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Merge pull request #214 from cecilehannay/main
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reorganize and develop some of the resources
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@cecilehannay
cecilehannay authored Jul 14, 2024
2 parents b7017dd + 663fe41 commit 813e864
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50 changes: 25 additions & 25 deletions _toc.yml
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- file: notebooks/sourcemods/exercises/exercise_add_field
- file: notebooks/sourcemods/exercises/exercise_rain_threshold

- file: notebooks/diagnostics/diagnostics
sections:
- file: notebooks/diagnostics/cam/cam
sections:
- file: notebooks/diagnostics/cam/basics_cam
- file: notebooks/diagnostics/cam/advanced_cam
- file: notebooks/diagnostics/cam/cam_se_native_example
- file: notebooks/diagnostics/cam-chem_waccm
- file: notebooks/diagnostics/clm_ctsm/clm_ctsm
sections:
- file: notebooks/diagnostics/clm_ctsm/basics_clm
- file: notebooks/diagnostics/pop/pop
sections:
- file: notebooks/diagnostics/pop/basics_pop
- file: notebooks/diagnostics/pop/advanced_pop
- file: notebooks/diagnostics/cice/cice
sections:
- file: notebooks/diagnostics/cice/basics_cice
- file: notebooks/diagnostics/cice/advanced_cice
- file: notebooks/diagnostics/additional/additional
sections:
- file: notebooks/diagnostics/additional/postprocessing
- file: notebooks/diagnostics/additional/cvdp
- file: notebooks/diagnostics/additional/analysis_tools

- file: notebooks/challenge/challenge
sections:
- file: notebooks/challenge/cam/cam
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sections:
- file: notebooks/challenge/bgc/bgc_exercise_1

- file: notebooks/diagnostics/diagnostics
sections:
- file: notebooks/diagnostics/cam/cam
sections:
- file: notebooks/diagnostics/cam/basics_cam
- file: notebooks/diagnostics/cam/advanced_cam
- file: notebooks/diagnostics/cam/cam_se_native_example
- file: notebooks/diagnostics/cam-chem_waccm
- file: notebooks/diagnostics/clm_ctsm/clm_ctsm
sections:
- file: notebooks/diagnostics/clm_ctsm/basics_clm
- file: notebooks/diagnostics/pop/pop
sections:
- file: notebooks/diagnostics/pop/basics_pop
- file: notebooks/diagnostics/pop/advanced_pop
- file: notebooks/diagnostics/cice/cice
sections:
- file: notebooks/diagnostics/cice/basics_cice
- file: notebooks/diagnostics/cice/advanced_cice
- file: notebooks/diagnostics/additional/additional
sections:
- file: notebooks/diagnostics/additional/postprocessing
- file: notebooks/diagnostics/additional/cvdp
- file: notebooks/diagnostics/additional/analysis_tools

- file: notebooks/resources/resources_overview
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- file: notebooks/resources/ncar_hpc
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257 changes: 0 additions & 257 deletions notebooks/prereqs/prereqs_overview.ipynb
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"</div>"
]
},
{
"cell_type": "markdown",
"id": "e731c34f-4386-4869-bdb7-a6e479f07a63",
"metadata": {},
"source": [
"### Running on derecho"
]
},
{
"cell_type": "markdown",
"id": "202de099-dc2d-47d2-99fb-b6f1b87d654c",
"metadata": {},
"source": [
"This tutorial material is designed for use with the derecho HPC system. All of your CESM experiment builds and jobs will be run on derecho.\n",
"\n",
"Please see the link below for more information about the derecho system, including a quick start guide with information about logging into derecho from a terminal, setting up your environment, submitting jobs, etc. "
]
},
{
"cell_type": "markdown",
"id": "235c1c69-da82-4cff-95bf-02c1bb2db897",
"metadata": {},
"source": [
"<div class=\"alert alert-info\" style=\"text-align: center;\">\n",
"\n",
"[CISL Documentation on Using derecho HPC](https://arc.ucar.edu/knowledge_base/74317833)\n",
" \n",
"</div>"
]
},
{
"cell_type": "markdown",
"id": "c7e2b935-85ea-47f1-b8f0-654d54714484",
"metadata": {},
"source": [
"#### Porting"
]
},
{
"cell_type": "markdown",
"id": "a47bc7ae-4bd8-4e55-87e8-27019a689099",
"metadata": {},
"source": [
"This tutorial assumes that you are using NCAR HPC assets. In order to run the CESM on a **_different_** computing platform, you will first need to port the CESM code to that environment/machine. We provide information about how to port the model code in the [porting section](https://ncar.github.io/CESM-Tutorial/notebooks/resources/porting.html)."
]
},
{
"cell_type": "markdown",
"id": "8a831d36-6629-4cd6-a247-2a8293aa2561",
"metadata": {},
"source": [
"### Using Casper"
]
},
{
"cell_type": "markdown",
"id": "2f8ad62c-89c5-49c3-9751-219303bce4c7",
"metadata": {},
"source": [
"The Casper cluster is a system of specialized data analysis and visualization resources. Casper is not used for building or running CESM, but it is used for CESM data analysis. We will use Casper for the diagnostics section of the lab activities. To utilize the **_additional_** analysis tools described in the [analysis tools section](https://ncar.github.io/CESM-Tutorial/notebooks/diagnostics/additional/analysis_tools.html) you will also want to use Casper."
]
},
{
"cell_type": "markdown",
"id": "aee2a810-f356-4c55-a19a-c0a32dfd504b",
"metadata": {},
"source": [
"<div class=\"alert alert-info\" style=\"text-align: center;\">\n",
"\n",
"[CISL Documentation on Using Casper Cluster](https://arc.ucar.edu/knowledge_base/70549550)\n",
" \n",
"</div>"
]
},
{
"cell_type": "markdown",
"id": "603c963b-4d65-4cd6-94a3-ea5ae932578e",
"metadata": {},
"source": [
"### Using JupyterHub"
]
},
{
"cell_type": "markdown",
"id": "a9423bae-be8c-4848-916c-926f86645da6",
"metadata": {},
"source": [
"The diagnostics section of this tutorial will use JupyterHub to run Jupyter Notebooks. You will need to login to the NCAR JupyterHub system to run the notebooks successfully.\n",
"\n",
"NOTE: To run a Jupyter cell\n",
"- Type your command into the cell\n",
"- To execute the command:\n",
" - Press **shift+return**\n",
" <div>\n",
" OR\n",
" <div>\n",
" - Select the cell then click the 'play' button at the top of the window\n",
"\n",
"To learn more about JupyterHub, please follow the link below."
]
},
{
"cell_type": "markdown",
"id": "6ae8710f-8dd2-4ed6-893f-d2de5b863b94",
"metadata": {},
"source": [
"<div class=\"alert alert-info\" style=\"text-align: center;\">\n",
"\n",
"[CISL Documentation about JupyterHub](https://arc.ucar.edu/knowledge_base/70549913)\n",
" \n",
"</div>"
]
},
{
"cell_type": "markdown",
"id": "144caca2-989b-40a5-b6c0-c8a0b7a470da",
"metadata": {},
"source": [
"## Modules on NCAR HPC"
]
},
{
"cell_type": "markdown",
"id": "52805170-9397-48b3-8bdf-a2c76fb45583",
"metadata": {},
"source": [
"NCAR maintains a number of different programs on the HPC systems that can be added to your user environment by executing the ``module load`` command. "
]
},
{
"cell_type": "markdown",
"id": "a551ace3-3b1a-4130-8084-3034842e0259",
"metadata": {},
"source": [
"We will use a few modules throughout this tutorial to visualize data, so you need to be able to check which modules you have loaded and to load necessary modules."
]
},
{
"cell_type": "markdown",
"id": "f6edec76-66ba-42f0-b3b2-00a4d90f15fd",
"metadata": {},
"source": [
"We provide basic instructions below on how to check and load Modules, but to learn more about Modules on NCAR HPC, please follow the link below."
]
},
{
"cell_type": "markdown",
"id": "b2aef333-82a9-4f3d-8afa-2f5c3df4ef4c",
"metadata": {},
"source": [
"<div class=\"alert alert-info\" style=\"text-align: center;\">\n",
"\n",
"[CISL documentation on modules](https://arc.ucar.edu/knowledge_base/72581272)\n",
"\n",
"</div>"
]
},
{
"cell_type": "markdown",
"id": "33d4014c-bc0f-4ab0-aaf3-cf6cf7572f22",
"metadata": {},
"source": [
"### Checking what modules are loaded in your environment\n",
"\n",
"To check what modules you have loaded in your environment, use the following at the command line:"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "3fe867e0-f0df-4d87-a9d6-169294ec222c",
"metadata": {},
"outputs": [],
"source": [
"module list"
]
},
{
"cell_type": "markdown",
"id": "2a5ec941-4f4a-4a99-a3a0-6e514c448805",
"metadata": {},
"source": [
"### Checking what modules are available\n",
"\n",
"You can see which modules are available on the HPC resources by using the following at the command line:"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "b974222c-a270-4075-b9b9-7be7b4550942",
"metadata": {},
"outputs": [],
"source": [
"module avail"
]
},
{
"cell_type": "markdown",
"id": "0d2cfc8e-2085-4b72-b917-9e98a1586e13",
"metadata": {},
"source": [
"The command returns a list to the terminal window of the modules available to load to your environment."
]
},
{
"cell_type": "markdown",
"id": "ec74810f-c422-468d-b30e-ddb9c41d878f",
"metadata": {},
"source": [
"![Modules](../../images/prereqs/modules.png)\n",
"\n",
"*<p style=\"text-align: center;\"> Figure: Some modules available on NCAR HPC resources. D: Default Module. L: Module is loaded. </p>*"
]
},
{
"cell_type": "markdown",
"id": "c523021e-9328-4e0b-8c40-15bcf2ebab75",
"metadata": {},
"source": [
"The modules highlighted in blue are text editors discussed further in the [text editors section](https://ncar.github.io/CESM-Tutorial/notebooks/resources/text_editors.html).\n",
"\n",
"The modules highlighted in red are netCDF tools that will be discussed further in the [netCDF section](https://ncar.github.io/CESM-Tutorial/notebooks/resources/netcdf.html).\n",
"\n",
"Note that there are many other analysis software tools available to load into your NCAR HPC environment. These include: idl, julia, matlab, R, python, ncl, etc. While some of these tools are discussed in the [analysis tools section](https://ncar.github.io/CESM-Tutorial/notebooks/diagnostics/additional/analysis_tools.html), we do not highlight them all here and encourage you to further explore your environment and needs."
]
},
{
"cell_type": "markdown",
"id": "65848ac8-1cad-47bf-b680-8b129ce4e25d",
"metadata": {},
"source": [
"### Loading a new module to your environment\n",
"\n",
"You can load one of the available modules (here we show loading ncview) using the following at the command line: "
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "ad9db6c8-91a9-4c3e-84b4-6e6fb65de213",
"metadata": {},
"outputs": [],
"source": [
"module load ncview"
]
},
{
"cell_type": "markdown",
"id": "a1e13c85-65d1-4904-a07b-6cba1249ddfd",
"metadata": {},
"source": [
"<div class=\"alert alert-warning\">\n",
"<strong>NOTE: We will provide a file that will load necessary modules for those attending the in person tutorial. </strong>\n",
"</div>"
]
},
{
"cell_type": "markdown",
"id": "3c9cc169-489e-427a-865a-539468cb060d",
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