Setting up a Case

Configuration

After creating a case, some aspects of the configuration are fixed (any variables in env_case.xml). But many can be changed before calling case.setup, which generates the files required to build and run the case. CIME provides xmlquery to view and xmlchange to modify the variables used in this process.

Querying

CIME provides the xmlquery command to view the configuration of a case. The configuration is a collection of variables stored in XML files. These variables are grouped together when defined in the model’s configuration.

The following will list all of the current configuration.

./xmlquery --listall

To view a specific group, replace <group> with the desired group name.

./xmlquery --subgroup <group> --listall

Modifying

The xmlchange command is used to modify the configuration of a case. The following will change the value of a variable.

./xmlchange <variable>=<value>

Some variables can exist in multiple groups. To change a variable in a specific group, use the --subgroup option.

./xmlchange JOB_WALLCLOCK_TIME=0:30 --subgroup case.run

Setting up the Case

Once all the configuration is done, it’s time to call case.setup from $CASEROOT. This will generate the files required to build and run the case.

Warning

If xmlchange is called after case.setup, the changes will not be reflected in the generated files. To update the files, call case.setup --reset.

Tracking changes with Git

When you set up a case, a new Git repository will be created within the $CASEROOT directory if a recent version of Git is installed. The repository will have a branch named after the case.

Warning

If you are using a version of Git older than 2.28, the repository will not be created automatically. In this case, you can create a repository manually and push the case to it.

Each time you run case.setup, case.build, case.submit, or xmlchange, a new commit is created. This allows you to track changes to the case over time.

If you set the CASE_GIT_REPOSITORY variable to a valid Git repository URL, the case will be pushed to that repository.

./xmlchange CASE_GIT_REPOSITORY=<repository>

Note

To disable this feature, call case.setup --disable-git.

Generated files

The following files and directories are generated in $CASEROOT:

.case.run	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 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.
.env_mach_specific.*	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.
CaseDocs/	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.
CaseStatus	File containing a list of operations done in the current case.
Depends.*	Lists of source code files that need special build options.
Macros.cmake	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.
case.st_archive	Script to perform short-term archiving to disk for your case output. Note that this script is run automatically by the normal CIME workflow.
cmake_macros/	Directory containing any CMake macros required for the machine/compiler combination.
user_nl_xxx[_NNNN]	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.
software_environment.txt	This file records some aspects of the computing system on which the case is built, such as the shell environment.