Updated files for creating CESM cases under git(hub) control #93
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| # DART_CASES | ||
| DART CASE directories from CESM+DART experiments. | ||
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| This presents ways to archive the experiment setups for publication purposes | ||
| and curate what happens during the continued cycling of a CESM experiment. | ||
| Some (most?) things are expected to stay static, but better to be safe than confused. | ||
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| Creating a CESM case setup under git control is reasonably straightforward. | ||
| Putting an existing case there is a little more complicated. | ||
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| The following strategies are based on making the 'main' ('master') branch | ||
| of the git repository have no case files in it, and each experiment/case | ||
| will be a unique branch named the same as the CESM 'CASE' name. | ||
| The separation is made clearer by also putting each case in a subdirectory | ||
| also named the same as the CASE. | ||
| The most useful way to do this is to make a new git clone for each new case. | ||
| This allows multiple cases to be active, and prevents a running job | ||
| from one case making changes to files belonging to a different branch. | ||
| All of these branches will be pushed to the same github repository. | ||
| They should not be merged into main, in order to keep the size of the branches small, | ||
| which allows more to fit within github's limit on free repositories. | ||
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| ## Terminology | ||
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| | Word | Meaning| | ||
| :--------------- |:-----------------------------------------------------------------------------------------| | ||
| |CASE | your CESM CASE name, which is the name of the assimilation and the git branch | | ||
| |DART\_CASES | your github repository for archiving assimilation setups | | ||
| |CASE_git | the local clone of DART\_CASES | | ||
| |EXP | the directory where you want the CASE_git clones to be created | | ||
| |CASEROOT | the path in which CESM builds CASE and from which assimilation jobs are launched. 'EXP/CASE_git/CASE' below | | ||
| |DART | your clone of DART | | ||
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| ## Create a New CASE Under git(hub) | ||
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| ### Preliminaries | ||
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| 0. If you're not an employee in NSF NCAR's Data Assimilation Research Section, | ||
| or are, but want to keep your cases separate from other DAReS CASEs, | ||
| fork https://github.com/NCAR/DART_CASES.git to your github. | ||
| 1. Put a copy of list\_of\_files\_to\_commit.csh (found in the top directory | ||
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Member
There was a problem hiding this comment. why not add everything in the case? |
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| of branch "main") into your shell\_scripts directory. | ||
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Member
There was a problem hiding this comment. this is shell_scripts in |
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| Edit it ( or rewrite in your favorite language) to specify which files | ||
| should be under git control. | ||
| See comments in that file about how to choose the files. | ||
| 2. In DART/models/\<your\_model\>/shell\_scripts/\<your\_setup\_script\> | ||
| 1. Set the CASE name for this assimilation. | ||
| If you're **re**using a DART\_CASES-controlled case name, | ||
| clean the existing git branch, which might mean just | ||
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| ` git rm -r $CASE ; git branch -d $CASE ` | ||
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Member
There was a problem hiding this comment. why would you delete an existing branch? |
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| 2. Specify that this case will be built in EXP/CASE\_git/CASE. | ||
| 3. Add lines like this before create\_newcase | ||
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| ``` | ||
| git clone [email protected]:<your_github>/DART_CASES.git $EXP/${CASE}_git ` | ||
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Member
There was a problem hiding this comment. this is for <your_github> rather than NCAR/DART_CASES |
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| git branch -a | grep $CASE | ||
| if ($status == 0) exit | ||
| ``` | ||
| 4. add lines near the end to put CASE under git control: | ||
| + cd \$CASEROOT | ||
| + git checkout -b \$CASE | ||
| + \$DART/\<your\_model\>/shell\_scripts/list\_of\_files\_to\_commit.csh | ||
| + git commit -m "First commit of files in case \$CASE " | ||
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| This will create a *branch* in your CASE_git clone which has the name \$CASE. | ||
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| ### Production | ||
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| 3. Run the setup script | ||
| This will create a *directory* in your CASE_git clone which has the name \$CASE. | ||
| Follow the instructions about checking the setup. | ||
| 4. If needed, in the CASEROOT directory, edit input.nml, \*.xml, etc. | ||
| to define your assimilation job correctly. | ||
| Add, commit, and push these to a new (-u) experiment git(hub) branch. | ||
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| ` git push -u origin ${CASE} ` | ||
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| 5. Submit the job | ||
| 6. If git-controlled files need to be changed for future DA cycles; | ||
| add, commit, and push them to the (correct) branch. | ||
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| ` git push origin ${CASE} ` | ||
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| ### Put an Existing CASE Under git(hub) Control in its Own Directory | ||
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| Example commands follow this list of steps. | ||
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| 1. Change the CASE directory name (made by CESM) to ${CASE}\_orig. (Not strictly necessary.) | ||
| 2. Clone the DART\_CASES repository into ${CASE}\_git. | ||
| 3. In ${CASE}\_git make a new *branch* with the name ${CASE} and check it out. | ||
| 4. Copy everything from ${CASE}\_orig into a new subdirectory ./${CASE} | ||
| 5. Compare this copy with ${CASE}\_orig | ||
| 6. Make ${CASE}\_orig read-only, so that you don't accidentally use it. | ||
| 7. Update the CASEROOT variable in CESM. | ||
| 8. `git add` the files that should be archived. You can use a variant of list\_of\_files\_to\_commit.csh | ||
| 9. Commit them (with a useful message) | ||
| 10. Push the contents of the CASE branch to DART\_CASES. There is a special syntax to push the new branch to the GitHub repository when the branch does not exist yet in the "origin". | ||
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Member
There was a problem hiding this comment. Are you taking about |
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| 11. Ongoing; add, commit, and push any changes to the CASE which should be archived. | ||
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| #### Tcsh Example | ||
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| ``` | ||
| [step 0]% set CASE = <your_casename> | ||
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| [step 1]% mv ${CASE} ${CASE}_orig | ||
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| [step 2]% git clone [email protected]:<your_github>/DART_CASES.git ${CASE}_git | ||
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| [step 3]% cd ${CASE}_git | ||
| [step 3]% git checkout -b ${CASE} | ||
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| [step 4]% rsync -av ../${CASE}_orig/ ${CASE} | ||
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| [step 5]% diff -r ../${CASE}_orig ${CASE} | less | ||
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| [step 6]% chmod 644 ../${CASE}_orig | ||
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| [step 7]% xmlchange --caseroot <full_path_new_CASEROOT> | ||
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| [step 8]% git add <files_you_want_to_archive> | ||
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| [step 9]% git commit -m "First commit of files which must be archived" | ||
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| [step 10]% git push -u origin ${CASE} | ||
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| ``` | ||
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| ## Wild West Method | ||
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| If the methods above aren't available to you, then hopefully you can use parts of them | ||
| to set up your case under git control. | ||
| There are too many degrees of freedom to describe how to do it | ||
| 1 operating system command at a time. | ||
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| #!/bin/tcsh | ||
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| # A CESM case + DART has a large number of files because of the ensemble size. | ||
| # Many of them change with every job submission, but have uninformative changes. | ||
| # Here is a list of files archived for the CAM6+DART Reanalysis | ||
| # before each month of assimilation or change in the setup. | ||
| # This may not be comprehensive for your case, and probably names files which you don't need, | ||
| # especially if you're running a non-F-compset (CAM) assimilation. | ||
| # File types that have a file for each instance (member) are represented in this list | ||
| # by only the first 2 instances, so that they can be compared to see whether there are | ||
| # differences between instances. | ||
| # | ||
| # This list uses csh wildcards (*, []) to shorten the list. | ||
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| foreach ftype ( \ | ||
| '*.csv' \ | ||
| '.case.run' \ | ||
| '.env_mach_specific.csh' \ | ||
| '.env_mach_specific.sh' \ | ||
| 'Buildconf/camconf/CESM_cppdefs' \ | ||
| 'Buildconf/camconf/Filepath' \ | ||
| 'Buildconf/camconf/atm_in' \ | ||
| 'Buildconf/camconf/chem_mech.doc' \ | ||
| 'Buildconf/camconf/chem_mech.in' \ | ||
| 'Buildconf/camconf/config_cache.xml' \ | ||
| 'Buildconf/camconf/docn_in' \ | ||
| 'Buildconf/camconf/drv_flds_in' \ | ||
| 'Buildconf/camconf/namelist' \ | ||
| 'Buildconf/cice.input_data_list' \ | ||
| 'Buildconf/ciceconf/ice_in' \ | ||
| 'Buildconf/ciceconf/namelist_infile' \ | ||
| 'Buildconf/clmconf/config_cache.xml' \ | ||
| 'Buildconf/clmconf/drv_flds_in' \ | ||
| 'Buildconf/clmconf/lnd_in' \ | ||
| 'Buildconf/clmconf/namelist' \ | ||
| 'Buildconf/cpl.input_data_list' \ | ||
| 'Buildconf/cplconf/*_modelio.nml_000[12]' \ | ||
| 'Buildconf/cplconf/drv_in' \ | ||
| 'Buildconf/cplconf/namelist_infile' \ | ||
| 'Buildconf/cplconf/seq_maps.rc' \ | ||
| 'Buildconf/docn.input_data_list' \ | ||
| 'Buildconf/docnconf/docn.streams.txt.prescribed_000[12]' \ | ||
| 'Buildconf/docnconf/docn_in' \ | ||
| 'Buildconf/docnconf/namelist_infile' \ | ||
| 'Buildconf/mosart.input_data_list' \ | ||
| 'Buildconf/mosartconf/mosart_in' \ | ||
| 'Buildconf/mosartconf/namelist_infile' \ | ||
| 'CaseDocs/*_in_000[12]' \ | ||
| 'CaseDocs/*_modelio.nml_000[12]' \ | ||
| 'CaseDocs/chem_mech.doc' \ | ||
| 'CaseDocs/chem_mech.in' \ | ||
| 'CaseDocs/docn.streams.txt.prescribed_000[12]' \ | ||
| 'CaseDocs/drv_flds_in' \ | ||
| 'CaseDocs/drv_in' \ | ||
| 'CaseDocs/seq_maps.rc' \ | ||
| 'CaseStatus' \ | ||
| 'DART_config' \ | ||
| 'Depends.intel' \ | ||
| 'Macros.make' \ | ||
| 'README.case' \ | ||
| 'SourceMods/*/*' \ | ||
| 'Tools/Makefile' \ | ||
| 'Tools/check_lockedfiles' \ | ||
| 'Tools/getTiming' \ | ||
| 'Tools/mkDepends' \ | ||
| 'Tools/mkSrcfiles' \ | ||
| 'Tools/save_provenance' \ | ||
| 'archive_metadata' \ | ||
| 'assimilate.csh' \ | ||
| 'case.build' \ | ||
| 'case.cmpgen_namelists' \ | ||
| 'case.qstatus' \ | ||
| 'case.setup' \ | ||
| 'case.st_archive' \ | ||
| 'case.submit' \ | ||
| 'check_case' \ | ||
| 'check_input_data' \ | ||
| 'compress.csh' \ | ||
| 'data_scripts.csh' \ | ||
| 'diags_rean.csh' \ | ||
| 'env_archive.xml' \ | ||
| 'env_batch.xml' \ | ||
| 'env_build.xml' \ | ||
| 'env_case.xml' \ | ||
| 'env_mach_pes.xml' \ | ||
| 'env_mach_specific.xml' \ | ||
| 'env_run.xml' \ | ||
| 'input.nml' \ | ||
| 'launch_cf.sh' \ | ||
| 'mv_to_campaign.csh' \ | ||
| 'no_assimilate.csh' \ | ||
| 'pelayout' \ | ||
| 'pre_purge_check.csh' \ | ||
| 'pre_submit.csh' \ | ||
| 'purge.csh' \ | ||
| 'repack_project.csh' \ | ||
| 'repack_st_arch.csh' \ | ||
| 'software_environment.txt' \ | ||
| 'stage_cesm_files' \ | ||
| 'stage_dart_files' \ | ||
| 'submit_compress.csh' \ | ||
| 'update_dart_namelists' \ | ||
| 'user_nl_*_000[12]' \ | ||
| 'user_nl_cpl' \ | ||
| ) | ||
| git add $ftype | ||
| end | ||
| exit | ||
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| -------------- | ||
| Other files archived in the Reanalysis github: | ||
| 'assimilate.csh.template' \ | ||
| '.gitignore' \ | ||
| 'README.md' \ | ||
| 'stage_cesm_files.template' \ | ||
| Buildconf/cam.input_data_list.sorted | ||
| Buildconf/clm.input_data_list.sorted | ||
| CaseDocs/nml_in_0001.tar | ||
| CESM_instructions.txt | ||
| DART_instructions.txt | ||
| O2-xHost_def-envir_2022-2-23/filter | ||
| O2-xHost_def-envir_2022-2-23/minimal_build.out | ||
| O2-xHost_def-envir_2022-2-23/obs_def_mod.f90 | ||
| O2-xHost_def-envir_2022-2-23/obs_kind_mod.f90 | ||
| O2-xHost_obs_typeOK_2022-3-10/filter | ||
| O2-xHost_obs_typeOK_2022-3-10/obs_def_mod.f90 | ||
| O2-xHost_obs_typeOK_2022-3-10/obs_kind_mod.f90 | ||
| O2-xHost_obs_typeOK_2022-3-10/quickbuild.out | ||
| add_user_docn.streams.csh | ||
| all_but_submit | ||
| assim.csh.added | ||
| assim_no_debug4ben.csh | ||
| assim_post_filter.csh | ||
| backup_manually.casper | ||
| backup_manually.cpl | ||
| backup_manually.csh | ||
| bias_from_obs_seq_output.csh | ||
| call_mv_to_cs.csh | ||
| case.setup.MPI_COMM_MAX | ||
| caseroot_script_list | ||
| cesm_exe_220214-143228.tgz | ||
| chng_hybrid2branch.csh | ||
| compress.csh_proj2camp | ||
| compress_hist.csh | ||
| compress_joblogs.csh | ||
| compress_st-arch.csh | ||
| copy_atts.csh | ||
| diff.csh | ||
| env_archive.xml.original | ||
| env_batch.xml.original | ||
| env_build.xml.original | ||
| env_case.xml.original | ||
| env_mach_pes.xml.original | ||
| env_mach_specific.xml.original | ||
| env_run.xml.original | ||
| env_run_branch_first_2012.xml | ||
| env_run_branch_second_2012.xml | ||
| env_run_pre_branch.xml | ||
| finish_june | ||
| first_try | ||
| fix_yearly_atts.csh | ||
| hist_cleanup_2012-10 | ||
| logs/run_environment.all_cycles_1_month | ||
| matlab_norm.csh | ||
| mover.csh | ||
| mover_proj2scratch.clm2_2011-3 | ||
| mover_proj2scratch.cpl_2011-3 | ||
| mover_proj2scratch.csh | ||
| mv_2011-05_to_CS_intera.atm.hist | ||
| mv_2011-05_to_CS_intera.esp.hist | ||
| mv_2011-05_to_CS_intera.logs | ||
| mv_2012-09-17-00000.csh | ||
| recreate_Reanalysis.notes | ||
| repack_hwm.csh | ||
| repack_st_arch-thru2013-12.csh | ||
| repack_st_arch.csh_proj2camp | ||
| repack_st_arch_tidy_mess.csh | ||
| sst+spinup.pptx | ||
| submit_compress_hist.csh | ||
| diags_batch.csh | ||
| not_in_DART |
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the GitHub limit is everything (all branches) in the repo.