Difference between revisions of "Tools portal"

m (Move Landlab to a standalone page)
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including links to its documentation and its source code repositories,
including links to its documentation and its source code repositories,
please see the [[CSDMS_Web_Modeling_Tool|CSDMS Web Modeling Tool]] wiki page.
please see the [[CSDMS_Web_Modeling_Tool|CSDMS Web Modeling Tool]] wiki page.
<div class=AutoScaleImage>[[ File:Pymt-logo-cropped.png | right ]]<div>
PyMT is an Open Source Python package, developed by the Community Surface Dynamics Modeling System, that provides the necessary tools used for the coupling of models that expose the Basic Modeling Interface (BMI). It contains:
* Tools necessary for coupling models of disparate time and space scales (including grid mappers)
* Time-steppers that coordinate the sequencing of coupled models
* Exchange of data between BMI-enabled models
* Wrappers that automatically load BMI-enabled models into the PyMT framework
* Utilities that support open-source interfaces (UGRID, SGRID, CSDMS Standard Names, etc.)
* A collection of community-submitted models, written in a variety of programming languages, from a variety of process domains - but all usable from within the Python programming language
* A plug-in framework for adding additional BMI-enabled models to the framework

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For more information on Dakotathon, including links to its documentation and its source code repository, please see the [[Dakotathon]] wiki page.
For more information on Dakotathon, including links to its documentation and its source code repository, please see the [[Dakotathon]] wiki page.
<div class=AutoScaleImage>[[ File:Landlab_logo_picture.jpg | 200px | right ]]<div>
[http://landlab.github.io LANDLAB] is an open-source Python library of code that enables users to easily build unique earth surface processes models to address specific hypotheses. The Landlab library contains gridding engines for building regular and irregular grids, process components that act on grid variables, tools for storing and sharing data among the grid and components, and plotting and analysis tools. Process components represent individual processes occurring at the earth’s surface (e.g. growth and death of vegetation, surface water infiltration, linear diffusion of sediment), or drivers of these processes (e.g. rainfall, solar radiation). Users can build models by combining existing process components, or build new components if a required process component does not exist. Landlab was developed by members of the CSDMS community with support from CSDMS and the National Science Foundation (two ACI - SI2 grants).
'''Why build another modeling tool?'''<br>Landlab has the rare distinction of being built to make modeling accessible to a wide variety of earth scientists, including those who do not traditionally use computational models. In contrast, most other models are designed to answer a specific hypothesis posed by the developers.
'''What does this mean for new users?'''
* Landlab is extensively [http://landlab.github.io/#/ documented.] 
* Users can contact developers with [https://github.com/landlab/landlab/issues issues.]
* There are [https://github.com/landlab/tutorials tutorials] to teach users how to use Landlab.
* There are [https://github.com/landlab/landlab_teaching_tools classroom tutorials] to teach students about different surface processes.
* Many Landlab tutorials are accessible through [https://www.hydroshare.org/ Hydroshare], an online collaborative environment for sharing data and models, which allows users to test-out Landlab without installing it locally.
* Landlab has integrated testing to ensure that new code contributions will not break existing code.
* There is [https://github.com/landlab/landlab/wiki/Develop-your-own-component documentation] to make contributing code a bit easier.
'''Landlab Components and Models'''<br>
Numerous people have contributed components and models to landlab. Of these, {{#ask:[[Model:+]] [[Source code availability::Through web repository||Through CSDMS repository]] [[ModelDomain::Terrestrial||Coastal||Marine||Hydrology||Carbonates and Biogenics‎||Climate||Geodynamic]] [[ModelFramework::LandLab]]
| format=count}} are described in the CSDMS repository and are listed below.
{{#ask: [[Model:+]] [[ModelDomain::Terrestrial||Coastal||Marine||Hydrology||Carbonates and Biogenics‎||Climate||Geodynamic]] [[Source code availability::Through CSDMS repository||Through web repository]] [[ModelFramework::LandLab]]
| ?One-line model description
| ?Last name
| ?First name
| ?Source code availability
| ?Source web address
| ?Model_also_known_as
| ?Source csdms web address
| limit=5000
| template=Model tables6
| format=template

==Permafrost Benchmark System==
==Permafrost Benchmark System==
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If you're already set up with a login on the PBS,
If you're already set up with a login on the PBS,
jump right to it at https://csdms.colorado.edu/pbs.
jump right to it at https://csdms.colorado.edu/pbs.

Latest revision as of 15:14, 7 February 2019

Modeling Tools

The CSDMS software engineers create tools to help CSDMS members couple and run models.

BMI Builder

The Basic Model Interface

The BMI Builder helps developers build a Basic Model Interface for their model by generating template source code which is then customized by the user for their particular model. Users provide some basic metadata for their model (such as names of input and output items, units, etc.) to the bmi builder which then creates creates BMI implementation files in their language of choice. The user then go through these file of files and implements the labeled sections.


  • Source code on GitHub
  • Documentation on how to use the BMI Builder is provided on GitHub in the read.me file

BMI Tester

The BMI Tester is a Python package that provides command-line utilities for testing Python classes that implement the Basic Model Interface (BMI). BMI Tester also provides a Python interface to the tester that allows users to run tests programmatically. The package is easily extendable so that new tests can be added to the suite.


Standard Names registry

The Standard Names registry is a Python library for working with CSDMS Standard Names.

The CSDMS Standard Names provide a comprehensive set of naming rules and patterns that are not specific to any particular modeling domain. They were also designed to have many other nice features such as parsability and natural alphabetical grouping. CSDMS Standard Names always consist of an object part and a quantity/attribute part and the quantity part may also have an operation prefix which can consist of multiple operations.

standard_names is a Python package to define, query, operate, and manipulate CSDMS Standard Names. It is distributed with a comprehensive list of the currently defined Standard Names.

The standard_names package consists of two basic classes:

  • StandardName: a single name
  • NamesRegistry: a collection of names.

The standard_names package has a complete set of unit tests that are continually tested on Mac, Linux, and Windows. It is distributed both as source code and as Anaconda packages from Anaconda Cloud.



The CSDMS Web Modeling Tool

The CSDMS Web Modeling Tool, WMT, is a web application that allows users on a desktop, laptop or tablet computer to build and run standalone or coupled Earth surface dynamics models on a supercomputer.

With WMT, users can:

  • Design a model from a set of CSDMS components
  • Edit model parameters
  • Save models to a web-accessible server
  • Share saved models with the community
  • Submit model runs to an HPC system
  • Download simulation results

The following components are currently available in WMT.

To see how you can use WMT to configure and run a standalone or a coupled model on the web, check out the WMT tutorial, or jump right into using WMT at https://csdms.colorado.edu/wmt.

For more information on WMT, including links to its documentation and its source code repositories, please see the CSDMS Web Modeling Tool wiki page.



Dakota is a software toolkit developed at Sandia National Laboratories that provides an interface between models and a library of analysis methods, including support for sensitivity analysis, uncertainty quantification, optimization, and calibration techniques. Dakota is a powerful tool, but its learning curve is steep: the user not only must understand the structure and syntax of the Dakota input file, but also must develop intermediate code that allows Dakota to set up and run a model, read outputs from the model, and calculate a response statistic from the outputs.

The CSDMS Dakota Interface, or Dakotathon, is a Python package that wraps and extends Dakota’s file-based user interface. It simplifies the process of configuring and running a Dakota experiment, and it allows a Dakota experiment to be scripted. Dakotathon creates the Dakota input file and provides a generic analysis driver. Any model componentized in the CSDMS modeling framework automatically works with Dakotathon. Dakotathon has a plugin architecture, so models not wrapped into the CSDMS modeling framework can be accessed by Dakotathon by programmatically extending a template; an example is provided in the Dakotathon distribution.

For more information on Dakotathon, including links to its documentation and its source code repository, please see the Dakotathon wiki page.

Permafrost Benchmark System

The Permafrost Benchmark System (PBS)

The Permafrost Benchmark System (PBS) wraps the command-line ILAMB benchmarking software with a customized version of WMT, and adds tools for uploading CMIP5-compatible model outputs and benchmark datasets. The PBS allows users to access and run ILAMB remotely, without having to install software or data locally; a web browser on a desktop, laptop, or tablet computer is all that’s needed.

For more information on the PBS, including links to documentation and source code repositories, please see the PBS home page at https://permamodel.github.io/pbs.

If you're already set up with a login on the PBS, jump right to it at https://csdms.colorado.edu/pbs.