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CSDMS annual meetingModeling Coupled Earth and Human Systems - The Dynamic Duo




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Objectives and general description

The CSDMS 2017 annual meeting will focus on “Modeling Coupled Earth and Human Systems”. Topics of interests also include modeling research that integrates different disciplines, different scales, and the synergy between models and Human Systems. As in past meetings, keynote speakers are by invitation only, and poster presentations are the general media. The meeting will include:

  1. State-of-the art keynote presentations in earth-surface dynamics and modeling coupled earth and human systems
  2. Hands-on clinics related to community models, tools and approaches
  3. Transformative software products and approaches designed to be accessible, easy to use, and relevant
  4. Breakout sessions for Working, Focus Research Groups and the Initiatives
  5. Poster Sessions
  6. Consider signing up for the pre- and post-conference meetings as well. See below for more information on these.


Poster Information: The poster boards are configured for 4' wide by 6' tall (portrait orientation) posters.

Agenda

Click here to view the draft agenda of 03/29/2017.

Keynote Speakers

Kim de Mutsert
GMU, Department of Environmental Science and Policy
Modeling a coastal environment with human elements
If one system comes to (my) mind where the human element is intertwined with the environment, it is the Louisiana coastal area in the Southern United States. Often referred to as the working coast, coastal Louisiana supports large industries with its ports, navigation channels, oil, and productive fisheries. In addition to that, Louisianians have a significant cultural connection to the coastal wetlands and their natural resources. Unfortunately, the land is disappearing into the sea with coastal erosion rates higher than anywhere else in the US. Due to these high rates of land loss, this system needs rigorous protection and restoration. While the restoration plans are mostly focused on building land, the effects on, for example, fisheries of proposed strategies should be estimated as well before decisions can be made on how to move forward. Through several projects I have been involved in, from small modeling projects to bold coastal design programs, I present how coupled models play a key role in science-based coastal management that considers the natural processes as well as the human element.

Scott Hagen
LSU, Center for Coastal Resiliency
Pathways at the coastal land margin to assess climate change impacts with transdisciplinary research outcomes
Our extensive transdisciplinary efforts since 2010 in the northern Gulf of Mexico (Mississippi, Alabama, and the Florida panhandle) have resulted in an advanced capability to model and assess hydrodynamic and ecological impacts of climate change at the coastal land margin (visit http://agupubs.onlinelibrary.wiley.com/hub/issue/10.1002/(ISSN)2328-4277.GULFSEARISE1/). The concerted efforts of natural and social scientists as well as engineers have contributed to a paradigm shift that goes well beyond “bathtub” approaches. Potential deleterious effects to barrier islands, shorelines, dunes, marshes, etc., are now better understood. This is because the methodology enables assessment of not just eustatic sea level rise (SLR), but gets to the basis of projections of climate change and the associated impacts, i.e., carbon emission scenarios. The paradigm shift, input from coastal resource managers, and future expected conditions now provides a rationale to evaluate and quantify the ability of natural and nature-based feature (NNBF) approaches to mitigate the present and future effects of surge and nuisance flooding.
Over the majority of the 20th century, the largely linear rate of eustatic SLR was realized by thermal expansion of seawater as a function of a gradual increase in the average annual global temperature. Global satellite altimetry indicates that the rate of global mean SLR has accelerated from approximately 1.6 to 3.4 mm/year. While the year-by-year acceleration of the rate of rise cannot be measured adequately, it is reasonable to assume that it was relatively stable throughout the 20th century. For the 21st century, general circulation models project that posed atmospheric carbon emission scenarios will result in higher global average temperatures. A warmer global system will introduce new mechanisms (e.g., land ice loss, isotatic adjustments, and changes in land water storage) that will contribute to relatively abrupt changes in sea state levels. The additions to thermal expansion will drive higher sea levels and the increases in sea level will be attained by further accelerations in the rate of the rise. Because of the nature of the new mechanisms that will govern sea levels, it is unlikely that future accelerations in the rate of rise will be smooth.
To further address the complications associated with relatively abrupt changes in SLR and related impacts of climate change at the coastal land margin we intend to: (1) refine, enhance, and extend the coupled dynamic, bio-geo-physical models of coastal morphology, tide, marsh, and surge; (2) advance the paradigm shift for climate change assessments by linking economic impact analysis and ecosystem services valuation directly to these coastal dynamics; (3) pursue transdisciplinary outcomes by engaging a management transition advisory group throughout the entire project process; and (4) deliver our results via a flexible, multi-platform mechanism that allows for region-wide or place-based assessment of NNBFs. This presentation will share examples of our recent efforts and discuss progress to-date.

Michael Young
UT, Bureau of Economic Geology
Improving soil models by connecting scientific disciplines
Michael H. Young1, Kris van Looy2, Harry Vereecken2, Martine van der Ploeg3
1 Bureau of Economic Geology, Jackson School of Geosciences, University of Texas at Austin
2 Agrosphere Inst., IBG-3, Inst. of Bio-geosciences, Forschungszentrum Jülich GmbH
3 Department of Soil Physics and Land Management, Wageningen University & Research

Soil science has developed as a critical discipline of the biosphere and continues to develop every day; yet state-of-the-art modeling is unable to adequately synthesize many processes in applied earth system models. If we agree that soil is a critical life-supporting compartment that supports ecosystem functions (e.g., habitat for biodiversity) and ecosystem services (e.g., water filtration, nutrient management), and that produces food, feed, fiber and energy for our societies, then our inability to integrate soil processes into the broader array of earth system models is an issue that needs solving. Integration is an achievable goal. Other research communities have collaborated intensively over the past decades—specifically the climate modeling community—but even many of their approaches overlook (or over-average) the detailed and advanced shared knowledge of the soil compartment. This represents a gap in how scientific knowledge is implemented. Over the recent decades, a new generation of soil models has been developed, based on a whole systems approach comprising all physical, mechanical, chemical, and biological processes. The processes are needed to fill these critical knowledge gaps and contribute to the preservation of ecosystem function, improve our understanding of climate-change feedback processes, bridge basic soil science research and management, and facilitate the communication between science and society. The International Soil Modeling Consortium (ISMC) was formed in 2016 as a new community effort of soil modelers to improve how soil processes are communicated to other scientific communities, from earth dynamics to biogeosciences to global climate modelers. ISMC was formed around three themes: linking data and observations to models; creating the means for soil model intercomparison studies; and connecting our soil-related knowledge between science communities. Within less than 12 months of inception, ISMC has warehoused nearly 40 soil-related models, initiated data sets and platforms for modeling studies, and facilitated collaborations with several international groups, including CSDMS. In this discussion, we will describe the motivation and genesis of ISMC, present current status of our research, and seek to create new research partnerships.

Greg Tucker and Eric Hutton
University of Colorado, Boulder
PyMT Demonstration

Jonathan Gilligan
Vanderbilt , Department of Earth and Environmental Sciences
Connecting Human and Natural Systems: The Role of Agent-Based Simulations
Human settlements in dynamic environmental settings face the challenges both of managing their own impact on their surroundings and also adapting to change, which may be driven by a combination of local and remote factors, each of which may involve both human and natural forcings. Impacts of and responses to environmental change play out at multiple scales which involve complex nonlinear interactions between individual actors. These interactions can produce emergent results where the outcome at the community scale is not easily predicted from the decisions taken by individuals within the community. Agent-based simulations can be useful tools to explore the dynamics of both the human response to environmental change and the environmental impacts of human activity. Even very simple models can be useful in uncovering potential for unintended consequences of policy actions. Participatory simulations that allow people to interact with a system that includes simulated agents can be useful tools for teaching and communicating about such unintended consequences. I will report on progress on agent-based simulations of environmentally stressed communities in Bangladesh and Sri Lanka and preliminary results of using a participatory coupled model of river flooding and agent-based real estate markets to teach about unintended consequences of building flood barriers.

Moira Zellner
UIC, Department of Urban Planning and Policy
Participatory Complex Systems Modeling for Environmental Planning: Opportunities and Barriers to Learning and Policy Innovation
Six years ago, we set out to study how complex systems simulations could support collaborative water planning. We hypothesized that, by allowing participants to see the hidden effects of land- and water-use decisions on water flow, such tools could provide a platform for collective and innovative solution-building to complex environmental problems. We first adopted a developmental and collaborative agent-based approach, where groups of stakeholders learned how to inform and use models to assess the impacts of different implementation strategies. Despite their improved understanding and enhanced exploration of solutions, participants resisted policy innovation beyond familiar strategies. We refined our approach towards facilitated interaction with complex systems models and additional interfaces to help stakeholders provide direct input to the simulations, comprehend model outputs, and negotiate tradeoffs. Participants challenged outdated and false assumptions and identified novel solutions to their water woes. Nevertheless, at times the dissonance between simulation outputs and participants’ expectations was too great to accept and own. We share three stories of the obstacles encountered and offer suggestions to overcome them: keep models and interfaces simple, make both biophysical processes and values visible and tangible, and explicitly structure the social aspects of the simulation’s use. We draw on our experiences to show what aspects of visualization can support participatory planning.

David Gochis
UCAR, Research Applications Laboratory
Process linkages in the WRF-Hydro/NOAA National Water Model: Different processes operating on different scales
The community WRF-Hydro system has evolved from a basic land surface modeling scheme for atmospheric models into a more comprehensive operational hydrologic prediction system.  Key to this evolution was explicit accounting for the need to represent different processes at different scales or with different types of spatial representations. The most recent evolution of the WRF-Hydro system was its implementation as the modeling system supporting the new NOAA National Water Model which become officially operational in August of 2016. This presentation will discuss the different kinds of configurations utilized within the NOAA National Water Model (NWM) and how the WRF-Hydro system was adapted to meet those requirements.   Specific emphasis will be placed on describing the spatial transformations and flux passing methods that were required to maintain coupling between different parts of the forecasting system.  Also discussed will be future work that is planned to enable new process representations within the NWM and how modeling approaches under the CSDMS has influenced this development.

Robert Nicholls
Southampton University, UK
Deltas as Coupled Socio-Ecological Systems
At a global scale, deltas significantly concentrate people by providing diverse ecosystem services and benefits for their populations. At the same time, deltas are also recognized as one of the most vulnerable coastal environments, due to a range of adverse drivers operating at multiple scales. These include global climate change and sea-level rise, catchment changes, deltaic-scale subsidence and land cover changes, such as rice to aquaculture. These drivers threaten deltas and their ecosystem services, which often provide livelihoods for the poorest communities in these regions. Responding to these issues presents a development challenge: how to develop deltaic areas in ways that are sustainable, and benefit all residents? In response to this broad question we have developed an integrated framework to analyze ecosystem services in deltas and their linkages to human well-being. The main study area is part of the world’s most populated delta, the Ganges-Brahmaputra-Meghna Delta within Bangladesh. The framework adopts a systemic perspective to represent the principal biophysical and socio-ecological components and their interaction. A range of methods are integrated within a quantitative framework, including biophysical and socio-economic modelling, as well as analysis of governance through scenario development. The approach is iterative, with learning both within the project team and with national policy-making stakeholders. The analysis allows the exploration of biophysical and social outcomes for the delta under different scenarios and policy choices. Some example results will be presented as well as some thoughts on the next steps.

Marco Janssen
Arizona State University, School of Sustainability
Two Modeling Cultures
The theme of this meeting is Modeling Coupled Earth and Human Systems. Since the World3 model and the Limits to Growth report of 1972 there has been a sustained effort of integrated modeling of human activities and the Earth system. Despite the existence of integrated models, there is an increasing recognition that the social science is largely lacking from the modeling efforts. Having worked in both natural science and social science departments, I reflect on the different modeling cultures and the challenges in social science to use simulation models. Building on the work of the CoMSES Net I also provide some promising examples of agent-based models advancing social science.

Brian Walsh
International Institute for Applied Systems Analysis
Integrated Assessment Models for decision making under uncertainty
The Sustainable Development Goals and of the Paris Agreement declare global commitments to climate stabilization and shared prosperity, but specific pathways for their simultaneous achievement remain unclear. On smaller time scales, governmental, agricultural, and economic systems require climate adaptation solutions. Integrated assessment models (IAMs) are essential tools for managing complex systems to meet these simultaneous imperatives, but are subject to theoretical, computational, and personal limitations. In this presentation, I will discuss the role of three IAMs (GLOBIOM, FeliX, and the Resilience Indicator Multihazard Model) in service of decision making under uncertainty for science and policy.

Julia Moriarty
Virginia Institute of Marine Science, College of William & Mary
Coupling Sediment Transport and Biogeochemical Processes: The Role of Resuspension on Oxygen & Nutrient Dynamics
Observations in coastal environments show that seabed resuspension can impact water quality and biogeochemical dynamics by vertically mixing sediment and water, and by redistributing material that has been entrained into the water column. Yet, ocean models that incorporate both sediment transport and biogeochemical processes are rare. The scientific community frequently utilizes hydrodynamic-sediment transport numerical models, but hydrodynamic-biogeochemical models ignore or simplify sediment processes, and have not directly accounted for the effect of resuspension on oxygen and nutrient dynamics.

This presentation focuses on development and implementation of HydroBioSed, a coupled hydrodynamic-sediment transport-biogeochemistry model that was developed within the open-source Regional Ocean Modeling System (ROMS) framework. HydroBioSed can account for processes including advection, resuspension, diffusion within the seabed and at the sediment-water interface, organic matter remineralization, and oxidation of reduced chemical species. Implementation of the coupled HydroBioSed model for different locations, including the Rhone River subaqueous delta and the northern Gulf of Mexico, have helped to quantify the effects of both sediment transport and biogeochemical processes. Results indicate that resuspension-induced exposure of anoxic, ammonium-rich portions of the seabed to the more oxic, ammonium-poor water column can significantly affect seabed-water column fluxes of dissolved oxygen and nitrogen. Also, entrainment of seabed organic matter into the water column may significantly draw down oxygen concentrations in some environments. Ongoing work focuses on how resuspension and redistribution of organic matter and sediment may influence oxygen dynamics in the Chesapeake Bay.

Zachary Flamig
University of Oklahoma
EF5: A hydrologic model for prediction, reanalysis and capacity building
The Ensemble Framework For Flash Flood Forecasting (EF5) was developed to address a critical need for rapidly updating distributed hydrologic models capable of predicting flash floods. In the U.S. EF5 is used to run a 3-member ensemble forced by radar based precipitation as part of the Flooded Locations And Simulated Hydrographs (FLASH) product suite used by NWS. As part of the FLASH project a reanalysis was conducted from 2002-2011 to examine a climatology of flash flood events across the U.S. EF5 is also used by a NASA SERVIR applied science team for capacity building in East Africa. EF5 was designed with this use case in mind and as such is user-friendly with helpful error messages, cross-platform support, and open source.

Harrison Gray
University of Colorado
Traveling at the speed of light: luminescence as a means to quantify fluvial sediment transport rates
Sediment transport in rivers is a key parameter in landscape evolution, fluvial sedimentation, and river engineering. In particular, information on the time-averaged virtual velocity and the channel/floodplain exchange rate of sediment is extremely useful for quantifying long-term sediment transport dynamics. This data is expensive and time-consuming to obtain. A potential solution is to use luminescence, a property of matter normally used for dating. I develop a model based on conservation of energy and sediment mass to explain the patterns of luminescence in river channel sediment. The parameters from the model can then be used to estimate the time-averaged virtual velocity, characteristic transport lengthscales, storage timescales, and floodplain exchange rates of fine sand-sized sediment in a fluvial system. I show that this model can accurately reproduce the luminescence observed in previously published field measurements. I test these predictions in three rivers where the sediment transport information is well known: the South River and Difficult Run in Virginia, and Linganore Creek in Maryland. Each of these rivers tests key predictions of the model with the South River having favorable conditions, Difficult Run having large amounts of human influence, and Linganore Creek switching from alluvial to bedrock and vice versa along its course. In the South River, the model successfully reproduces the virtual-velocity and exchange rates from previously published data. In Difficult Run, we find that the influx of sediment from human development obfuscates the model-predicted pattern as expected. In Linganore Creek, the shift from alluvial covered to bedrock and back produces a change in the luminescence consistent with the predictions made by the model. From these results, I conclude that when model assumptions are upheld, luminescence can provide a useful method to obtain sediment transport information. This finding, coupled with the advent of portable luminescence technology, opens the door for rapid and inexpensive collection of long-term sediment transport data.


Clinic Leaders

Tuesday (1st day)

Irina Overeem & Mark Piper
CU, CSDMS-IF
People attending: 32
Bringing CSDMS Models into the Classroom
Evaluation link: https://cuboulder.qualtrics.com/jfe/form/SV_1A2YTtDtiNX3Ez3
CSDMS has developed a Web-based Modeling Tool – the WMT. WMT allows users to select models, to edit model parameters, and run the model on the CSDMS High-Performance Computing System. The web tool makes it straightforward to configure different model components and run a coupled model simulation. Users can monitor progress of simulations and download model output.

CSDMS has designed educational labs that use the WMT to teach quantitative concepts in geomorphology, hydrology, coastal evolution and coastal sediment transport. These labs are intended for use by Teaching assistants and Faculty alike. Descriptions of 2 to 4-hr hands-on labs have been developed for HydroTrend, Plume, Sedflux, CHILD, TOPOFLOW and ROMS-Lite. These labs include instructions for students to run the models and explore dominant parameters in sets of simulations. Learning objectives are split between topical concepts, on climate change and sediment transport amongst many others, and modeling strategies, modeling philosophy and critical assessment of model results.

In this clinic, we will provide an overview of the available models and labs, and their themes and active learning objectives. We will discuss the requirements and logistics of using the WMT in your classroom. We will run some simulations hands-on, and walk through one lab in more detail as a demonstration. Finally, the workshop intends to discuss future developments for earning assessment tools with the participants.

Mariela Perignon
CU, CSDMS-IF
People attending: 38
ANUGA - An open-source model of river flood morphodynamics (and other hydrological disasters)
ANUGA is an open source software package capable of simulating small-scale hydrological processes such as dam breaks, river flooding, storm surges and tsunamis. Thanks to its modular structure, we’ve incorporated additional components to ANUGA that allow it to model suspended sediment transport and vegetation drag. ANUGA is a Python-language model that solves the Shallow Water Wave Equation on an unstructured triangular grid and can simulate shock waves and rapidly changing flows. It was developed by the Australian National University and Geosciences Australia and has an active developer and user community.

This clinic will provide a hands-on introduction to hydrodynamic modeling using ANUGA. We will discuss the structure and capabilities of the model as we build and run increasingly complex simulations. No previous knowledge of Python is required. Example input files will be provided and participants will be able to explore the code and outputs at their own pace.

Jean-Arthur Olive
Lamont-Doherty Earth Observatory
People attending: 15
Introduction to coupled geodynamics-surface process modeling with SiStER
This clinic will provide an introduction to the MATLAB-based geodynamic modeling code SiStER (Simple Stokes solver with Exotic Rheologies, available at: https://csdms.colorado.edu/wiki/Model:SiStER), with particular emphasis on problems that couple solid-Earth deformation and surface processes. Attendees will develop and run simulations where fault evolution (in rifts or orogens), lithospheric flexure and/or mantle flow interact with surficial mass redistribution through erosion and sedimentation.

Tatiana Filatova
University of Twente, Faculty of Behavioral, Management and Social sciences
People attending: 47
Spatial agent-based models: introducing individual interacting actors in environmental models
Agent-based modeling (ABM) developed as a method to simulate systems that include a number of agents – farmers, households, governments as well as biological organisms – that make decisions and interact according to certain rules. In environmental modeling, ABM is one of the best ways to explicitly account for human behavior, and to quantify cumulative actions of various actors distributed over the spatial landscape. This clinic provides an introduction to ABM and covers such topics as:
  1. Modeling heterogeneous agents that vary in attributes and follow different decision-strategies
  2. Going beyond rational optimization and accommodating bounded rationality
  3. Designing/representing agents’ interactions and learning.
The clinic provides hands-on examples using the open-source modeling environment NetLogo https://ccl.northwestern.edu/netlogo. While no prior knowledge of NetLogo is required, participants are welcome to explore its super user-friendly tutorial. The clinic concludes with highlighting the current trends in ABM such as its applications in climate change research, participatory modeling and its potential to link with other types of simulations.

Wednesday (2nd day)

Irina Overeem1 & Elchin Jafarov2 & Kang Wang1
1) CU, CSDMS-IF
2) LANL

People attending: 18
Modeling Permafrost; a new software toolbox to explore frozen grounds
Permafrost is one of the Arctic climate indicators, and feedback of thawing permafrost to the global climate system through the impacts on the carbon cycle remains an important research topic. Observations can assess the current state of permafrost, but models are eventually essential to make predictions of future permafrost state.
In this 2hr clinic, we will present a new, easy-to-access and comprehensive cyberinfrastructure for permafrost modeling. The ‘PermaModel Integrated Modeling Toolbox’ includes three permafrost models of increasing complexity. The IMT is embedded within the Community Surface Dynamics Modeling System Web Modeling Tool (WMT). We include multiple sets of sample inputs, representing a variety of climate and soil conditions and locations, to enable immediate use of the IMT.
The hands-on clinic teaches students and researchers how to run and use several permafrost models. The presented models are envisioned to be the suitable for quick exploration of hypotheses and for teaching purposes.

Nicole Gasparini
TU, Department of Earth and Environmental Sciences
People attending: 40
Modeling Earth-Surface Dynamics with Landlab 1.0
Nicole M. Gasparini and Erkan Istanbulluoglu with Sai S. Nudurupati, Jordan M. Adams, Eric Hutton, Katherine R. Barnhart and Gregory E. Tucker.

Landlab a Python toolkit for building, coupling, and exploring two-dimensional numerical models of Earth-surface dynamics. This clinic will provide a hands-on introduction to Landlab's features and capabilities, including how to create a model grid, populate it with data, and run numerical algorithms for surface hydrology, hillslope sediment creation and transport, and stream incision. We will highlight the structure and examples from two complete models built within the Landlab framework: a ecohydrology model and an overland flow model. For participants interested in both Landlab and the Dakota toolkit, we encourage you to sign up for both this clinic and a following clinic on using Dakota in the context of Landlab models. Participants are encouraged to install Landlab on their computers prior to the clinic. Installation instructions can be found at: http://landlab.github.io (select "Install" from the menu bar at the top of the page).

Allen Lee
Arizona State University
People attending: 38
Good enough practices for reproducible scientific computation
How difficult would it be to create a transparent, fully reproducible codebase that can be downloaded from a trusted digital repository, compiled, and then run with minimal effort? How about a codebase that can be understood, reparameterized with coherent alternative assumptions, and analyzed by other researchers or future graduate students? As of this writing, it appears to be quite hard just to locate the code necessary to build / run an executable [1] [2] and this is a problem that only gets worse over time as software and system dependencies evolve. Luckily there are many Good Enough [3] practices that can be added incrementally to your development workflow to help others understand, properly review, and build on the software artifacts that increasing numbers of research findings depend upon.
This clinic will cover practical tips, workflows, and tools to help you create reproducible [4] and citable [5] computational pipelines while avoiding common pitfalls and potential issues. We will go over good practices for version control, documentation, data and metadata management, and demonstrate how CoMSES Net is using emerging technologies like Docker containerization to facilitate reproducible computational pipelines. Other topics (depending on participant interest and experience) include automated tests, continuous integration, and modular components / microservices.

[1] - http://reproducibility.cs.arizona.edu/
[2] - https://cbie.asu.edu/practice-archiving-model-code-agent-based-models
[3] - https://swcarpentry.github.io/good-enough-practices-in-scientific-computing
[4] - https://www.practicereproducibleresearch.org
[5] - https://www.force11.org/group/software-citation-working-group

Raleigh Martin
University of California, Los Angeles
People attending: 32
The Sediment Experimentalist Network (SEN) Knowledge Base
The Sediment Experimentalist Network (SEN) integrates the efforts of sediment experimentalists to build a Knowledge Base for guidance on best practices for data collection and management. The network facilitates cross-institutional collaborative experiments and communicates with the research community about data and metadata guidelines for sediment-based experiments. This effort aims to improve the efficiency and transparency of sedimentary research for field geologists and modelers as well as experimentalists.

The purpose of this clinic is to familiarize participants, experimentalists and modelers alike, with how to use and contribute to the SEN Knowledge Base (SEN-KB, www.sedexp.net). SEN-KB provides a wiki-like forum for sharing information on experimental methods, equipment, set-ups, and facilities. It also serves as a portal for discovery of datasets tied to the descriptions of experimental techniques. Such datasets are not hosted on SEN-KB; rather, data descriptions are linked to datasets stored on external servers, such as SEAD (“Sustainable Environment Actionable Data”, https://sead2.ncsa.illinois.edu/). SEAD is a resource for storing and curating large (10’s-100’s of GB) experimental datasets, and it provides the capability for submitting these data for publication, issuance of DOIs (“digital object identifiers”), and long-term archiving on disciplinary data repositories.

After a brief introduction to using SEN-KB and SEAD, participants will divide into two groups depending on their interests. The first group of “Data Contributors” will engage in a focused session of contributing new entries and/or editing existing entries on SEN-KB and SEAD based on their own experimental work. The second group of “Data Utilizers” will formulate and begin executing plans for addressing scientific questions of interest based on utilization of existing datasets described on SEN-KB and SEAD, such as those generated at the pre-JpGU Kyoto-SEN workshop (Morphodynamics and Genetic Stratigraphy for Understanding Landforms and Strata) to be held a few days before the clinic. We expect experimentalists to affiliate with the “Data Contributors” group, whereas modelers and other non-experimentalists will affiliate with the “Data Utilizers” group. Nonetheless, participants are open to choose for themselves. Both groups will be guided by SEN-KB leaders on hand to answer questions and document software issues. Toward the end of the clinic, both groups will reconvene to discuss lessons learned a path forward.

Enrollees will be contacted a couple weeks prior to the CSDMS meeting to engage in some brief pre-workshop activities to prepare for the clinic.

Tasks for participants prior to clinic:
  • Fill out survey (edit here).
  • Set up an account on SEN-KB - include in email, remind the day before - http://sedexp.net/
  • You have two choices (1) Click “Create new account” OR (2) “Log in with Google”
  • Set up an account on SEAD
  • Bring laptop to session - remind the day before

Thursday (3rd day)

Reed Maxwell
CSM, Department of Geology and Geological Engineering
People attending: 33
Beyond Groundwater Modeling: Integrated Simulation of Watershed Systems using ParFlow (sold out as of April 6th)
Reed Maxwell, Colorado School of Mines
Laura Condon, Syracuse University
Nicholas Engdahl, Washington State University


Accurately characterizing the spatial and temporal variability of water and energy fluxes in many hydrologic systems requires an integrated modeling approach that captures the interactions and feedbacks between groundwater, surface water, and land- surface processes. Increasing recognition that these interactions and feedbacks play an important role in system behavior has lead to exciting new developments in coupled surface-subsurface modeling, with coupled surface-subsurface modeling becoming an increasingly useful tool for describing many hydrologic systems.

This clinic will provide a brief background on the theory of coupled surface-subsurface modeling techniques and parallel applications, followed by examples and hands-on experience using ParFlow, an open-source, object-oriented, parallel watershed flow model. ParFlow includes fully-integrated overland flow; the ability to simulate complex topography, geology and heterogeneity; and coupled land-surface processes including the land-energy budget, biogeochemistry, and snow processes. ParFlow is multi-platform and runs with a common I/O structure from laptop to supercomputer. ParFlow is the result of a long, multi-institutional development history and is now a collaborative effort between CSM, LLNL, UniBonn, and UC Berkeley. Many different configurations related to common hydrologic problems will be discussed through example problems.

Kim de Mutsert
GMU, Department of Environmental Science and Policy
People attending: 15
Introduction to EcoPath with Ecosim
This clinic will offer you an introduction to developing food web models using Ecopath with Ecosim software. Ecopath with Ecosim (EwE) is an ecological modeling software suite for personal computers that has been built and extended on for almost thirty years. EwE is the first ecosystem level simulation model to be widely and freely accessible. EwE is the most applied tool for modeling marine and aquatic ecosystems globally, with over 400 models published to date, making EwE an important modeling approach to explore ecosystem related questions in marine science. In addition, Ecopath software was recognized as one of NOAA’s top ten scientific breakthroughs in the last 200 years. In this clinic, we will start with a brief introduction, then download the freeware and start setting up some simple models which we will use in example exercises. Note: the software works in a Windows environment; Mac computers can be used if they are set up with Parallels Desktop or a similar application to run programs in a Windows environment on a Mac.

Mark Piper & Eric Hutton
CU, CSDMS-IF
People attending: 24
BMI: Live! (sold out as of April 6th)
In software engineering, an interface is a set of functions with prescribed names, argument types, and return types. When a developer implements an interface for a piece of software, they fill out the details of the function, while keeping the signatures intact. CSDMS has developed the Basic Model Interface (BMI) for simplifying the conversion of an existing model in C, C++, Fortran, Python or Java into a reusable, plug-and-play component. By design, BMI functions are straightforward to implement. However, when trying to match BMI functions to model behaviors, the devil is often in the details.
In this hands-on clinic, we will take a simple model -- in this case, an implementation of the two-dimensional heat equation in Python -- and together, we will write the BMI functions to transform it into a component. As we develop, we’ll unit test our component with nose, and we’ll explore how to use the component with a Jupyter Notebook. Optionally, we can set up a GitHub repository to store and to track changes to the code we write. To get the most out of this clinic, come prepared to code! We have a lot to write in the time allotted for the clinic. Attendees must bring a laptop, and we recommend installing the Anaconda Python distribution. We also request that you read over:before participating in the clinic.

Katy Barnhart
CU, Department of Geological Sciences
People attending: 47
Model sensitivity analysis and optimization with Dakota and Landlab
Katherine Barnhart with Charles Shobe, Gregory Tucker, and Mark Piper

Dakota is a flexible toolkit with algorithms for parameter optimization, uncertainty quantification, parameter estimation, and sensitivity analysis. In this clinic we will work through examples of using Dakota to compare field observations with model output using methods of sensitivity analysis and parameter optimization. We will also examine how the choice of comparison metrics influences results. Methods will be presented in the context of the Landlab Earth-surface dynamics framework but are generalizable to other models. Participants who are not familiar with Landlab are encouraged (but not required) to sign up for the Landlab clinic, which will take place before this clinic.

Participants are encouraged to install both Landlab and Dakota on their computers prior to the clinic. Installation instructions for Landlab can be found at: http://landlab.github.io (select "Install" from the menu bar at the top of the page). Installation instructions for Dakota can be found at https://dakota.sandia.gov/content/install-dakota.



Participants

Who is registered for what as of 06/25/2017?

Reimbursement

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Thank you CSDMS community members for a record-breaking number of registrations for the 2017 Annual Meeting! Due to this overwhelming response, we are no longer able to provide registration reimbursement or hotel support for the standard registration period commencing April 2nd. You are still welcome to register and attend the meeting, but you will need to make and pay for your own hotel accommodations and daily transportation to/from the meeting venue and the Wednesday evening banquet. Abstract submission is closed as of April 2nd.

For those who registered before April 2nd: "Within its budget, CSDMS intends to support member applicants to attend the annual meeting. Towards this goal, we encourage members to fully or partially cover their expenses if capable. We additionally thank those in the industry and agency fields for understanding that 1) we cannot compensate federal agency participants since our own funding is from NSF, and 2) we request that our industrial/ corporate participants cover their own costs thereby allowing more academic participants to attend.

To the extent possible, CSDMS intends to reimburse the registration fee (for those that registered before April 2nd and who send a request after the meeting to Lynn McCready at csdms@colorado.edu by the deadline of June 30th, 2017), lodging (shared rooms at 100% and single rooms at 50% at conference hotels for the evenings of May 22nd, 23rd and 24th), and a limited amount of travel expenses for qualified registrants (keynote speakers and clinic leaders and student scholarship awardees)."

Important for foreign travelers: If you need a visa to travel to USA, select a business visa. If you need an invitation letter, please email csdms@colorado.edu as soon as possible. Also indicate whether specific wording is required in the letter.

Travel, Lodging and Conference Center Information

The meeting will be held at SEEC
Hotel: Millennium Harvest House Hotel
Transportation: You can book transportation between DIA and Boulder here: Green Ride Boulder. And information on how to find Green Ride Boulder at DIA.
We will provide a bus between the Millennium Harvest House Hotel and the meeting venue each day (the shuttle is not able to stop at other area hotels). We will also provide transportation from the Millennium Harvest House Hotel to the banquet (again, the shuttle is not able to stop at other area hotels). Please note that the parking adjacent to the SEEC building now requires payment for non-permit holders. You will need to park in the limited designated areas and provide payment in the adjacent kiosks.

Pre-conference events

The following will apply to both the Software Carpentry bootcamp and the HPC workshop pre-conference events:

  • Registration is open till April 1st (or until program fills) and is handled through the 2017 meeting site.
  • Each is capped at 30 participants (first paid first serve), and it has a $30 registration fee.
  • Participant will be responsible for cost / organization of their extra day of hotel accommodation and dinner. Costs will not be reimbursed.
  • We will cover coffee, continental breakfast and lunch during each of the events.

Software Carpentry bootcamp

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CSDMS will host a one-day pre-conference Software Carpentry bootcamp on Monday May 22nd, 2017, led by Mariela Perignon and Mark Piper.
The objective of the bootcamp is to teach basic programming skills that will be useful for scientific computing and model development. This is an intensive, hands-on workshop, during which certified instructors will cover basic elements of:
  1. the Unix bash shell,
  2. Python programming and NumPy, and
  3. Github for version control.

Our instructors are earth scientists and have familiarity with the CSDMS framework, such that lessons and examples will be targeted toward relevant problems in your field. The bootcamp intentionally precedes the CSDMS meeting, so the skills participants develop should be useful in the clinics during the meeting.

HPC workshop

CSDMS will host a one-day pre-conference HPC workshop on Monday May 22nd, 2017, led by Thomas Hauser and his HPC Research Computing team.
The objective of the workshop is to teach basic parallel programming skills. This will be an hands-on workshop, cover the following topics:

  1. Basics of Parallelism
  2. Optimizing for current CPUs
  3. Parallelizing your code with OpenMP
  4. Introduction to MPI


Post-conference hackathon

CSDMS will host a one-day post-conference hackathon on Friday May 26th, 2017, organized by Eric Hutton and Mark Piper.

A hackathon is loosely defined as a social gathering with the goal of collaboratively creating usable software. Here, we’ll hack BMIs. The motivation is that a BMI-ed model can be converted into a CSDMS component, which allows it to be called from PyMT and included in WMT, thereby increasing the visibility and use of the model. Each attendee is invited to bring a model of their choice1 to wrap with a BMI. The model can be in any CSDMS-supported language (C, C++, Fortran, Java, Python). Attendees should be proficient in the language of their chosen model. Attendees will be required to submit their model code to CSDMS staff before April 1, so that the hackathon organizers have time to familiarize themselves with the code. The attendees will work together to add BMIs to models. CSDMS staff will guide participants and provide technical assistance. The ultimate goal of the hackathon is to get each participant's model wrapped with a BMI. This is a lofty goal. The more likely outcome is that each participant will have a good start on getting their model wrapped.

Before the hackathon, attendees are expected to have read:

and to have attended a BMI clinic in the current or in an earlier year. Attendees need a laptop with either a working compiler for the language of their choice or an account on beach​. To make the most of the hackathon, attendees should attempt to prepare their model for a BMI by refactoring it into initialize (sets the initial state of the model), update (advances the model by one time step), and finalize (shuts down the model) subprograms.

1 If an attendee doesn’t have a model to wrap, but does express a language preference, we will provide them with a simple model in their language that they can wrap; however, attendees who bring their own model will have precedence if space is an issue.

Note:

  • Registration is open till April 1st (or until program fill) and is handled through the 2017 meeting site.
  • The hackathon is capped at 12 participants (first paid first serve), and it has a $30 registration fee.
  • Participant will be responsible for cost / organization of their extra day of hotel accommodation and dinner. Costs will not be reimbursed.
  • We will cover coffee, continental breakfast and lunch during the hackathon.

Student Scholarships

This year CSDMS is offering a limited number of scholarships (up to 5) for graduate students to attend the CSDMS annual meeting. These scholarships will be offered for the purpose of increasing participation of underrepresented students or those that have not previously attended. To be eligible, graduate students need to meet the following requirements:

  • Attend the whole meeting (May 23-25, 2017)
  • Submit an abstract
  • Be enrolled as a graduate student at the time of the meeting (bring proof)
  • Submit a letter of motivation that states why you wish to participate in the meeting, and explain how your participation would enhance diversity in the field of surface dynamics modeling. Be sure to mention if it is your first time attending.

Send your application materials to csdms@colorado.edu by February 13th, 2017. The CSDMS scholarships will cover:

  • Registration costs (you will still need to pay the registration fee, but will be reimbursed after attending the meeting)
  • Hotel accommodations for three nights, starting May 22nd. (as outlined in Travel/Lodging section above - 100% paid if you agree to a roommate)
  • Travel (air fare ONLY within the United States and local transport)
  • Per diem to help reimburse the cost of meals from 23-25 May 2017 not offered in the conference schedule

All applicants will receive confirmation of their submission. Please notify us at csdms@colorado.edu if you do not receive confirmation within 24 hours of submission.

Important dates

  • January 20th: Registration opens
  • February 13th: Deadline for student scholarship applications CSDMS
  • April 1st: Deadline for abstract submission & discounted early registration
  • May 15th: Deadline regular registration. Notice additional costs do apply.
  • May 22nd: Optional: pre-conference bootcamp
  • May 22nd: Optional: pre-conference HPC workshop
  • May 23-25th: CSDMS annual meeting
  • May 26th: Optional: post-conference hackathon
  • May 26th: CSDMS Executive and Steering committees meetings (by invitation only)



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