Material for the GEOframe Winter School - Getting Started with OMS and Jupyterlab

Day first of the Winter School on GEOframe was conceived to give people the taste of what OMS is and how to use it with Python lab. For the Installations, please refer to the Installation page. 

Not much information about Jupyterlab though. It will be given interactively using notebooks and explaining their contents.

• The philosophy behind OMS/GEOframe (YouTube video)
• The GEOframe deployment
• A brief introduction to the Object Modelling System (YouTube video)
• OMS User Manual - Introduction (pdf, epub) 
• The OMS working environment (YouTube video)
• OMS User Manual - The working Environment (pdf, epub)
• The structure of a .sim file (YouTube video)
• The existing manual excerpt (outdated but still useful) (pdf, epub)
• Examples (All the material in the .zip files. Notebooks in /docs folder)
• ex_00 (zip files)
• Examples-basic (zip files). Please find Jupyter notebook shown in video below in the doc directory of the zipped files.
• Example 001YouTube video
• Controlling Iteration (Ex 05) YouTube video.
• Going on with examples: Again on You Tube Video Iteration, Bulk connect, Feedbacks
• Exercises 1&2
• Watertank  Example (zip files). Documentation in the doc folder.
• Water Tank example - Part I YouTube video
• Exercises 3&4
• Creating a notebook from the scratch (Live YouTube video by Niccolò Tubini)
• Open directions

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Material for the Winter School on the GEOframe System - Installations

The Winter School on the GEOframe system is approaching.  In this webpost you will find all the preparatory material of the school indexed.

Installations

You are not assumed to know Python or Java to participate to the School. However programs runs on Java.. We will not do any Java programming though.  Input/Output of models will be treated by using some scripting in Python. We will communicate the appropriate notions during the classes. However, for the interested there are plenty of courses on the web (for instance this comes from SciPy 2018. Other from SciPy here.)

• Java. GEOframe and OMS are written in Java and they require to have installed Java on your computer. Here you can find instructions to install Java on your computer.  OMS need Java 8 JDK.  Please note that you need the Java Development Toolkit (JDK) installed not the Java Runtime Environment (JRE).  The official Oracle's pages are here. You can watch several videos for Windows: here. Googling you can get videos for your platform.
• We are going to use Docker for our modelling. Therefore you need to install it (here for Linuxes) on your computer. To quickly understand what Docker is, you can see here. Or read this tutorial. This video could be useful too. The knowledge of Docker required will be extremely elementary. You will not be required to do Docker applications. You simply use one and, at the end, is just matter of executing a command. 
• During the School we will use Jupyter and Python 3 for data management and visualisation. It would be great if you could arrive
• The post at this link contains all the information needed. For installation of the software, we suggest Anaconda. For any problem contact us through the mailing list. 
• To understand what a Jupyter notebook is about, please see its manual. However, we will use Jupyterlab.  (You can see a YouTube video about here).  One can think that Jupyter was heavily based on the look-and-feel of Mathematica notebooks: but Jupyterlab is a step ahead to something different. Installing Anaconda, you also have already installed Jupyter notebook. So you have just to try it issuing the command: 
• Jupyter notebook
• You still do not know what to do with it, but we will lear step by step during the Winter School
• For Jupyter lab, you have to do installation  explictly: 
•  conda install -c conda-forge jupyterlab 
• The manual of Jupyterlab is here.
• Finally, at least for MacOs user, due to a bug either in the Docker or in GEOtools, it is necessary to use the OMS Console.  You can download the beta 3.5.62 release from here.

• If you want to further with Jupiter and Jupiterlab, you can  install BeakerX. For its installation, please follow verbatim the instructions here. The instructions given at the main page of BeakerX are incomplete ;-).

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Updated material on Horton Machine

The Horton Machine is our set of tools for terrain analysis actually maintained by Hydrologis. They since 2000 and something took care of keeping my tools alive on various platforms: GRASS, JGrass, uDig and now on gvSIG. We also have a porting of the Horton machine that works under GEOframe but is the same codebase.

Silvia Franceschi and Andrea Antonello gave a tutorial at this year gvSIG conference and here it is the material.

You can find the same material also at this osf project. Soon they will follow some theoretical lectures.

Life After Ph.D. (especially for Italians but of general interest)

This is part of the Ph.D. days of Department of Civil, Environmental and Mechanical Engineering of University of Trento. October 29, 30, 31 were used to check the advancement of our almost one hundred Ph.D. students. Who was moving to the first to the second year, who from the second to the third, who had to prove to be able to write the final Thesis after the third year.

I think professor Scardi offered a good overview, worth to be listened to.

Parallel Computing in GEOframe

Inside our University we have a group that works on parallel computing. My colleagues work in various directions, using standard technologies as OpenMP or MPI. I confess I am very ignorant on the details. However, starting from our hydrological problems, it happens that we embraced OMS that implements an intrinsic parallelism which acts between components. Besides, my PhD student Francesco Serafin, introduced a new way to parallelize our problems called Net3. All of these things are shortly presented in the slides below.

The link, here.

HPC school for PhD students at Department of Civil, Environmental and Mechanical Engineering

Among the initiative organized by our doctoral school there is this introduction to computing that can be od interest for beginners (with a little attitude).

Here below, please find the Software Carpentry lectures that were streamed on YouTube and are now present at our Department page.

Unix Shell introduction

Jupyter notebooks and a little of Python programming

Crocus and Snowpack in a nutshell

There is not an enormous choice of process based models that treat snow Among them, two that are a reference for us are Snowpack and Crocus. Here it is their essential references.

SNOWPACK

• Bartelt, P., & Lehning, M. (2002). A physical SNOWPACK model for the Swiss avalanche warning Part I. Numerical model. Cold Regions Science and Technology, 35(3), 123–145. https://doi.org/10.1016/S0165-232X(02)00073-3
• Lehning, M., Bartelt, P., Brown, B., Fierz, C., & Satyawali, P. (2002). A physical SNOWPACK model for the Swiss avalanche warning Part II. Snow microstructure. Cold Regions Science and Technology, 35(3), 147–167. Retrieved from www.elsevier.com/locate/coldregions
• Lehning, M., Bartelt, P., Brown, B., & Fierz, C. (2002). A physical SNOWPACK model for the Swiss avalanche warning Part III: meteorological forcing, thin layer formation and evaluation. Cold Regions Science and Technology, 35(3), 169–184. Retrieved from www.elsevier.com/locate/coldregions

CROCUS

• Brun, E., David, P., Sudul, M., & Brunot, G. (1992). A numerical model to simulate snow-cover stratigraphy for operational avalanche forecasting. Journal of Glaciology (Vol. 38).
• Brun, E., Martin, E., Simon, V., Gendre, C., & Coleou, C. (1989). AN ENERGY AND MASS MODEL OF SNOW COVER SUITABLE FOR OPERATIONAL AVALANCHE FORECASTING. Journal of Glaciology (Vol. 35)
• Vionnet, V., Brun, E., Morin, S., Boone, A., Faroux, S., Le Moigne, P., … Willemet, J. M. (2012). The detailed snowpack scheme Crocus and its implementation in SURFEX v7.2. Geoscientific Model Development. https://doi.org/10.5194/gmd-5-773-2012