2. Creating a Case¶
This and following sections provide more detail about the basic commands of the CIME Case Control System: create_newcase, case.setup, case.build and case.submit. On a supported system, you can configure, build and run many complex climate model configurations with only these 4 commands.
To see if your machine is supported try:
> query_config --machines
If you are not on an out-of-the box CIME-supported platform, you will need to port CIME to your system before proceeding.
2.1. Calling create_newcase¶
The first step in creating a CIME-based experiment is to use create_newcase.
See the options for create_newcase in the help text.:
> create_newcase --help
The only required arguments to create_newcase are:
> create_newcase --case CASENAME --compset COMPSET --res GRID
Creating a CIME experiment or case requires, at a minimum, specifying a compset and a model grid and a case directory. CIME supports out-of-the-box component sets, model grids and hardware platforms (machines).
Warning
The --case
argument must be a string and may not contain any of the following special characters
> + * ? < > { } [ ] ~ ` @ :
The --case
argument is used to define the name of your case, a very important piece of
metadata that will be used in filenames, internal metadata and directory paths. The
CASEROOT
is a directory create_newcase will create with the same name as the
CASENAME
. If CASENAME
is simply a name (not a path), CASEROOT
is created in
the directory where you execute create_newcase. If CASENAME
is a relative or absolute
path, CASEROOT
is created there, and the name of the case will be the last component
of the path.
2.2. Results of calling create_newcase¶
Suppose create_newcase was called as follows. Here, $CIMEROOT is the full pathname of the root directory of the CIME distribution:
> cd $CIMEROOT/scripts
> create_newcase --case ~/cime/example1 --compset A --res f09_g16_rx1
In the example, the command creates a $CASEROOT
directory: ~/cime/example1
.
If that directory already exists, a warning is printed and the command aborts.
In the argument to --case
, the case name is taken from the string after the last slash
— so here the case name is example1
.
The output from create_newcase includes information such as.
The compset longname is
2000_DATM%NYF_SLND_DICE%SSMI_DOCN%DOM_DROF%NYF_SGLC_SWAV
The model resolution is
a%0.9x1.25_l%0.9x1.25_oi%gx1v6_r%r05_m%gx1v6_g%null_w%null
create_newcase installs files in $CASEROOT
that will build and run the model and to optionally archive the case on the target platform.
Running create_newcase creates the following scripts, files and directories in $CASEROOT
:
User Scripts
- case.build
Script to build component and utility libraries and model executable.
- case.setup
Script used to set up the case (create the case.run script, Macros file and user_nl_xxx files).
- 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.
- case.submit
Script to submit the case to run using the machine’s batch queueing system.
- case.cmpgen_namelist
Script to perform namelist baseline operations (compare, generate, or both).”
- xmlchange
Script to modify values in the xml files.
- xmlquery
Script to query values in the xml files.
- preview_namelists
Script for users to see their component namelists in
$CASEROOT/CaseDocs
before running the model.
- preview_run
Script for users to see batch submit and mpirun command.”
- check_input_data
Script for checking for various input data sets and moving them into place.
- check_case
Script to verify case is set up correctly.
XML Files
- env_archive.xml
Defines patterns of files to be sent to the short-term archive. You can edit this file at any time. You CANNOT use xmlchange to modify variables in this file.”
- env_mach_specific.xml
Sets a number of machine-specific environment variables for building and/or running. You CANNOT use xmlchange to modify variables in this file.
- env_build.xml
Sets model build settings. This includes component resolutions and component compile-time configuration options. You must run the case.build command after changing this file.
- env_run.xml
Sets runtime settings such as length of run, frequency of restarts, output of coupler diagnostics, and short-term and long-term archiving. This file can be edited at any time before a job starts.
- env_mach_pes.xml
Sets component machine-specific processor layout (see changing pe layout ). The settings in this are critical to a well-load-balanced simulation (see load balancing).
- env_batch.xml
Sets batch system settings such as wallclock time and queue name.”
User Source Mods Directory
- SourceMods
Top-level directory containing subdirectories for each compset component where you can place modified source code for that component. You may also place modified buildnml and buildlib scripts here.”
Provenance
- README.case
File detailing create_newcase usage. This is a good place to keep track of runtime problems and changes.”
- CaseStatus
File containing a list of operations done in the current case.
Non-modifiable work directories
- Buildconf,
Work directory containing scripts to generate component namelists and component and utility libraries (PIO or MCT, for example). You should never have to edit the contents of this directory.
- LockedFiles/
Work directory that holds copies of files that should not be changed. Certain xml files are locked after their variables have been used by should no longer be changed (see below).
- Tools/
Work directory containing support utility scripts. You should never need to edit the contents of this directory.”
2.3. Locked files in your case directory¶
The $CASEROOT
xml files are organized so that variables can be
locked at certain points after they have been resolved (used) in other
parts of the scripts system.
CIME does this by locking a file in $CASEROOT/LockedFiles
and
not permitting you to modify that file unless, depending on the file,
you call case.setup –clean or
case.build –clean .
CIME locks your $CASEROOT
files according to the following rules:
- Locks variables in env_case.xml after create_newcase.
The env_case.xml file can never be unlocked.
- Locks variables in env_mach_pes.xml after case.setup.
To unlock env_mach_pes.xml, run case.setup –clean.
- Locks variables in env_build.xml after completion of case.build.
To unlock env_build.xml, run case.build –clean
Variables in env_run.xml, env_batch.xml and env_archive.xml are never locked, and most can be changed at any time.
There are some exceptions in the env_batch.xml file.
2.4. Adding a –user-mods-dir argument to create_newcase¶
A user may want to customize a target case with a combination of
user_nl_xxx
file modifications and/or SourceMods
for some
components and/or xmlchange commands. As an example, the user
might want to carry out a series of experiments based on a common set
of changes to the namelists, source code and/or case xml settings.
Rather than make these changes each time a new experimental
CASEROOT
is generated, the user can create a directory on local
disk with a set of changes that will be applied to each case.
As an example, the directory could contain the following files:
> user_nl_cpl
> shell_commands (this would contain ./xmlchange commands)
> SourceMods/src.cam/dyncomp.F90
When the user calls create_newcase with the --user-mods-dir
pointing to the
full pathname of the directory containing these changes, then the CASEROOT
will be
created with these changes applied.