Form:CSDMS annual meeting
From CSDMS
Models meet Data, Data meet Models
May 26 - 28, 2014, Boulder Colorado, USA
Registration
Registration will open soon. Please email csdms@colorado.edu with questions.
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Objectives and general description
The CSDMS Meeting 2014 will bring Uncertainty and Sensitivity in Surface Dynamics Modeling to your attention.
The meeting includes: 1) State-of-the art keynote presentations in earth-surface dynamics and modeling; 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; and more.
Poster Information: The poster boards are configured for 4' wide by 6' tall (portrait orientation) posters. The deadline to submit abstracts is April 1, 2014.
Meeting Agenda & Announcements
View the latest agenda here:
agenda
- Those who are participating in the "WMT: The CSDMS Web Modeling Tool" clinic or the "SNAC: A 3D parallel explicit finite element code for long-term lithospheric deformation modeling" clinic must apply for a HPCC account by May 1st.
Invited Keynote speakers
Brian Fath
Towson University & International Society for Ecological Modeling
{{{participants}}}Ecosystem Dynamics Randy LeVeque
University of Washington
{{{participants}}}GeoClaw Joellen Russell
University of Arizona
{{{participants}}}Paleo-climate Modeling Kyle Straub
Tulane
{{{participants}}}Signals of Relative Sea Level perturbations: Defining the divide between autogenic signal shredding vs. preservation in the stratigraphic record Mary Hill
University of Kansas
{{{participants}}}Data/model assessment Raleigh Hood
University of Maryland
{{{participants}}}Modeling the Chesapeake Bay Ehab Meselhe
The Water Institute of the Gulf
{{{participants}}}Integrated Compartment Model (ICM)
Clinic Invitees
Ali Khosronejad
University of Minnesota
{{{participants}}}The SAFL Virtual StreamLab (VSL3D): High Resolution Simulation of Turbulent Flow, Sediment Transport, and Morphodynamics in Waterways Ali Khosronejad and Fotis Sotiropoulos
St, Anthony Falls Laboratory and Department of Civil Engineering
University of Minnesota
Minneapolis, MN
fotis@umn.edu
The St. Anthony Falls Laboratory Virtual StreamLab (VSL3D) is a powerful multi-resolution and multi-physics Computational Fluid Dynamics (CFD) model for simulating 3D, unsteady, turbulent flows and sediment transport processes in real-life streams and rivers with arbitrarily complex structures, such as man-made hydraulic structures, woody debris, and even hydrokinetic turbine arrays. The code can handle arbitrarily complex geometry of waterways and embedded structures using novel immersed boundary strategies. Turbulence can be handled either via Reynolds-averaged Navier-Stokes (RANS) turbulence models or via large-eddy simulation (LES) coupled with wall models. Free-surface effects are simulated using a level-set, two-phase flow approach, which can capture complex free-surface phenomena, including hydraulic jumps, over arbitrarily complex bathymetry. A fully-coupled hydro-morphodynamic module has also been developed for simulating bedload and suspended load sediment transport in meandering rivers. A novel dual time-stepping quasi-synchronized approach has been developed to decouple the flow and sediment transport time scales, enabling efficient simulations of morphodynamic phenomena with long time scales, such as dune migration in rivers. The code is parallelized using MPI. This clinic will present a comphrehensive overview of the VSL3D, report extensive grid sensivity and validation studies with experimental data, and present a series of applications, including: 1) LES and unsteady RANS of turbulent flow and scalar transport in natural meandering streams; 2) LES of sand wave growth and evolution in a laboratory scale flume; 2) unsteady RANS of dune formation and migration in large scale meandering rivers with in stream rock structures (rock vanes, j-hooks, w-weirs, etc.); 3) LES of free-surface flows in natural and enginnered open channels; and 4) LES of gravity currents.
Representative references about the VSL3D code
1. Khosronejad, A., Hill, C., Kang, S., and Sotiropoulos, F., “Computational and Experimental Investigation of Scour Past Laboratory Models of Stream Restoration Rock Structures,” Advances in Water Resources, Volume 54, Pages 191–207, 2013.
2. Kang, S., and Sotiropoulos, F., “Assessing the predictive capabilities of isotropic, eddy-viscosity Reynolds-averaged turbulence models in a natural-like meandering channel,” Water Resources Research, Volume: 48, Article Number: W06505, DOI: 10.1029/2011WR011375, 2012.
3. Kang, S., Khosronejad, A., and Sotiropoulos, F., “Numerical simulation of turbulent flow and sediment transport processes in arbitrarily complex waterways,” Environmental Fluid Mechanics, Memorial Volume in Honor of Prof. Gerhard H. Jirka, Eds. W. Rodi & M Uhlmann, CRC Press (Taylor and Francis group), pp. 123-151, 2012.
4. Kang, S., and Sotiropoulos, F., “Numerical modeling of 3D turbulent free surface flow in natural waterways,” Advances in Water Resources, Volume: 40, Pages: 23-36, DOI: 10.1016/j.advwatres.2012.01.012, 2012.
5. Kang, S., and Sotiropoulos, F., “Flow phenomena and mechanisms in a field-scale experimental meandering channel with a pool-riffle sequence: Insights gained via numerical simulation,” Journal of Geophysical Research – Earth Surface, Volume: 116, Article Number: F03011 DOI: 10.1029/2010JF001814 Published: AUG 20 2011.
6. Khosronejad, A., Kang, S., Borazjani, I., and Sotiropoulos, F., “Curvilinear Immersed Boundary Method For Simulating Coupled Flow and Bed Morphodynamic Interactions due to Sediment Transport Phenomena,” Advances in Water Resources, Volume: 34, Issue: 7, Pages: 829-843 DOI: 10.1016/j.advwatres.2011.02.017, Published: JUL 2011.
7. Kang, S., Lightbody, A., Hill, C., and Sotiropoulos, F., “High-resolution numerical simulation of turbulence in natural waterways,” Advances in Water Resources, Volume 34, Issue 1, January 2011, Pages 98-113.Greg Tucker & Daniel Hobley
CIRES
{{{participants}}}Creative computing with Landlab: A flexible Python package for rapidly building and exploring 2D surface-dynamics models Daniel E. J. Hobley(Daniel.hobley@colorado.edu)(2), Jordan M. Adams(2), Nicole M. Gasparini(2), Eric Hutton(3), Erkan Istanbulluoglu(4), Sai Siddhartha(4), Gregory E. Tucker(1)
1. CIRES and Department of Geological Sciences, University of Colorado, Boulder, CO, USA
2. Department of Earth and Environmental Sciences, Tulane University, New Orleans, LA, USA
3. Community Surface Dynamics Modeling System (CSDMS), University of Colorado, CO, USA
4. Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
Computer models help us explore the consequences of scientific hypotheses at a level of precision and quantification that is impossible for our unaided minds. The process of writing and debugging the necessary code is often time-consuming, however, and this cost can inhibit progress. The code-development barrier can be especially problematic when a field is rapidly unearthing new data and new ideas, as is presently the case in surface dynamics.
To help meet the need for rapid, flexible model development, we have written a prototype software framework for two-dimensional numerical modeling of planetary surface processes. The Landlab software can be used to develop new models from scratch, to create models from existing components, or a combination of the two. Landlab provides a gridding module that allows you to create and configure a model grid in just a few lines of code. Grids can be regular or unstructured, and can readily be used to implement staggered-grid numerical solutions to equations for various types of geophysical flow. The gridding module provides built-in functions for common numerical operations, such as calculating gradients and integrating fluxes around the perimeter of cells. Landlab is written in Python, a high-level language that enables rapid code development and takes advantage of a wealth of libraries for scientific computing and graphical output. Landlab also provides a framework for assembling new models from combinations of pre-built components.
In this clinic we introduce Landlab and its capabilities. We emphasize in particular its flexibility, and the speed with which new models can be developed under its framework. In particular, we will introduce the many tools available within Landlab that make development of new functionality and new descriptions of physical processes both easy and fast. Participants will finish the clinic with all the knowledge necessary to build, run and visualize 2D models of various types of earth surface systems using Landlab.Eunseo Choi
Center for Earthquake Research and Information
University of Memphis
{{{participants}}}SNAC: A 3D parallel explicit finite element code for long-term lithospheric deformation modeling Eunseo Choi
echoi2@memphis.edu
Center for Earthquake Research and Information, University of Memphis
SNAC (StGermaiN Analysis of Continua) is a 3D parallel explicit finite element code for modeling long-term deformations of lithosphere. It is an open source being distributed through Computational Infrastructure for Geodynamics (http://geodynamics.org/cig/software/snac/) as well as through CSDMS web site (http://csdms.colorado.edu/wiki/Model:SNAC).
This clinic will provide an overview of SNAC and lead participants through a typical work procedure for producing a 3D lithospheric deformation model on a high performance cluster. Specifically, participants will take the following steps: 0) acquiring an account on the CSDMS HPC (to be done before the clinic); 1) checking out the source code through a version control system; 2) building SNAC on the cluster; 3) getting familiar with SNAC by running a cookbook example in parallel and visualizing outputs; 4) modifying the source codes to customize a model.Courtney Harris
VIMS
{{{participants}}}Sediment transport in an idealized domain using ROMS Participants in this clinic will learn how to compile and run a Regional Ocean Modeling (ROMS) test case for an idealized continental shelf. The hydrodynamic model that we will use includes wave forcing and suspended sediment transport.
ROMS is an open source, three dimensional primitive equation hydrodynamic ocean model that uses a structured curvilinear horizontal grid and a stretched terrain following vertical grid. For more information see https://www.myroms.org. It currently has more than 4,000 registered users, includes modules for sediment transport and biogeochemistry, and has several options for turbulence closures and numerical schemes. Model input is specified using a combination of ASCII text files and NetCDF (Network Common Data Form) files. Output is written to NetCDF files. In part because ROMS was designed to provide flexibility for the choice of model parameterizations and processes, and to run in parallel, implementing the code can seem daunting, but in this clinic we will present an idealized ROMS model that can be run on the CSDMS cluster.
As a group, we will compile and run an idealized ROMS model on the CSDMS computer, Beach. The group will choose a modification to the standard model. While the modified model runs, we will explore methods for visualizing model output. Participants who have an account on Beach can try to run the model themselves. Clinic participants who have Matlab set up to visualize NetCDF files will be able to browse model output files during the clinic.
Following the clinic, participants should have access to tools for looking at ROMS output, an example ROMS model run, and experience with ROMS input and output files.Chris Jenkins
INSTAAR
{{{participants}}}Carbonate Models Clinic - carbo* suite Chris Jenkins, Peter Burgess, Donald Potts
The carbo* set of modules use Lotka-Volterra population ecology, hydrodynamics, mesoscale simulators, an organism knowledge base (OKB), and habitat suitability indexes to model benthic carbonate production. The modeling covers coral reef, Halimeda and maerl, oyster, deep-water coral and bryozoan facies but can be extended to other types using the OKB. Recently the creation of rubble bioclasts has been addressed by modeling bioerosion, skeleton breakage, water column turbulence statistics, and clast ballistic trajectories in extreme weather.
Model runs are initiated for modern situations by automatically gathering data from global database and remote sensed resources such as MODIS AQUA, World Ocean Atlas, WaveWatch, GEBCO. Idealized scenarios – from paleogeography - can also be constructed and submitted for modeling. Time spans of up to 10,000 years have been run, using a burst technique with annual time-stepping. Seasonal stepping for shorter time span is also possible. The model outputs include profiles of organism biofacies, accumulation geometries, (1m3) ‘block of rock’ fabric & porosity models for generated materials, and 3D and animated mappings of the sediment facies.
The clinic will go through a typical setup and run, with some variations within the group. One of the modeled areas will be Molokai, Hawaii. Participants on the day will receive a copy of the software. Images of recent outputs are shown at http://instaar.colorado.edu/~jenkinsc/carboClinic2014/carboClinicImages2014.htm. Future developments will be discussed, particularly integration with terrigenous sediment and suspendate models, and nutrient loadings.Laura Swiler & Adam Stephens
Sandia National Laboratories
{{{participants}}}Dakota: A Toolkit for Sensitivity Analysis, Uncertainty Quantification, and Calibration Dakota is an open-source toolkit with several types of algorithms, including sensitivity analysis (SA), uncertainty quantification (UQ), optimization, and parameter calibration. Dakota provides a flexible, extensible interface between computational simulation codes and iterative analysis methods such as UQ and SA methods. Dakota has been designed to run on high-performance computing platforms and handles a variety of parallelism. In this clinic, we will provide an overview of Dakota algorithms, specifically focusing on uncertainty quantification (including various types of sampling, reliability analysis, stochastic expansion, and epistemic methods), sensitivity analysis (including variance-based decomposition methods and design of experiments), and parameter calibration (including nonlinear least squares and Bayesian methods). The tutorial will provide an overview of the methods and discuss how to use them. In addition, we will briefly cover how to interface your simulation code to Dakota. Mark Piper & Irina Overeem
CSDMS
{{{participants}}}WMT: The CSDMS Web Modeling Tool Mark Piper, Eric Hutton and Irina Overeem, CSDMS Integration Facility Boulder Colorado, United States
(mark.piper@colorado.edu)
The CSDMS Web Modeling Tool (WMT) is the web-based successor to the desktop Component Modeling Tool (CMT). WMT presents a drag-and-drop interface that allows users to build and run coupled surface dynamics models from a web browser on a desktop, laptop or tablet computer.
With WMT, a user can:
• Design a coupled model from a list of available components
• Edit the parameters of the model components
• Save the coupled model to a server, where it can be accessed from any computer
• Set run parameters, including the computer/cluster on which to run the model
• Share saved modeling projects with others in the community
• Submit jobs to the high-performance computing system
Although WMT is web-based, the building and configuration of a model can be done offline. The user can then reconnect to save a model and submit it for a run.
In this clinic we present an overview of WMT, including an explanation of the user interface, a listing of the currently available models and a discussion of how models can be run in operational mode or in reduced-input mode for teaching. We cap the clinic with a live demonstration of setting up, saving and running a coupled model on the CSDMS supercomputer system.
Scott Peckham
University of Colorado
{{{participants}}}Introduction to the Basic Model Interface and CSDMS Standard Names In order to simplify conversion of an existing model to a reusable, plug-and-play model component, CSDMS has developed a simple interface called the Basic Model Interface or BMI that model developers are asked to implement. In this context, an interface is a named set of functions with prescribed function names, argument types and return types. By design, the BMI functions are straightforward to implement in any of the languages supported by CSDMS, which include C, C++, Fortran (all years), Java and Python. Also by design, the BMI functions are noninvasive. A BMI-compliant model does not make any calls to CSDMS components or tools and is not modified to use CSDMS data structures. BMI therefore introduces no dependencies into a model and the model can still be used in a "stand-alone" manner. Any model that provides the BMI functions can be easily converted to a CSDMS plug-and-play component that has a CSDMS Component Model Interface or CMI.
Once a BMI-enabled model has been wrapped by CSDMS staff to become a CSDMS component, it automatically gains many new capabilities. This includes the ability to be coupled to other models even if their (1) programming language, (2) variable names, (3) variable units, (4) time-stepping scheme or (5) computational grid is different. It also gains (1) the ability to write output variables to standardized NetCDF files, (2) a "tabbed-dialog" graphical user interface (GUI), (3) a standardized HTML help page and (4) the ability to run within the CSDMS Modeling Tool (CMT).
This clinic will explain the key concepts of BMI, with step-by-step examples. It will also include an overview of the new CSDMS Standard Names, which provide a standard way to map input and output variable names between component models as part of BMI implementation. Participants are encouraged to read the associated CSDMS wiki pages in advance and bring model code with specific questions.
See
1) BMI Page: BMI_Description
2) Standard Names Page: CSDMS_Standard_NamesMonte Lunacek
University of Colorado
{{{participants}}}Interactive Data Analysis with Python Recent additions to Python have made it an increasingly popular language for data analysis. In particular, the pandas library provides an R-like data-fame in Python, which is data structure that resembles a spreadsheet. This provides an efficient way to load, slice, reshape, query, summarize, and visualize your data. Combining this with numpy, maplotlib, and scikit-learn creates a powerful set of tools for data analysis. In this hands-on tutorial, we will cover the basics of numpy, matplotlib, pandas, and introduce scikit-learn. Joshua Watts
Arizona State University
{{{participants}}}Agent-Based Modeling Research: Topics, Tools, and Methods Agent-Based Modeling (ABM) or Individual-Based Modeling is a research method rapidly increasing in popularity -- particularly among social scientists and ecologists interested in using simulation techniques to better understand the emergence of interesting system-wide patterns from simple behaviors and interactions at the individual scale. ABM researchers frequently partner with other scientists on a wide variety of topics related to coupled natural and human systems. Human societies impact (and are impacted by) various earth systems across a wide range of spatial and temporal scales, and ABM is a very useful tool for better understanding the effect of individual and social decision-making on various surface processes. The clinic will focus on introducing the basic toolkit needed to understand and pursue ABM research, and consider how ABM work differs from other computational modeling approaches. The clinic: - Will explore examples of the kinds of research questions and topics suited to ABM methods. - Will (attempt to) define some key concepts relevant to ABM research, such as emergence, social networks, social dilemmas, and complex adaptive systems. - Will provide an introduction to ABM platforms, particularly focused on NetLogo. - Discuss approaches to verification, validation, and scale dependency in the ABM world. - Introduce the Pattern-Oriented Modeling approach to ABM. - Discuss issues with reporting ABM research (ODD specification, model publishing). - Brainstorm tips and tricks for working with social scientists on ABM research.
Participants
Interested to see who registered for the meeting?
Reimbursement
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, lodging (shared rooms at 100% and single rooms at 50% at Millennium Harvest House Hotel), and a limited amount of travel expenses of qualified registrants - those members who have attended all three days of the meeting and are not industry or federal employees.
Registration fee, lodging and possible additional travel costs for the one day Post-meeting Software Bootcamp will not be reimbursed.
Important for foreign travelers requesting reimbursement: If you need a visa to travel to USA, select a business visa. If you need an invitation letter, please email csdms@colorado.edu soonest. Also indicate whether specific wording is required in the letter. Second, we will need to copy the entry stamp in your passport sometime during the meeting as proof that you were here on business as required by US tax laws for reimbursement (especially when dealing with airfare.) We are only able to provide reimbursement for airfare within the U.S.
Travel, Lodging and Conference Center Information
The meeting will be held at UCAR Conference Center
Lodging for meeting participants is at the Millennium Harvest House Hotel
SuperShuttle is offering $48 round trip transportation from DIA to Boulder via the following code & link: ALP44 http://www.supershuttle.com/default.aspx?GC=ALP44
Please visit the CSDMS contact page for advice on ways to reach Boulder from the Denver Airport.
Student Scholarships
Note: Scholarship submissions closed. For those who applied, we will reveal soon if you won a student scholarship.
Important dates
- February 1st: Registration opens
- March 1st: Deadline for student scholarship applications
- April 1st: Deadline for abstract submission & registration
- May 26-28th: CSDMS annual meeting
- May 29th: CSDMS Executive and Steering committees meeting (by invitation only)
Helpful Information for Travels Home
SuperShuttle: 303-227-0000 Boulder Taxi Cab Service: 303-777-7777
If booking SuperShuttle, they will ask you if you are South or North of Jay Road. The UCAR Facility is SOUTH of Jay Road.
The meeting facility address is UCAR Center Green, Bldg. #CG1, 3080 Center Green Drive, Boulder CO 80301
Program
Program Schedule updated March 23rd
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