7. Customizing your input variables

CIME and CIME-compliant components primarily use Fortran namelists to control runtime options. Some components use other text-based files for runtime options.

All CIME-compliant components generate their input variable files using a buildnml script typically located in the component’s cime_config directory (or other location as set in config_file.xml). buildnml may call other scripts to complete construction of the input file.

For example, the CIME data atmosphere model (DATM) generates namelists using the script $CIMEROOT/components/data_comps/datm/cime_config/buildnml.

You can customize a model’s namelists in one of two ways:

  1. by editing the $CASEROOT/user_nl_xxx files
These files should be modified via keyword-value pairs that correspond to new namelist or input data settings. They use the syntax of Fortran namelists.
  1. by calling xmlchange to modify xml variables in your $CASEROOT.

    Many of these variables are converted to Fortran namelist values for input by the models. Variables that have to be coordinated between models in a coupled system (such as how many steps to run for) are usually in a CIME xml file.

You can generate the component namelists by running preview_namelists from $CASEROOT.

This results in the creation of component namelists (for example, atm_in, lnd_in, and so on) in $CASEROOT/CaseDocs/.

Warning

The namelist files in CaseDocs are there only for user reference and SHOULD NOT BE EDITED since they are overwritten every time preview_namelists and case.submit are called and the files read at runtime are not the ones in CaseDocs.

7.1. Customizing driver input variables

The driver input namelists/variables are contained in the files, drv_in, drv_flds_in and seq_maps.rc. Note that seq_maps.rc has a different file format than the other two input files.

All driver namelist variables are defined in the file $CIMEROOT/src/drivers/mct/cime_config/namelist_definition_drv.xml.

The variables that can be changed only by modifying xml variables appear with the entry attribute modify_via_xml="xml_variable_name".

All other driver namelist variables can be modified by by adding a keyword value pair at the end of user_nl_cpl.

For example, to change the driver namelist value of eps_frac to 1.0e-15, add the following line to the end of the user_nl_cpl:

eps_frac = 1.0e-15

On the hand, to change the driver namelist value of the starting year/month/day, start_ymd to 18500901, use the command:

./xmlchange RUN_STARTDATE=1850-09-01

Note that

To see the result of change, call preview_namelists and verify that the new value appears in CaseDocs/drv_in.

7.1.1. Setting up a multi-year run

This shows all of the steps necessary to do a multi-year simulation starting from a “cold start” for all components. The compset and resolution in this example are for a CESM fully-coupled case but the steps are similar for other models and cases.

  1. Create a new case named EXAMPLE_CASE in your $HOME directory.

    > cd $CIME/scripts
    > ./create_newcase --case ~/EXAMPLE_CASE --compset B1850 --res f09_g17
    
  2. Check the pe-layout by running ./pelayout. Make sure it is suitable for your machine. If it is not use xmlchange or pelayout to modify your pe-layout. Then setup your case and build your executable.

    > cd ~/EXAMPLE_CASE
    > ./case.setup
    > ./case.build
    

    Warning

    The case.build script can be compute intensive and may not be suitable to run on a login node. As an alternative you would submit this job to an interactive queue. For example, on the NCAR cheyenne platform, you would use qcmd – ./case.build to do this.

  3. In your case directory, set the job to run 12 model months, set the wallclock time, and submit the job.

    > ./xmlchange STOP_OPTION=nmonths
    > ./xmlchange STOP_N=12
    > ./xmlchange JOB_WALLCLOCK_TIME=06:00 --subgroup case.run
    > ./case.submit
    
  4. Make sure the run succeeded.

    You should see the following line or similar at the end of the cpl.log file in your run directory or your short term archiving directory, set by $DOUT_S_ROOT.

    (seq_mct_drv): ===============       SUCCESSFUL TERMINATION OF CPL7-cesm ===============
    
  5. In the same case directory, Set the case to resubmit itself 10 times so it will run a total of 11 years (including the initial year), and resubmit the case. (Note that a resubmit will automatically change the run to be a continuation run).

    > ./xmlchange RESUBMIT=10
    > ./case.submit
    

    By default resubmitted runs are not submitted until the previous run is completed. For 10 1-year runs as configured in this example, CIME will first submit a job for one year, then when that job completes it will submit a job for another year. There will be only one job in the queue at a time. To change this behavior, and submit all jobs at once (with batch dependencies such that only one job is run at a time), use the command:

    > ./case.submit --resubmit-immediate
    

7.1.2. Setting up a branch or hybrid run

A branch or hybrid run uses initialization data from a previous run. Here is an example in which a valid load-balanced scenario is assumed.

  1. The first step in setting up a branch or hybrid run is to create a new case. A CESM compset and resolution is assumed below.

    > cd $CIMEROOT/scripts
    > create_newcase --case ~/NEW_CASE --compset B1850 --res f09_g17
    > cd ~/NEW_CASE
    
  2. For a branch run, use the following xmlchange commands to make NEW_CASE be a branch off of EXAMPLE_CASE at year 0001-02-01.

    > ./xmlchange RUN_TYPE=branch
    > ./xmlchange RUN_REFCASE=EXAMPLE_CASE
    > ./xmlchange RUN_REFDATE=0001-02-01
    
  3. For a hybrid run, use the following xmlchange command to start NEW_CASE from EXAMPLE_CASE at year 0001-02-01.

    > ./xmlchange RUN_TYPE=hybrid
    > ./xmlchange RUN_REFCASE=EXAMPLE_CASE
    > ./xmlchange RUN_REFDATE=0001-02-01
    

    For a branch run, your env_run.xml file for NEW_CASE should be identical to the file for EXAMPLE_CASE except for the $RUN_TYPE setting.

    Also, modifications introduced into user_nl_ files in EXAMPLE_CASE should be reintroduced in NEW_CASE.

  4. Next, set up and build your case executable.

    > ./case.setup
    > ./case.build
    
  5. Pre-stage the necessary restart/initial data in $RUNDIR. Assume for this example that it was created in the /rest/0001-02-01-00000 directory shown here:

    ::

    > cd $RUNDIR > cp /user/archive/EXAMPLE_CASE/rest/0001-02-01-00000/* .

    It is assumed that you already have a valid load-balanced scenario. Go back to the case directory, set the job to run 12 model months, and submit the job.

    > cd ~/NEW_CASE
    > ./xmlchange STOP_OPTION=nmonths
    > ./xmlchange STOP_N=12
    > ./xmlchange JOB_WALLCLOCK_TIME=06:00
    > ./case.submit
    
  6. Make sure the run succeeded (see above directions) and then change the run to a continuation run. Set it to resubmit itself 10 times so it will run a total of 11 years (including the initial year), then resubmit the case.

    > ./xmlchange CONTINUE_RUN=TRUE
    > ./xmlchange RESUMIT=10
    > ./case.submit
    

7.2. Customizing data model input variable and stream files

Each data model can be runtime-configured with its own namelist.

7.2.1. Data Atmosphere (DATM)

DATM is discussed in detail in data atmosphere overview. DATM can be user-customized by changing either its namelist input files or its stream files. The namelist file for DATM is datm_in (or datm_in_NNN for multiple instances).

  • To modify datm_in or datm_in_NNN, add the appropriate keyword/value pair(s) for the namelist changes that you want at the end of the user_nl_datm file or the user_nl_datm_NNN file in $CASEROOT.
  • To modify the contents of a DATM stream file, first run preview_namelists to list the streams.txt files in the CaseDocs/ directory. Then, in the same directory:
    1. Make a copy of the file with the string “user_” prepended.
      > cp datm.streams.txt.[extension] user_datm.streams.txt[extension.
    2. Change the permissions of the file to be writeable. (chmod 644)
      chmod 644 user_datm.streams.txt[extension
    3. Edit the user_datm.streams.txt.* file.

Example

If the stream txt file is datm.streams.txt.CORE2_NYF.GISS, the modified copy should be user_datm.streams.txt.CORE2_NYF.GISS. After calling preview_namelists again, your edits should appear in CaseDocs/datm.streams.txt.CORE2_NYF.GISS.

7.2.2. Data Ocean (DOCN)

DOCN is discussed in detail in data ocean overview. DOCN can be user-customized by changing either its namelist input or its stream files. The namelist file for DOCN is docn_in (or docn_in_NNN for multiple instances).

  • To modify docn_in or docn_in_NNN, add the appropriate keyword/value pair(s) for the namelist changes that you want at the end of the file in $CASEROOT.
  • To modify the contents of a DOCN stream file, first run preview_namelists to list the streams.txt files in the CaseDocs/ directory. Then, in the same directory:
    1. Make a copy of the file with the string “user_” prepended.
      > cp docn.streams.txt.[extension] user_docn.streams.txt[extension.
    2. Change the permissions of the file to be writeable. (chmod 644)
      chmod 644 user_docn.streams.txt[extension
    3. Edit the user_docn.streams.txt.* file.

Example

As an example, if the stream text file is docn.stream.txt.prescribed, the modified copy should be user_docn.streams.txt.prescribed. After changing this file and calling preview_namelists again, your edits should appear in CaseDocs/docn.streams.txt.prescribed.

7.2.3. Data Sea-ice (DICE)

DICE is discussed in detail in data sea-ice overview. DICE can be user-customized by changing either its namelist input or its stream files. The namelist file for DICE is dice_in (or dice_in_NNN for multiple instances) and its values can be changed by editing the $CASEROOT file user_nl_dice (or user_nl_dice_NNN for multiple instances).

  • To modify dice_in or dice_in_NNN, add the appropriate keyword/value pair(s) for the namelist changes that you want at the end of the file in $CASEROOT.
  • To modify the contents of a DICE stream file, first run preview_namelists to list the streams.txt files in the CaseDocs/ directory. Then, in the same directory:
    1. Make a copy of the file with the string “user_” prepended.
      > cp dice.streams.txt.[extension] user_dice.streams.txt[extension.
    2. Change the permissions of the file to be writeable. (chmod 644)
      chmod 644 user_dice.streams.txt[extension
    3. Edit the user_dice.streams.txt.* file.

7.2.4. Data Land (DLND)

DLND is discussed in detail in data land overview. DLND can be user-customized by changing either its namelist input or its stream files. The namelist file for DLND is dlnd_in (or dlnd_in_NNN for multiple instances) and its values can be changed by editing the $CASEROOT file user_nl_dlnd (or user_nl_dlnd_NNN for multiple instances).

  • To modify dlnd_in or dlnd_in_NNN, add the appropriate keyword/value pair(s) for the namelist changes that you want at the end of the file in $CASEROOT.
  • To modify the contents of a DLND stream file, first run preview_namelists to list the streams.txt files in the CaseDocs/ directory. Then, in the same directory:
    1. Make a copy of the file with the string “user_” prepended.
      > cp dlnd.streams.txt.[extension] user_dlnd.streams.txt[extension.
    2. Change the permissions of the file to be writeable. (chmod 644)
      chmod 644 user_dlnd.streams.txt[extension
    3. Edit the user_dlnd.streams.txt.* file.

7.2.5. Data River (DROF)

DROF is discussed in detail in data river overview. DROF can be user-customized by changing either its namelist input or its stream files. The namelist file for DROF is drof_in (or drof_in_NNN for multiple instances) and its values can be changed by editing the $CASEROOT file user_nl_drof (or user_nl_drof_NNN for multiple instances).

  • To modify drof_in or drof_in_NNN, add the appropriate keyword/value pair(s) for the namelist changes that you want at the end of the file in $CASEROOT.
  • To modify the contents of a DROF stream file, first run preview_namelists to list the streams.txt files in the CaseDocs/ directory. Then, in the same directory:
    1. Make a copy of the file with the string “user_” prepended.
      > cp drof.streams.txt.[extension] user_drof.streams.txt[extension.
    2. Change the permissions of the file to be writeable. (chmod 644)
      chmod 644 user_drof.streams.txt[extension
    3. Edit the user_drof.streams.txt.* file.

7.3. Customizing CESM active component-specific namelist settings

7.3.1. CAM

CIME calls $SRCROOT/components/cam/cime_config/buildnml to generate the CAM’s namelist variables.

CAM-specific CIME xml variables are set in $SRCROOT/components/cam/cime_config/config_component.xml and are used by CAM’s buildnml script to generate the namelist.

For complete documentation of namelist settings, see CAM namelist variables.

To modify CAM namelist settings, add the appropriate keyword/value pair at the end of the $CASEROOT/user_nl_cam file. (See the documentation for each file at the top of that file.)

For example, to change the solar constant to 1363.27, modify user_nl_cam file to contain the following line at the end:

solar_const=1363.27

To see the result, call preview_namelists and verify that the new value appears in CaseDocs/atm_in.

7.3.2. CLM

CIME calls $SRCROOT/components/clm/cime_config/buildnml to generate the CLM namelist variables.

CLM-specific CIME xml variables are set in $SRCROOT/components/clm/cime_config/config_component.xml and are used by CLM’s buildnml script to generate the namelist.

For complete documentation of namelist settings, see CLM namelist variables.

To modify CLM namelist settings, add the appropriate keyword/value pair at the end of the $CASEROOT/user_nl_clm file.

To see the result, call preview_namelists and verify that the changes appear correctly in CaseDocs/lnd_in.

7.3.3. MOSART

CIME calls $SRCROOT/components/mosart/cime_config/buildnml to generate the MOSART namelist variables.

To modify MOSART namelist settings, add the appropriate keyword/value pair at the end of the $CASEROOT/user_nl_rtm file.

To see the result of your change, call preview_namelists and verify that the changes appear correctly in CaseDocs/rof_in.

7.3.4. CICE

CIME calls $SRCROOT/components/cice/cime_config/buildnml to generate the CICE namelist variables.

For complete documentation of namelist settings, see CICE namelist variables.

To modify CICE namelist settings, add the appropriate keyword/value pair at the end of the $CASEROOT/user_nl_cice file. (See the documentation for each file at the top of that file.) To see the result of your change, call preview_namelists and verify that the changes appear correctly in CaseDocs/ice_in.

In addition, case.setup creates CICE’s compile time block decomposition variables in env_build.xml as follows:

7.3.5. POP2

CIME calls $SRCROOT/components/pop2/cime_config/buildnml to generate the POP2 namelist variables.

For complete documentation of namelist settings, see POP2 namelist variables.

To modify POP2 namelist settings, add the appropriate keyword/value pair at the end of the $CASEROOT/user_nl_pop2 file. (See the documentation for each file at the top of that file.) To see the result of your change, call preview_namelists and verify that the changes appear correctly in CaseDocs/ocn_in.

In addition, case.setup generates POP2’s compile-time block decomposition variables in env_build.xml as shown here:

7.3.6. CISM

See CISM namelist variables for a complete description of the CISM runtime namelist variables. This includes variables that appear both in cism_in and in cism.config.

To modify any of these settings, add the appropriate keyword/value pair at the end of the user_nl_cism file. (See the documentation for each file at the top of that file.) Note that there is no distinction between variables that will appear in cism_in and those that will appear in cism.config: simply add a new variable setting in user_nl_cism, and it will be added to the appropriate place in cism_in or cism.config. To see the result of your change, call preview_namelists and verify that the changes appear correctly in CaseDocs/cism_in and CaseDocs/cism.config.

Some CISM runtime settings are sets via env_run.xml, as documented in CISM runtime variables.