Building and running SkyLab

List of spack, software, and AMIs

Versions used:

  • spack-stack-1.2.0 from December 20, 2022

  • AMIs available in us-east-1 region (N. Virginia)

    • Ubuntu 20.04 with gnu-10.3.0 and mpich-4.0.2:

      AMI Name skylab-3.0.0-ubuntu20

      AMI ID ami-0b112e4c34b83c3b2

      It is necessary to use c6i.2xlarge or larger instances of this family.

    • Red Hat 8 with gnu-11.2.1 and openmpi-4.1.4:

      AMI Name skylab-3.0.0-redhat8

      AMI ID ami-0b7ee6595f9f79860

      It is necessary to use c6i.2xlarge or larger instances of this family.

Developer section

Note. To follow this section, one needs read access to the JCSDA-internal GitHub org.

1- Load modules

First, you need to load all the modules needed to build jedi-bundle and solo/r2d2/ewok. Note loading modules only set up the environment for you. You still need to build jedi-bundle, run ctests, and install solo/r2d2/ewok/simobs.

Please note that currently we only support Orion, Discover, S4, and AWS platforms. If you are working on a system not specified below please follow the instructions on JEDI Portability.

Users are responsible for setting up their GitHub and AWS credentials on the platform they are using.

The commands for loading the modules to compile and run Skylab are provided in separate sections for HPC platforms and AWS instances (AMIs). Users need to execute these commands before proceeding with the build of jedi-bundle below.

2- Build jedi-bundle

Once the stack is installed and the corresponding modules loaded, the next step is to get and build the JEDI executables.

The first step is to create your work directory. In this directory you will clone the JEDI code and all the files needed to build, test, and run JEDI and SkyLab. We call this directory JEDI_ROOT throughout this document.

The next step is to clone the code bundle to a local directory:

mkdir $JEDI_ROOT
git clone --branch 3.0.0

The example here is for jedi-bundle, the instructions apply to other bundles as well.

From this point, we will use two environment variables:

  • $JEDI_SRC which should point to the base of the bundle to be built (i.e. the directory that was cloned just above, where the main CMakeLists.txt is located or $JEDI_ROOT/jedi-bundle). $JEDI_SRC=$JEDI_ROOT/jedi-bundle

  • $JEDI_BUILD which should point to the build directory or $JEDI_ROOT/build. Create the directory if it does not exist. $JEDI_BUILD=$JEDI_ROOT/build


It is recommended these two directories are not one inside the other.

  • Orion: it’s recommended to use $JEDI_ROOT=/work/noaa/da/${USER}/jedi.

  • Discover: it’s recommended to use $JEDI_ROOT=/discover/nobackup/${USER}/jedi.

  • On the preconfigured AWS AMIs, use $JEDI_ROOT=$HOME/jedi

Building JEDI then can be achieved with the following commands:

ecbuild $JEDI_SRC
make -j8

Feel free to have a coffee while it builds. Once JEDI is built, you should check the build was successful by running the tests (still from $JEDI_BUILD):


If you are on an HPC you may need to provide additional flags to the ecbuild command, or login to a compute node, or submit a batch script for running the ctests. Please refer the documentation for more details.

(You might have another coffee.) You have successfully built JEDI!


Even if you are a master builder and don’t need to check your build, if you intend to run experiments with ewok, you still need to run a few of the tests that download data (this is temporary) and generate static files. You can run these tests with:

ctest -R get_
ctest -R bumpparameters

3- Build solo/r2d2/ewok/simobs

We recommend that you use a python3 virtual environment (venv) for building solo/r2d2/ewok/simobs

git clone --branch 1.1.0
git clone --branch 1.2.0
git clone --branch 0.3.1
git clone --branch 1.1.0

python3 -m venv --system-site-packages --without-pip venv
source venv/bin/activate

cd $JEDI_SRC/solo
python3 -m pip install -e .
cd $JEDI_SRC/r2d2
python3 -m pip install -e .
cd $JEDI_SRC/ewok
python3 -m pip install -e .
cd $JEDI_SRC/simobs
python3 -m pip install -e .

Note: You need to run source venv/bin/activate every time you start a new session on your machine.

4- Setup SkyLab

Create and source $JEDI_ROOT/

We recommend creating this bash script and sourcing it before running the experiment. This bash script sets environment variables such as JEDI_BUILD, JEDI_SRC, EWOK_WORKDIR and EWOK_FLOWDIR required by ewok. If these variables are not defined they will be set from JEDI_ROOT. Users may set JEDI_SRC, JEDI_BUILD, EWOK_WORKDIR and EWOK_FLOWDIR to point to relevant directories on their systems or use the default template in the sample script below. Note that JEDI_SRC, JEDI_BUILD and EWOK_WORKDIR are experiment specific, i.e. you can run several experiments at the same time, each having their own definition for these variables.

The user further has to set the environment variable R2D2_HOST in the script on pre-configured platforms, or unset this variable on generic platforms. R2D2_HOST is required by r2d2, ewok, and to determine the location EWOK_STATIC_DATA of the static data used by ewok. This data is staged on the preconfigured platforms. On generic platforms, the script sets EWOK_STATIC_DATA to ${JEDI_ROOT}/static.

Please don’t forget to source this script after creating it: source $JEDI_ROOT/



if [ -z $JEDI_ROOT ]; then
  export JEDI_ROOT=**Set this based on your set up if JEDI_SRC, JEDI_BUILD, EWOK_WORKDIR or EWOK_FLOWDIR are not defined.**

if [ -z $JEDI_SRC ]; then
  export JEDI_SRC=${JEDI_ROOT}/jedi-bundle

# Set host name for R2D2/EWOK

# On Orion:
export R2D2_HOST=orion
# On Discover:
export R2D2_HOST=discover
# On Cheyenne:
export R2D2_HOST=cheyenne
# On S4:
export R2D2_HOST=s4
# On AWS Parallel Cluster
export R2D2_HOST=aws-pcluster
# On your local machine / AWS single node
unset R2D2_HOST

# Most users won't need to change the following settings

# Source source this file for ewok ecFlow workflows
source $JEDI_ROOT/venv/bin/activate

if [ -z $JEDI_BUILD ]; then
  export JEDI_BUILD=${JEDI_ROOT}/build

if [ -z $EWOK_WORKDIR ]; then
  export EWOK_WORKDIR=${JEDI_ROOT}/workdir

if [ -z $EWOK_FLOWDIR ]; then
  export EWOK_FLOWDIR=${JEDI_ROOT}/ecflow

# Add ioda python bindings to PYTHONPATH
PYTHON_VERSION=`python3 -c 'import sys; version=sys.version_info[:2]; print("{0}.{1}".format(*version))'`

# necessary user directories for ewok and ecFlow files

# ecFlow vars
myid=$(id -u ${USER})
if [[ $myid -gt 64000 ]]; then
  myid=$(awk -v min=3000 -v max=31000 -v seed=$RANDOM 'BEGIN{srand(seed); print int(min + rand() * (max - min + 1))}')
export ECF_PORT=$((myid + 1500))

# The ecflow hostname (e.g. a specific login node) is different from the R2D2/EWOK general host (i.e. system) name
host=$(hostname | cut -f1 -d'.')
export ECF_HOST=$host

if [[ x"${R2D2_HOST}" == "x" ]]; then
  export EWOK_STATIC_DATA=${JEDI_ROOT}/static
  case $R2D2_HOST in
      export EWOK_STATIC_DATA=/work/noaa/da/role-da/static
      export EWOK_STATIC_DATA=/discover/nobackup/projects/jcsda/s2127/static
      export EWOK_STATIC_DATA=/glade/p/mmm/jedipara/static
      export EWOK_STATIC_DATA=/data/prod/jedi/static
      export EWOK_STATIC_DATA=${JEDI_ROOT}/static
      echo "Unknown host name $R2D2_HOST"
      exit 1

5- Run SkyLab

Now you are ready to start an ecflow server and run an experiment. Make sure you are in your python virtual environment (venv).

To start the ecflow server: -p $ECF_PORT

Note: On Discover, users need to set ECF_PORT manually:

export ECF_PORT=2500 -p $ECF_PORT

Please note “Host” and “Port Number” here. Also note that each user must use a unique port number (we recommend using a random number between 2500 and 9999)

To view the ecflow GUI:

ecflow_ui &

When opening the ecflow GUI flow for the first time you will need to add your server to the GUI. In the GUI click on “Servers” and then “Manage servers”. A new window will appear. Click on “Add server”. Here you need to add the Name, Host, and Port of your server. For “Host” and “Port” please refer to the last section of output from the previous step.

To stop the ecflow server: -p $ECF_PORT

To start your ewok experiment: $JEDI_SRC/ewok/experiments/your-experiment.yaml