Quick Start: CESM Model Workflow (CESM2.1)

The following quick start guide is for versions of CESM2 that have already been ported to the local target machine. CESM2 is built on the CIME (Common Infrastructure for Modeling Earth) framework. Please refer to the CIME Porting Documentation if CIME has not yet been ported to the target machine.

If you are new to CESM2, please consider reading the CIME Case Control System Part 1: Basic Usage guide first.

This is the procedure for quickly setting up and running a CESM2 case.

Download CESM2 (see Downloading CESM2).

Select a component set, and a resolution for your case. Details of available component sets and resolutions are available from the query_config tool located in the my_cesm_sandbox/cime/scripts directory

cd my_cesm_sandbox/cime/scripts
./query_config --help

See the supported component sets, supported model resolutions and supported machines for a complete list of CESM2 supported component sets, grids and computational platforms.

Note

Variables presented as $VAR in this guide typically refer to variables in XML files in a CESM case. From within a case directory, you can determine the value of such a variable with ./xmlquery VAR. In some instances, $VAR refers to a shell variable or some other variable; we try to make these exceptions clear.

Create a case

The create_newcase command creates a case directory containing the scripts and XML files to configure a case (see below) for the requested resolution, component set, and machine. create_newcase has three required arguments: --case, --compset and --res (invoke create_newcase –help for help).

On machines where a project or account code is needed (including NCAR’s machines), you must either specify the --project argument to create_newcase or set the $PROJECT variable in your shell environment.

If running on a supported machine, that machine will normally be recognized automatically and therefore it is not required to specify the --machine argument to create_newcase.

Invoke create_newcase as follows:

./create_newcase --case CASENAME --compset COMPSET --res GRID

where:

  • CASENAME defines the name of your case (stored in the $CASE XML variable). This is a very important piece of metadata that will be used in filenames, internal metadata and directory paths. create_newcase will create the case directory with the same name as the CASENAME. If CASENAME is simply a name (not a path), the case directory is created in the directory where you executed create_newcase. If CASENAME is a relative or absolute path, the case directory is created there, and the name of the case will be the last component of the path. The full path to the case directory will be stored in the $CASEROOT XML variable. See CESM2 Experiment Casenames for details regarding CESM experiment case naming conventions.

  • COMPSET is the component set.

  • GRID is the model resolution.

Here is an example on NCAR machine cheyenne with the $USER shell environment variable set to your cheyenne login name:

./create_newcase --case /glade/scratch/$USER/cases/b.e20.B1850.f19_g17.test --compset B1850 --res f19_g17

Setting up the case run script

Issuing the case.setup command creates scripts needed to run the model along with namelist user_nl_xxx files, where xxx denotes the set of components for the given case configuration. Before invoking case.setup, modify the env_mach_pes.xml file in the case directory using the xmlchange command as needed for the experiment.

cd to the case directory. Following the example from above:

cd /glade/scratch/$USER/cases/b.e20.B1850.f19_g17.test

Modify settings in env_mach_pes.xml (optional). (Note: To edit any of the env xml files, use the xmlchange command. invoke xmlchange –help for help.)

Invoke the case.setup command.

./case.setup

Build the executable using the case.build command

Modify build settings in env_build.xml (optional).

Run the build script.

./case.build

Users of the NCAR cheyenne system should consider using qcmd to compile CESM2 on a compute node as follows:

qcmd -- ./case.build

The CESM executable will appear in the directory given by the XML variable $EXEROOT, which can be queried using:

./xmlquery EXEROOT

Run the case

Modify runtime settings in env_run.xml (optional). Two settings you may want to change now are:

  1. Run length: By default, the model is set to run for 5 days based on the $STOP_N and $STOP_OPTION variables:

    ./xmlquery STOP_OPTION,STOP_N

    These default settings can be useful in troubleshooting runtime problems before submitting for a longer time, but will not allow the model to run long enough to produce monthly history climatology files. In order to produce history files, increase the run length to a month or longer:

    ./xmlchange STOP_OPTION=nmonths,STOP_N=1

  2. You can set the $DOUT_S variable to FALSE to turn off short term archiving:

    ./xmlchange DOUT_S=FALSE

Submit the job to the batch queue using the case.submit command.

./case.submit

When the job is complete, most output will NOT be written under the case directory, but instead under some other directories (on NCAR’s cheyenne machine, these other directories will be in /glade/scratch/$USER). Review the following directories and files, whose locations can be found with xmlquery (note: xmlquery can be run with a list of comma separated names and no spaces):

./xmlquery RUNDIR,CASE,CASEROOT,DOUT_S,DOUT_S_ROOT

  • $RUNDIR

    This directory is set in the env_run.xml file. This is the location where CESM2 was run. There should be log files there for every component (i.e. of the form cpl.log.yymmdd-hhmmss) if $DOUT_S == FALSE. Each component writes its own log file. Also see whether any restart or history files were written. To check that a run completed successfully, check the last several lines of the cpl.log file for the string “SUCCESSFUL TERMINATION OF CPL7-cesm”.

  • $DOUT_S_ROOT/$CASE

    $DOUT_S_ROOT refers to the short term archive path location on local disk. This path is used by the case.st_archive script when $DOUT_S = TRUE. See CESM Model Output File Locations for details regarding the component model output filenames and locations.

    $DOUT_S_ROOT/$CASE is the short term archive directory for this case. If $DOUT_S is FALSE, then no archive directory should exist. If $DOUT_S is TRUE, then log, history, and restart files should have been copied into a directory tree here.

  • $DOUT_S_ROOT/$CASE/logs

    The log files should have been copied into this directory if the run completed successfully and the short-term archiver is turned on with $DOUT_S = TRUE. Otherwise, the log files are in the $RUNDIR.

  • $CASEROOT

    There could be standard out and/or standard error files output from the batch system.

  • $CASEROOT/CaseDocs

    The case namelist files are copied into this directory from the $RUNDIR.

  • $CASEROOT/timing

    There should be two timing files there that summarize the model performance.