5. Running a Case

5.1. Calling case.submit

The script case.submit will submit your run to the batch queueing system on your machine. If you do not have a batch queueing system, case.submit will start the job interactively, given that you have a proper MPI environment defined. Running case.submit is the ONLY way you should start a job.

To see the options to case.submit, issue the command

> ./case.submit --help

A good way to see what case.submit will do, is to first call preview_run

> ./preview_run

which will output the environment for your run along with the batch submit and mpirun commands. As an example, on the NCAR machine, cheyenne, for an A compset at the f19_g17_rx1 resolution, the following is output from preview_run:

   nodes: 1
   total tasks: 36
   tasks per node: 36
   thread count: 1

   FOR JOB: case.run
   module command is /glade/u/apps/ch/opt/lmod/7.5.3/lmod/lmod/libexec/lmod python purge
   module command is /glade/u/apps/ch/opt/lmod/7.5.3/lmod/lmod/libexec/lmod python load ncarenv/1.2 intel/17.0.1 esmf_libs mkl esmf-7.0.0-defio-mpi-O mpt/2.16 netcdf-mpi/4.5.0 pnetcdf/1.9.0 ncarcompilers/0.4.1
   Setting Environment OMP_STACKSIZE=256M
   Setting Environment TMPDIR=/glade/scratch/mvertens
   Setting Environment MPI_TYPE_DEPTH=16
   qsub    -q regular -l walltime=12:00:00 -A P93300606 .case.run

FOR JOB: case.st_archive
      module command is /glade/u/apps/ch/opt/lmod/7.5.3/lmod/lmod/libexec/lmod python purge
      module command is /glade/u/apps/ch/opt/lmod/7.5.3/lmod/lmod/libexec/lmod python load ncarenv/1.2 intel/17.0.1 esmf_libs mkl esmf-7.0.0-defio-mpi-O mpt/2.16 netcdf-mpi/4.5.0 pnetcdf/1.9.0 ncarcompilers/0.4.1
      Setting Environment OMP_STACKSIZE=256M
      Setting Environment TMPDIR=/glade/scratch/mvertens
      Setting Environment MPI_TYPE_DEPTH=16
      Setting Environment TMPDIR=/glade/scratch/mvertens
      Setting Environment MPI_USE_ARRAY=false
   qsub    -q share -l walltime=0:20:00 -A P93300606  -W depend=afterok:0 case.st_archive

   mpiexec_mpt  -np 36 -p "%g:"  omplace -tm open64  /glade/scratch/mvertens/jim/bld/cesm.exe  >> cesm.log.$LID 2>&1

Each of the above sections is defined in the various $CASEROOT xml files and the associated variables can be modified using the xmlchange command (or in the case of tasks and threads, this can also be done with the pelayout command).

  • The PE layout is set by the xml variables NTASKS, NTHRDS and ROOTPE. To see the exact settings for each component, issue the command


    To change all of the NTASKS settings to say 30 and all of the NTHRDS to 4, you can call

    ./xmlchange NTASKS=30,NTHRDS=4

    To change JUST the ATM NTASKS to 8, you can call

    ./xmlchange NTASKS_ATM=8
  • Submit parameters are set by the xml variables in the file env_batch.xml. This file is special in certain xml variables can appear in more than one group. NOTE: The groups are the list of jobs that are submittable for a case. Normally, the minimum set of groups are case.run and case.st_archive. We will illustrate how to change an xml variable in env_batch.xml using the xml variable JOB_WALLCLOCK_TIME.

    • To change JOB_WALLCLOCK_TIME for all groups to 2 hours for cheyenne, use

      ./xmlchange JOB_WALLCLOCK_TIME=02:00:00
    • To change JOB_WALLCLOCK_TIME to 20 minutes for cheyenne for just case.run, use

      ./xmlchange JOB_WALLCLOCK_TIME=00:20:00 --subgroup case.run

Before you submit the case using case.submit, make sure the batch queue variables are set correctly for your run In particular, make sure that you have appropriate account numbers (PROJECT), time limits (JOB_WALLCLOCK_TIME), and queue (JOB_QUEUE).

Also modify $CASEROOT/env_run.xml for your case using xmlchange.

Once you have executed case.setup and case.build , call case.submit to submit the run to your machine’s batch queue system.

> ./case.submit

5.1.1. Result of running case.submit

When called, the case.submit script will:

  • Load the necessary environment.

  • Confirm that locked files are consistent with the current xml files.

  • Run preview_namelist, which in turn will run each component’s cime_config/buildnml script.

  • Run check_input_data to verify that the required data are present.

  • Submit the job to the batch queue. which in turn will run the case.run script.

Upon successful completion of the run, case.run will:

  • Put timing information in $CASEROOT/timing. See model timing data for details.

  • Submit the short-term archiver script case.st_archive to the batch queue if $DOUT_S is TRUE. Short-term archiving will copy and move component history, log, diagnostic, and restart files from $RUNDIR to the short-term archive directory $DOUT_S_ROOT.

  • Resubmit case.run if $RESUBMIT > 0.

5.1.2. Monitoring case job statuses

The $CASEROOT/CaseStatus file contains a log of all the job states and xmlchange commands in chronological order. Below is an example of status messages:

2017-02-14 15:29:50: case.setup starting
2017-02-14 15:29:54: case.setup success
2017-02-14 15:30:58: xmlchange success <command> ./xmlchange STOP_N=2,STOP_OPTION=nmonths  </command>
2017-02-14 15:31:26: xmlchange success <command> ./xmlchange STOP_N=1  </command>
2017-02-14 15:33:51: case.build starting
2017-02-14 15:53:34: case.build success
2017-02-14 16:02:35: case.run starting
2017-02-14 16:20:31: case.run success
2017-02-14 16:20:45: st_archive starting
2017-02-14 16:20:58: st_archive success


After a successful first run, set the env_run.xml variable $CONTINUE_RUN to TRUE before resubmitting or the job will not progress.

You may also need to modify the env_run.xml variables $STOP_OPTION, $STOP_N and/or $STOP_DATE as well as $REST_OPTION, $REST_N and/or $REST_DATE, and $RESUBMIT before resubmitting.

See the basic example for a complete example of how to run a case.

5.1.3. Troubleshooting a job that fails

There are several places to look for information if a job fails. Start with the STDOUT and STDERR file(s) in $CASEROOT. If you don’t find an obvious error message there, the $RUNDIR/$model.log.$datestamp files will probably give you a hint.

First, check cpl.log.$datestamp, which will often tell you when the model failed. Then check the rest of the component log files. See troubleshooting run-time problems for more information.

5.2. Input data

The check_input_data script determines if the required data files for your case exist on local disk in the appropriate subdirectory of $DIN_LOC_ROOT. It automatically downloads missing data required for your simulation.


It is recommended that users on a given system share a common $DIN_LOC_ROOT directory to avoid duplication on disk of large amounts of input data. You may need to talk to your system administrator in order to set this up.

The required input data sets needed for each component are found in the $CASEROOT/Buildconf directory. These files are generated by a call to preview_namlists and are in turn created by each component’s buildnml script. For example, for compsets consisting only of data models (i.e. A compsets), the following files are created:


You can independently verify the presence of the required data by using the following commands:

> ./check_input_data --help
> ./check_input_data

If data sets are missing, obtain them from the input data server(s) via the commands:

> ./check_input_data --download

check_input_data is automatically called by the case control system, when the case is built and submitted. So manual usage of this script is optional.

5.2.1. Distributed Input Data Repositories

CIME has the ability to utilize multiple input data repositories, with potentially different protocols. The repositories are defined in the file $CIMEROOT/config/$model/config_inputdata.xml. The currently supported server protocols are: gridftp, subversion, ftp and wget. These protocols may not all be supported on your machine, depending on software configuration.


You now have the ability to create your own input data repository and add it to the config_inputdata.xml. This will permit you to easily collaborate by sharing your required inputdata with others.

5.3. Starting, Stopping and Restarting a Run

The file env_run.xml contains variables that may be modified at initialization or any time during the course of a model run. Among other features, the variables comprise coupler namelist settings for the model stop time, restart frequency, coupler history frequency, and a flag to determine if the run should be flagged as a continuation run.

At a minimum, you will need to set the variables $STOP_OPTION and $STOP_N. Other driver namelist settings then will have consistent and reasonable default values. The default settings guarantee that restart files are produced at the end of the model run.

By default, the stop time settings are:

STOP_N = 5
STOP_DATE = -999

The default settings are appropriate only for initial testing. Before starting a longer run, update the stop times based on the case throughput and batch queue limits. For example, if the model runs 5 model years/day, set RESUBMIT=30, STOP_OPTION= nyears, and STOP_N= 5. The model will then run in five-year increments and stop after 30 submissions.

5.3.1. Run-type initialization

The case initialization type is set using the $RUN_TYPE variable in env_run.xml. A CIME run can be initialized in one of three ways:


In a startup run (the default), all components are initialized using baseline states. These states are set independently by each component and can include the use of restart files, initial files, external observed data files, or internal initialization (that is, a “cold start”). In a startup run, the coupler sends the start date to the components at initialization. In addition, the coupler does not need an input data file. In a startup initialization, the ocean model does not start until the second ocean coupling step.


In a branch run, all components are initialized using a consistent set of restart files from a previous run (determined by the $RUN_REFCASE and $RUN_REFDATE variables in env_run.xml). The case name generally is changed for a branch run, but it does not have to be. In a branch run, the $RUN_STARTDATE setting is ignored because the model components obtain the start date from their restart data sets. Therefore, the start date cannot be changed for a branch run. This is the same mechanism that is used for performing a restart run (where $CONTINUE_RUN is set to TRUE in the env_run.xml file). Branch runs typically are used when sensitivity or parameter studies are required, or when settings for history file output streams need to be modified while still maintaining bit-for-bit reproducibility. Under this scenario, the new case is able to produce an exact bit-for-bit restart in the same manner as a continuation run if no source code or component namelist inputs are modified. All models use restart files to perform this type of run. $RUN_REFCASE and $RUN_REFDATE are required for branch runs. To set up a branch run, locate the restart tar file or restart directory for $RUN_REFCASE and $RUN_REFDATE from a previous run, then place those files in the $RUNDIR directory. See Starting from a reference case.


A hybrid run is initialized like a startup but it uses initialization data sets from a previous case. It is similar to a branch run with relaxed restart constraints. A hybrid run allows users to bring together combinations of initial/restart files from a previous case (specified by $RUN_REFCASE) at a given model output date (specified by $RUN_REFDATE). Unlike a branch run, the starting date of a hybrid run (specified by $RUN_STARTDATE) can be modified relative to the reference case. In a hybrid run, the model does not continue in a bit-for-bit fashion with respect to the reference case. The resulting climate, however, should be continuous provided that no model source code or namelists are changed in the hybrid run. In a hybrid initialization, the ocean model does not start until the second ocean coupling step, and the coupler does a “cold start” without a restart file.

The variable $RUN_TYPE determines the initialization type. This setting is only important for the initial production run when the $CONTINUE_RUN variable is set to FALSE. After the initial run, the $CONTINUE_RUN variable is set to TRUE, and the model restarts exactly using input files in a case, date, and bit-for-bit continuous fashion.

The variable $RUN_STARTDATE is the start date (in yyyy-mm-dd format) for either a startup run or a hybrid run. If the run is targeted to be a hybrid or branch run, you must specify values for $RUN_REFCASE and $RUN_REFDATE.

5.3.2. Starting from a reference case (REFCASE)

There are several xml variables that control how either a branch or a hybrid case can start up from another case. The initial/restart files needed to start up a run from another case are required to be in $RUNDIR. The xml variable $GET_REFCASE is a flag that if set will automatically prestaging the refcase restart data.

  • If $GET_REFCASE is TRUE, then the the values set by $RUN_REFDIR, $RUN_REFCASE, $RUN_REFDATE and $RUN_TOD are used to prestage the data by symbolic links to the appropriate path.

    The location of the necessary data to start up from another case is controlled by the xml variable $RUN_REFDIR.

    • If $RUN_REFDIR is an absolute pathname, then it is expected that initial/restart files needed to start up a model run are in $RUN_REFDIR.

    • If $RUN_REFDIR is a relative pathname, then it is expected that initial/restart files needed to start up a model run are in a path relative to $DIN_LOC_ROOT with the absolute pathname $DIN_LOC_ROOT/$RUN_REFDIR/$RUN_REFCASE/$RUN_REFDATE.

    • If $RUN_REFDIR is a relative pathname AND is not available in $DIN_LOC_ROOT then CIME will attempt to download the data from the input data repositories.

  • If $GET_REFCASE is FALSE then the data is assumed to already exist in $RUNDIR.

5.4. Controlling output data

During a model run, each model component produces its own output data sets in $RUNDIR consisting of history, initial, restart, diagnostics, output log and rpointer files. Component history files and restart files are in netCDF format. Restart files are used to either restart the same model or to serve as initial conditions for other model cases. The rpointer files are ascii text files that list the component history and restart files that are required for restart.

Archiving (referred to as short-term archiving here) is the phase of a model run when output data are moved from $RUNDIR to a local disk area (short-term archiving). It has no impact on the production run except to clean up disk space in the $RUNDIR which can help manage user disk quotas.

Several variables in env_run.xml control the behavior of short-term archiving. This is an example of how to control the data output flow with two variable settings:

DOUT_S_ROOT = /$SCRATCH/$user/$CASE/archive

The first setting above is the default, so short-term archiving is enabled. The second sets where to move files at the end of a successful run.


  • All output data is initially written to $RUNDIR.

  • Unless you explicitly turn off short-term archiving, files are moved to $DOUT_S_ROOT at the end of a successful model run.

  • Users generally should turn off short-term archiving when developing new code.

Standard output generated from each component is saved in $RUNDIR in a log file. Each time the model is run, a single coordinated datestamp is incorporated into the filename of each output log file. The run script generates the datestamp in the form YYMMDD-hhmmss, indicating the year, month, day, hour, minute and second that the run began (ocn.log.040526-082714, for example).

By default, each component also periodically writes history files (usually monthly) in netCDF format and also writes netCDF or binary restart files in the $RUNDIR directory. The history and log files are controlled independently by each component. History output control (for example, output fields and frequency) is set in each component’s namelists.

The raw history data does not lend itself well to easy time-series analysis. For example, CAM writes one or more large netCDF history file(s) at each requested output period. While this behavior is optimal for model execution, it makes it difficult to analyze time series of individual variables without having to access the entire data volume. Thus, the raw data from major model integrations usually is post-processed into more user-friendly configurations, such as single files containing long time-series of each output fields, and made available to the community.

For CESM, refer to the CESM2 Output Filename Conventions for a description of output data filenames.

5.5. Restarting a run

Active components (and some data components) write restart files at intervals that are dictated by the driver via the setting of the $REST_OPTION and $REST_N variables in env_run.xml. Restart files allow the model to stop and then start again with bit-for-bit exact capability; the model output is exactly the same as if the model had not stopped. The driver coordinates the writing of restart files as well as the time evolution of the model.

Runs that are initialized as branch or hybrid runs require restart/initial files from previous model runs (as specified by the variables $RUN_REFCASE and $RUN_REFDATE). Pre-stage these files to the case $RUNDIR (normally $EXEROOT/../run) before the model run starts. Normally this is done by copying the contents of the relevant $RUN_REFCASE/rest/$RUN_REFDATE.00000 directory.

Whenever a component writes a restart file, it also writes a restart pointer file in the format rpointer.$component. Upon a restart, each component reads the pointer file to determine which file to read in order to continue the run. These are examples of pointer files created for a component set using full active model components.

- rpointer.atm
- rpointer.drv
- rpointer.ice
- rpointer.lnd
- rpointer.rof
- rpointer.cism
- rpointer.ocn.ovf
- rpointer.ocn.restart

If short-term archiving is turned on, the model archives the component restart data sets and pointer files into $DOUT_S_ROOT/rest/yyyy-mm-dd-sssss, where yyyy-mm-dd-sssss is the model date at the time of the restart. (See below for more details.)

5.5.1. Backing up to a previous restart

If a run encounters problems and crashes, you will normally have to back up to a previous restart. If short-term archiving is enabled, find the latest $DOUT_S_ROOT/rest/yyyy-mm-dd-ssss/ directory and copy its contents into your run directory ($RUNDIR).

Make sure that the new restart pointer files overwrite older files in in $RUNDIR or the job may not restart in the correct place. You can then continue the run using the new restarts.

Occasionally, when a run has problems restarting, it is because the pointer and restart files are out of sync. The pointer files are text files that can be edited to match the correct dates of the restart and history files. All of the restart files should have the same date.

5.6. Archiving model output data

The output data flow from a successful run depends on whether or not short-term archiving is enabled, as it is by default.

5.6.1. No archiving

If no short-term archiving is performed, model output data remains remain in the run directory as specified by $RUNDIR.

5.6.2. Short-term archiving

If short-term archiving is enabled, component output files are moved to the short-term archiving area on local disk, as specified by $DOUT_S_ROOT. The directory normally is $EXEROOT/../../archive/$CASE. and has the following directory structure:


The logs/ subdirectory contains component log files that were created during the run. Log files are also copied to the short-term archiving directory and therefore are available for long-term archiving.

The rest/ subdirectory contains a subset of directories that each contains a consistent set of restart files, initial files and rpointer files. Each subdirectory has a unique name corresponding to the model year, month, day and seconds into the day when the files were created. The contents of any restart directory can be used to create a branch run or a hybrid run or to back up to a previous restart date.

5.6.3. Long-term archiving

Users may choose to follow their institution’s preferred method for long-term archiving of model output. Previous releases of CESM provided an external long-term archiver tool that supported mass tape storage and HPSS systems. However, with the industry migration away from tape archives, it is no longer feasible for CIME to support all the possible archival schemes available.

5.7. Data Assimilation and other External Processing

CIME provides a capability to run a task on the compute nodes either before or after the model run. CIME also provides a data assimilation capability which will cycle the model and then a user defined task for a user determined number of cycles.

5.7.1. Pre and Post run scripts

Variables PRERUN_SCRIPT and POSTRUN_SCRIPT can each be used to name a script which should be exectuted immediately prior starting or following completion of the CESM executable within the batch environment. The script is expected to be found in the case directory and will recieve one argument which is the full path to that directory. If the script is written in python and contains a subroutine with the same name as the script, it will be called as a subroutine rather than as an external shell script.

5.7.2. Data Assimilation scripts

Variables DATA_ASSIMILATION, DATA_ASSIMILATION_SCRIPT, and DATA_ASSIMILATION_CYCLES may also be used to externally control model evolution. If DATA_ASSIMILATION is true after the model completes the DATA_ASSIMILATION_SCRIPT will be run and then the model will be started again DATA_ASSIMILATION_CYCLES times. The script is expected to be found in the case directory and will recieve two arguments, the full path to that directory and the cycle number. If the script is written in python and contains a subroutine with the same name as the script, it will be called as a subroutine rather than as an external shell script.

..: A simple example pre run script.

#!/usr/bin/env python3
import sys
from CIME.case import Case

def myprerun(caseroot):
    with Case(caseroot) as case:
         print ("rundir is ",case.get_value("RUNDIR"))

 if __name__ == "__main__":
   caseroot = sys.argv[1]