diff --git a/_toc.yml b/_toc.yml index e0132cd87..a3aa79e21 100644 --- a/_toc.yml +++ b/_toc.yml @@ -102,31 +102,6 @@ chapters: - 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 @@ -172,6 +147,31 @@ chapters: 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 sections: - file: notebooks/resources/ncar_hpc diff --git a/notebooks/prereqs/prereqs_overview.ipynb b/notebooks/prereqs/prereqs_overview.ipynb index 9e74d5263..c5400c658 100644 --- a/notebooks/prereqs/prereqs_overview.ipynb +++ b/notebooks/prereqs/prereqs_overview.ipynb @@ -134,263 +134,6 @@ "" ] }, - { - "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": [ - "
\n", - "\n", - "[CISL Documentation on Using derecho HPC](https://arc.ucar.edu/knowledge_base/74317833)\n", - " \n", - "
" - ] - }, - { - "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": [ - "
\n", - "\n", - "[CISL Documentation on Using Casper Cluster](https://arc.ucar.edu/knowledge_base/70549550)\n", - " \n", - "
" - ] - }, - { - "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", - "
\n", - " OR\n", - "
\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": [ - "
\n", - "\n", - "[CISL Documentation about JupyterHub](https://arc.ucar.edu/knowledge_base/70549913)\n", - " \n", - "
" - ] - }, - { - "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": [ - "
\n", - "\n", - "[CISL documentation on modules](https://arc.ucar.edu/knowledge_base/72581272)\n", - "\n", - "
" - ] - }, - { - "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", - "*

Figure: Some modules available on NCAR HPC resources. D: Default Module. L: Module is loaded.

*" - ] - }, - { - "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": [ - "
\n", - "NOTE: We will provide a file that will load necessary modules for those attending the in person tutorial. \n", - "
" - ] - }, { "cell_type": "markdown", "id": "3c9cc169-489e-427a-865a-539468cb060d", diff --git a/notebooks/resources/ncar_hpc.ipynb b/notebooks/resources/ncar_hpc.ipynb index 9e74d5263..cbebba625 100644 --- a/notebooks/resources/ncar_hpc.ipynb +++ b/notebooks/resources/ncar_hpc.ipynb @@ -5,89 +5,7 @@ "id": "f406f992-92bd-4b17-9bd3-b99c5c8abaf3", "metadata": {}, "source": [ - "# Prerequisites for Success\n" - ] - }, - { - "cell_type": "markdown", - "id": "4651282a-0c4f-449a-bf36-74af04e7281e", - "metadata": {}, - "source": [ - "NOTE: Although the materials and notebooks in this tutorial are published as a Jupyter Book, **you will need to use a terminal window to actually run the commands presented in this tutorial.**\n", - "\n", - "To successfully complete this tutorial you will:\n", - "- Utilize a **terminal** window\n", - "- Issue commands at the **command line** using **UNIX**\n", - "- Need to be able to access and run on the **NCAR HPC systems** (HPC = High Performance Computing)\n", - "- Use **JupyterHub** for some basic diagnostic plotting\n", - "\n", - "The links below provide more information about these topics. **If you are not familiar any of the four topics above, we strongly recommend that you read through the following sections.**" - ] - }, - { - "cell_type": "markdown", - "id": "24e22d53-7b0b-4fb8-82ad-360e75e64ac0", - "metadata": {}, - "source": [ - "## Terminal windows" - ] - }, - { - "cell_type": "markdown", - "id": "14f5fe74-cc59-4ccc-af62-e31650e1372c", - "metadata": {}, - "source": [ - "For most of these tutorial exercises, we assume that you will use the online documentation in tandem with an open terminal window. The commands described in these materials will be entered at the command line in your terminal window.\n", - "\n", - "If you are unfamiliar with opening terminal windows, we suggest you use the link below to learn more about terminal windows. " - ] - }, - { - "cell_type": "markdown", - "id": "01790d14-4535-4e0a-a7da-38ac467717de", - "metadata": {}, - "source": [ - "
\n", - "\n", - "[Terminals](https://ncar.github.io/CESM-Tutorial/notebooks/resources/terminals.html#terminal-windows)\n", - " \n", - "
" - ] - }, - { - "cell_type": "markdown", - "id": "37406e6f-57c2-4493-86a9-52bc2d5eb3f8", - "metadata": {}, - "source": [ - "## UNIX" - ] - }, - { - "cell_type": "markdown", - "id": "6572f442-e01a-4809-a90d-c251ff79f8af", - "metadata": {}, - "source": [ - "The commands described in these materials will be entered in a UNIX environment. If you are unfamiliar with navigating a UNIX environment, we suggest you use the link below to learn more about UNIX. " - ] - }, - { - "cell_type": "markdown", - "id": "e664eb92-e98d-4c3d-afbe-ea517b71439b", - "metadata": {}, - "source": [ - "
\n", - "\n", - "[UNIX](https://ncar.github.io/CESM-Tutorial/notebooks/resources/unix.html#unix)\n", - " \n", - "
" - ] - }, - { - "cell_type": "markdown", - "id": "16324ba6-5c27-41c2-8e62-dc2ccc817527", - "metadata": {}, - "source": [ - "## NCAR High Performance Computing (HPC)" + "# NCAR High Performance Computing (HPC)ΒΆ" ] }, { diff --git a/notebooks/resources/porting.ipynb b/notebooks/resources/porting.ipynb index 9172b18cf..c84e59b20 100644 --- a/notebooks/resources/porting.ipynb +++ b/notebooks/resources/porting.ipynb @@ -76,7 +76,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.12" + "version": "3.10.13" } }, "nbformat": 4, diff --git a/notebooks/resources/profile.ipynb b/notebooks/resources/profile.ipynb index 70c82a473..49820ac92 100644 --- a/notebooks/resources/profile.ipynb +++ b/notebooks/resources/profile.ipynb @@ -5,15 +5,7 @@ "id": "b2cd974a-dfbb-4937-8ed0-ab87ab60f1ef", "metadata": {}, "source": [ - "# NCAR HPC Environment" - ] - }, - { - "cell_type": "markdown", - "id": "e9b16469-3477-46cc-aa03-9a865f80256e", - "metadata": {}, - "source": [ - "## 2023 CESM in person tutorial specific instructions" + "# 2024 CESM Tutorial specific instructions" ] }, { @@ -412,7 +404,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.12" + "version": "3.10.13" }, "toc-showcode": false }, diff --git a/notebooks/resources/unix.ipynb b/notebooks/resources/unix.ipynb index 5e71d532d..503347b7b 100644 --- a/notebooks/resources/unix.ipynb +++ b/notebooks/resources/unix.ipynb @@ -37,20 +37,6 @@ "\n", "
" ] - }, - { - "cell_type": "markdown", - "id": "805c8473-8106-4ba6-9d8e-c27cee7fcd7d", - "metadata": {}, - "source": [] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "96f010ce-2005-4a69-9081-7ced219e66ea", - "metadata": {}, - "outputs": [], - "source": [] } ], "metadata": {