This is a quick start guide for CESM at Yale. You will still need to read the CESM User Guide and work with your fellow research group members to design and run your simulations, but this guide covers the basics that are specific to running CESM at Yale.
CESM User Guides
- CESM1.0.4 User’s Guide
- CESM1.1.z User’s Guide
- CESM User’s Guide (CESM1.2 Release Series User’s Guide) (PDF)
CESM 1.0.4, 1.2.2, 2.x are available on Grace.
For CESM 2.1.0, load the following modules
module load CESM/2.1.0-iomkl-2018a
For older versions of CESM, you will need to use the old modules. These old version of CESM do not work with the new modules
module use /apps/hpc/Modules module use /apps/hpc.rhel7/Modules module avail CESM
Once you have located your module, run
module load <module-name>
with the module name from above.
With either module, the module will configure your environment with the Intel compiler, OpenMPI and NetCDF libraries as well as set the location of the Yale’s repository of CESM input data.
If you will be primarily using CESM, you can avoid rerunning the module load command every time you login by saving it to your default environment:
module load <module-name> module save
To reduce the amount of data duplication on the cluster, we keep one centralized repository of CESM input data. The YCRC staff are only people who can add to that directory. If your build fails due to missing inputdata, contact us with your
create_newcase line and we will download that data for you.
CESM needs to be rebuilt separately for each run. As a result, running CESM is more complicated than a standard piece of software where you would just run the executable.
Create Your Case
Each simulation is called a “case”. Loading a CESM module will put the create_newcase script in your path, so you can call it as follows. This will create a directory with your case name, that we will refer to as
$CASE through out the rest of the guide.
create_newcase -case $CASE -compset=<compset> -res=<resolution> -mach=<machine> cd $CASE
The mach parameters for Grace is
yalegrace for CESM 1.x and
gracempi for CESM 2.x , respectively. For example
create_newcase --case $CASE --compset=B1850 --res=f09_g17 --mach=gracempi cd $CASE
Setup Your Case
If you are making any changes to the namelist files (such as increasing the duration of the simulation), do those before running the setup scripts below.
CESM 1.1.X and CESM 1.2.X
Build Your Case
After you run the setup script, there will be a set of the scripts in your case directory that start with your case name. To compile your simulation executable, first move to an interactive job and then run the build script corresponding to your case.
# CESM 1.x srun --pty -c 4 -p interactive bash module load <module-name> # <module-name> = the appropriate module for your CESM version ./$CASE.$mach.build
# CESM 2.x srun --pty -c 4 -p interactive bash module load <module-name> # <module-name> = the appropriate module for your CESM version ./case.build --skip-provenance-check
--skip-provenance-check flag is required with CESM 2.x due to the changes made to port the code to Grace.
For more details on interactive jobs, see our Slurm documentation.
During the build, CESM will create a corresponding directory in your scratch60 or project directory at
This directory will contain all the outputs from your simulation as well as logs and the cesm.exe executable.
Common Build Issues
Make sure you compile on an interactive node as described above. If you build fails, it will direct you to look in a bldlog file. If that log complains that it can’t find mpirun, NetCDF or another library or executable, make sure you have the correct CESM module loaded. It can helpful to run
module purge before the
module load to ensure a reproducible environment.
If you get an error saying
ERROR: Error gathering provenance information from manage_externals, rerun the build using the suggested flag, e.g.
Submit Your Case
Once the build is complete, which can take 5-15 minutes, you can submit your case with the submit script.
# CESM 1.x ./$CASE.$mach.submit
# CESM 2.x ./case.submit
For more details on monitoring your submitted jobs, see our Slurm documentation.
Changing Slurm Partition
In CESM 2.x, to change the partition in which your main jobs will run, use the following command:
./xmlchange JOB_QUEUE=scavenge --subgroup case.run
The associated archive job will still be submitted to the day partition.
Troubleshoot Your Run
If your run doesn’t complete, there are a few places to look to identify the error. CESM writes to multiple log files for the different components and you will likely have to look in a few to find the root cause of your error.
In your case directory, there will be a file that looks like
slurm-<job_id>.log. Check that file first to make sure the job started up properly. If the last few lines in the file redirect you to look at
cpl.log.<some_number> file in your scratch directory, see below. If there is another error, try to address it and resubmit.
CESM Run Logs
If the last few lines of the slurm log direct you to look at
cpl.log.<some_number> file, change directory to your case “run” directory in your scratch directory:
The pointer to the cpl file is often misleading as I have found the error is usually located in one of the other logs. Instead look in the
cesm.log.xxxxxx file. Towards the end there may be an error or it may signify which component was running. Then look in the log corresponding to that component to track down the issue.
One shortcut to finding the relevant logs is to sort the log files by the time to see which ones were last updated:
ls -ltr *log*
Look at the end of the last couple logs listed and look for an indication of the error.
Once you have identified the lines in the logs corresponding to your error:
If your log says something like
Disk quota exceeded, your group is out of space in the fileset you are writing to. You can run the
getquota script to get details on your disk usage. Your group will need to reduce their usage before you will be able to run successfully.
If it looks like a model error and you don’t know how to fix it, we strongly recommend Googling your error and/or looking in the CESM forums.
If you are still experiencing issues, contact us.
Alternative Submission Parameters
By default, the submission script will submit to the "mpi" partition for 1 day. To change this, edit your case’s
run script and change the partition and time. The maximum walltime in the mpi partition is 24 hours. The maximum walltime in scavenge is 24 hours on Grace. For example:
## scavenge partition #SBATCH --partition=scavenge #SBATCH --time=1-
## day partition #SBATCH --partition=pi_fedorov #SBATCH --time=7-
Then you can submit by running the submit script
- We recommend referencing the User Guides listed at the top of this page.
- CESM User Forum
- Our Slurm Documentation
- CESM is a very widely used package, you can often find answers by simply using Google. Just make sure that the solutions you find correspond to the approximate version of CESM you are using. CESM changes in subtle but significant ways between versions.