–8, 2017, was “Cloud Computing, Internet of Things, andAI for Discovery and Innovation.” Organized by NCHC withfunding from the Ministry of Science and Technology, as
well as from NARlabs, the atmosphere of the workshop was
informal and conducive to learning and developing collaborations. The first sessions were held at the National Centerfor High-performance Computing’s Taichung Office in Taichung, Taiwan. A second session was held on the campus of
National Chi Nan University in Nantou, Taiwan. Part of thisyear’s SEAIP meeting focused on community, technical, analytic, and application challenges in a time of rapid changes
in information and communications technology research.
Each year, the SEAIP workshop brings together researchers
from Europe, the United States, Northeast Asia, and Southeast Asia. This year, the meeting was held in conjunction
with the ICT Virtual Organization of ASEAN Institutes and
NICT (ASEAN IVO) meeting. The SEAIP venue provides aforum for PRAGMA researchers to share their experienceand to meet researchers from Southeast Asia that might
not be able to attend PRAGMA workshops, thus broadening
PRAGMA’s impact and involvement with others.
In 2018, this series of meetings was renamed the International Joint-Research and Training Program to more accurately reflect its global perspective. The next meeting will
be held in Taiwan, November 26–30, 2018.
CHAIR OF SEAIP AND THE INTERNATIONAL JOINT-RESEARCH AND TRAINING PROGRAM: Fang-Pang Lin, Na­tional Center for High-performance Computing.

46
2018 COLLABORATIVE OVERVIEWEXPLORING NEW RESEARCH TOPICS AND BROADENING
ENGAGEMENTPRAGMA explores new areas of research and is always looking for new communities of users who will benefit from advancing cyberinfrastructure technologies. As
examples, we highlight several efforts either associated with PRAGMA workshops
or from separate workshops that PRAGMA members attended in order to start a
dialog with new communities.

Understanding the New AI Bridging Cloud Infrastructure
The Workshop on High Performance Infrastructure for AI, Tokyo, May 9, was held inconjunction with PRAGMA 34. This meeting provided attendees with an overview
and update of the National Institute of Advanced Industrial Science and Technology’s (AIST) investment in and development of the state-of-the-art AI Bridging
Cloud Infrastructure (ABCI). The ABCI platform, housed on the University of Tokyo’s campus, is aimed at pushing the research envelope of artificial intelligence,machine learning, and deep learning applications. In addition to the overview of thearchitecture and engineering of the deployment, attendees also heard about pilot
applications and a related activity by the National Center for High-performance
Computing in Taiwan. At the end of the presentation, participants were given a tourof the new ultra-green datacenter and computer facility. See the AI Bridging Cloud
Infrastructure highlight for more information.

Empowering Malaysian and Pacific Rim Researchers with Current Trends in
Data Analytics
As a part of Big Data Week Asia, the 2018 Big Data Summit 2 was held in conjunction with the PRAGMA 35 conference in Kuala Lumpur and Penang, October 2–6.
The objective of the workshop was to empower researchers with current trends indata analytics, focusing on the application of high-performance computing and artificial intelligence for data analytics, to enable sharing advances both among Malaysian researchers and also between Malaysian and international researchers. PRAGMA elected to hold its 35th workshop in conjunction with Big Data Week Asia tofoster greater collaborations in this emerging area, and it was a great success. At the
PRAGMA 35 meeting, PRAGMA members discussed advances in the newly created AI Bridging Cloud Infrastructure, advances in visualization, and developments in
the Pacific Research Platform. In addition, Malaysian attendees learned more about
PRAGMA and its activities and were invited to participate as collaborators. Several
participants stayed for the PRAGMA 35 workshop and engaged in PRAGMA’s working groups. Several projects were identified to pursue, including use of visualization
for understanding neurological signals in the brain and the application of AI to smart
cities data. These participants want to become part of the PRAGMA.

Exploring Opportunities with an International Network of Bays
The 2018 World Congress of the Most Beautiful Bays in the World Club was held inPenghu Bay, Taiwan during September and October 2018 (see world-bays.com).
One of the efforts of PRAGMA’s Telescience Working Group has been to explore
the application of distributed technologies in smart cities and in the environment.
Interactions between Telescience Working Group Chair Fang-Pang Lin and Con47
THE PACIFIC RIM APPLICATIONS AND GRID MIDDLEWARE ASSEMBLY

gress organizers led
to several membersof the Most Beautiful Bays in the WorldClub attending PRAGMA 34 in Tokyo inMay. At the PRAGMA
conference, representatives of the Most
Beautiful Bays Club
explained the goalsof their organization Most Beautiful Bays meeting.
and invited PRAGMA
members to participate in the XIV World Bays Congress
held on Penghu Bay in Taiwan, which had an emphasis onenvironmental health and sustainability, climate change,
and renewable energy. Several PRAGMA members accepted the invitation and attended as guests of thePenghu County Government, giving a presentation thatprovided an overview on PRAGMA and continued the
dialog to understand the needs of the members of the
Most Beautiful Bays Club. PRAGMA members along with
the Penghu County Government representative also met
with several members from National Penghu Universityof Science and Technology, including the University President, Dean of Student Affairs, and Professors, to discussproject ideas and student involvement related to “blueeconomy” environment and tourism projects in Penghu
as starting points for collaboration.

Assisting Mekong River Basin Researchers Address
Technical Barriers to Modeling the Environment andSharing Data
The 2018 Mekong Research Symposium was held in Ho
Chi Minh City, Vietnam on September 6–7, 2018 (see www.
lowermekong.org/events/lower-mekong-research-sym-

posium). As a follow-up to a co-located event at PRAGMA
31 (Bangkok, September 7, 2016),
researchers at the
University of Virginia
helped organize thesymposium, which
engaged both PRAGMA and CENTRA
members to attend.
As noted in the invitation to the event (see website previously mentioned), “the Mekong, one of the world’s mostsignificant rivers, is central to its inhabitants’ livelihood,
imperative to an emerging world economy, and a criticallyimportant paragon of the challenges in achieving global environmental sustainability. The Lower Mekong Basin(LMB) is placed in the Indo-Burma hotspot by biologists;
an area of great interest to scholars due to an extraordinary diversity of plant and animal life. Today, rapid infrastructure development and land use conversions coupledwith climate change threats such as sea level rise andextreme weather conditions are resulting in acceleratedchanges to the basin’s physical and ecological processes.”
At the end of the workshop, participants had agreed that
better data access will allow more researchers to participate and contribute to sustainable development in theregion, starting with creating an inventory of existing Mekong data and assessing infrastructure resources available in the region. The infrastructure for data sharing isa starting point for future collaboration among regional
scientists and their international colleagues in PRAGMA
and CENTRA.

48
2018 COLLABORATIVE OVERVIEWCENTRA-PRAGMA COLLABORATIONSDiversifying opportunities for the CENTRA and PRAGMA communities

CENTRA: YEAR 3
The Collaborations to Enable Transnational Applications(CENTRA) aims to advance and catalyze international
collaborations and enable them to be long lived throughsupport of travel, exchange visits, and collaboration
mechanisms. CENTRA grew out of interactions among
PRAGMA members, with CENTRA’s founding members
being the Advanced Computing and Information Systems (ACIS) laboratory of the University of Florida withsupport from the National Science Foundation, the Center of Excellence for Cyber-Enablement of Applications(CECEA) of the National Center for High-performance
Computing (NCHC) of Taiwan with support from the
Ministry of Science and Technology of Taiwan, and theASEAN International Virtual Organization (IVO) fundedby the National Institute of Information and Communications Technology (NICT) of Japan.
This year, CENTRA turned three years old. It held its third
annual meeting (CENTRA 3) in Tokyo, Japan on May

14–16, 2018, hosted by NICT. It was timed to follow the
PRAGMA 34 meeting and leverage the continuing interactions between CENTRA researchers and PRAGMA investigators. A total of 86 participants from 35 institutionsin 12 countries attended CENTRA 3.
At the CENTRA 3 meeting, several ongoing collaborative
projects reviewed their progress since CENTRA 2, including “Dynamically Aggregating Smart Community Sensors, Edge, and Cloud Resources with Overlay VPNs,” ledby Renato Figueiredo of the University of Florida; “SDNIP Peering for IoT Data Transmission,” led by Te-Lung Liuof NCHC; “IT for Natural Disaster Management & Visualization Alliance,” led by Jason Haga of AIST; “ASEAN
IVO: Software Defined System on Disaster Mitigation andSmart Cities,” led by Hong-Hoe Ong, with Luke Jing Yuan
of MIMOS; “AirBox: a Participatory Ecosystem for PM2.5
Monitoring,” led by Ling-Jyh Chen of Academia Sinica in
Taipei ; and “Distributed Lifemapper,” led by Aimee Stewart of the University of Kansas. In addition, new projects

CENTRA 3 All-hands group photo, Tokyo, May 201849
THE PACIFIC RIM APPLICATIONS AND GRID MIDDLEWARE ASSEMBLY

were proposed on “Privacy-preserving Cloud Computing
for IoT,” led by Joao Paulo of INESC TEC; “Network Congestion Issues in Disaster Scenarios,” led by Krishna Kantof Temple University in Philadelphia; “PADE: Precision
Agriculture with Drones and Edge,” led by Christopher
Stewart of Ohio State University; “Using UAV Images to
Monitor Rice Paddies with Artificial Intelligence,” led by
Hui-Ping Tsai of the National Chung Hsing University in
Taichung, and “Secure Data Collaboration Using GFFS,”
led by Andrew Grimshaw of the University of Virginia.
Examples of exchange activities enabled by CENTRA
include a visit by U.S. PhD student Kensworth Subratie(University of Florida) to CENTRA member site NICT in
Japan on March 4–16, 2018. The purpose of the short stay
was to set up the necessary networking infrastructure for
an international Internet of Things (IoT) testbed between
NICT and ACIS. The testbed is to be used as a collaborativeenvironment among multiple CENTRA research groups
for the design and evaluation of the various componentsthat must function together toimplement next generation
IoT services and applications. These components
include,but are not limited
to, IoT hardware
devices, virtual
networking in-

frastructure and application packages, as well as their orchestration and management. Parts of this work benefit
from earlier research led by Renato Figueiredo (Ken’s adviser) under PRAGMA’s auspices on trusted networking.
Another example is the visit by U.S. researchers Aimee
Stewart and C.J. Grady, both from the University of Kansas, to Taiwan, May 2–7, 2018 to lead CENTRA’s SAGE-Lifemapper Workshops and Marine Science Collaboration
Meetings. One workshop was hosted at NCHC’s Hsinchu headquarters and included using Lifemapper on a
SAGE2-enabled visualization wall to test its capabilities
and future implementation at the CENTRA member siteat the University of Kansas (KU). The other was presented at the National Museum of Marine Science andTechnology (NMMST). Both were very successful, wellattended, hands-on workshops. Results include plans forLifemapper deployments at NMMST and participating
universities and plans by NCHC and KU for additional follow-up workshops. Lifemapper activities leverage PRAGMA-sponsored work on backend middleware (see the
Virtual Biodiversity Expedition and Lifemapper higlight),
whereas CENTRA has contributed to the redesign of theLifemapper frontend and (SAGE2) browser interface.
Among other activities, CENTRA hosted a webinar series from Fall 2017 through Spring 2018, which included
12 sessions on cyberinfrastructure-enabled research andapplications in areas such as software-defined networking, the Internet of Things, edge computing, artificial intelligence, and various smart and connected communi-

50
2018 COLLABORATIVE OVERVIEW

ties applications. The series was attended
by a total of 117 unique participants from
14 countries, with 55% from Asia, 34%
from North America and 11% from Europe and Oceania. The webinar series engaged a high percentage of early-career
researchers (38%), including students(34%) and post-docs (4%). All webinar
video recordings are documented on the
CENTRA website for on-demand viewing.
The series speakers included two members of PRAGMA, and many of the webinar attendees are involved in PRAGMA
activities.
PRAGMA 34, held in conjunction with CENTRA 3, Tokyo, May 2018

CENTRA continues to follow its intentional growth path. Last year, the Institutefor Systems and Computer Engineering, Technology and
Science (INESC TEC) became a member, and after the
CENTRA 2 meeting, the Korea Institute for Science andTechnology Information (KISTI) became CENTRA’s fifth
member.

PARTICIPANTS
Leaders of Global CENTRA: US-CENTRA at U Florida:
Jose Fortes; ASEAN-IVO at NICT: Shinji Shimojo; CECEA
at NCHC: Fang-Pang Lin; INESC TEC: Rui Oliveira; KISTI:
Kum Won Cho

WEBSITESCENTRA: www.globalcentra.org. CENTRA Webinars are
documented at vimeo.com/globalcentra.
The Collaborations to Enable Transnational Cyberinfrastructure Applications (CENTRA) is supported by NSF
ACI award #1550126 and aims to advance the scientific understanding and applications of distributed software-defined cyberinfrastructure.

51
THE PACIFIC RIM APPLICATIONS AND GRID MIDDLEWARE ASSEMBLY&

workshops
working groups

52
2018 COLLABORATIVE OVERVIEWWORKSHOPS AND WORKING GROUPS
Reviewing, planning, and organizing activities and introducing new members

PRAGMA workshops are meetings of all members of the
PRAGMA community. They are the major vehicle for information exchange between and among working groups,
expeditions, researchers, and institutions; they also provide excellent opportunities to engage new researchersand students at the host sites. New participants bringnew perspectives, applications, technologies, students,
and resources to these events. These workshops are a
critical opportunity to demonstrate progress on projects
and to create action plans for accomplishing tasks prior
to the next subsequent workshop.
Workshops are hosted by different organizations to provide a forum for PRAGMA members to meet and discussresearch interests and ideally develop new collaborations
with members of the hosting institutions.
The workshops are organized according to the activitiesof the following four working groups in PRAGMA:• RESOURCES WORKING GROUP: Working to make the
distributed resources of PRAGMA useful to diverse applications via development and use of tools and tech-

nologies like PRAGMA Cloud Testbed, PRAGMA ENT,
Open Data Platform and others. Co-leaders: Nadya
Williams (SDSC/UC San Diego) and Hsiu-Mei Chou
(NCHC).
• TELESCIENCE WORKING GROUP: Focusing on a variety of activities that require access to, or use of, remoteequipment, such as tiled-display walls (TDW) and sensors. Co-leaders: Shinji Shimojo (NICT and Osaka U)
and Fang-Pang Lin (NCHC). This group also includes
activities on disaster management.
• BIOSCIENCES WORKING GROUP: Focusing much of
its efforts over the last several years on infrastructuredevelopment that enables virtual screening experiments and computational genomics analyses with anemphasis on combating infectious diseases and, more
recently, on rice breeding. Leader: Jason Haga (AIST).
• CYBER-LEARNING WORKING GROUP: Focusing on
the use of technologies to improve understanding inseveral areas of computational science through theuse and improvement of EDISON. Co-leaders: Ruth Lee(KISTI) and Hsi-ching Lin (NCHC).
53

THE PACIFIC RIM APPLICATIONS AND GRID MIDDLEWARE ASSEMBLYHIGHLIGHTED WORKING GROUP 2018:
TELESCIENCEThe Telescience working group focuses on technologies
that are related to smart and connected communities,
which include collaborative and advanced visualization,
collaboration on SDN clouds, and the Internet of Things(IoT). The application areas focus on both natural to urban environments as well as on newly developed robotics. Traffic and crowd monitoring and behavior reasoning is just one example of an application area that wasrecently investigated in the group. In that study, traffic

information was translated to define the contribution ofcar exhaust to air particulate PM2.5 and was added to thecontribution of power plants, which was then modeledby down-scale meso weather forecasting. Collaborativevisualization based on the SAGE2 network on disastermanagement and marine biology study is another casethat exemplified the group’s efforts. The group also helps
build communities, including the newly formed Smart
Bay Cities collaboration, which will expand on the experiences and technologies developed this year to project
future opportunities for societal impact.

54
2018 COLLABORATIVE OVERVIEWPRAGMA WORKSHOPS
In 2018, two PRAGMA Workshops were held:• PRAGMA 34: May 9–12, 2018, Akihabara, Tokyo, Japan.
Co-hosted by AIST and Osaka University. PRAGMA 34
was held in conjunction with a Workshop on High Performance Infrastructure for AI, in conjunction with the
3rd annual CENTRA meeting.
• PRAGMA 35: October 3–6, 2018, Penang, Malaysia.
Hosted by Universiti Sains Malaysia. Co-sponsored by
Big Data Week Asia. Held in conjunction with Big Data
Week Asia and the Big Data Summit 2. In addition, a

MYREN (Malaysia Research and Education Network)
and Network Startup Research Center co-located aworkshop, and Kamal Hisham Kamaruddin, head of
MYREN, gave a keynote at PRAGMA 35, and discussed
connectivity between Malaysia and other PRAGMA sites.
More information about the PRAGMA 34 and 35 workshops can be found at www.pragma-grid.net/pragma34
and www.pragma-grid.net/pragma35, respectively.
In addition, training programs such as the Southeast Asia
International Joint Research and Training Program (SEAIP,
seaip.narlabs.org.tw), newly renamed the International
Joint-Research and Training Program, provided PRAGMA
with new members (See Building Community section).
Looking to the future, we will continue to use these strategies to engage new researchers. In addition, we will workwith our members to identify strategic partners and engage them through focused scientific or technical workshops. Listed below are our planned upcoming workshops:• PRAGMA 36: April 25–27, 2019, to be hosted by the
Korea Institute of Science and Technology Information(KISTI) in Jeju, Korea in conjunction with the 4th CENTRA Workshop (April 22–24, 2019).
• PRAGMA 37: September 11–13, 2019, to be hosted by
UC San Diego, La Jolla, California, USA.
We acknowledge the many contributions of members inhosting PRAGMA workshops and thank the organizers andhost institutions for their efforts to ensure PRAGMA’s continued success.
PRAGMA 35 Workshop, USM, Penang Malaysia, October 201855
THE PACIFIC RIM APPLICATIONS AND GRID MIDDLEWARE ASSEMBLYMEMBERS & PARTNERS
PRAGMA is an institution- and people-based organization governed by a steering committee (SC) that invites
new members, determines locations of workshops, and sets overall direction for PRAGMA initiatives. More information about SC members (denoted with an asterisk * ) can be found at www.pragma-grid.net/people.php.

ACTIVE MEMBERS
A key component of PRAGMA is active involvement by participating in workshops, contributing resources, hosting
workshops, and/or promoting and supporting student and researcher exchanges. The following institutions and members have contributed to PRAGMA activities in the past year:
ADVANCED SCIENCE AND TECHNOLOGY INSTITUTE (ASTI): Jelina Tanya H.

ka*, yoshio.tanaka@aist.go.jp; Jason
Haga*, jh.haga@aist.go.jp; Ryousei
Takano, takano-ryousei@aist.go.jp

CYBERMEDIA CENTER (CMC), OSAKAUNIVERSITY: Shinji Shimojo*, shimo-

NATIONAL INSTITUTE OF SUPERCOMPUTING AND NETWORKING (NISN),
KOREA INSTITUTE OF SCIENCE ANDTECHNOLOGY INFORMATION (KISTI):

Tetangco*, jeng@asti.dost.gov.ph

jo@cmc.osaka-u.ac.jp; Susumu Date*,
date@cmc.osaka-u.ac.jp: Yoshiyuki
Kido, kido@cmc.osaka-u.ac.jp
DATA TO INSIGHT CENTER, INDIANAUNIVERSITY (IU): Beth Plale, plale@indiana.edu

KASETSART UNIVERSITY (KU): Pu-tchong Uthayopas* (ex-officio),putchong@ku.th
KONKUK UNIVERSITY (Konkuk):Karpjoo Jeong* (ex-officio), jeongk@
konkuk.ac.kr
NARA INSTITUTE OF SCIENCE ANDTECHNOLOGY (NAIST): Kazutoshi

Fujikawa*, fujikawa@itc.naist.jp, Kohei
Ichikawa*, ichikawa@is.naist.jp
NATIONAL CENTER FOR HIGH-PERFORMANCE COMPUTING (NCHC),NATIONAL APPLIED RESEARCH LABORATORIES (NARL): Whey-Fone Tsai*(ex-officio), wftsai@nchc.narl.org.tw;
Fang-Pang Lin*, fplin@nchc.narl.org.
tw; Weicheng Huang*, whuang@nchc.
narl.org.tw, Hsiu-Mei Chou, hmchou@nchc.narl.org.tw
NATIONAL INSTITUTE OF ADVANCEDINDUSTRIAL SCIENCE AND TECHNOLOGY (AIST): Satoshi Sekiguchi*,s.sekiguchi@aist.go.jp; Yoshio Tana-

Kumwon Cho*, ckw@kisti.re.kr; JongSuk Ruth Lee*, jsruthlee@kisti.re.kr
THAMMASAT UNIVERSITY: Prapaporn

Rattanatamrong*, rattanat@gmail.
com; Wanida Putthividhya*, wput­
thividhya@gmail.com

UNIVERSITY OF FLORIDA (UF), theAdvanced Computing and Information
Systems Laboratory and the Florida Museum of Natural History: José Fortes*,

fortes@acis.ufl.edu; Renato Figueiredo*, renato@acis.ufl.edu; Matthew
Collins, mcollins@acis.ufl.edu, Grace
Hong, gshong@acis.ufl.edu
UNIVERSITY OF HONG KONG (HKU):

Wing Keung Kwan* (ex-officio), hcx­
ckwk@hku.hk; P.T. Ho, hcxchpt@hku.
hk; Lilian Y.L. Chan, lilianyl@hku.hk

UNIVERSITAS INDONESIA: Heru

UNIVERSITY OF WISCONSIN-MADISON(UW-Madison), the Center for Limnology: Paul Hanson, pchanson@wisc.edu

UNIVERSITI SAINS MALAYSIA (USM):

OTHER MEMBERS

Suhartanto*, heru@cs.ui.ac.id; Wisnu
Jatmiko, wisnuj@cs.ui.ac.id
Habibah A. Wahab*, habibahw@usm.
my; Nurul Malim*, nurulhashimah@usm.
my; Chan Huah Yong, hychan@usm.my;
Mohd Azam Osman; azam@usm.my
UC SAN DIEGO: including the California Institute for Telecommunications &Information Technology (Calit2), San
Diego Supercomputer Center (SDSC),
Center for Research in Biological Systems (CRBS): Shava Smallen*, ssmal­

len@sdsc.edu; Philip Papadopoulos*(ex-officio, as of July 1, 2018 at UC
Irvine), philip.papadopoulos@gmail.
com; Peter Arzberger*, parzberg@
ucsd.edu; Nadya Williams, nwilliams@
ucsd.edu; Teri Simas, simast@sdsc.edu(until June 1, 2018)

CENTER FOR COMPUTATIONAL SCIENCES (CCS), UNIVERSITY OF TSUKUBA: Osamu Tatebe, tatebe@cs.tsuku­

ba.ac.jp; Taisuke Boku, taisuke@
cs.tsukuba.ac.jp

COLLEGE OF COMPUTER SCIENCE ANDTECHNOLOGY (CCST), JILIN UNIVERSITY(JLU): Xiaohui Wei, weixh@jlu.edu.cn
COMPUTER NETWORK INFORMATIONCENTER (CNIC), CHINESE ACADEMY OFSCIENCES (CAS): Ze Luo, luoze@cnic.

cn; Yu Chen, cy@cnic.cn

MIMOS: Hong-Hoe Ong, hh.ong@

mimos.my; Jing-Yuan Luke, jyluke@
mimos.my56
2018 COLLABORATIVE OVERVIEWMONASH UNIVERSITY (Monash):David Abramson*, david.abramson@monash.edu, Paul Bonnington, paul.
bonnington@monash.edu; Maria
Indrawan, maria.indrawan@infotech.
monash.edu.au
NATIONAL ELECTRONICS AND COMPUTER TECHNOLOGY CENTER (NECTEC): Piyawut Srichaikul, piyawut.

srichaikul@nectec.or.th

UNIVERSITY OF HYDERABAD (UoH):

Rajeev Wankar, wankarcs@uohyd.er­
net.in and rajeev.wankar@gmail.com

NETWORKING MEMBERS
Networking partners provide access toexpertise to improve the efficiency of
the resource’s groups in running distributed experiments and applications.
ASIA-PACIFIC ADVANCED NETWORK(APAN): Markus Buchhorn, markus@

apan.net

PACIFIC WAVE: John Silvester, jsil­

vest@usc.edu

STARLIGHT IRNC & SDX, AND GLOBALRESEARCH PLATFORM INITIATIVES:

Maxine Brown, maxine@uic.edu; Joe
Mambretti, j-mambretti@northwest­
ern.edu; Thomas DeFanti, tdefanti@
ucsd.edu
TransPAC, INDIANA UNIVERSITY:

Jennifer Schopf, jmschopf@indiana.
edu; Andrew Lee, leea@indiana.edu
For more information about PRAGMA
Members, visit www.pragma-grid.net/
members-partners.php

ADDITIONALORGANIZATIONS ACTIVE IN
PRAGMA
BIODIVERSITY INSTITUTE,
UNIVERSITY OF KANSAS (biodiver­sity.ku.edu), and its researchers andstudents conduct research on sevencontinents in biodiversity informatics,
systematics and ecology and evolutionary biology. They have contributed to the biodiversity expedition
through participation in workshops
and in the use and extension of theLifemapper software.

NATIONAL APPLIED RESEARCHLABORATORY (NARL; www.narl.org.

tw/en) was established in 2003 toconsolidate nine national laboratories
into a single nonprofit organization to
construct, operate and maintain thelarge-scale R&D facility and platformin support of academic research andfoster the necessary manpower invarious advanced fields focused onby the nation. NCHC is one of thelaboratories in NARL. NARL can bring
to bear several other laboratories at
NARL for PRAGMA collaborations.
NATIONAL INSTITUTE FOR INFORMATIONAND COMMUNICATION TECHNOLOGY(NICT; www.nict.go.jp) is an incorporated administrative agency that conducts
general research and development on
information technology supporting theubiquitous society of the future. NICT
supported PRIME students 2009–2015
and has participated in the activities of
the Telescience Working Group throughsupport of the high-definition videoconferencing testing.
UNIVERSITY OF QUEENSLAND (www.

uq.edu.au) has recently become
involved in PRAGMA through David
Abramson’s move there. David remains
actively involved in PRAGMA and
PRIME, supporting two students fromUC San Diego from June to August
2013 and sending students to PRAGMA
sites (see MURPA/QURPA section).
VIRGINIA TECH Cayelan Carey andcolleagues in Project EDDIE (Environmental Data-Driven Inquiry andExploration; projecteddie.org, an
NSF-funded project) have developed
sensor-based and time series data
analysis activities that can be integrated into classrooms to improve quantitative skills, reasoning, and increase
student engagement. Prof. Carey is
expanding this effort by developing
additional teaching modules that use
the overlay network developed aspart of PRAGMA to run lake simulations of climate change scenarios. The
modules were piloted at eight universities in the 2015–2016 academic year
and were assessed to determine how
participation in the module activities
alter student reasoning about climatechange and computing.

PARTNERSGLEON (www.gleon.org) the Glob-al Lakes Ecological Observatory
Network, is a grassroots network oflimnologists, ecologists, information
technology experts and engineers
who use GLEON’s network of people, sensors and data to understandissues such as eutrophication or
climate change at regional to global
scales. GLEON, which was established based on an early PRAGMA
expedition to place sensors on a lakein Taiwan in 2004, has grown to a
network of more than 500 members.
It has developed new knowledge andinsights, created new data products
and developed a very successful
Graduate Student Association (GSA).
There are several ties between
GLEON and PRAGMA, including
shared personnel, shared learningfrom the GLEON GSA to develop the
PRAGMA Student Group, the sharedscientific expedition on Lake Eutrophication, and the joint hosting of aworkshop on big data in Taiwan in
December 2012.
NETWORK STARTUP RESOURCE CENTER (NSRC, nsrc.org), has longstand-ing experience in running hands-on
networking training workshops andproviding engineering assistance atboth the campus and national network
levels. They have worked in more than
one hundred countries throughout theworld over the past 20+ years. NSRC
has recently worked with PRAGMA in
Southeast Asia to support researchers
from Myanmar to attend PRAGMA
24. In addition, NSRC has been able
to encourage participation in PRAGMA workshops, such as collocating a
NSRC tutorial for MYREN (Malaysian
Research and Education Network)
concurrently with PRAGMA 35, andencouraging MYREN to provided aplenary talk at PRAGMA 35, bringing
together these two communities.

57
THE PACIFIC RIM APPLICATIONS AND GRID MIDDLEWARE ASSEMBLYSPONSORSPRAGMA is supported by its member institutions and the U.S. National Science
Foundation (NSF OCI 1234983, PI: Smallen, Co-PI: Williams), involving and supporting researchers at UC San Diego, University of Florida, Indiana University,
University of Wisconsin, University of Kansas, and Virginia Tech. This involves
support from the NSF Office of Cyberinfrastructure, Office of International
Science and Engineering, Division of Information and Intelligent Systems in the
Directorate for Computer and Information Science and Engineering, and theEmerging Frontiers Office of the Directorate for Biological Science. In addition,
previous support came from NSF OCI-0627026, PI: Papadopoulos and involved
support from NSF’s Office of Shared Cyberinfrastructure, Office of International
Science and Engineering, Division of Information and Intelligent Systems, andDivision of Biological Infrastructure.

58
2018 COLLABORATIVE OVERVIEWAIST’s research activities are partly
supported by Japan Science and Technology Agency (JST), the New Energy
and Industrial Technology Development
Organization (NEDO), Japan, and AIST
International Collaboration Fund.
ASTI’s grid activities are funded by the
Department of Science and Technology (DOST), Philippines.
CCS’s (at the University of Tsukuba)
PRAGMA participation is partially
supported by the JST CREST Grant
Numbers JPMJCR1303 and JPMJCR1414, and JSPS KAKENHI Grant
Number JP17H01748.
CCST at Jilin University receives funding support from the Chinese Natural
Science Foundation (61170004) andthe Chinese Ministry of Education(20130061110052).
CNIC’s sponsors include the Chinese
Academy of Sciences, the Ministryof Science and Technology of China,
and the Natural Science Foundationof China.
Indiana University receives additional
support from NSF 1659310 fundedrobust PID testbed, called the RPID
testbed (pronounced “rapid”).
Kasetsart University’s PRAGMA
participation has been partly fundedby an SRU Grant, Kasetsart University

Research and Development Institute(KURDI), and the National ResearchCouncil of Thailand.
KISTI receives major funding fromMSIP through the EDISON Project and
KISTI through its Supercomputing
R&D Program.
Monash University’s PRAGMA activities (including MURPA) are supported
by a range of grants from the Australian Research Council and Monash
University internal funding. In particular, the MURPA program wishes toacknowledge the financial support of
the Faculty of Information Technology
and the Monash e-Research Centre.
NCHC is one of the institutes monitored by the National Applied Research Laboratories that receives major funding support from the Ministryof Science and Technology, Taiwan.
NECTEC receives its funding throughThailand’s National Science and Technology Development Agency.
Osaka University and National Instituteof Information and Communications
Technology (NICT) research was supported in part by institutional funding
for their collaborative research project
titled “Research on High Functional
Network Platform Technology forLarge-scale Distributed Computing.”

PRAGMA-ENT is supported in part by
JGN of the National Institute of Information and Communications Technology (NICT), Japan and SINET5 of
the National Institute of Informatics(NII), Japan.
StarLight receives major funding from
NSF (ACI-1450871) for the project
titled “IRNC:RXP: StarLight SDX A
Software Defined Networking Exchange for Global Science Researchand Education.”TransPAC receives major funding from
NSF and collaborates closely withPacificWave, Japan’s National Instituteof Information and Communications
Technology, APAN, TEIN, and other
Asian networking groups.
Universitas Indonesia’s PRAGMA
participation has been partly fundedby the Faculty of Computer Scienceand through research grants from The
Ministry of Research Technology andHigher Education, Republic Indonesia.
USM’s grid activities in Malaysia arefunded mainly through E-science and
USM Central Funding.
Virginia Tech and University of Florida
receive additional funding from NSF
1737424 for the Smart and Connected
Water Systems project as part of its
Smart and Connected Communities
program.

PRAGMA would like to acknowledge and thank those who helped prepare this report: Jennifer Matthews for graphic design; Molly Wofford for editing; Grace Hong coordination at PRAGMA 34 and 35; and all of the individuals who contributed
photos, including Jason Haga, Paul Hanson, Grace Hong, Shava Smallen, Nadya Williams, Wassapon Watanakeesuntorn,
Gerald Pao, and students in the MURPA/QURPA program.
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THE PACIFIC RIM APPLICATIONS AND GRID MIDDLEWARE ASSEMBLY

www.pragma-grid.net