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Building the Singularity container

singularity build cgenie_muffin.sif singularity_cgenie_muffin.def

Using cgenie.muffin from a Slurm script

  1. Modify all Slurm directives inside the script submit_muffin.sh.

  2. Submit the slurm script using:

sbatch submit_muffin.sh

Using cgenie.muffin in an interactive session

  1. Start an interactive session

  2. From the terminal load singularity:

ml singularity/3.7.4
  1. Change to the cgenie_muffin directory. If you just copied the example directory using "cp -r /curc/sw/containers/examples/cgenie_muffin .", then you can do:
cd ./cgenie_muffin
  1. Start an interactive singularity session using cgenie_muffin container:
singularity shell $CURC_CONTAINER_DIR/cgenie_muffin.sif
  1. Within the container set the environmental variable CGENIE_MUFFIN_LOCATION this should point to the "cegenie_muffin" path. Since we are in "./cgenie_muffin" (based on step 4) this can be done as follows:
export CGENIE_MUFFIN_LOCATION=$PWD
  1. Now, go to the genie-main directory:
cd ./cgenie.muffin/genie-main/
  1. To run the test "testbiogem" do the following:
make cleanall
make testbiogem
  1. To run the muffin Earth system model:
make cleanall
./runmuffin.sh cgenie.eb_go_gs_ac_bg.worbe2.BASE LABS LAB_0.EXAMPLE 10