Quick Start (RCESM Model Workflow)

The following quick start guide is for versions of RCESM that have already been ported to the local target machine. RCESM 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 RCESM or 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 RCESM case.

Download the RCESM source (see Downloading RCESM).

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_cresm_sandbox/cime/scripts directory

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

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

Note

The CRESM was developed and tested around a fully-coupled Gulf of Mexico (GOM) case. We will use this case as the example throughout this quick start guide. There are options for other grids and configurations available. Please see the available RCESM component sets and supported model resolutions for more information.

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. RCESM case names should follow the CESM naming conventions. See CESM2 Experiment Casenames for details regarding CESM experiment case naming conventions.
  • COMPSET is the component set.
  • GRID is the model resolution.
  • run-unsupported is required for all RCESM compsets as these should all be considered scientifically experimental within the RCESM/CESM code base.

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

my_cresm_sandbox/cime/scripts/create_newcase --case my_case_dirs/p.r10.pbsgulf2010.tx9k_g3x.my_new_test.001 --compset PBSGULF2010 -res tx9k_g3x --run-unsupported

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 my_case_dirs/p.r10.pbsgulf2010.tx9k_g3x.my_new_test.001

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 RCESM on a compute node as follows:

qcmd -- ./case.build

The RCESM 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).

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. The Gulf of Mexico example from above has mostly been tested for this 5 day period. If you wanted to run it for an entire month, you would change:

./xmlchange STOP_OPTION=nmonths,STOP_N=1

After setting the run lenght, 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

  • $RUNDIR

    This directory is set in the env_run.xml file. This is the location where RCESM was run. There should be log files there for every component (i.e. of the form cpl.log.yymmdd-hhmmss). 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”.

  • $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.

Restart the case

The RCESM supports the ability to restart from any point that restart files are written. To set the frequency that restart files are written, first check the $REST_N and $REST_OPTION variables:

./xmlquery REST_OPTION,REST_N

The default values for these variables are set to the end of the simulation (so they should be the same as $STOP_N and $STOP_OPTION variables initially). To set the frequency so that restart files are written more often, change the variables to reflect the values you want. For example, to write daily restart files, set:

./xmlchange REST_OPTION=ndays,REST_N=1

Once your simulation is finished and you want to restart the run, you will need to change the $CONTINUE_RUN xml variable to true, and then submit the run again.

./xmlchange CONTINUE_RUN=TRUE
./case.submit

This change on its own will restart the model from the point of the last written restart. This is because the model uses the rpointer.* files in the case run directory to determine the restart date and time. These files are automatically set to point to the most recently written set of restart files. If you were interested in restarting from an earlier write, you would need to manually edit the filenames in each of the rpointer.* files in the case run directory.