From 0edc6a7e3061843ad98487c63e4d6fde7e5738dc Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 14 Oct 2026 16:47:20 -0600 Subject: [PATCH 1/3] Rename everything that had cesm in the filenames to be ctsm instead --- notebooks/basics/{cesm_workflow.ipynb => ctsm_workflow.ipynb} | 0 .../basics/{cesm_workflow => ctsm_workflow}/case_build.ipynb | 0 .../basics/{cesm_workflow => ctsm_workflow}/case_setup.ipynb | 0 .../basics/{cesm_workflow => ctsm_workflow}/case_submit.ipynb | 0 .../checking_jobs_and_status.ipynb | 0 .../basics/{cesm_workflow => ctsm_workflow}/create_clone.ipynb | 0 .../basics/{cesm_workflow => ctsm_workflow}/create_newcase.ipynb | 0 .../basics/{cesm_workflow => ctsm_workflow}/model_output.ipynb | 0 notebooks/basics/{cesm_workspaces.ipynb => ctsm_workspaces.ipynb} | 0 9 files changed, 0 insertions(+), 0 deletions(-) rename notebooks/basics/{cesm_workflow.ipynb => ctsm_workflow.ipynb} (100%) rename notebooks/basics/{cesm_workflow => ctsm_workflow}/case_build.ipynb (100%) rename notebooks/basics/{cesm_workflow => ctsm_workflow}/case_setup.ipynb (100%) rename notebooks/basics/{cesm_workflow => ctsm_workflow}/case_submit.ipynb (100%) rename notebooks/basics/{cesm_workflow => ctsm_workflow}/checking_jobs_and_status.ipynb (100%) rename notebooks/basics/{cesm_workflow => ctsm_workflow}/create_clone.ipynb (100%) rename notebooks/basics/{cesm_workflow => ctsm_workflow}/create_newcase.ipynb (100%) rename notebooks/basics/{cesm_workflow => ctsm_workflow}/model_output.ipynb (100%) rename notebooks/basics/{cesm_workspaces.ipynb => ctsm_workspaces.ipynb} (100%) diff --git a/notebooks/basics/cesm_workflow.ipynb b/notebooks/basics/ctsm_workflow.ipynb similarity index 100% rename from notebooks/basics/cesm_workflow.ipynb rename to notebooks/basics/ctsm_workflow.ipynb diff --git a/notebooks/basics/cesm_workflow/case_build.ipynb b/notebooks/basics/ctsm_workflow/case_build.ipynb similarity index 100% rename from notebooks/basics/cesm_workflow/case_build.ipynb rename to notebooks/basics/ctsm_workflow/case_build.ipynb diff --git a/notebooks/basics/cesm_workflow/case_setup.ipynb b/notebooks/basics/ctsm_workflow/case_setup.ipynb similarity index 100% rename from notebooks/basics/cesm_workflow/case_setup.ipynb rename to notebooks/basics/ctsm_workflow/case_setup.ipynb diff --git a/notebooks/basics/cesm_workflow/case_submit.ipynb b/notebooks/basics/ctsm_workflow/case_submit.ipynb similarity index 100% rename from notebooks/basics/cesm_workflow/case_submit.ipynb rename to notebooks/basics/ctsm_workflow/case_submit.ipynb diff --git a/notebooks/basics/cesm_workflow/checking_jobs_and_status.ipynb b/notebooks/basics/ctsm_workflow/checking_jobs_and_status.ipynb similarity index 100% rename from notebooks/basics/cesm_workflow/checking_jobs_and_status.ipynb rename to notebooks/basics/ctsm_workflow/checking_jobs_and_status.ipynb diff --git a/notebooks/basics/cesm_workflow/create_clone.ipynb b/notebooks/basics/ctsm_workflow/create_clone.ipynb similarity index 100% rename from notebooks/basics/cesm_workflow/create_clone.ipynb rename to notebooks/basics/ctsm_workflow/create_clone.ipynb diff --git a/notebooks/basics/cesm_workflow/create_newcase.ipynb b/notebooks/basics/ctsm_workflow/create_newcase.ipynb similarity index 100% rename from notebooks/basics/cesm_workflow/create_newcase.ipynb rename to notebooks/basics/ctsm_workflow/create_newcase.ipynb diff --git a/notebooks/basics/cesm_workflow/model_output.ipynb b/notebooks/basics/ctsm_workflow/model_output.ipynb similarity index 100% rename from notebooks/basics/cesm_workflow/model_output.ipynb rename to notebooks/basics/ctsm_workflow/model_output.ipynb diff --git a/notebooks/basics/cesm_workspaces.ipynb b/notebooks/basics/ctsm_workspaces.ipynb similarity index 100% rename from notebooks/basics/cesm_workspaces.ipynb rename to notebooks/basics/ctsm_workspaces.ipynb From a574c312b94f1397cbdf68ab0a406a704062b830 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 15 Oct 2026 01:43:16 -0600 Subject: [PATCH 2/3] Initial go through to change basics for CLM cases rather than general CESM cases --- notebooks/basics/code/git_download_ctsm.ipynb | 57 +--- notebooks/basics/ctsm_workflow.ipynb | 180 ++++++------ .../basics/ctsm_workflow/case_build.ipynb | 2 +- .../basics/ctsm_workflow/case_setup.ipynb | 5 +- .../basics/ctsm_workflow/case_submit.ipynb | 76 ++--- .../basics/ctsm_workflow/create_newcase.ipynb | 270 +++++++++++++----- .../basics/ctsm_workflow/model_output.ipynb | 2 +- notebooks/basics/ctsm_workspaces.ipynb | 4 +- notebooks/basics/exercises_overview.ipynb | 2 +- notebooks/resources/unix.ipynb | 2 +- 10 files changed, 342 insertions(+), 258 deletions(-) diff --git a/notebooks/basics/code/git_download_ctsm.ipynb b/notebooks/basics/code/git_download_ctsm.ipynb index 847aa87..4f900dd 100644 --- a/notebooks/basics/code/git_download_ctsm.ipynb +++ b/notebooks/basics/code/git_download_ctsm.ipynb @@ -22,9 +22,9 @@ "metadata": {}, "source": [ "
\n", - "We will use the CLM6 tutorial tag: `ctsm6.0_Tutorial2026`

\n", + "We will use the CLM6 tutorial tag: `clm5.4.063`

\n", "\n", - "Note: At the time of the tutorial, the final CLM6 release has not yet been completed. Therefore, we will use a preliminary tutorial tag (`ctsm6.0_Tutorial2026`) that contains the CLM6 code base and configuration needed for the exercises. The exact tag used in the tutorial may differ from the final CLM6 release.\n", + "Note: At the time of the tutorial, the final CLM6 release has not yet been completed. Therefore, we will use a preliminary tag (`ctsm5.4.063`) that contains the CLM6 code base and configuration needed for the exercises. The exact tag used in the tutorial may differ from the final CLM6 release.\n", "
" ] }, @@ -52,7 +52,7 @@ "\n", "First, create a location in the **glade** file system where you will store your CLM source code.\n", "\n", - "Throughout this tutorial, `$USER` is a placeholder for your NCAR HPC username." + "Throughout this tutorial, `$USER` is the environment variable already set for you that is your NCAR HPC username." ] }, { @@ -101,9 +101,9 @@ "```\n", " git clone https://github.com/ESCOMP/CTSM.git my_clm_code\n", " cd my_clm_code\n", - " git checkout clm6.0_Tutorial2026\n", + " git checkout ctsm5.4.063\n", "```\n", - "The directory name `my_clm_code` is only an example. You may choose any directory name you prefer. Outside of this tutorial, many users choose names that identify the CLM version they are working with (for example, `ctsm6.0`, or `clm6.0_Tutorial2026`).\n", + "The directory name `my_clm_code` is only an example. You may choose any directory name you prefer. Outside of this tutorial, many users choose names that identify the CLM version they are working with (for example, `ctsm6.0`, `ctsm5.5` or `clm6.0_Tutorial2026`).\n", "\n", "- **Verify the Tutorial Tag**\n", "\n", @@ -116,7 +116,7 @@ "which should return:\n", "\n", "```\n", - " clm6.0_Tutorial2026\n", + " clm5.4.063\n", "```\n", "" ] @@ -143,9 +143,9 @@ "- Consistency with community experiments or previous studies.\n", "- Compatibility with analysis tools and workflows.\n", "\n", - "For example, if you plan to compare your simulations with a community project, you should generally use the same CESM version as that project.\n", + "For example, if you plan to compare your simulations with a community project, you should generally use the same CESM or CLM version as that project.\n", "\n", - "More information can be found on the [CESM Models website](https://www.cesm.ucar.edu/models).\n" + "More information can be found on the [CLM github Page](https://github.com/ESCOMP/CTSM.git).\n" ] }, { @@ -155,48 +155,11 @@ "source": [ "
\n", " \n", - "To see available CLM tags that were used in CESM releases, use:\n", - "\n", - "\n", - "```bash\n", - "git tag --list 'release-cesm*'\n", - "```\n", - "\n", - "\n", + "To see available CLM tags that have a release tag (and thus a DOI to go with them) go to the release page on CLM github. It's under the Code tab on the far left of the page, and then \"Tags\" two to the right of the \"master\" pulldown, and then Releases. (https://github.com/ESCOMP/CTSM/releases)\n", "\n", "
" ] }, - { - "cell_type": "markdown", - "id": "195d4a4b-514b-446e-9d2b-4c7aeae60aa2", - "metadata": {}, - "source": [ - "\n", - "
\n", - "
\n", - "\n", - " Click here for example output \n", - "
\n", - " \n", - "```\n", - "release-cesm2.0.01\n", - "release-cesm2.0.02\n", - "release-cesm2.2.01\n", - "release-cesm2.2.01.asd01\n", - "release-cesm2.2.01.asd02\n", - "release-cesm2.2.02\n", - "release-cesm2.2.03\n", - "release-cesm2.2.04\n", - "```\n", - "\n", - "**Note** *CESM3 has not yet been officially released at the time of this tutorial. As a result, you will only see CESM2 release tags when listing official releases. The tutorial tag `clm6.0_Tutorial2026` is a pre-release CESM3 tag created specifically for this tutorial and therefore does not appear in the list of official CESM releases.*\n", - "\n", - "\n", - "
\n", - "
\n" - ] - }, { "cell_type": "markdown", "id": "88bd0742-e990-4fcf-9b40-5c8b21a9ec43", @@ -207,7 +170,7 @@ "\n", "The CTSM repository itself does not contain all component model source code. **Individual model components are maintained in separate repositories** and must be downloaded after cloning CLM. \n", "\n", - "CESM3 uses `git-fleximod` to manage external repositories. \n", + "CESM3/CLM uses `git-fleximod` to manage external repositories. \n", "\n", "From your CLM source directory, run: \n", "\n", diff --git a/notebooks/basics/ctsm_workflow.ipynb b/notebooks/basics/ctsm_workflow.ipynb index c3317de..8be417e 100644 --- a/notebooks/basics/ctsm_workflow.ipynb +++ b/notebooks/basics/ctsm_workflow.ipynb @@ -1,92 +1,92 @@ { - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# CESM Workflow" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "CLM has been designed to be easy to use. Once you have downloaded the CLM code, a CLM `case` can be run with a set of 4 commands. \n", - "\n", - "*Note: In CLM jargon, a case refers to a specific instance of a model simulation.*" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "
\n", - "\n", - "1) Create a new case using `create_newcase`\n", - "2) Set up the case by invoking `case.setup`\n", - "3) Build the executable using `case.build`\n", - "4) Run your case using `case.submit`\n", - " \n", - "
\n" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "The following sections will go into more detail about these 4 commands and also provide information about how to check your job status or create a clone of a previous case." - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## More information" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "While there is not published documentation for CESM3 workflow yet, it is very similar to the CESM2 workflow. And more detailed information on the CESM3 Workflow is documented in the following links. Check these out later to learn more." - ] - }, - { - "cell_type": "markdown", - "metadata": { - "tags": [] - }, - "source": [ - "
\n", - "\n", - "[CESM2 release](https://escomp.github.io/CESM/release-cesm2/)\n", - " \n", - "[CIME](https://esmci.github.io/cime/versions/master/html/index.html)\n", - "\n", - "
" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Bash", - "language": "bash", - "name": "bash" - }, - "language_info": { - "codemirror_mode": "shell", - "file_extension": ".sh", - "mimetype": "text/x-sh", - "name": "bash" - } - }, - "nbformat": 4, - "nbformat_minor": 4 + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# CTSM Workflow" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "CLM has been designed to be easy to use. Once you have downloaded the CLM code, a CLM `case` can be run with a set of 4 commands. \n", + "\n", + "*Note: In CLM jargon, a case refers to a specific instance of a model simulation.*" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "
\n", + "\n", + "1) Create a new case using `create_newcase`\n", + "2) Set up the case by invoking `case.setup`\n", + "3) Build the executable using `case.build`\n", + "4) Run your case using `case.submit`\n", + " \n", + "
\n" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "The following sections will go into more detail about these 4 commands and also provide information about how to check your job status or create a clone of a previous case." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## More information" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "While there is not yet fully published documentation for CLM6/CESM3 workflow yet, it is very similar to the CLM5/CESM2 workflow. And we have documentation for the latest model version, with the caveat that it isn't fully accurate or completed yet. Detailed information on the CLM6/CESM2 Workflow is in the following links. Check these out later to learn more." + ] + }, + { + "cell_type": "markdown", + "metadata": { + "tags": [] + }, + "source": [ + "
\n", + "\n", + "- [CTSM latest](https://escomp.github.io/CTSM)\n", + "- [CESM2 release](https://escomp.github.io/CESM/release-cesm2/)\n", + "- [CIME](https://esmci.github.io/cime/versions/master/html/index.html)\n", + "\n", + "
" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Bash", + "language": "bash", + "name": "bash" + }, + "language_info": { + "codemirror_mode": "shell", + "file_extension": ".sh", + "mimetype": "text/x-sh", + "name": "bash" + } + }, + "nbformat": 4, + "nbformat_minor": 4 } diff --git a/notebooks/basics/ctsm_workflow/case_build.ipynb b/notebooks/basics/ctsm_workflow/case_build.ipynb index 31e76e3..b703749 100644 --- a/notebooks/basics/ctsm_workflow/case_build.ipynb +++ b/notebooks/basics/ctsm_workflow/case_build.ipynb @@ -29,7 +29,7 @@ "id": "0d8b2ab4-7976-48b7-81e4-e2ae0f28cd97", "metadata": {}, "source": [ - "![CESM case.build](../../../images/basics/CESM_case_build.png)\n", + "![CLM/CESM case.build](../../../images/basics/CESM_case_build.png)\n", "*

Figure: Detailed view of the location of case.build

*\n", "\n", "\n", diff --git a/notebooks/basics/ctsm_workflow/case_setup.ipynb b/notebooks/basics/ctsm_workflow/case_setup.ipynb index 46320cb..d095864 100644 --- a/notebooks/basics/ctsm_workflow/case_setup.ipynb +++ b/notebooks/basics/ctsm_workflow/case_setup.ipynb @@ -95,6 +95,9 @@ "
\n", " \n", "```\n", + "\n", + "WARNING: Macros of the form COMPILER_MACHINE.cmake are deprecated and should be replaced with the form MACHINE_COMPILER.cmake\n", + "\n", "job is case.run USER_REQUESTED_WALLTIME None USER_REQUESTED_QUEUE None WALLTIME_FORMAT %H:%M:%S\n", "Creating batch scripts\n", "Writing case.run script from input template /glade/u/home/$USER/code/my_cesm_code/ccs_config/machines/template.case.run\n", @@ -102,9 +105,9 @@ "Writing case.st_archive script from input template /glade/u/home/$USER/code/my_cesm_code/ccs_config/machines/template.st_archive\n", "Creating file case.st_archive\n", "Writing case.cupid script from input template /glade/u/home/$USER/code/my_cesm_code/ccs_config/machines/template.cupid\n", + "Could not resolve $CUPID_MEM_PER_TASK using a value of 10\n", "Creating file case.cupid\n", "Creating user_nl_xxx files for components and cpl\n", - "Running cam.case_setup.py\n", "If an old case build already exists, might want to run 'case.build --clean' before building\n", "You can now run './preview_run' to get more info on how your case will be run\n", "```\n", diff --git a/notebooks/basics/ctsm_workflow/case_submit.ipynb b/notebooks/basics/ctsm_workflow/case_submit.ipynb index 16d240f..8648653 100644 --- a/notebooks/basics/ctsm_workflow/case_submit.ipynb +++ b/notebooks/basics/ctsm_workflow/case_submit.ipynb @@ -42,12 +42,6 @@ "- `$RUNDIR` =`/glade/derecho/scratch/$USER/$CASE/run` " ] }, - { - "cell_type": "markdown", - "id": "579cb4c8-03f1-4c9f-913f-de2ffeccfbc5", - "metadata": {}, - "source": [] - }, { "cell_type": "markdown", "id": "d8e6525b-31d9-450d-a3b9-e3b435fc231a", @@ -95,59 +89,51 @@ "
\n", " \n", "```\n", - " 2026-06-30 21:32:46 atm \n", - "Create namelist for component cam\n", - " Calling /glade/u/home/$USER/my_cesm_code/components/cam//cime_config/buildnml\n", - "CAM namelist copy: file1 /glade/u/home/$USER/cases/b1850.basics/Buildconf/camconf/atm_in file2 /glade/derecho/scratch/$USER/b1850.basics/run/atm_in \n", - " 2026-06-30 21:32:49 lnd \n", + " 2026-10-15 01:08:47 atm \n", + "Create namelist for component datm\n", + " Calling /glade/u/home/$USER/code/my_clm_code//components/cdeps/datm/cime_config/buildnml\n", + " 2026-10-15 01:08:47 lnd \n", "Create namelist for component clm\n", - " Calling /glade/u/home/$USER/my_cesm_code/components/clm//cime_config/buildnml\n", - " 2026-06-30 21:32:50 ice \n", - "Create namelist for component cice\n", - " Calling /glade/u/home/$USER/my_cesm_code/components/cice//cime_config/buildnml\n", - "RUN: /glade/u/home/$USER/my_cesm_code/components/cice/bld/generate_cice_decomp.pl -ccsmroot /glade/u/home/$USER/my_cesm_code -res tx2_0v1 -nx 180 -ny 128 -nproc 256 -thrds 1 -output all \n", - "FROM: /glade/u/home/$USER/cases/b1850.basics\n", - " output: 180 128 5 4 5 sectrobin square-ice\n", - "\n", - " 2026-06-30 21:32:51 ocn \n", - "Create namelist for component mom\n", - " Calling /glade/u/home/$USER/my_cesm_code/components/mom//cime_config/buildnml\n", - " 2026-06-30 21:32:52 rof \n", + " Calling /glade/u/home/$USER/code/my_clm_code/cime_config/buildnml\n", + " 2026-10-15 01:08:47 ice \n", + "Create namelist for component sice\n", + " Calling /glade/u/home/$USER/code/my_clm_code/cime/CIME/non_py/src/components/stub_comps_nuopc/sice/cime_config/buildnml\n", + " 2026-10-15 01:08:47 ocn \n", + "Create namelist for component socn\n", + " Calling /glade/u/home/$USER/code/my_clm_code/cime/CIME/non_py/src/components/stub_comps_nuopc/socn/cime_config/buildnml\n", + " 2026-10-15 01:08:47 rof \n", "Create namelist for component mosart\n", - " Calling /glade/u/home/$USER/my_cesm_code/components/mosart//cime_config/buildnml\n", - " 2026-06-30 21:32:52 glc \n", + " Calling /glade/u/home/$USER/code/my_clm_code/components/mosart//cime_config/buildnml\n", + " 2026-10-15 01:08:47 glc \n", "Create namelist for component dglc\n", - " Calling /glade/u/home/$USER/my_cesm_code/components/cdeps/dglc/cime_config/buildnml\n", - " 2026-06-30 21:32:52 wav \n", - "Create namelist for component ww3\n", - " Calling /glade/u/home/$USER/my_cesm_code/components/ww3//cime_config/buildnml\n", - " Running /glade/u/home/$USER/my_cesm_code/components/ww3//cime_config/buildnml \n", - " 2026-06-30 21:33:04 esp \n", + " Calling /glade/u/home/$USER/code/my_clm_code/components/cdeps/dglc/cime_config/buildnml\n", + " 2026-10-15 01:08:47 wav \n", + "Create namelist for component swav\n", + " Calling /glade/u/home/$USER/code/my_clm_code/cime/CIME/non_py/src/components/stub_comps_nuopc/swav/cime_config/buildnml\n", + " 2026-10-15 01:08:47 esp \n", "Create namelist for component sesp\n", - " Calling /glade/u/home/$USER/my_cesm_code/cime/CIME/non_py/src/components/stub_comps_nuopc/sesp/cime_config/buildnml\n", - " 2026-06-30 21:33:04 cpl \n", + " Calling /glade/u/home/$USER/code/my_clm_code/cime/CIME/non_py/src/components/stub_comps_nuopc/sesp/cime_config/buildnml\n", + " 2026-10-15 01:08:47 cpl \n", "Create namelist for component drv\n", - " Calling /glade/u/home/$USER/my_cesm_code/components/cmeps/cime_config/buildnml\n", - "Writing nuopc_runconfig for components ['CPL', 'ATM', 'LND', 'ICE', 'OCN', 'ROF', 'GLC', 'WAV']\n", + " Calling /glade/u/home/$USER/code/my_clm_code//answer_changes/components/cmeps/cime_config/buildnml\n", + "Writing nuopc_runconfig for components ['CPL', 'ATM', 'LND', 'ROF', 'GLC']\n", "Checking that inputdata is available as part of case submission\n", "Loading input file list: 'Buildconf/ctsm.input_data_list'\n", "Loading input file list: 'Buildconf/cpl.input_data_list'\n", - "Loading input file list: 'Buildconf/mom.input_data_list'\n", - "Loading input file list: 'Buildconf/ww3.input_data_list'\n", - "Loading input file list: 'Buildconf/cice.input_data_list'\n", + "Loading input file list: 'Buildconf/datm.input_data_list'\n", "Loading input file list: 'Buildconf/mosart.input_data_list'\n", - "Loading input file list: 'Buildconf/cam.input_data_list'\n", "Loading input file list: 'Buildconf/dglc.input_data_list'\n", "Check case OK\n", "submit_jobs case.run\n", + "Could not resolve $CUPID_MEM_PER_TASK using a value of 10\n", "Submit job case.run\n", - "Submitting job script qsub -q main -l walltime=12:00:00 -A P93300606 -l job_priority=regular -v ARGS_FOR_SCRIPT='--resubmit' /glade/u/home/$USER/cases/b1850.basics/.case.run\n", - "Submitted job id is 6606898.desched1\n", + "Submitting job script qsub -q main -l walltime=12:00:00 -A P93300606 -l job_priority=regular -M $USER@ucar.edu -m a -v ARGS_FOR_SCRIPT='--resubmit' /glade/u/home/$USER/cases/i1850_sp.basics/.case.run\n", + "Submitted job id is 7827012.desched1\n", "Submit job case.st_archive\n", - "Submitting job script qsub -q develop -l walltime=00:20:00 -A P93300606 -l job_priority=regular -W depend=afterok:6606898.desched1 -v ARGS_FOR_SCRIPT='--resubmit' /glade/u/home/$USER/cases/b1850.basics/case.st_archive\n", - "Submitted job id is 6606899.desched1\n", - "Submitted job case.run with id 6606898.desched1\n", - "Submitted job case.st_archive with id 6606899.desched1\n", + "Submitting job script qsub -q develop -l walltime=00:20:00 -A P93300606 -l job_priority=regular -W depend=afterok:7827012.desched1 -M $USER@ucar.edu -m a -v ARGS_FOR_SCRIPT='--resubmit' /glade/u/home/$USER/cases/i1850_sp.basics/case.st_archive\n", + "Submitted job id is 7827013.desched1\n", + "Submitted job case.run with id 7827012.desched1\n", + "Submitted job case.st_archive with id 7827013.desched1\n", "```\n", "\n", "\n", diff --git a/notebooks/basics/ctsm_workflow/create_newcase.ipynb b/notebooks/basics/ctsm_workflow/create_newcase.ipynb index 09beb9e..1d83d1a 100644 --- a/notebooks/basics/ctsm_workflow/create_newcase.ipynb +++ b/notebooks/basics/ctsm_workflow/create_newcase.ipynb @@ -182,7 +182,7 @@ "id": "8f080dc7-3bfb-4e61-b112-af418f52018a", "metadata": {}, "source": [ - "In this tutorial we will use fairly simple names for the cases you create, build, and run. However, most CLM experiments have much longer casenames that provide information about the experiment at a glance. Knowing the and CLM case naming conventions will help you navigate and CLM community experiments. Information about the CESM naming is available at:" + "In this tutorial we will use fairly simple names for the cases you create, build, and run. However, most CLM experiments have much longer casenames that provide information about the experiment at a glance. Knowing CESM/CLM case naming conventions will help you navigate CESM and CLM community experiments. Information about the CESM naming is available below. Also below are the CESM and LMWG experiments github pages that give information on the latest CESM and CLM production experiments:" ] }, { @@ -192,7 +192,9 @@ "source": [ "
\n", "\n", - "[CESM case naming conventions](https://www.cesm.ucar.edu/models/cesm2/naming-conventions)\n", + "- [CESM case naming conventions](https://www.cesm.ucar.edu/models/cesm2/naming-conventions)\n", + "- [CESM development experiments](https://github.comr/NCAR/CESM_dev)\n", + "- [LMWG CLM development experiments](https://github.comr/NCAR/LMWG_dev)\n", "\n", "
" ] @@ -267,7 +269,11 @@ "\n", "
\n", " \n", + "Below we show the header and some of the grids that are are useful for CLM simulations.\n", + "\n", "```\n", + "Schema validity test fails for /glade/u/home/$USER/my_cesm_code/ccs_config/config_grids_nuopc.xml\n", + "\n", " =========================================\n", " GRID naming convention\n", " =========================================\n", @@ -287,7 +293,7 @@ " Note that the mask is for information only - and is not an attribute of the grid\n", " By default, if the mask is not specified below, it will be set to the ocnice grid\n", " And if there is no ocnice grid (such as for single column, the mask is null since it does not mean anything)\n", - "\n", + " \n", " -------------------------------------------------------------\n", " default component grids:\n", "\n", @@ -314,20 +320,86 @@ " wav XWAV wgx3v7 \n", " iac SIAC null \n", " -------------------------------------------------------------\n", + ".\n", + ".\n", + ".\n", + " alias: CLM_USRDAT (only for compsets that are DATM.+CLM|DATM.+SLND )\n", "\n", - " alias: g16_g16 (only for compsets that are DATM.+DROF )\n", + " longname: a%CLM_USRDAT_l%CLM_USRDAT_oi%null_r%null_g%null_w%null_z%null_m%null\n", + " non-default grids are: atm:CLM_USRDAT lnd:CLM_USRDAT rof:null \n", "\n", - " longname: a%gx1v6_l%gx1v6_oi%gx1v6_r%null_g%null_w%null_z%null_m%gx1v6\n", - " non-default grids are: atm:gx1v6 lnd:gx1v6 ocnice:gx1v6 \n", - " \n", - " gx1v6 is displaced Greenland pole v6 1-deg grid: with domain file(s): \n", + " alias: 1x1_numaIA (only for compsets that are DATM.+CLM|DATM.+SLND )\n", "\n", - " alias: g17_g17 (only for compsets that are DATM.+DROF only for compsets that are not _MOM )\n", + " longname: a%1x1_numaIA_l%1x1_numaIA_oi%null_r%null_g%null_w%null_z%null_m%null\n", + " non-default grids are: atm:1x1_numaIA lnd:1x1_numaIA rof:null \n", "\n", - " longname: a%gx1v7_l%gx1v7_oi%gx1v7_r%null_g%null_w%null_z%null_m%gx1v7\n", - " non-default grids are: atm:gx1v7 lnd:gx1v7 ocnice:gx1v7 \n", - " \n", - " gx1v7 is displaced Greenland pole 1-deg grid with Caspian as a land feature: with domain file(s): \n", + " alias: 1x1_brazil (only for compsets that are DATM.+CLM|DATM.+SLND )\n", + "\n", + " longname: a%1x1_brazil_l%1x1_brazil_oi%null_r%null_g%null_w%null_z%null_m%null\n", + " non-default grids are: atm:1x1_brazil lnd:1x1_brazil rof:null \n", + "\n", + " alias: 1x1_smallvilleIA (only for compsets that are DATM.+CLM|DATM.+SLND )\n", + "\n", + " longname: a%1x1_smallvilleIA_l%1x1_smallvilleIA_oi%null_r%null_g%null_w%null_z%null_m%null\n", + " non-default grids are: atm:1x1_smallvilleIA lnd:1x1_smallvilleIA rof:null \n", + "\n", + " alias: 1x1_cidadinhoBR (only for compsets that are DATM.+CLM|DATM.+SLND )\n", + "\n", + " longname: a%1x1_cidadinhoBR_l%1x1_cidadinhoBR_oi%null_r%null_g%null_w%null_z%null_m%null\n", + " non-default grids are: atm:1x1_cidadinhoBR lnd:1x1_cidadinhoBR rof:null \n", + "\n", + " alias: 1x1_camdenNJ (only for compsets that are DATM.+CLM|DATM.+SLND )\n", + "\n", + " longname: a%1x1_camdenNJ_l%1x1_camdenNJ_oi%null_r%null_g%null_w%null_z%null_m%null\n", + " non-default grids are: atm:1x1_camdenNJ lnd:1x1_camdenNJ rof:null \n", + "\n", + " alias: 1x1_mexicocityMEX (only for compsets that are DATM.+CLM|DATM.+SLND )\n", + "\n", + " longname: a%1x1_mexicocityMEX_l%1x1_mexicocityMEX_oi%null_r%null_g%null_w%null_z%null_m%null\n", + " non-default grids are: atm:1x1_mexicocityMEX lnd:1x1_mexicocityMEX rof:null \n", + "\n", + " alias: 1x1_vancouverCAN (only for compsets that are DATM.+CLM|DATM.+SLND )\n", + "\n", + " longname: a%1x1_vancouverCAN_l%1x1_vancouverCAN_oi%null_r%null_g%null_w%null_z%null_m%null\n", + " non-default grids are: atm:1x1_vancouverCAN lnd:1x1_vancouverCAN rof:null \n", + "\n", + " alias: 1x1_urbanc_alpha (only for compsets that are DATM.+CLM|DATM.+SLND )\n", + "\n", + " longname: a%1x1_urbanc_alpha_l%1x1_urbanc_alpha_oi%null_r%null_g%null_w%null_z%null_m%null\n", + " non-default grids are: atm:1x1_urbanc_alpha lnd:1x1_urbanc_alpha rof:null \n", + ".\n", + ".\n", + ".\n", + " alias: nldas2_rnldas2_mnldas2 (only for compsets that are DATM.+CLM )\n", + "\n", + " longname: a%0.125nldas2_l%0.125nldas2_oi%0.125nldas2_r%0.125nldas2_g%null_w%null_z%null_m%0.125nldas2\n", + " non-default grids are: atm:0.125nldas2 lnd:0.125nldas2 ocnice:0.125nldas2 rof:0.125nldas2 \n", + " mask is: 0.125nldas2\n", + ".\n", + ".\n", + ".\n", + " alias: f09_f09_mt233 (only for compsets that are not _MOM )\n", + "\n", + " longname: a%0.9x1.25_l%0.9x1.25_oi%0.9x1.25_r%null_g%null_w%null_z%null_m%tx2_3v3\n", + " non-default grids are: atm:0.9x1.25 lnd:0.9x1.25 ocnice:0.9x1.25 \n", + " mask is: tx2_3v3\n", + ".\n", + ".\n", + ".\n", + " alias: f19_f19_mt233 (only for compsets that are not _MOM )\n", + "\n", + " longname: a%1.9x2.5_l%1.9x2.5_oi%1.9x2.5_r%null_g%null_w%null_z%null_m%tx2_3v3\n", + " non-default grids are: atm:1.9x2.5 lnd:1.9x2.5 ocnice:1.9x2.5 \n", + " mask is: tx2_3v3\n", + "\n", + ".\n", + ".\n", + ".\n", + " alias: ne30pg3_ne30pg3_mt233 (only for compsets that are not _MOM )\n", + "\n", + " longname: a%ne30np4.pg3_l%ne30np4.pg3_oi%ne30np4.pg3_r%null_g%null_w%null_z%null_m%tx2_3v3\n", + " non-default grids are: atm:ne30np4.pg3 lnd:ne30np4.pg3 ocnice:ne30np4.pg3 \n", + " mask is: tx2_3v3\n", "\n", "...\n", "```\n", @@ -371,35 +443,17 @@ "- Compsets determine which grid is required." ] }, - { - "cell_type": "markdown", - "id": "0d522ed3-098c-4194-be32-f219be984248", - "metadata": {}, - "source": [ - "#### CESM2 Supported Compsets" - ] - }, - { - "cell_type": "markdown", - "id": "e8b7943e-0be5-4feb-9b3f-cb8d4fe4aac0", - "metadata": {}, - "source": [ - " Link for CESM2 Supported Compsets: \n", - "
\n", - "[http://www.cesm.ucar.edu/models/cesm2/config/compsets.html](http://www.cesm.ucar.edu/models/cesm2/config/compsets.html)" - ] - }, { "cell_type": "markdown", "id": "e91dff67-7992-48d2-afba-c0acb5528fb8", "metadata": {}, "source": [ "
\n", - "Cime Tool for listing configurations:

\n", + "Cime Tool for listing CLM configurations:

\n", "\n", "```\n", "cd /glade/u/home/$USER/code/my_cesm_code/cime/scripts/\n", - "./query_config --compsets\n", + "./query_config --compsets clm\n", "```\n", "
" ] @@ -418,45 +472,123 @@ "
\n", " \n", "```\n", - "Active component: allactive\n", - " --------------------------------------\n", - " Compset Alias: Compset Long Name \n", - " --------------------------------------\n", - " B1850C_MTt4s : 1850C_CAM70%MT%CT4S2_CLM60%BGC-CROP_CICE_MOM6_MOSART_DGLC%NOEVOLVE_WW3\n", - " B1850CM : 1850C_CAM70%MT%CT4S2_CLM60%BGC-CROP_CICE_MOM6_MOSART_DGLC%NOEVOLVE_WW3\n", - " B1850C_MTso : 1850C_CAM70%MT_CLM60%BGC-CROP_CICE_MOM6_MOSART_DGLC%NOEVOLVE_WW3\n", - " BHISTC_MTso : HISTC_CAM70%MT_CLM60%BGC-CROP_CICE_MOM6_MOSART_DGLC%NOEVOLVE_WW3\n", - " BHISTC_MTt4s : HISTC_CAM70%MT%CT4S2_CLM60%BGC-CROP_CICE_MOM6_MOSART_DGLC%NOEVOLVE_WW3\n", - " BHISTCM : HISTC_CAM70%MT%CT4S2_CLM60%BGC-CROP_CICE_MOM6_MOSART_DGLC%NOEVOLVE_WW3\n", - " BHISTC_MTso : HISTC_CAM70%MT_CLM60%BGC-CROP_CICE_MOM6_MOSART_DGLC%NOEVOLVE_WW3\n", - " B1850C_LTso : 1850C_CAM70%LT_CLM60%BGC-CROP_CICE_MOM6_MOSART_DGLC%NOEVOLVE_WW3\n", - " BHISTC_LTso : HISTC_CAM70%LT_CLM60%BGC-CROP_CICE_MOM6_MOSART_DGLC%NOEVOLVE_WW3\n", - " BHISTC_LT_DART : HISTC_CAM70%LT_CLM60%BGC_CICE_MOM6_MOSART_DGLC%NOEVOLVE_SWAV\n", - " B1850E_MTt4s : 1850E_CAM70%MT%CT4S2_CLM60%BGC-CROP_CICE_MOM6_MOSART_DGLC%NOEVOLVE_WW3\n", - " B1850EM : 1850E_CAM70%MT%CT4S2_CLM60%BGC-CROP_CICE_MOM6_MOSART_DGLC%NOEVOLVE_WW3\n", - " BHISTE_MTt4s : HISTE_CAM70%MT%CT4S2_CLM60%BGC-CROP_CICE_MOM6_MOSART_DGLC%NOEVOLVE_WW3\n", - " BHISTEM : HISTE_CAM70%MT%CT4S2_CLM60%BGC-CROP_CICE_MOM6_MOSART_DGLC%NOEVOLVE_WW3\n", - " ETEST : 2000_CAM60_CLM50%SP_CICE_DOCN%SOM_MOSART_SGLC_SWAV_TEST\n", - " E1850TEST : 1850_CAM60_CLM50%SP_CICE_DOCN%SOM_MOSART_SGLC_SWAV_TEST\n", - "\n", - "Active component: drv\n", + "\n", + "Active component: clm\n", " --------------------------------------\n", " Compset Alias: Compset Long Name \n", " --------------------------------------\n", - " AA : 2000_DATM%NYF_DLND%LCPL_DICE%SSMI_DOCN%DOM_DROF%NYF_SGLC_DWAV\n", - " A : 2000_DATM%NYF_SLND_DICE%SSMI_DOCN%DOM_DROF%NYF_SGLC_SWAV\n", - " ADSOM : 2000_DATM%NYF_SLND_DICE%SSMI_DOCN%SOM_DROF%NYF_SGLC_SWAV_TEST\n", - " ADSOMAQP : 2000_DATM%NYF_SLND_SICE_DOCN%SOMAQP_SROF_SGLC_SWAV\n", - " ADAQP3 : 2000_DATM%NYF_SLND_SICE_DOCN%AQP3_SROF_SGLC_SWAV\n", - " ADAQPFILE : 2000_DATM%NYF_SLND_SICE_DOCN%AQPFILE_SROF_SGLC_SWAV\n", - " A1850DLND : 1850_SATM_DLND%SCPL_SICE_SOCN_SROF_SGLC_SWAV\n", - " ADWAV : 2000_SATM_SLND_SICE_SOCN_SROF_SGLC_DWAV%CLIMO\n", - " ADESP : 2000_DATM%NYF_SLND_SICE_DOCN%SOMAQP_SROF_SGLC_SWAV_DESP%NOOP\n", - " ADESP_TEST : 2000_DATM%NYF_SLND_SICE_DOCN%SOMAQP_SROF_SGLC_SWAV_DESP%TEST\n", - " AIAF : 2000_DATM%IAF_SLND_DICE%IAF_DOCN%IAF_DROF%IAF_SGLC_SWAV\n", - " S : 2000_SATM_SLND_SICE_SOCN_SROF_SGLC_SWAV_SESP\n", - " X : 2000_XATM_XLND_XICE_XOCN_XROF_XGLC_XWAV\n", - "\n", + " I1PtClm60BgcRsGs : 2000_DATM%1PT_CLM60%BGC_SICE_SOCN_SROF_SGLC_SWAV\n", + " I1PtClm60FatesRsGs : 2000_DATM%1PT_CLM60%FATES_SICE_SOCN_SROF_SGLC_SWAV\n", + " IHist1PtClm60BgcRsGs : HIST_DATM%1PT_CLM60%BGC_SICE_SOCN_SROF_SGLC_SWAV\n", + " IHist1PtClm60FatesRsGs : HIST_DATM%1PT_CLM60%FATES_SICE_SOCN_SROF_SGLC_SWAV\n", + " I1PtClm60SpRsGs : 2000_DATM%1PT_CLM60%SP_SICE_SOCN_SROF_SGLC_SWAV\n", + " I1PtClm50SpRsGs : 2000_DATM%1PT_CLM50%SP_SICE_SOCN_SROF_SGLC_SWAV\n", + " I2000Clm50Sp : 2000_DATM%GSWP3v1_CLM50%SP_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " I2000Clm50SpRsGs : 2000_DATM%GSWP3v1_CLM50%SP_SICE_SOCN_SROF_SGLC_SWAV\n", + " I2000Clm60SpRsGs : 2000_DATM%GSWP3v1_CLM60%SP_SICE_SOCN_SROF_SGLC_SWAV\n", + " I2000Clm60SpCrujraRsGs : 2000_DATM%CRUJRA2024b_CLM60%SP_SICE_SOCN_SROF_SGLC_SWAV\n", + " I2000Clm60Sp : 2000_DATM%GSWP3v1_CLM60%SP_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " I2000Clm60SpCrujra : 2000_DATM%CRUJRA2024b_CLM60%SP_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " I2000Clm60SpMiz : 2000_DATM%GSWP3v1_CLM60%SP_SICE_SOCN_MIZUROUTE_DGLC%NOEVOLVE_SWAV\n", + " I2000Clm60SpMizGs : 2000_DATM%GSWP3v1_CLM60%SP_SICE_SOCN_MIZUROUTE_SGLC_SWAV\n", + " I2000Clm60SpMizNldasGs : 2000_DATM%NLDAS2_CLM60%SP_SICE_SOCN_MIZUROUTE_SGLC_SWAV\n", + " I2010Clm50Sp : 2010_DATM%GSWP3v1_CLM50%SP_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " I2000Clm50Bgc : 2000_DATM%GSWP3v1_CLM50%BGC_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " I2000Clm50BgcCru : 2000_DATM%CRUv7_CLM50%BGC_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " I2000Clm50BgcCropRtm : 2000_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_RTM_DGLC%NOEVOLVE_SWAV\n", + " I2000Clm50BgcCrop : 2000_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " I2000Clm60BgcCrop : 2000_DATM%GSWP3v1_CLM60%BGC-CROP_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " I2000Clm60BgcCropCrujra : 2000_DATM%CRUJRA2024b_CLM60%BGC-CROP_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " I2000Clm60BgcCropCrujraRsGs : 2000_DATM%CRUJRA2024b_CLM60%BGC-CROP_SICE_SOCN_SROF_SGLC_SWAV\n", + " I2000Clm60Bgc : 2000_DATM%GSWP3v1_CLM60%BGC_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " I2000Clm60BgcCrujra : 2000_DATM%CRUJRA2024b_CLM60%BGC_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " I1850Clm50Sp : 1850_DATM%GSWP3v1_CLM50%SP_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " I1850Clm60SpCrujra : 1850_DATM%CRUJRA2024b_CLM60%SP_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " I1850Clm50BgcCrop : 1850_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " I1850Clm50BgcCropRsGs : 1850_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_SROF_SGLC_SWAV\n", + " I1850Clm60BgcCrop : 1850_DATM%GSWP3v1_CLM60%BGC-CROP_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " I1850Clm60BgcCropCrujra : 1850_DATM%CRUJRA2024b_CLM60%BGC-CROP_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " I1850Clm60Sp : 1850_DATM%GSWP3v1_CLM60%SP_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " I1850Clm60BgcCropCrujraRsGs : 1850_DATM%CRUJRA2024b_CLM60%BGC-CROP_SICE_SOCN_SROF_SGLC_SWAV\n", + " I1850Clm60Bgc : 1850_DATM%GSWP3v1_CLM60%BGC_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " I1850Clm60BgcCrujra : 1850_DATM%CRUJRA2024b_CLM60%BGC_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " I1850Clm50BgcCropCmip6 : 1850_DATM%GSWP3v1_CLM50%BGC-CROP-CMIP6DECK_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " I1850Clm60BgcCropCmip6 : 1850_DATM%GSWP3v1_CLM60%BGC-CROP-CMIP6DECK_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " I1850Clm60BgcCropCrujraCmip6 : 1850_DATM%CRUJRA2024b_CLM60%BGC-CROP-CMIP6DECK_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " I1850Clm50BgcCropCmip6waccm : 1850_DATM%GSWP3v1_CLM50%BGC-CROP-CMIP6WACCMDECK_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " I1850Clm60BgcCropCmip6waccm : 1850_DATM%GSWP3v1_CLM60%BGC-CROP-CMIP6WACCMDECK_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " I1850Clm60BgcCropCrujraCmip6waccm : 1850_DATM%CRUJRA2024b_CLM60%BGC-CROP-CMIP6WACCMDECK_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " I2000Clm60BgcCropQianRsGs : 2000_DATM%QIA_CLM60%BGC-CROP_SICE_SOCN_SROF_SGLC_SWAV\n", + " I2000Clm50BgcCropQianRsGs : 2000_DATM%QIA_CLM50%BGC-CROP_SICE_SOCN_SROF_SGLC_SWAV\n", + " I2000Clm50FatesQian : 2000_DATM%QIA_CLM50%FATES_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " I2000Clm50BgcCruRsGs : 2000_DATM%CRUv7_CLM50%BGC_SICE_SOCN_SROF_SGLC_SWAV\n", + " I2000Clm50SpRtmFl : 2000_DATM%GSWP3v1_CLM50%SP_SICE_SOCN_RTM%FLOOD_DGLC%NOEVOLVE_SWAV\n", + " I2000Clm60Fates : 2000_DATM%GSWP3v1_CLM60%FATES_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " I2000Clm50Fates : 2000_DATM%GSWP3v1_CLM50%FATES_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " I2000Clm50FatesCruRsGs : 2000_DATM%CRUv7_CLM50%FATES_SICE_SOCN_SROF_SGLC_SWAV\n", + " I2000Clm60FatesSpCrujraRsGs : 2000_DATM%CRUJRA2024b_CLM60%FATES-SP_SICE_SOCN_SROF_SGLC_SWAV\n", + " I2000Clm60FatesSpCrujra : 2000_DATM%CRUJRA2024b_CLM60%FATES-SP_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " I2000Clm60FatesSpRsGs : 2000_DATM%GSWP3v1_CLM60%FATES-SP_SICE_SOCN_SROF_SGLC_SWAV\n", + " I2000Clm50FatesRsGs : 2000_DATM%GSWP3v1_CLM50%FATES_SICE_SOCN_SROF_SGLC_SWAV\n", + " I2000Clm60FatesRsGs : 2000_DATM%GSWP3v1_CLM60%FATES_SICE_SOCN_SROF_SGLC_SWAV\n", + " I2000Clm60FatesCrujraRsGs : 2000_DATM%CRUJRA2024b_CLM60%FATES_SICE_SOCN_SROF_SGLC_SWAV\n", + " I1850Clm50Bgc : 1850_DATM%GSWP3v1_CLM50%BGC_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " I1850Clm60BgcNoAnthroRtm : 1850_DATM%GSWP3v1_CLM60%BGC-NOANTHRO_SICE_SOCN_RTM_DGLC%NOEVOLVE_SWAV\n", + " I1850Clm60BgcCrujraNoAnthroRtm : 1850_DATM%CRUJRA2024b_CLM60%BGC-NOANTHRO_SICE_SOCN_RTM_DGLC%NOEVOLVE_SWAV\n", + " I1850Clm60SpNoAnthroRtm : 1850_DATM%GSWP3v1_CLM60%SP-NOANTHRO_SICE_SOCN_RTM_DGLC%NOEVOLVE_SWAV\n", + " I1850Clm60SpCrujraNoAnthroRtm : 1850_DATM%CRUJRA2024b_CLM60%SP-NOANTHRO_SICE_SOCN_RTM_DGLC%NOEVOLVE_SWAV\n", + " I1850Clm50BgcNoAnthroRtm : 1850_DATM%GSWP3v1_CLM50%BGC-NOANTHRO_SICE_SOCN_RTM_DGLC%NOEVOLVE_SWAV\n", + " I1850Clm50SpNoAnthroRtm : 1850_DATM%GSWP3v1_CLM50%SP-NOANTHRO_SICE_SOCN_RTM_DGLC%NOEVOLVE_SWAV\n", + " IHistClm50BgcCrop : HIST_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " IHistClm60Sp : HIST_DATM%GSWP3v1_CLM60%SP_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " IHistClm60SpCrujra : HIST_DATM%CRUJRA2024b_CLM60%SP_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " IHistClm60SpRsGs : HIST_DATM%GSWP3v1_CLM60%SP_SICE_SOCN_SROF_SGLC_SWAV\n", + " IHistClm60SpCrujraRsGs : HIST_DATM%CRUJRA2024b_CLM60%SP_SICE_SOCN_SROF_SGLC_SWAV\n", + " IHistClm60Bgc : HIST_DATM%GSWP3v1_CLM60%BGC_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " IHistClm60BgcCrop : HIST_DATM%GSWP3v1_CLM60%BGC-CROP_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " IHistClm60BgcCropCrujra : HIST_DATM%CRUJRA2024b_CLM60%BGC-CROP_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " IHistClm50Sp : HIST_DATM%GSWP3v1_CLM50%SP_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " IHistClm50Bgc : HIST_DATM%GSWP3v1_CLM50%BGC_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " IHistClm50BgcQian : HIST_DATM%QIA_CLM50%BGC_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " IHistClm50BgcQianRsGs : HIST_DATM%QIA_CLM50%BGC_SICE_SOCN_SROF_SGLC_SWAV\n", + " IHistClm60BgcQianRsGs : HIST_DATM%QIA_CLM60%BGC_SICE_SOCN_SROF_SGLC_SWAV\n", + " ISSP585Clm50BgcCrop : SSP585_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " ISSP585Clm60BgcCropCrujra : SSP585_DATM%CRUJRA2024b_CLM60%BGC-CROP_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " ISSP126Clm50BgcCrop : SSP126_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " ISSP119Clm50BgcCrop : SSP119_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " ISSP245Clm50BgcCrop : SSP245_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " ISSP245Clm60BgcCropCrujra : SSP245_DATM%CRUJRA2024b_CLM60%BGC-CROP_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " ISSP370Clm50BgcCrop : SSP370_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " ISSP370Clm60BgcCropCrujra : SSP370_DATM%CRUJRA2024b_CLM60%BGC-CROP_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " ISSP434Clm50BgcCrop : SSP434_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " ISSP460Clm50BgcCrop : SSP460_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " ISSP534Clm50BgcCrop : SSP534_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " ISSP585Clm60BgcCrop : SSP585_DATM%GSWP3v1_CLM60%BGC-CROP_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " IHistClm50BgcCropQianRsGs : HIST_DATM%QIA_CLM50%BGC-CROP_SICE_SOCN_SROF_SGLC_SWAV\n", + " IHistClm60BgcCropQianRsGs : HIST_DATM%QIA_CLM60%BGC-CROP_SICE_SOCN_SROF_SGLC_SWAV\n", + " IHistClm50BgcCropRsGs : HIST_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_SROF_SGLC_SWAV\n", + " I1850Clm50BgcSpinup : 1850_DATM%CPLHIST-CESM3_CLM50%BGC_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " I1850Clm60BgcCropSpinup : 1850_DATM%CPLHIST-CESM3_CLM60%BGC-CROP_SICE_SOCN_MOSART_DGLC%NOEVOLVE_SWAV\n", + " I2000Ctsm50NwpSpGswpGs : 2000_DATM%GSWP3v1_CLM50%NWP-SP_SICE_SOCN_MOSART_SGLC_SWAV\n", + " I2000Ctsm50NwpSpNldasGs : 2000_DATM%NLDAS2_CLM50%NWP-SP_SICE_SOCN_MOSART_SGLC_SWAV\n", + " I2000Ctsm50NwpSpNldasRsGs : 2000_DATM%NLDAS2_CLM50%NWP-SP_SICE_SOCN_SROF_SGLC_SWAV\n", + " I1850Clm50SpG : 1850_DATM%GSWP3v1_CLM50%SP_SICE_SOCN_MOSART_CISM2%GRIS-EVOLVE_SWAV\n", + " I1850Clm50SpGa : 1850_DATM%GSWP3v1_CLM50%SP_SICE_SOCN_MOSART_CISM2%AIS-EVOLVE_SWAV\n", + " I1850Clm50SpGag : 1850_DATM%GSWP3v1_CLM50%SP_SICE_SOCN_MOSART_CISM2%AIS-EVOLVE%GRIS-EVOLVE_SWAV\n", + " IHistClm50SpG : HIST_DATM%GSWP3v1_CLM50%SP_SICE_SOCN_MOSART_CISM2%GRIS-EVOLVE_SWAV\n", + " I1850Clm50BgcCropG : 1850_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_CISM2%GRIS-EVOLVE_SWAV\n", + " IHistClm50BgcCropG : HIST_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_CISM2%GRIS-EVOLVE_SWAV\n", + " I1850Clm60SpG : 1850_DATM%GSWP3v1_CLM60%SP_SICE_SOCN_MOSART_CISM2%GRIS-EVOLVE_SWAV\n", + " I1850Clm60SpGa : 1850_DATM%GSWP3v1_CLM60%SP_SICE_SOCN_MOSART_CISM2%AIS-EVOLVE_SWAV\n", + " I1850Clm60SpGag : 1850_DATM%GSWP3v1_CLM60%SP_SICE_SOCN_MOSART_CISM2%AIS-EVOLVE%GRIS-EVOLVE_SWAV\n", + " I1850Clm60BgcCropG : 1850_DATM%GSWP3v1_CLM60%BGC-CROP_SICE_SOCN_MOSART_CISM2%GRIS-EVOLVE_SWAV\n", + " I1850Clm60BgcCropCrujraG : 1850_DATM%CRUJRA2024b_CLM60%BGC-CROP_SICE_SOCN_MOSART_CISM2%GRIS-EVOLVE_SWAV\n", + " IHistClm60BgcCropCrujraG : HIST_DATM%CRUJRA2024b_CLM60%BGC-CROP_SICE_SOCN_MOSART_CISM2%GRIS-EVOLVE_SWAV\n", + " I1850Clm50SpRsGag : 1850_DATM%GSWP3v1_CLM50%SP_SICE_SOCN_SROF_CISM2%AIS-EVOLVE%GRIS-EVOLVE_SWAV\n", + " I1850Clm60SpRsGag : 1850_DATM%GSWP3v1_CLM60%SP_SICE_SOCN_SROF_CISM2%AIS-EVOLVE%GRIS-EVOLVE_SWAV\n", + " I1850Clm60SpRsGs : 1850_DATM%GSWP3v1_CLM60%SP_SICE_SOCN_SROF_SGLC_SWAV\n", + " I1850Clm60SpCrujraRsGs : 1850_DATM%CRUJRA2024b_CLM60%SP_SICE_SOCN_SROF_SGLC_SWAV\n", + " I2000Ctsm50NwpSpAsRsGs : 2000_SATM_CLM50%NWP-SP_SICE_SOCN_SROF_SGLC_SWAV\n", "...\n", "```\n", "\n", diff --git a/notebooks/basics/ctsm_workflow/model_output.ipynb b/notebooks/basics/ctsm_workflow/model_output.ipynb index f6a5a13..8099669 100644 --- a/notebooks/basics/ctsm_workflow/model_output.ipynb +++ b/notebooks/basics/ctsm_workflow/model_output.ipynb @@ -16,7 +16,7 @@ "id": "d8e6525b-31d9-450d-a3b9-e3b435fc231a", "metadata": {}, "source": [ - "If the model run is successful, the CESM netCDF history files are automatically moved to a short term archive (`$DOUT_S_ROOT`) by `case.st_archive`." + "If the model run is successful, the CLM netCDF history files are automatically moved to a short term archive (`$DOUT_S_ROOT`) by `case.st_archive`." ] }, { diff --git a/notebooks/basics/ctsm_workspaces.ipynb b/notebooks/basics/ctsm_workspaces.ipynb index 93f3adb..c219cc2 100644 --- a/notebooks/basics/ctsm_workspaces.ipynb +++ b/notebooks/basics/ctsm_workspaces.ipynb @@ -88,7 +88,7 @@ "metadata": {}, "source": [ "- ### Create CLM Code Directory\n", - "Create a workspace location to put your CLM code on Derecho. In all exercises in this tutorial `$USER` is a placeholder and it refers to NCAR HPC login name. (In the exercises: replace `$USER` with your login name)\n" + "Create a workspace location to put your CLM code on Derecho. In all exercises in this tutorial `$USER` is an environment variable preset for you that refers to your NCAR HPC login name.\n" ] }, { @@ -150,7 +150,7 @@ "id": "4e972986-5267-43a8-917b-1e36c7117323", "metadata": {}, "source": [ - "You do not need to create the input data directory (`$DIN_LOC_ROOT`) on NCAR systems, as these datasets are already available in a shared location. This location is shared by all CESM users to save space on the NCAR supercomputer. \n", + "You do not need to create the input data directory (`$DIN_LOC_ROOT`) on NCAR systems, as these datasets are already available in a shared location. This location is shared by all CESM/CLM users to save space on the NCAR supercomputer. \n", "\n", "Similarly, the build (`$EXEROOT`), run (`$RUNDIR`), and archive (`$DOUT_S_ROOT`) directories are created automatically when you create a CLM case." ] diff --git a/notebooks/basics/exercises_overview.ipynb b/notebooks/basics/exercises_overview.ipynb index d52b1ac..b78fcc6 100644 --- a/notebooks/basics/exercises_overview.ipynb +++ b/notebooks/basics/exercises_overview.ipynb @@ -11,7 +11,7 @@ "## Learning Goals:\n", "\n", "- The student will successfully set up and run their first (short) CLM simulation.\n", - "- This lab exercise is designed to build off the one-time setup section and uses the CESM workflow information presented. \n", + "- This lab exercise is designed to build off the one-time setup section and uses the CLM workflow information presented. \n", "\n", "## Exercise overview:\n", "\n", diff --git a/notebooks/resources/unix.ipynb b/notebooks/resources/unix.ipynb index 461dfca..81aa5c5 100644 --- a/notebooks/resources/unix.ipynb +++ b/notebooks/resources/unix.ipynb @@ -13,7 +13,7 @@ "id": "011c91f1-75f0-496e-a329-45ed70297e86", "metadata": {}, "source": [ - "Most CESM users and developers use the UNIX environment to set up CESM experiments and do preliminary analysis of their CESM model output data. We strongly suggest those using CESM become familiar with working in a command line environment." + "Most CESM/CLM users and developers use the UNIX environment to set up CLM experiments and do preliminary analysis of their CLM model output data. We strongly suggest those using CLM become familiar with working in a command line environment." ] }, { From a964da36e73e932d4c9b8595fefb98630095ce0a Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 15 Oct 2026 01:49:09 -0600 Subject: [PATCH 3/3] Update TOC with renamed files --- _toc.yml | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/_toc.yml b/_toc.yml index ac86611..0b9f5bf 100644 --- a/_toc.yml +++ b/_toc.yml @@ -26,20 +26,20 @@ chapters: - file: notebooks/basics/basics_overview sections: - - file: notebooks/basics/cesm_workspaces + - file: notebooks/basics/ctsm_workspaces - file: notebooks/basics/code_overview sections: - file: notebooks/basics/code/git_download_ctsm - file: notebooks/basics/code/ctsm_code_explore - - file: notebooks/basics/cesm_workflow + - file: notebooks/basics/ctsm_workflow sections: - - file: notebooks/basics/cesm_workflow/create_newcase - - file: notebooks/basics/cesm_workflow/case_setup - - file: notebooks/basics/cesm_workflow/case_build - - file: notebooks/basics/cesm_workflow/case_submit - - file: notebooks/basics/cesm_workflow/model_output - - file: notebooks/basics/cesm_workflow/checking_jobs_and_status - - file: notebooks/basics/cesm_workflow/create_clone + - file: notebooks/basics/ctsm_workflow/create_newcase + - file: notebooks/basics/ctsm_workflow/case_setup + - file: notebooks/basics/ctsm_workflow/case_build + - file: notebooks/basics/ctsm_workflow/case_submit + - file: notebooks/basics/ctsm_workflow/model_output + - file: notebooks/basics/ctsm_workflow/checking_jobs_and_status + - file: notebooks/basics/ctsm_workflow/create_clone - file: notebooks/basics/exercises_overview sections: - file: notebooks/basics/exercises/first_I1850