access_JEDIAtNCI_MiniAcademyJune2020_Activity2

This page is discontinued!!!!

Interactive activity 2

This covers "Monday B: Running an Application, Git Flow, and ZenHub"

Steps 1

In the original tutorial all the scripts, configurations and data files were installed on AWS instances. Unfortunately these are not available. What we will do instead is to use some of the CTest tests which you built in "Interactive activity 1". To do this you will manually copy some files and then run the example applications.

Here we will run an executable built (fv3jedi_var.x) in the previous exercise using a yaml configuration file (hyb-3dvar_gfs.yaml). A script to be qsub'ed (run_fv3jedi_var.bash) is provided. All the input files are under Data/ directory.

Prepare by running the following commands,

cd ${TOP_DIR}/academy/jedi/build      # go to the build directory
cd fv3-jedi                           # this is where fv3-jedi subproject was built
cd test                               # where CTest tests are
mkdir mytest                          # where we will set up our tests
cd mytest
cp ../../../bin/fv3jedi_var.x .       # copy one of the executables built
cp ../testinput/hyb-3dvar_gfs.yaml .  # copy a config file
cp -r --preserve=all ../Data .        # copy all the input data files
cp /home/548/jtl548/academy/public/activity2/step1/scripts/run_fv3jedi_var.bash .  # copy script that runs fv3jedi_var.x

Have a look at the yaml configuration file (explanation on yaml is in Lecture Tuesday, Feb 25 - System Configuration) and identify various input files including observations.

Instead of running ./run.bash hyb-3dvar as suggested in the Monterey tutorial use the script you copied to launch MPI processes,

qsub run_fv3jedi_var.bash

The outputs come out in CWD and subdirectories underneath. Browse through some of the output files,

• hyb-3dvar_gfs.run and hyb-3dvar_gfs.run.* - log output
• Data/analysis - analysis

Steps 2

In the Monterey academy participants used AWS instances where all the software packages were pre-installed. We don't have access to AWS so we will have to do this step differently.

All the Python scripts used in this step are available from the feature/academy branch of fv3-jedi. I have copied them so that participants can use them without checking them out. To use the Python scripts do,

export PATH=/home/548/jtl548/academy/public/activity2/step2/scripts:${PATH}  # add location of tools to PATH

ToDo. May need to change location by removing step?

Now use convergence.py to plot how cost function changes during inner-loop iteration,

convergence.py --help                   # help on commandline options
convergence.py -l hyb-3dvar_gfs.run     # produce convergence plot

Use ImageMagick or your favourite graphics viewer to look at the plot. Try plotting other cost functions.

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And then add the location of the installed libraries to the run-time library search path environment variable,

export LD_LIBRARY_PATH=$WHERE_YOU_WANT_INSTALL_TO_BE/lib

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Steps 4