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CESM

CESM (Community Earth System Model) is a fully coupled global climate model developed by NCAR. It simulates Earth's past, present, and future climate states using interacting components for atmosphere, ocean, land, sea ice, and more.

Keywords: climate, earth system model, atmospheric science, oceanography, coupled model

Module design

CESM modules on RCC clusters come in two tiers, both of which are available for each version:

Module type Purpose
cesm/<version> (base) Loads the full build environment (compiler, MPI, NetCDF, etc.) and sets CESMROOT. Use this to compile any compset of your choice with create_newcase.
cesm/<version>-<compset>-<res>-<compiler>-<mpi> (compset) Loads the base environment and points to a pre-built cesm.exe for a specific compset/resolution. Clone with --keepexe to skip recompilation entirely.

If you just want to run one of the standard pre-built compsets, the compset module is all you need.

Available modules

-------------------- /software/modulefiles2 --------------------
cesm/2.1.5                              cesm/2.2.2
cesm/2.1.5-BW1850-f19_g17-gnu-openmpi   cesm/2.2.2-F2000climo-f19_g17-gnu-openmpi(default)
cesm/2.1.5-BWma1850-f19_g17-gnu-openmpi

-------------------- /software/modulefiles ---------------------
cesm/2.1.5(default)
cesm/2.1.5-BW1850-f19_g17-gnu-openmpi
cesm/2.1.5-BWma1850-f19_g17-gnu-openmpi
cesm/2.2.2
cesm/2.2.2-F2000climo-f19_g17-gnu-openmpi

To see what a module sets up: 

module show cesm/2.2.2-F2000climo-f19_g17-gnu-openmpi

For built-in usage instructions: 

module help cesm/2.1.5-BW1850-f19_g17-gnu-openmpi

Quick start — CESM 2.2.2 (F2000climo, atmosphere-only)

This compset runs CAM6 in forced-SST mode. It is the fastest to run and a good starting point.

module load cesm/2.2.2-F2000climo-f19_g17-gnu-openmpi

# Clone the pre-built template (skips compilation entirely)
python3 $CESMROOT/cime/scripts/create_clone \
    --case /scratch/$USER/my_f2000 \
    --clone $CESM_TEMPLATE_CASE \
    --keepexe

cd /scratch/$USER/my_f2000

# Set output directory and run length
./xmlchange CIME_OUTPUT_ROOT=/scratch/$USER/cesm_output
./xmlchange STOP_N=5,STOP_OPTION=ndays

./case.submit

Quick start — CESM 2.1.5 (BW1850 / BWma1850, fully coupled)

These compsets run a fully coupled ocean-atmosphere-land-ice model (BGC + MA variants). They are memory-intensive and require a PE layout adjustment before submitting.

module load cesm/2.1.5-BW1850-f19_g17-gnu-openmpi

python3 $CESMROOT/cime/scripts/create_clone \
    --case /scratch/$USER/my_bw1850 \
    --clone $CESM_TEMPLATE_CASE \
    --keepexe

cd /scratch/$USER/my_bw1850

PE layout fix required for BW1850 and BWma1850

CIME's default layout places too many tasks per node (~3.5 GB/task), causing out-of-memory failures on coupled runs. Always apply this fix before submitting: 

sed -i 's/^#SBATCH  --nodes=2$/#SBATCH  --nodes=8/' .case.run
sed -i 's/^#SBATCH  --ntasks-per-node=28$/#SBATCH  --ntasks-per-node=4/' .case.run
This gives ~12.6 GB/task, which is sufficient.

./xmlchange CIME_OUTPUT_ROOT=/scratch/$USER/cesm_output
./xmlchange STOP_N=5,STOP_OPTION=ndays

./case.submit

Example job scripts

Midway3 (caslake partition)

case.submit generates and submits the SLURM script automatically — you never invoke cesm.exe directly. CIME places the executable in $EXEROOT and prepares all runtime files in $RUNDIR. To inspect the generated script before submitting:

cat /scratch/$USER/my_f2000/.case.run

A typical generated script for CESM 2.2.2 F2000climo looks like:

#!/bin/bash
#SBATCH --job-name=cesm
#SBATCH --account=pi-[cnetid]   # replace with your allocation (e.g. rcc-[cnetid], cil)
#SBATCH --partition=caslake
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=48
#SBATCH --time=02:00:00
#SBATCH --exclusive

# ... CIME-generated environment setup ...

mpirun -np 48 $EXEROOT/cesm.exe

Do not submit .case.run manually — always use ./case.submit so CIME stages input files and manages job dependencies correctly.

Job efficiency

Use seff <jobid> after a run completes to check CPU and memory efficiency. CESM coupled runs on a single caslake node typically achieve >90% CPU efficiency.

Midway2

For Midway2, the module built-in help is self-contained and includes the full workflow, PE layout settings, and ready-to-run example commands — run:

module help cesm/2.1.5-BW1850-f19_g17-gnu-openmpi
module help cesm/2.1.5-BWma1850-f19_g17-gnu-openmpi
module help cesm/2.2.2-F2000climo-f19_g17-gnu-openmpi

Compiling your own compset

If you want to run a compset not covered by the pre-built modules, use the base module:

module load cesm/2.2.2

python3 $CESMROOT/cime/scripts/create_newcase \
    --case /scratch/$USER/my_custom_case \
    --compset <COMPSET_LONGNAME> \
    --res <RESOLUTION> \
    --machine simple_linux \
    --compiler gnu

cd /scratch/$USER/my_custom_case
./case.setup
./case.build
./case.submit

See the CIME documentation for available compsets and resolutions.

Notes

  • Input data: pre-staged at $DIN_LOC_ROOT (set automatically by the module). Do not copy or move this directory.
  • Output: goes to CIME_OUTPUT_ROOT; set this to your /scratch/$USER/ directory.
  • UCX: RCC clusters use an OpenMPI UCX bypass for memory-pinning compatibility. This is already set in the module — no action needed.
  • Restart files: CESM writes restart files at intervals set by REST_N/REST_OPTION. To continue a run, set CONTINUE_RUN=TRUE and update the run length, then resubmit: 
    ./xmlchange CONTINUE_RUN=TRUE
./xmlchange STOP_N=5,STOP_OPTION=ndays   # set the next segment length
./case.submit