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Note: You can set up cylc-flow and cylc-uiserver in separate virtual environments. If you install cylc-flow in your JEDI-Skylab virtual environment, you can then install cylc-uiserver in a separate virutal virtual env and use that environment to kick off the GUI. Follow steps "Adding cylc to your workflow" and then "Setting up venv for cylc GIU".

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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

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

which

4. sudo su apt install -y rsync exit

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

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

Setting up venv for cylc GUI (ex: mac):

1. Needs python3.9 for the UI, therefore run: 
   

   Code Block
   language shell
   brew install python@3.9

2. Update PYTHONPATH:
   

   Code Block
   language shell
   module purge unset PYTHONPATH unset PYTHONHOME

3. Created venv without spack-stack:
   

   Code Block
   language shell
   python3.9 -m venv --system-site-packages cylc-venv

4. Activate venv:
   

   Code Block
   language shell
   source cylc-venv/bin/activate

5. Install cylc:
   

   Code Block
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   pip install cylc-flow pip install cylc-uiserver pip install cylc-rose metomi-rose

6. Install optional:
   

   Code Block
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   pip install 'cylc-flow[tutorial]' pip install 'cylc-uiserver[hub]'

7. Graphviz:
   

   Code Block
   language shell
   brew install graphviz

To test the GUI:
Code Block

language	shell

cylc gui

8. graphviz

9. To test the GUI:
   

   Code Block
   language shell
   cylc gui

Setting up cylc localhost configuration:

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. 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.

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

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
	    """	

Hercules Note:

On Hercules, it appears that the aws package is not found when only running source {JEDI_ROOT}venv/bin/activate . Therefore it is best to source your setup.sh script instead of just the virtual environment. Replace the global init-script = ${JEDI_ROOT}/venv/bin/activate  with global init-script = ${JEDI_ROOT}/setup.sh  or wherever you keep setup.sh. Then you will want to comment out all of the ecflow lines in setup.sh. 

Discover via spack-stack:

1. Load spack-stack modules
   

   Code Block
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   #!/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
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   # 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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