Template:Updates from the director

Updates from the director

→ August 2013

Dear CSDMS members,

1. New Reports 1: See link for all who want a single report outlining the contributions and achievements of CSDMS1.0 (2007-12)
2. New Reports 2: And here is the first Annual Report of CSDMS2.0 (2013)
3. New Chairs: The 2013 Annual Report provides you with an update on our Steering Committee and Executive Committee including our new chairs: 1) Courtney Harris (VIMS) Chair of the Marine WG; 2) Sam Bentley (LSU) Chair of the Education and Knowledge Transfer WG; 3) Chris Duffy (Penn State) Chair of the Critical Zone FRG; 4) Kathleen Galvin (CSU) and Mike Ellis (BGS) Co-Chairs of the Anthropocene FRG; 4) Phaedra Upton (GNS) and Mark Behn (WHOI) Co-Chairs of the Geodynamics FRG; 5) Pat Wiberg (UVA) Chair of the CSDMS Steering Committee. Brad Murray (Duke U), Chair of the Coastal WG, will initially oversee the new initiative on Coastal Vulnerability and Courtney Harris (VIMS) will initially oversee the new initiative on Continental Margins. See this link for further details and Bios.
4. Sign Up: Please sign up (log into the website, click on your username appearing at the top in red, start editing) to receive information and contribute to our new Focus Research Groups (FRGs):
   • Geodynamics http://csdms.colorado.edu/wiki/Geodynamics_Focus_Research_Group
   • Anthropocene http://csdms.colorado.edu/wiki/Anthropocene_Focus_Research_Group
   • the Critical Zone http://csdms.colorado.edu/wiki/CZ
   • the Coastal Vulnerability Initiative http://csdms.colorado.edu/wiki/Coastal_Vulnerability_Initiative
   • the Continental Margin Initiative http://csdms.colorado.edu/wiki/Continental_Margin_Initiative
5. CSDMS Annual meeting 2013: Our largest and arguably best annual meeting created quite a buzz for attendees. Keynote addresses, clinic presentations, poster presentations, and break out group discussions are all available on line http://csdms.colorado.edu/wiki/CSDMS_meeting_2013 Further our annual report provides abstracts of these presentations.
6. Mark your Calendars: Plan on attending the 2014 Annual CSDMS meeting, held in Boulder CO, May 20, 22, & 23, 2014. --- http://csdms.colorado.edu/wiki/Form:CSDMS_annual_meeting
7. CSDMS2.0 Strategic Plans: For draft version of the CSDMS2.0 plans please download http://csdms.colorado.edu/mediawiki/images/2013_CSDMS_annual_report.pdf . It is still not too late to read these preliminary draft vision statements for each of the working groups, and offer suggestions. You may choose to do this through the working group CSDMS wiki pages, or send comments directly to the appropriate Group Chairs.
8. Integration Facility Staff Positions: CSDMS is seeking applicants for a full time Software Engineer. CSDMS is also seeking applicants for the position of CSDMS Executive Assistant (position will soon be posted on the CSDMS web site, but in the meantime please send applications to csdms@colorado.edu).
9. Getting Big: There are over 1040 CSDMS members (56% U.S.) representing 166 U.S. institutions (123 academic, 22 private, 21 federal) and 275 non-U.S. institutions from 67 countries (171 academic, 22 private, 70 government). There are now ~443 affiliated institutions.
10. The 2013 lifetime achievement award was presented to Professor Alan Howard (UVA), as part of the 2013 CSDMS Annual Meeting. Rebecca Caldwell won a Kindle for Best Poster. The CSDMS Student Modeler of the Year Award for 2012 goes to Surendra Adhikara (CalTech). We will soon open nominations for 2013. Read more about these winners on our web site or in our Annual Report.
11. IF staff continue to advance and refine our plug and play component modeling tools. Learn more about the Basic Modeling Interface, the CSDMS Component Modeling Interface, CMT, use of Standard names, and our plans for advancing our modeling framework to other platforms in our 2013 Annual Report.

With best wishes for the coming fall season
James P.M. Syvitski
CSDMS Executive Director



→ August 2012

Dear CSDMS members,

1. CSDMS1.0 (2007-12) has now come to a close. During these first five years CSDMS has grown from a group of 80 numerically oriented earth scientists, to 850 members from more than 380 research institutions (universities, government labs and industry) from more than 60 countries. Growth appears to be accelerating.
2. CSDMS2.0 (2012-17) will be launched in October 2012, with new funding of the CSDMS initiative through NSF Ocean Sciences, NSF Earth Sciences, and NSF Biological Sciences. The new start date shifts operations and reporting by six months. The current CSDMS Modeling Framework will be extended for use within a web browser, on a wider variety of computational platforms, and on other high performance computing clusters to ensure robustness and sustainability of the framework. The latest 2012 Semiannual Report provides more details on CSDMS 2.0 including plans for componentizing models more quickly through automated wrapping tools, quantifying model uncertainty, model benchmarking and inter-comparison, semantic mediation and ontologies, and developing a quantitative surface dynamics educational toolbox.
3. Six new community initiatives will be pursued in CSDMS2.0:
   1. an earth - ecosystem modeling initiative to capture ecosystem dynamics and ensuing interactions with landscapes,
   2. a geodynamics initiative to investigate the interplay among climate, geomorphology, and tectonic processes,
   3. an Anthropocene modeling initiative, to incorporate mechanistic models of human influences,
   4. a coastal vulnerability modeling initiative, with emphasis on deltas and their multiple threats and stressors,
   5. a continental margin modeling initiative, to capture extreme oceanic and atmospheric events generating turbidity currents in the Gulf of Mexico, and
   6. a CZO Focus Research Group, to develop compatibility between CSDMS architecture and protocols and Critical Zone Observatory-developed models and data.
4. To guaranty access to source code of numerical models CSDMS in close cooperation with Dr. K. Lehnert and Dr. L. Hsu (Integrated Earth Data Applications, LDEO), requested a DOI for each Model in the CSDMS Source Code Repository. Despite over 50 million DOI strings, CSDMS is the first in history to request DOIs for numerical models. A list of all the numerical models of the CSDMS model database together with limited metadata for each model is provided to IEDA. Read more in the 2012 Semiannual Report.
5. Several hands-on modeling labs are now fully documented and available from the educational repository. Below examples are designed to have societal and scientific relevance. Read more in the 2012 Semiannual Report:
   1. Glacio-Hydrological Processes,
   2. River-Delta Interactions,
   3. Sediment Supply, and
   4. Stratigraphic Processes.
6. Contributed models need a Basic Model Interface (BMI) if they are to be converted into a plug and play component. This includes mapping input and output variable names to CSDMS Standard Names and providing model metadata. The CSDMS Standard Names follow an object + quantity pattern with an optional operation prefix. A draft of these are available for comment
7. Euro-CSDMS is a new initiative to enhance Earth surface modeling in Europe as a major contributor to the existing NSF CSDMS effort. Euro-CSDMS will be an IT infrastructure and an associated group of researchers that marry and leverage the science, engineering, social & economic communities to develop and provide practical tools, applications and solutions for environmental security and industry innovation. Its main purpose will be to foster collaborative research in order to develop open-source technologies to evaluate and predict the global, regional and local response to environmental change. Read more in the 2012 Semiannual Report.
8. The CSDMS Annual meeting is scheduled for March 23-25, 2013, Boulder Colorado. Registration and Abstract submission deadline is Jan 1, 2013. Details will be available soon through the CSDMS web site. The last meeting proved such a success with its many keynote and poster presentations, and model clinics. We intend to continue this tradition and also use the meeting to kick start CSDMS2.0 and the new initiatives (see above) and thus update our Strategic Plan.
9. Elections! Vote !!!!!!!!!!

With best wishes for the coming fall season
James P.M. Syvitski
CSDMS Executive Director


→ February 2012

Dear CSDMS members,

CSDMS continues to gain momentum. In 2011 membership grew by 46% (220 new members — 710 members in total from 142 U.S. institutions and 183 non-US institutions from 51 countries). There was a 22% growth in models and components (191 open-source models), a 41% growth in model code (now 4.85 million lines of code), a 66% growth in CSDMS HPCC users, and a 267% growth in visits to the CSDMS web resources. These 5.45 million visits suggest that CSDMS is now the “go to” site for models and related data and educational products including animations, modeling labs and lecture materials. The CSDMS YouTube channel now offers 122 movies & animations, generating more than 36,001 views and placing the CSDMS YouTube channel from time to time in the “Top 50 most viewed channels” in the “non profit” category. CSDMS penetration of computational tools into the earth-science community should provide valuable future dividends. Please download the recent 2011 Annual Report and read up on the details.

Work is afoot to try to get a CSDMS-related program up and running in Europe, with plans to coordinate these activities with the European Commission funding activities. See Peter Burgess for developing details: p.burgess@es.rhul.ac.uk

Plans are in the works to develop a taskforce of the CSDMS Interagency Committee to explore early adoption strategies of CSDMS models and products. Most agencies use models to address practical applied problems: operational forecasts; regulatory assessments, permitting, risk assessments, remedial action plans, emergency response, and outreach to stakeholders. Agencies often rely on models developed or are funded in-house, for reasons of quality control, specificity, familiarity (with developers, users, and contractors). CSDMS can contribute to agency understanding on how to build and deploy coupled models and individual agencies might be “early adopters” and leverage CSDMS to develop coupled models to address specific topics. As a proof of concept, the Bureau of Ocean Energy Management (BOEM) is funding Rutgers, VIMS, and UC-Santa Barbara to work with CSDMS to develop a coupled modeling system to provide insights into areas most likely to be impacted by turbidity currents, and the factors that precondition or trigger the flow. The Gulf of Mexico has more than 28,000 miles of underwater pipes exposed to different types of structural damage — 5% of the pipelines are broken or damaged by sudden and violent cascading of sediments.

The 2011 Annual CSDMS Award winners are:

1. Best Poster — “Direct Numerical Simulation of Sediment Erosion” Zachary Borden (UC Santa Barbara),
2. Student Modeler Award — “A reduced-complexity channel-resolving model for sedimentary delta formation” — Man Liang (SAFL, U Minnesota) and
3. Lifetime Achievement Award — Professor Rudy L. Slingerland (Penn State). -- detailed in the Annual Report.

A key CSDMS achievement of the past year is the development of an innovative, two-level wrapping process (BMI/CMI) that greatly simplifies the process of converting contributed models into interoperable, plug-and-play components. Model contributors are asked to make relatively small changes and additions (e.g. functions that describe their model's attributes in a standard way) to their source code to provide a Basic Model Interface or BMI. BMI implementation is noninvasive and straightforward --- it requires no calls to CSDMS code and no knowledge of CSDMS framework concepts or protocols. By design, BMI provides all of the model information (grid type, information on input and output variables, etc.) that is needed by a second-level wrapper that converts the model to a CSDMS component. The second-level wrapper provides a Component Model Interface or CMI that enables coupling to other CSDMS components and automatically calls service components when needed to accommodate numerous differences between models such as programming language, computational grid, time-stepping scheme, variable names and units. Service components provide additional added value such as output to NetCDF files, unit conversion and spatial regridding. By design, BMI allows the same CMI wrapper to be used for every model written in a given language. This greatly simplifies and reduces maintenance associated with the wrapping process and reduces the burden on code contributors.

The CSDMS special issue on Environmental Modeling is almost complete and most papers are now available as ‘in press’ and are ‘on line’ for download at Computers & Geosciences. The second all hands meeting: “Impact of time and process scales” was attended by 101 CSDMS members. The meeting offered 1) 20-keynote lectures on insights on time and space issues and how this is addressed in the software subtleties that is at the heart of all surface dynamic modeling efforts, 2) 12-clinics on a variety of models, on model coupling and visualization, and parallel programming, and 3) well-attended poster sessions most of which can be found on the CSDMS web: http://csdms.colorado.edu/wiki/CSDMS_meeting_2011 along with keynote videos of presentations. Six new community initiatives will be pursued in the coming years:

1. an earth - ecosystem modeling initiative to capture ecosystem dynamics and ensuing interactions with landscapes,
2. a geodynamics initiative to investigate the interplay among climate, geomorphology, and tectonic processes,
3. an Anthropocene modeling initiative, to incorporate mechanistic models of human influences,
4. a coastal vulnerability modeling initiative, with emphasis on deltas and their multiple threats and stressors,
5. a continental margin modeling initiative, to capture extreme oceanic and atmospheric events generating turbidity currents in the Gulf of Mexico, and
6. a CZO Focus Research Group, to develop compatibility between CSDMS architecture and protocols and Critical Zone Observatory-developed models and data.

CSDMS is a contributing member of the NSF Frontiers of Earth System Dynamics Delta Dynamics Collaboratory (DDC) that will develop and test high-resolution, quantitative models incorporating morphodynamics, ecology, and stratigraphy to predict river delta dynamics over engineering to geologic time-scales, and to address questions of system dynamics, resiliency, and sustainability. This DDC opportunity will see a suite of 1D (reduced complexity) to 3D (ecogeomorphodynamic flow and sediment transport) models be developed using existing CMT components and components developed in the course of that research. CSDMS will also contribute to developing a NASA "fingerprinting" system able to identify hot spots of key delta systems as they respond to environmental stressors, under contemporary societal vulnerabilities and future threats. CSDMS is also a strong supporter with other international communities in calling for an International Year of Deltas. On behalf of all the staff of the Integration Facility (IF) we wish all of our CSDMS contributors the best for upcoming spring season. Again thanks for your efforts!

James P.M. Syvitski
CSDMS Executive Director, February 15^th, 2012


→ August 2011

Dear CSDMS members,

1) Just 3 Weeks Left for registering your attendance for the Annual CSDMS 2011 Meeting Impact of Time and Process Scale in Boulder CO (Oct. 28-30): CSDMS 2011 meeting

• Our theme on time and space scales addresses the software subtleties at the heart of all surface dynamic modeling efforts — whether stratigraphic, landscape-evolution, morphodynamics or transport of material. Through keynote presentations, posters, and hands-on clinics, we will look at modeling questions over a variety of time and spatial scales and how we can appropriately nest modelsover diverse scales. Community contributed standalone models will take the limelight. This year’s focus on stand-alone models aims to familiarize our community with our growing Model Repository of 182 models and modeling tools.
• And don’t forget about the “don’t miss” banquet where we are to award our 2nd lifetime achievement award(who will it be)? Send in your recommendations
• Within its budget CSDMS intends to support the greatest number of members to attend the meeting. Early registration is required therefore to secure your place given the limitations of our UCAR venue. Remember that our Community now approaches 600 members, so please secure your space NOW.

2) We have released our latest 2011 Semiannual Report

The report provides the latest CSDMS information and achievements including the many improvements to the CSDMS Component Modeling Tool CMT and improvements to the CSDMS Repositories for Models, Components, Data and Education. The 2011 semiannual report also provides updates on each of the Year 5 Goals. Below are a few teasers!

• Did you know that you can vote on which models should be prioritized for conversion into a CMT component model? See: Why vote for model incorporation
• Did you know that you can track the progress of this model conversion?
• Did you know that CSDMS has its own YouTube Channel that has been highlighted several times for being in the “Top 50 most viewed channel” of the “non profit” category? http://www.youtube.com/user/CSDMSmovie
• Classes are starting — have you made plans to incorporate CSDMS movies, labs, simulations and lectures into your class?

3) The CSDMS High Performance Computing Cluster (HPCC) Beach continues to grow in capability (cores, memory) and CSDMS-users supported. Hardware troubles in mid-spring have been resolved. http://csdms.colorado.edu/wiki/HPCC_portal

A second HPCC, Janus is now available to appropriate CSDMS users for larger model applications. With more than 16,000 cores, Janus offers CSDMS modelers new limits for their surface dynamics modeling efforts.

On behalf of all the staff of the Integration Facility (IF) we wish all of our CSDMS contributors the best for upcoming fall season. We want to see you in Boulder in October. Again thanks for your efforts!

James P.M. Syvitski

CSDMS Executive Director, August 10, 2011

→ January 2011

Dear CSDMS members,

On behalf of the CSDMS integration staff we wish you all the very best for the New Year.

CSDMS continues to gain momentum, with 140 new members in 2010 (>480 members in total). CSDMS has become the international coordinator of open source surface dynamics models and modeling efforts, with more than 120 U.S. institutions and more than 100 foreign institutions from 30 countries. The CSDMS Model Repository offers >160 open-source models registering more than 8000 downloads. This penetration of models directly addresses the historical lack of readily available models for research and application. During the last year CSDMS saw continued growth and advances in community products, including

1. a completely revised web portal and services (check it out!),
2. the first official release of the CSDMS model-coupling tool CMT (and even newer release is coming within the month),
3. an 800% increase in the number of models made into CMT components,
4. an alpha-version of the CSDMS Domain Architecture SedGrid,
5. new data handling abilities (NetCDF, WML),
6. the first all-hands conference Modeling for Environmental Change, and
7. numerous tested educational modules, clinics, and courses.

The CSDMS Web Portal with more than 1.5 million visits is becoming a “go to” site for models and CSDMS-related data and educational products including animations and images, modeling labs and lecture materials. The new site remains in use but is still under construction. If you need to find something (like our latest annual report) you might need to use the search engine, until the site is completed.

The Annual Report is a must read for all members. The report provides the 5 year strategic plans developed at our Annual Meeting and also the work plans for the Integration Facility over the coming year and detailed description of accomplishments over the last year.

Our 110 users of the CSDMS HPCC Beach will be pleased to hear that the system has grown with another 128 compute cores due to the generosity of the U.S.G.S. and the Univ of Colorado. Beach now offers members 704 cores @ 3.0 GHz E5472 (≈8 Tflops). If anyone desires even more computational horsepower, they should contact me and I will try to find time on the large CU supercomputer Janus (>150Tflops). Remember it is free J.

Proposals submitted to NSF on or after January 18, 2011, must include a supplementary document of no more than two pages labeled “Data Management Plan”. Designed to deal with both models and data, CSDMS is supporting this NSF requirement by offering an acceptable vehicle through its community portal. See:NSF_data_management_plan.

The 2010 annual report also publishes the abstracts from our Annual Meeting, for those who could not attend. The report includes the Dave Furbish dedication to Professor Gary Parker who was recipient of the first CSDMS Lifetime Achievement Award. Gary was awarded the honor along with a gentle roasting at the San Antonio meeting. As Professor Furbish writes: “Gary has fundamentally contributed to steering the course of scientific thinking. The breadth of his impact is impressive.” The 2010 Student Award has yet to be announced given the larger than expected and great nominations. Watch for that announcement in the coming month.

On behalf of all the staff of the Integration Facility (IF) we thank our hard working CSDMS members and look forward to working with them in the New Year!

James P.M. Syvitski,

CSDMS Executive Director,
Jan 7, 2011


→ July 2010

Dear CSDMS members,

Just 2 Weeks Left: for registering for the all hands CSDMS 2010 Meeting ‘Modeling for Environmental Change’ in San Antonio TX (Oct. 14-17). The meeting will offer an all-star cast of keynote speakers, teaching clinics, strategizing session, and banquet. A CSDMS Special Issue of ‘Computers and Geosciences’ will publish the findings and papers of the participants. Follow this link for more information and to register.

We have released our latest semiannual report. The report introduces a new Just the Facts concept for updates on:

1. Our growing Community of more than 420 members.
2. Model Repository: >150 open-source models, >3.0 million lines of code
3. Data Repository: The Dartmouth Flood Observatory is moving to CSDMS and into the CSDMS Repository will soon host:
   1. Global Flood Atlas,
   2. River Watch (estimated daily river discharge values from remote sensing for ~2500 sites, distributed along major rivers and tributaries on all continents, July 1, 2002 to present),
   3. Global Active Archive of Large Flood Events.
4. The CSDMS Modeling Tool with its improved help system, and greater ease of download and use.
5. CSDMS High Performance Computing Cluster (HPCC): now supports the modeling needs of 109 CSDMS members. The CSDMS HPCC will grow with another 128 compute cores (fall of 2010) and associated RAID.

The 2010 semiannual report provides updates on each of the Year 4 Goals. These updates are a ‘must read’ for those using the newly released CSDMS Modeling Tool (CMT). The report contains the survey results of 36 AAU universities, to assess how surface process modeling is currently being taught. This Sample Inventory of Modeling Courses documents the courses highly relevant to CSDMS modeling and educational efforts, and the schools with the richest course offerings. The report also provides a CSDMS Modeling Course “Use Case”, for those interested in adopting CSDMS modules for upcoming course.

On behalf of all the staff of the Integration Facility (IF) we wish all of our hard working CSDMS members an interesting or relaxing summer. Again thanks for your efforts!

James P.M. Syvitski
CSDMS Executive Director
July 27, 2010


→ January 2010

Dear CSDMS members,

On behalf of all the staff of the Integration Facility (IF) we wish all of our hard working members the very best for the New Year. Below I provide brief snippets of updates. For those wanting more details on all of these topics please see the CSDMS 2009 Annual report.

Our Community:

350 members, 76 US Academic Institutions, 63 Foreign Institutes from 17 countries, 17 US Federal labs and agencies, 11 companies

CSDMS Model Protocols:

Now streamlined and being adopted by the journal Computers & Geosciences (International Association of Mathematical Geosciences), to better penetrate the research community.

Repositories:

Model	97 open-source models, >2.9 million lines of code, 7 computer languages, 250 downloads per month. We are working to get the source code, or clean pathway for members to get the code for on another 55 models.
Data	Grown by 61% in 2009 to now include: ICE-5G Model Data, Sea Ice data, Harmonized World Soil Database, Sea Level Data, Human dimensions data, ASTER Global Digital Elevation Model. CSDMS distinguishes between at least 3 data types relevant for modeling: 1) boundary or initialization data, 2) model algorithm test or benchmark data, and 3) integrated datasets for model validation of coupled systems.
EKT	4 modeling courses, educational codes (~ 60 modules) associated with 3 major modeling textbooks, 20 modeling labs, 25 model animations

CSDMS High Performance Computing Cluster (HPCC):

Fully functional, presently supporting 7 major projects using multiple processors, and provides the backbone for the CSDMS Modeling Framework for model coupling.

CSDMS Ccaffeine GUI:

Fully functional GUI allowing users to graphically build applications from CSDMS components on their own platforms (PC, OX, Linux) and then run them on the CSDMS HPCC server "Beach" You can download the GUI through this link. The new GUI also offers VisIt, a multi-dimensional graphic package designed for Terra-scale, multi-processor rendering for HPC models in a client-server configuration. This valuable CSDMS functionality is being underwritten through the generous support of StatOil and ConocoPhillips.

Proof-of-Concept Projects:

Completed 3 highly varied exercises in linking six models (SedFlux, GC2D, CHILD, TopoFlow, CEM, HydroTrend) written by 6 authors, in 4 computer languages (c, c++, IDL, Matlab), 3 different grids (raster, non-uniform mesh, spatially-averaged), and 2 levels of granularity (process and modular) {and a partridge in a pear tree}. Valuable lessons learned, including the need for faster more robust grid meshing routines.

Year 4 Goals:

1. CSDMS Website ‘A Gateway into the CSDMS World’,
2. Usability of the ‘CSDMS Modeling Framework’,
3. Componentizing the CSDMS Model Repository,
4. Advancing WG & FRG Goals,
5. All-hands Jamboree (either San Antonio or Hawaii) and associated Special Issue,
6. More Technical Advances,
7. Pedagogical EKT modules.

New CSDMS staff:

Dr. Maureen Berlin who is presently working on plume dynamics in Greenland fjords (satellites and modeling) to invert for time-dependent Ice Sheet melt (with Irina Overeem), will be later transitioning to a CSDMS CDI community coordinator and EKT innovator.

Student Modelers Award Winners:

1. Adam Campbell 'Numerical Model investigations … — ice sheet dynamics from a physics-based perspective.
2. Elchin Jafarov for his 'Numerical Modeling of Permafrost Dynamics … Using a High Spatial Resolution Dataset'.

CSDMS will fund their visit to Boulder CO to work with staff scientists and develop their models into a CSDMS component.

Reminders:

Get your abstracts in (deadline April 30) to the Special CSDMS Symposia SS-11 Recent advances in numerical model on morphodynamics, sediment transport and stratigraphy, part of the 18th Intl Sedimentological Congress, Mendoza Argentina
 (Sept 26-Oct 1).

Again thanks for your efforts!

James P.M. Syvitski

CSDMS Executive Director
January 6, 2010

→ August 2009

Dear CSDMS members,

I hope your summer is progressing smoothly. CSDMS is now four members short of 300, (with a surprise gift to the 300th member)! So we continue to expand our presence within the community. Below are brief snippets of updates. The CSDMS 2009 semi-annual report is now posted on our web site, for those wanting technical details. Year 3 continues its focus on:

1. developing the CSDMS architecture and interface standards,
2. model, data and educational repositories, and
3. members conducting advanced simulations on the new CSDMS High Performance Computing Cluster (HPCC).

Some Technical Update Examples:

1. CSDMS interface standards that define how model components can be connected are largely in place.
2. The ElementMapper tool in the OpenMI SDK has been employed to pass data from the CHILD TIN-mesh to the SedFlux Raster-mesh, for example. This will soon be implemented as a CCA "MappingTool" component. Many of the other OpenMI service tools will soon be wrapped for CCA compliance.
3. We have extended an open-source application called I2PY so as to better convert IDL code to Python. We are examining whether to develop a similar converter (M2PY) to covert MatLab code, or rather convert MatLab code as platform-specific C library files that can be used on the CSDMS HPCC server running RedHat Linux. These approaches allow the community to continue to use proprietary, high-level languages such as MatLab and IDL, yet incorporate their software as components in the CSDMS plug-and-play framework.
4. The new CSDMS GUI for Ccaffeine allows CSDMS users to build applications from CSDMS components on their own PCs and then run them on our HPCC server called "beach". Messages and files are passed between the user's PC and our HPCC server via SSH tunneling, while data generated by model runs reside on our server. Work is ongoing to incorporate visualization tools into the new GUI, starting with HPCC-compatible Visit. Our goal is make the CSDMS version of the Ccaffeine GUI be "bullet-proof" as it will serve as the main means for CSDMS users to perform model runs on our supercomputer.

Repository Updates:

1. The CSDMS model repository has doubled in the last 6 months, and members have provided us with indications of substantial growth over the next 6 months. Hundreds of models have been downloaded in the last few months alone, indicating rapid penetration of CSDMS models into the science community.
2. Check out the new repository data holding . Working with NCED and other labs, we plan to grow the data repository through holdings of flume experimental data, from which models can be benchmarked.
3. Irina Overeem has accepted the new CSDMS Education and Knowledge Transfer position and is offering weekly improvements in the Educational Repository, including modeling lectures and labs, and a new instructive movie gallery. Please support her efforts with new product offerings - keep those contributions coming!

Community Updates:

1. The semi-annual report provides members with summaries from each of the working and focus research groups. The report provides expanded findings of the Terrestrial WG and the Coastal WG. Members might take some time to peruse these findings, and also consider participating in one of the 2009 autumn meetings that are being held at the CSDMS Integration Facility in Boulder Colorado. Each Chair is receiving expanded funding for their respective activities, and more members should be able to receive "partial" travel support. Upcoming group meetings will be held jointly with another group to expand our cross-disciplinary CSDMS mission. For instance, the Terrestrial Working Group and Coastal Working Group are planning a joint workshop to be held October 26th -28th in Boulder. In the next week, dates of other joint workshops. Over the next week, dates of other joint workshops will be finalized and posted on our web site.
2. We encourage members to visit the meeting web site to find timeless content from past meetings, and to see of the many sponsored CSDMS upcoming meetings. CSDMS is co-sponsor of the upcoming:
   • IAMG Computational Methods for the Earth, Energy and Environmental Sciences;
   • RCEM symposium on River, Coastal and Estuarine Morphodynamics,
   • Fall AGU session: Computational Modeling of Landscapes and Seascapes: Models, Data Sets, and Applications (EP03);
   • Fall AGU session: Quantifying the Sensitivity of Landscapes to Climate-Change (U07);
   • Fall AGU session: Challenges in Achieving Integrated Earth System Modeling (IN11), and
   • ISC Special Session: Recent advances in numerical model on morphodynamics, sediment transport and stratigraphy, in Mendoza Argentina. Please submit abstracts soon, to this last one, as this meeting in 2010 will allow CSDMS members to shine internationally and greatly influence the direction of our science.
3. The Semi-annual Report 2009 also contains two CSDMS-specific papers as appendices. The first is Morphodynamic Models: An Overview that integrates overviews from each of the CSDMS Chairs. The second Producing CSDMS-compliant Morphodynamic Code to Share with the RCEM Community sets the scene on how models will be linked.
4. A number of outstanding proposals have been submitted to NSF and other agencies, from CSDMS members over the last six months. Keep those collaborations going! Two recently funded examples include:
   • Professor Galewsky leading an NSF-funded Cyberinfrastructure for a Western Consortium of Idaho, Nevada, and New Mexico to allow users to specify, maintain and update, through a central user interface and a common methodology, a collection of software and interconnection tools, needed to accomplish climate research tasks. The project will follow CSDMS protocols to couple surface process and hydrologic models with WRF.
   • Leaders in community modeling and cyber-infrastructure (Community Climate Systems Model; Community Surface Dynamics Modeling System; National Unified Operational Prediction Capability; Earth System Modeling Framework; Earth System Grid; and Common Metadata for Climate Modelling Digital Repositories) have received Cyber-Enabled Discovery and Innovation (CDI) funds to enable virtual organizations (VOs) in the Earth sciences to scale to massive interdisciplinary “communities of communities.” A key project element is commodity governance, which encodes social and technical aspects of governance in cyberinfrastructure to create virtual units that can operate, aggregate, and coordinate in a decentralized fashion. CDI is NSF's bold five-year initiative to create revolutionary science and engineering research outcomes made possible by innovations and advances in computational thinking.

New CSDMS staff:

1. Jisamma Kallumadikal is our new CSDMS Computer Scientist (Industrial Consortium). Jisamma received her Bachelors in Computer Science & Engineering, Cochin U. of Science & Technology, India, and her Masters in Computer Engineering, U. Duisburg – Essen, Germany. Her work experience includes being a systems engineer or software developer for T Systems Enterprise Services, Bonn, Germany; Fraunhofer SCAI, Sankt Augustin, Germany; Nokia Networks R&D, Düsseldorf, Germany; Teles Computer Systems, Bangalore, India; & BNS Solutions, Trivandrum, India.
2. Beichuan Yan joins CSDMS as a software engineer. Beichuan received his B.E. and M.S. in Civil Eng. from Tsinghua U., Beijing, China and his Ph.D. in Civil Eng. from the University of Colorado – Boulder. His research experience includes work on stress-strain and consolidation simulation (FEM) and discrete element modeling of granular materials and coupling with FEM.
3. Carl Friedrichs is the new Chair of CSDMS Chesapeake Focus Research Group. Carl received his B.A from Amherst College, his Ph.D. from MIT/WHOI and is presently a Professor of Marine Sciences at the Virginia Institute for Marine Sciences. Carl’s long-term research goals are to better understand the fundamental aspects of coastal and estuarine physics, which control sediment and other material fluxes at time-and length-scales important to geology, biogeochemistry, and ecology.

Learn more about them and their backgrounds in the semi-annual report.

Remember:

• Submit your abstracts to one of the AGU or ISC CSDMS sessions,
• Participate in upcoming CSDMS Working Group and Focus Research Group meetings and activities,
• Submit your latest advances to the CSDMS model, data, and educational repositories,
• Visit the CSDMS website for the latest information about upcoming meetings, new models and available educational products.

Again thanks for your efforts!

James P.M. Syvitski

CSDMS Executive Director
August 6, 2009

→ February 2009

Dear CSDMS members,

Every 4 months I try to stay connected to our now >250 members, providing brief updates. Like you I do not like getting too many emails, our web site is always up to date, however.

Year 1 & 2 largely dealt with logistics, organization, governance and communication (e.g. wiki). Year 2 & 3 has its focus on middleware (architecture, frameworks, and interface standards) and model and data repositories). Year 3-5 will be focused on members conducting advanced simulations, on the new CSDMS High Performance Computing Cluster (HPCC).

We have initially focused on community leaders, to get their many models into our repository, along with their metadata, all the models from the Slingerland book, the Pelletier book, and soon, the Parker e-book. We heartily thank the many individuals who have taken the time to submit their models along with their metadata, test cases, example input and output files. This is so important to our effort, and your favorite funding managers are noting which members are fulfilling their requirement to make their models and modeling tools publicly available.

We are hoping that members will become familiar with the concept of ‘Initialize, Run, Finalize’ or IRF that is so important for component modeling. Details can be found in the CSDMS Handbook, and to further help we will soon issue a very short How To help letter. AND if needed, please contact one of the software engineers (Beichuan Yan, Eric Hutton or Scott Peckham) to ask to schedule individual help.

The NSF program managers are hoping that CSDMS members will flood their offices with CSDMS-related proposals. These can be individual efforts, or more collaborative with other working group members. They can be cyber-related, or advancing science through HPCC simulations, or provide new module connectivity, development of new algorithms, or be related to or in support of field programs. My only advice is for you to pay attention to the deliberations that are found in the CSDMS Strategic Plan, or information on the CSDMS web site, or the reports from Working or Focus Research Group meetings (see past meetings and their ppts or pdfs). The appropriate Chair, or I, or both, would be happy to provide letters of support for your CSDMS efforts. The proposals will be looked at NSF with favor, but still must pass the muster of panels, if applicable, and peer-review, who will continue to look to see if your proposals are indeed coherent and transformative.

The CSDMS high performance computing cluster (HPCC) is up and running. We will soon, through our web site, be offering members access to the system, with accounts and login instructions. The HPCC is for members who have submitted code into the CSDMS Model Repository, to either run their models in advance of science, or to advance developing modeling efforts that will ultimately become part of the Repository. This is the pay to play rule. The HPCC is also for members who wish to apply compliant CSDMS models developed by others within the CSDMS framework, to help them advance their science. The caveat here is that many of the models in the Repository are still not CCA/OpenMI compliant. Finally the HPCC is for members who wish to experiment with new data systems in support CSDMS models, or visualizations of the model runs. You can read more about the HPCC and the ribbon-cutting ceremony held February 4, 2009 by visiting this link.

Depending on the size and maturity of the CSDMS Group, between $8K and $9K is made available to Chairs in support of their annual meeting. This money is obviously not enough to cover the attendance of all members. Partial support is the norm for active members; so don’t forget to budget for travel cost in your research grants. Also, for those that cannot attend in person, you may be able to attend via Skype or similar connection, for some of the meetings. All ppts presented can be found on the CSDMS Wiki page under past meetings. I will also be working with NSF directors to see if we can find the funds for an all-hands meeting, likely near the end of Year 3 or beginning of Year 4.

I will soon be attending the S2S MARGINS meeting, as it looks to its future, representing CSDMS. If you would like to influence the site selection for this program or the sampling strategy related to CSDMS models or efforts, please send me an email ASAP, with your thoughts, as I will be presenting in NZ on this issue in early April.

Finally, reminders:

1. Get your Wiki account (it is easy and fast through our CSDMS web site), and always log in through your account, to participate in on-line group discussions, or to add or edit on-line material.
2. Periodically check out upcoming CSDMS related meetings, and sponsored workshops, and participate where possible. We are supporting AAPG, IAMG, RCEM, and Turbidity Current workshops over the next few months. Please participate.
3. Download the CSDMS handbook from our web site, and learn about component modeling. Get familiar with IRF!

Again thanks for your efforts!

Yours sincerely,

James P.M. Syvitski
CSDMS Executive Director.
February 24th, 2008

→ November 2008

Dear CSDMS members

Below I provide some brief updates on CSDMS developments (Fall 2008 quarterly missive).

1. Those of you attending AGU, please plan on attending the CSDMS Town Hall Meeting
   1. When: Thursday, December 18, 2008, 6:15 PM
   2. Where: San Francisco Moscone Convention Center, West, Room 3016
2. There will be a buffet and cash bar provided. Come and meet CSDMS Staff, Working Group and Focus Research Group Chairs, program managers, and industry representatives. We will present updates and demonstrations of our modeling efforts. We will also be presenting the winner of the first annual CSDMS Student Modeler Award!
3. The Hydrology Focus Research Group will be meeting January 20-21, 2009, in Boulder CO. All interested members should contact the Chair, Professor Jay Famiglietti, or Marlene Lofton to sign up for the meeting, and enquire about travel support.
4. The Carbonate Focus Research Group will be meeting January 26-27, 2009, in Boulder CO. All interested members should contact the Chair, Professor Peter Burgess, or Marlene Lofton to sign up for the meeting, and enquire about travel support.
5. The Terrestrial Working Group will be meeting Feb. 2-4, 2009, in Boulder CO. All interested members should contact the Chair, Professor Greg Tucker, or Marlene Lofton to sign up for the meeting, and enquire about travel support.
6. The CSDMS Education and Knowledge Transfer Meeting met on Oct. 10, 2008, in Boulder CO. Working Group members elected Karen Campbell as Chair of the EKT Working Group. Karen is located at the National Center of Earth-surface Dynamics, University of Minnesota. Researchers prioritized their goals and set future priorities, and updated each other on progress to date. For more information, including meeting notes and ppt/pdf presentations CSDMS members may go to EKT wiki page.
7. The CSDMS Inter-Agency Committee met at NSF Headquarters and discussed the congressional mandate requirement for all Federally funded PIs to make their software code publicly available, along with supporting metadata and documentation. Exceptions to the rule were all discussed. Discussions also centered on minimum standards needed to be met by individual PIs, and the role the CSDMS Integration Facility and its 200+ member community in supporting this effort. The CSDMS IF is working with the Agencies in supporting this mandate. The community is advised to be aware of the mandate and to work with CSDMS in helping them achieve this goal.
8. A CSDMS handbook is now available that provides much information on the background of model integrations, modular modeling concepts and other cyber-infrastructure concepts (see below for outline of the handbook). The CSDMS architecture being developed is explained in this document.
9. The CSDMS community is extending into Australasia. James Syvitski, CSDMS ED, met recently with Taiwanese scientist at an International Workshop on Sediment Transport in Taiwanese Rivers - Coastal Seas and Other Coastal Systems (Nov 3-5, 2008). Plans are underway to have appropriate Taiwanese scientists to join the CSDMS effort. The CSDMS Integration Facility is hosting for AY2008/09 Visiting Scientist Yun-zhen Chen from Nanjing University to work on model simulations of the Yellow River and its delta environment. Professor Syvitski will also soon be meeting with interested academics from the Sydney regional community and later with New Zealand representatives in Wellington and Christchurch.
10. Presentations from the CSDMS co-sponsored SEDIBUD workshop are now available online at the SEDIBUD wiki page.
11. CSDMS is co-sponsoring the River Coastal and Estuarine Morphodynamics (RCEM) 2009 Meeting, September 21 - 25, 2009 to be held in Santa Fe City, Argentina. In addition to sponsorship, James Syvitski and Eric Hutton from the CSDMS Integration Facility will be presenting a 7 hour short course on Earth-surface Dynamic Modeling and Model Coupling to include modules such as
    1. S2S process-response modeling: S2S Modelers checklist, example, definitions; From Concept to Model; Constraints, Sensitivity & Scaling
    2. Modeling discharge and Sediment Flux DEM to flow paths; Climate to discharge; Paleo-discharge; Hydrological Modeling; Sediment Delivery;
    3. Landscape Evolution Modeling Weathering Module, Mass Wasting Module, Fluvial Transport Module,
    4. Nearshore Modeling: Coastal modeling approaches; Delta lobe avulsion 2D & 3D; Littoral sediment transport modeling: along shore; off shore;
    5. Plume modeling: Hyperpycnal Models, Hypopycnal Models; Shelf Sediment Transport Modeling
    6. Sediment Failure and Sediment Gravity Flow Modeling (turbidity currents, debris flows)
    7. Whole Basin Modeling
    Gary Parker will be providing a short course on Morphodynamics of Lowland Rivers

So all the best to everyone, thanks for all of your hardwork ------ and see you soon at AGU!!!!!!

James P.M. Syvitski
CSDMS Executive Director.
November 9th, 2008

→ August 2008

Dear Community here are some recent highlights

• The CSDMS community continues to grow. While the main body of membership approaches to 200 Working Group members, our Executive Committee has authorized the establishment of two Focus Research Groups (FRG), that cut across our Environmental Working Groups:
  1. Carbonate Modeling Community-FRG,
  2. Hydrology Modeling Community-FRG, the later to be co-sponsored by CUAHSI.
  A third Geographically-Focused Research Group (GFRG) is being developed with co-sponsorship with the Chesapeake Community Modeling Program (CCMP). Details are still being worked out with the co-sponsors, and eventually chairs of the FRG's will be appointed, CSDMS-wiki web pages developed, and FRG membership lists and activities established. Stay tuned.
• Members should create an account (its free) on the CSDMS web site by clicking on the "create account" link on the Mississippi image, and thereafter sign in with the "log in" link also found on the Mississippi image. This will allow the user to enter the wiki side of the CSDMS web site and edit pages appropriately and take in community discussions. Not all pages can be changed, and there are still a few hiccups. But get used to logging in through the wiki.
• The CSDMS Integration Facility is hiring one (possibly two) computational and/or geophysical post-doctoral fellow with experience in software development, to work in a team as a software engineer in the development of an integrated framework for the modular modeling of Earth-surface dynamics.
• A CSDMS Industrial Consortium is being established after a successful launch meeting associated with the AAPG/SEPM 2008 San Antonio meeting. The first priority will be to hire a dedicated software engineer to speed in the development of the CSDMS framework and interface standards and work as a liaison with the Consortium and the CSDMS community.
• The CSDMS architecture is to be the DoE Common Component Architecture (CCA) that employs SIDL (Scientific Interface Definition Language) to allow rapid communication of various component models through its language neutral compiler (BABEL). As an aid to users the BOCCA GUI allows ease in this operation. A "idiots guide" is being developed and will be soon released to the community as a how to guide. Most importantly is for users to get their code written in the IRF method: Initialize, Run, Finalize. This typically takes less than a day to get completed.
  The CSDMS interface standard will be based on OpenMI. OpenMI also comes with a Windows based framework that will not be employed (rather we will use the CCA architecture and framework). OpenMI allows for 1D and 2D models to be coupled, smoothing and interpolation routines to be used and shared with component models of different grids and time stepping. Documentation on its use will be part of the "idiots guide" being developed. Most importantly for users is to learn how to write up their "get values" routines, to allow models to communicate through CCA.
• The Integration Facility is busy learning to do the coupling and writing the glue code. As a proof of concept they are taking a glacier model (GC2D) written in MATLAB and to be combined with a flow routing model (TopoFlow) written IDL. To accomplish this the MATLAB and IDL code had to be each re-written in Python (to make the code open-source and CCA compliant), each had to be refactored, made OpenMI compliant and tested. The IF is also combining a 2D landscape evolution model (CHILD) written in C++ using tins, with a sedtrans-strat model (SedFlux2D) written in C that is raster-based. Again the models needed to be made CCA and OpenMI compliant, and tested (the models were already refactored). The lessons learned from these exercises will be shared with the community on the CSDMS web site and idiots guide.
• We say goodbye to Andrew Svec who has been terrific but for a variety of considerations has moved back to U. Minnesota @C to become the combined Director of Communication and Marketing. We wish Andrew all the best in his new position. The new Executive Assistant for CSDMS is S. Marlene Lofton who has a graduate degree community psychology and another in business administration, much experience in running workshops and retreats, and was once a computer science teacher. She joins CSDMS on Aug. 1.
• The Chairs of the Working Groups will be working with Marlene on their next meetings and agendas. Stay tuned.

I hope your summer is going well! All the best

James P.M. Syvitski
CSDMS Executive Director.
July 30th, 2008

→ April 2008

Dear CSDMS members

1. What a first year, with much accomplished, and a membership growing faster than anticipated. We now exceed 175 Working Group members, and this is a doubling of members within the first year. First I would like to thank all who have helped to shepherd this initiative to where we are today. You know who you are --- Kudos. This thanks extends to members of the Executive Committee, our Working Group Chairs, members of the Steering Committee, industrial and government partners, and particularly the local Integration Office staff, who have been putting in long hours to keep us all on track.
2. Our web site is now a Wiki. To participate in the on line discussion, we ask that you open up an account, thus allowing you to edit on-line material. To do that, please locate the create account link (just above the Mississippi delta image). Once done you will need to log in to contribute and edit. You can easily set this up so that you log in from your computer automatically. CSDMS staff can only edit a few of the structural pages, but our members can edit much. The Working Group Chairs will be conducting more and more business with their members on line.
3. The CSDMS Five Year Strategic Plan has been uploaded to the CSDMS website on the CSDMS Documents page: http://csdms.colorado.edu/wiki/index.php/CSDMS_docs.
   You will be getting a shiny version in the mail, so you don't need to print it out. However feel free to pass on the PDF version to colleagues and program managers. The Strategic Plan will be updated every year, some things dropped & some things added, so this is the evolving blueprint of our initiative. Please take the time to familiarize yourself with the plan.
4. Year 2 begins to day. We will be planning our next meetings, our five Working Groups, our management meetings, our science Workshops, and a coding camp. Stay tuned and stay in contact with your WG chairs.

Again thanks for your efforts!

James P.M. Syvitski
CSDMS Executive Director.
April 8th, 2008

→ February 2008

Dear CSDMS Members

Annual Report: Enclosed please find the first CSDMS annual report. We were caught off guard in finding out that the NSF Annual Report is due 90 days before the end of our fiscal year (April 1). Most organizations issue their annual report after the end of the FY. The enclosed report, while informative, lacks graphics / photos. To better reflect all of our participants 2007 surface dynamic modeling efforts, we plan on releasing a FY annual report in April. Therefore would you please send in (to csdms@colorado.edu):

1. full references for any 2007 peer-reviewed CSDMS-related papers that you wish to highlight to the community and our program directors, and
2. figures/photos (e.g. cool-model simulations etc) that you own the copyright to and wouldn't mind seeing them displayed in CSDMS publications.

Strategic Plan: The CSDMS ExCom is busy working to complete the first draft of the CSDMS 5yr Strategic Plan. When asked, please offer your insight.

Workshops and Meetings: The Cyber-informatics and Numerics WG recently met for two days and accomplished much on the CSDMS cyberinfrastructure (see enclosed annual report for details). Tao Sun and members are greatly thanked for their effort. Next up is the Community Sediment Model for Carbonate Systems, Feb. 27-29, 2008, Golden, CO; followed by the Coastal WG and Marine WG startup meetings, Orlando, FL, March 8, 2008. CSDMS is a co-sponsor with SEPM for the research conference Clinoform sedimentary deposits: The processes producing them and the stratigraphy defining them, Aug. 15-18, 2008, Rock Springs, WY. We encourage interested parties to participate in these efforts.

Dedicated CSDMS Experimental Supercomputer: Great News!! The CSDMS Integration Facility is securing funds, largely through the University of Colorado, but with additional support from the U.S.G.S and possibly NOAA, to acquire a CSDMS-operated and dedicated Experimental Supercomputer (ES). The CSDMS ES is dedicated to support modeling efforts of our community. CSDMS choice of DOE's Common Component Architecture (CCA) with its supporting tools (e.g. Babel, Bocca, Ccaffeine) provides a mature high-performance computing (HPC) framework. ES details are in flux, but initial estimates suggest it will comprise between 256 - 400 cores, offering 3 to 5 teraflops of computing power, and configured with two HPC approaches - 1) massive shared memory among fewer processors, and 2) the more typical parallel configuration - each running Linux with Fortran, C and C++ compilers. Plans have the CSDMS ES linked to an NSF-proposed Front Range HPC with 7000 core, >100 teraflops, which in turn would be linked to the US TerraGrid, and/or the proposed Cheyenne NCAR/UCAR Petascale HPC dedicated to support the NSF Geoscience Collaboratory. To find out more please read the enclosed Annual Report. When up and running, we will provide CSDMS members information on how to access (free!) time on the ES for their CSDMS-related research and simulations.

CSDMS Compliant Repository: CSDMS has developed a wiki-based website that is home to the CSDMS-CCA development project (http://csdms-cca.googlecode.com) to present CSDMS latest developments on model protocols, model components, and instructive information about how scientists can use CCA in this environment. The website allows CSDMS members to easily add information to the website, to stay current and to further foster community around the project. The website presently contains a description on how to install the CCA development tools on various platforms (platforms include fedora, ubuntu, OSX10.5, and Solaris 8).

Coding Camps: We are looking into running coding camps for both training in the use of the Common Component Architecture and its related tools, and for migrating code over to use in an HPC environment. More info as it develops.

James P.M. Syvitski
CSDMS Executive Director.
February 14th, 2008