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1. Activate your Skylab virtual environment, if you haven't already. 
   

   Code Block
   language shell
   source $JEDI_ROOT/venv/bin/activate

2. Force install cylc-flow. Note, cylc is installed in spack-stack but it has some compatibility issues so it is easiest at the point to re-install in your venv. 
   

   Code Block
   language shell
   pip install cylc-flow --force-reinstall

3. (*Optional - as needeed) rsync  is required for the workflow.  If a which rsync  does not return this application (if one is on a brand new OrbStack machine):
   

   Code Block
   language shell
   sudo su apt install -y rsync exit

4. Check cylc location and test with skylab/experiments/workflow-engine-test.yaml: 
   

   Code Block
   language shell
   which cylc create_experiment.py skylab/experiments/workflow-engine-test.yaml

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[install]
    [[symlink dirs]]  
        [[[localhost]]]
            work = ${EWOK_WORKDIR}
            run = ${EWOK_FLOWDIR}

[platforms]
    [[localhost]]
        hosts = localhost
        job runner = background
	global init-script = source ${JEDI_ROOT}venv/bin/activate 

    [[compute]]
	hosts = localhost
	job runner = slurm
	install target = localhost
	global init-script = """
	    source source$${JEDI_ROOT}/venv/bin/activate
	    export SLURM_EXPORT_ENV=ALL
	    export HDF5_USE_FILE_LOCKING=FALSE
	    ulimit -s unlimited || true
	    ulimit -v unlimited || true
	    """	

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1. Load spack-stack modules
   

   Code Block
   language shell
   #!/usr/bin/env bash # Initialize modules source $MODULESHOME/init/bash # Load python dependencies echo "Using SLES15 modules" module use /discover/swdev/jcsda/spack-stack/scu17/modulefiles module use /gpfsm/dswdev/jcsda/spack-stack/scu17/spack-stack-1.9.0/envs/ue-intel-2021.10.0/install/modulefiles/Core module load stack-intel/2021.10.0 module load stack-intel-oneapi-mpi/2021.10.0 module load stack-python/3.11.7 module load py-pip/23.1.2

   
   
2. Load cylc module and test
   

   Code Block
   language shell
   # Load the cylc module module use -a /discover/nobackup/projects/gmao/advda/swell/dev/modulefiles/core/ module load cylc/sles15_8.4.0 # Run cylc command cylc "$@"

   
   
3. You might need to create a file called $HOME/bin/cylc, and make sure it is executable in order to run locally: chmod +x $HOME/bin/cylc
1. Note, I did not have to do this when setting up and running on discover-mil with spack-stack 1.9.0 intel
4. Add the example of ~/.cylc/flow/global.cylc see above for HPCs that use slurm/sbatch for job submission.

FAQ

How to remove an experiment from ecflow?

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