The run script defines a workflow that is needed to run a variational data assimilation application with FV3-JEDI and the B-Matrix Unstructured Mesh Package ( BUMP). Take a look at the files you just copied over. Singularity shell -home = $PWD -e jedi-tutorial_latest.sifįor further details see Working with Singularity. To proceed, let’s create a new directory suitable for running the application and then copy the files over for this tutorial: In addition to the executables and test data files in /opt/jedi/build, there are also various configuration files in the /opt/jedi/fv3-bundle/tutorials directory. The container contains everything you need to run a Data Assimilation (DA) application. Here the QG and Lorentz 95 toy models have their own test directories ( oops/qg/test and oops/l95/test respectively), with a few other test configurations in oops/src/test.
#Panoply x run code#
As the top-level code component, OOPS is structured a bit differently. See, for example, the ufo/test and saber/test subdirectories in /opt/jedi/build. So, they can be found within each corresponding directory, usually in a subdirectory called test. The tests for each code repository are defined within that repository. And, since the unit tests in general produce output files, you will not be able to run the tests in the /opt/jedi/build directory. Furthermore, the files in the container read-only. The files in the /opt/jedi directory are part of the container and cannot be readily accessed after you exit singularity. This contains the compiled code, including the executables that are located in /opt/jedi/build/bin. So, you will see the fv3-bundle components of OOP, IODA, UFO, SABER, and FV3-JEDI, along with a few other supporting code repositories.Īlso in the /opt/jedi directory is a subdirectory called build. As described above, jedi applications are best built as part of bundles that include all the different JEDI code repositories needed to compile that particular application. To avoid this, run the following commands: But, it also means that some things, like this $HOME/.openmpi directory are shared by your container enviroment and your host environment.Īnother common source of spurious test failure is memory faults due to an insufficient stack size.
#Panoply x run software#
This is a Good Thing it provides a convenient work environment that is familiar to most scientists and software engineers, where you can see the files in your home directory without having to explicitly mount it in the container (as you would with Docker). When you are inside the singularity container, you have the same home directory (and user name) as you do outside of the container. It is interesting to note that this is something that we cannot include in the container. This turns on OpenMPI’s “oversubscribe” mode. If the $HOME/.openmpi directory already exists, edit it to make sure it contains an nf file with the line rmaps_base_oversubscribe = 1. In this activity we’ll use the jedi-tutorial container:Įcho 'rmaps_base_oversubscribe = 1' > $HOME/.openmpi/nf
![panoply x run panoply x run](https://estylecdn.com/manufcols/houseofwu/current/zoomalt/44244_F_0074_.jpg)
#Panoply x run download#
The first step in this and all JEDI tutorials is to download the appropriate JEDI tutorial Singularity container.
![panoply x run panoply x run](https://www.estylecdn.com/manufcols/morilee/morilee-current/zoomalt/99101_2.jpg)
Step 1: Download and Enter the JEDI Container ¶ Which JEDI bundle you build depends on which atmospheric or oceanic model you plan to work with. Some bundles may also include supplementary repositories that support different observation types, such as an alternative radiative transfer model or tools for working with radio occultation measurements from global navigation satellite systems. Most bundles will also include additional repositories that provide the forecast model and the physics packages or software infrastructure that supports it. The interface between FV3-based models and JEDI is implemented through the FV3-JEDI code repository. In this tutorial, we will be building fv3-bundle.Īll JEDI bundles include the base JEDI component of the Object Oriented Prediction System ( OOPS), the Interface for Observational Data Access ( IODA), the Unified Forward Operator ( UFO) and the System-Agnostic Background Error Representation ( SABER). A bundle includes a collection of GitHub repositories needed to build and run JEDI with a particular model. JEDI packages are organized into bundles.
![panoply x run panoply x run](https://zet4.pl/zul_pl_BUTY-ROBOCZE-XR302-S1P-PANOPLY-DELTAPLUS-41601_1.jpg)
Along the way, we will get to know the JEDI singularity container we will run these applications without compiling any code - JEDI is already in the container and ready to go. We’ll run both 3D and 4D ensemble variational applications (3DEnVar, 4DEnVar) and compare the increments that each produces. In this tutorial we will be running a low-resolution version of the FV3 model as implemented in NOAA’s Global Forecast System, FV3-GFS.
#Panoply x run how to#
How to run a JEDI DA application inside the container Introduction to the JEDI source code and directory structure How to download and run/enter a JEDI application container Tutorial: Run JEDI-FV3 in a Container ¶ Learning Goals: