...
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> cd components/clm
> git fetch origin
> git checkout release-cesm2.2.01/hist_opt |
(B) Create a new case
2. Use the code in the model directory $CESM_ROOT to create a new case called $CASENAME:
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> $CESM_ROOT/cime/scripts/create_newcase --case <your_path/$CASENAME> --mach cheyenne --res f09_f09_mg17 --compset FCnudged |
From section A, $CESM_ROOT would be /glade/work/$USER/my_cesm_sandbox
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| A new directory $CASEROOT = <your_path+$CASENAME> is created. You may need to add --run_unsupported to the call line if you are not running with a scientifically validated compset and resolution combination. Note 1: If you need to specify a project on cheyenne, the command is --project $PROJECT_NUMBER. Note 2: For additional help and options, type ./create_newcase -h Note 3: To find the possible compset types $CESM_ROOT/cime/scripts/query_config --compsets cam. Note 4: The above call uses the new nudging scheme on 32 model layers, to use the old nudging scheme with 56 model layers use the compset: --compset FCSD, and adjust met files accordingly.
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(C) Set up your case
3. From within$CASEROOT
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| 4. Make changes to the model configuration using the *.xml files; you can edit the files directly or use the xmlchange tool (in your case |
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directory). Changes to env_build.xml must be made before building, or you will need to re-build.
See advanced pages to change the chemistry source code. (D) Build the Executable |
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| You can use script xmlquery to query a variable in the xml files before modifying a variable with xmlchange command. For example: >./xmlquery CALENDAR |
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5. Compile and build the model in $CASEROOT
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First address any current bug-fixes: Bugs and Updates |
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>qcmd -- ./case.build
Note: you cannot run ./case.build interactively from the cheyenne prompt because it uses too much memory: you must use 'qcmd'. |
Note 1: You may need a project number to run qcmd: qcmd -A $PROJECT_NUMBER -- ./case.build
6. (Optional) Make changes to the model runtime setup: Changes to env_run.xml can be made at any time:
a. If not starting in the default 2005, change dates: see Changing Dates of a Run (also see relevant namelist changes)
b. The default option for biogeochemistry is “specified phenology” (satellite LAI) with CLM5 physics:
<entry id="CLM_BLDNML_OPTS" value="-bgc sp">
<entry id="CLM_PHYSICS_VERSION" value="clm5_0">
Other options are available, such as irrigated crops - please see the CLM documentation.
c. The default simulation is a test run for 5 days. ChangeSTOP_OPTION and STOP_N to alter this to desired values.
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| 7. (Optional) Check namelist settings in the namelist files user_nl_cam and user_nl_clm. Most CAM-chem related namelist variables are in CaseDocs/atm_in, but MEGAN and drydep are in CaseDocs/drv_flds_in (these files are created during build). To modify any of these, copy the appropriate lines to user_nl_cam and edit there. For example, if the startdate has been changed in env_run.xml, you have to also change the date of the initial meteorology file in user_nl_cam to start at the corresponding date. For other changes see namelist changes or advanced options page. After adding changes to user_nl_* files, optionally run: | Code Block |
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| >./preview_namelists |
NOTE: most changes in user_nl_* files do not require re-building. However, during a run (CONTINUE_RUN = TRUE) no changes can be made to history output (fincl lists). If you want to change history output, create a new or branch run. |
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8. Check the run setup. In the env_batch.xml file make sure to have your project added correctly: <entry id="PROJECT" value=$YOUR_PROJECT_CODE> Depending on the version of CESM, you may instead find the entry id for PROJECT in env_workflow.xml
Change your walltime if desired: <entry id="JOB_WALLCLOCK_TIME" value="12:00:00"> (12 hours max)
9. If you make changes to env_build.xml variables or SourceMods after setting up and building, you may have to clean your setup and build again:
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>./case.setup --clean
>./case.setup |
OR
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>./case.setup --reset |
(which cleans, then does setup)
followed by
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>./case.build --clean
>qcmd -- ./case.build |
(E) Run the Model
10. Submit run to queue:
While running, output is written to <run_dir>: /glade/scratch/<username>/$CASENAME/run
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| After the run completes successfully, output files are moved to the short term archive: /glade/scratch/<username>/archive/$CASENAME/atm/hist (similar directories exist for other model components: lnd, etc.).
Restart and initial conditions files are written to: /glade/scratch/<username>/archive/$CASENAME/rest Note: long term archiving is currently not working |
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| Default output is monthly, so if you run a test 5-day simulation with monthly output, you will not see any files in the atm/hist location. However, restart files will have been created. |
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11. Useful commands while model is running:
check your run progress:
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>qstat –u <user> |
If you find an issue and need to delete your run:
If your model run doesn't complete, try some of the suggestions on the troubleshooting page.
12. To continue a run from restart files, for example after an initial start up, change CONTINUE_RUN to TRUE in the env_run.xml file.
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High performance computing systems often have maximum wall times (e.g. JOB_WALLCLOCK_TIME = 12 hours), meaning a long run will need to be split into several smaller runs. In this case, change the “RESUBMIT” value in env_run.xml file to greater than zero. For example, you can simulate 10 years by changing STOP_OPTION=nyears, STOP_N=1 and RESUBMIT=9. This will perform an initial run of 1 years + (9 resubmits x 1 years per job) = 10 years. |