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In order to run Skylab with the correct virtual environment, since cylc ignores PYTHONPATH, you need to add a global.cylc file to run an init-script before runtime that will activate the JEDI venv. This should go in ~/.cylc/flow/global.cylc. Replace <JEDI_ROOT> with your path to your JEDI venv. The install The install block is optional for now, but it sets your cylc work directory and run directory to mimic ecflow. Note, these will automatically put a cylc-run directory under the parent EWOK_WORKDIR and EWOK_FLOWDIR directories.

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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>${JEDI_ROOT}/venv/bin/activate

Setting up cylc HPC configuration:

Similar to the localhost setup, you will need to add or update ~/.cylc/flow/global.cylc. The install block is optional for now, but it sets your cylc work directory and run directory to mimic ecflow. Note, these will automatically put a cylc-run directory under the parent EWOK_WORKDIR and EWOK_FLOWDIR directories. Example of global.cylc file for HPCs that use slurm/sbatch for jobs:

vi ~/.cylc/flow/global.cylc

[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${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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