3. Setting up a Case

After creating a case, some aspects of the case are fixed (any variables in env_case.xml). Changing the pe-layout (see Changing Pes) or some aspects of the batch system you may be using must be modified before running case.setup.

3.1. Calling case.setup

After creating a case or changing aspects of a case, such as the pe-layout, call the case.setup command from $CASEROOT. This creates the following additional files and directories in $CASEROOT:


A (hidden) file with the commands that will be used to run the model (such as “mpirun”) and any batch directives needed. The directive values are generated using the contents of env_mach_pes.xml. Running case.setup –clean will remove this file. This file should not be edited directly and instead controlled through XML variables in env_batch.xml. It should also never be run directly.


File containing machine-specific makefile directives for your target platform/compiler. This file is created if it does not already exist.

The user can modify the file to change certain aspects of the build, such as compiler flags. Running case.setup –clean will not remove the file once it has been created. However. if you remove or rename the Macros.make file, running case.setup recreates it.


Files where all user modifications to component namelists are made.

xxx is any one of the set of components targeted for the case. For example, for a full active CESM compset, xxx is cam, clm or rtm, and so on.

NNNN goes from 0001 to the number of instances of that component. (See multiple instances)

For a case with 1 instance of each component (default), NNNN will not appear in the user_nl file names.

A user_nl file of a given name is created only once.

Calling case.setup –clean will not remove any user_nl files.

Changing the number of instances in the env_mach_pes.xml file will cause only new user_nl files to be added to $CASEROOT.


Directory that contains all the component namelists for the run.

This is for reference only and files in this directory SHOULD NOT BE EDITED since they will be overwritten at build time and runtime.


Files summarizing the module load commands and environment variables that are set when the scripts in $CASEROOT are called. These files are not used by the case but can be useful for debugging module load and environment settings.


This file records some aspects of the computing system on which the case is built, such as the shell environment.