GEOS-Chem in CESM: Difference between revisions
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=== Downloading the model === | === Downloading the model === | ||
Relevent CESM docs: | Relevent CESM docs: [https://escomp.github.io/CESM/versions/master/html/downloading_cesm.html Downloading CESM] | ||
```To use GEOS-Chem you should checkout CESM tag cesm2_3_alpha17e or later. This version uses CAM tag cam6_3_160 which includes GEOS-Chem v14.1.2.``` | |||
The NCAR CESM documentation will guide you through downloading CESM and populating the externals. "Externals" mean source code repositories that are separate from the CESM source code repository that you download. This is similar to how the GC-Classic initial download is mostly an empty set of directories until you run 'git submodule update --init --recursive' which checks out git submodules. CESM uses a package called manage_externals rather than git submodules and stores information about the externals in local configuration file Externals.cfg (see [https://github.com/ESCOMP/CESM/blob/master/Externals.cfg here] for example file). All externals are checked out with command "./manage_externals/checkout_externals". The checkout is recursive, meaning any externals that have custom externals config files are also checked out. This is the case for downloading HEMCO which is specified in HEMCO_CESM/Externals_HCO.cfg (example [https://github.com/ESCOMP/HEMCO_CESM/blob/master/Externals_HCO.cfg here]), and also GEOS-Chem which is specified in CAM/Externals_CAM.cfg (example [https://github.com/ESCOMP/CAM/blob/cam_development/Externals_CAM.cfg here]). | The NCAR CESM documentation will guide you through downloading CESM and populating the externals. "Externals" mean source code repositories that are separate from the CESM source code repository that you download. This is similar to how the GC-Classic initial download is mostly an empty set of directories until you run 'git submodule update --init --recursive' which checks out git submodules. CESM uses a package called manage_externals rather than git submodules and stores information about the externals in local configuration file Externals.cfg (see [https://github.com/ESCOMP/CESM/blob/master/Externals.cfg here] for example file). All externals are checked out with command "./manage_externals/checkout_externals". The checkout is recursive, meaning any externals that have custom externals config files are also checked out. This is the case for downloading HEMCO which is specified in HEMCO_CESM/Externals_HCO.cfg (example [https://github.com/ESCOMP/HEMCO_CESM/blob/master/Externals_HCO.cfg here]), and also GEOS-Chem which is specified in CAM/Externals_CAM.cfg (example [https://github.com/ESCOMP/CAM/blob/cam_development/Externals_CAM.cfg here]). | ||
=== Creating a case (run directory) === | === Creating a case (run directory) === | ||
Revision as of 18:17, 13 May 2024
Overview
This page serves as a resource for using GEOS-Chem in the Community Earth System Model (CESM). It is meant to supplement not replace existing CESM documentation and therefore includes a guide to navigating CESM resources maintained by NCAR. The rest of the page focuses on aspects of the model specific to GEOS-Chem and is written primarily to help offline GEOS-Chem users get started. CESM users interested in using GEOS-Chem chemistry may also find it useful but should additionally look at GEOS-Chem documentation listed on the main page of this wiki.
(Brief history of GEOS-Chem in CESM with citable references...here or in a new section)
CESM Resources
Model documentation
The best way to successfully use GEOS-Chem chemistry in CESM is to become familiar with CESM documentation and guides maintained by NCAR. The CESM2 Quickstart Guide contains an overview of the model and instructions for downloading, building, and running CESM2. CESM2 is built upon a framework called Common Infrastructure for Modeling the Earth (CIME, pronounced "SEAM") which handles configuring, compiling, testing, and running the model. Offline GEOS-Chem users can think of CIME as run directory management and testing, containing the equivalent of what is found in the 'run' and 'test' directories within GEOS-Chem. Read through the CIME documentation to become familiar with the concepts of CIME and to get detailed instructions for creating run directories, configuring a run, building the source code, and running the model. Community Atmosphere Model (CAM) is the atmospheric component of CESM and includes both GEOS-Chem and HEMCO as subcomponents. The CAM6.3 documentation builds upon information in the CESM Quickstart Guide and the CIME documentation. Read through it to learn about the atmospheric component's configuration options, data inputs, and model outputs.
Model websites
NCAR maintains several websites with up-to-date information about CESM. The CAM website and CESM with Chemistry Wiki page are of particular interest to GEOS-Chem users.
Data visualization and analysis
See the NCAR Python Resources for Chemistry Modeling for jupyter notebook examples of visualizing and analyzing CESM output data. Examples for atmospheric chemistry modeling with CAM-Chem are also relevant for modeling with GEOS-Chem.
Getting help
CESM help requests are handled on a searchable forum maintained by NCAR. Consider registering for a free account if you plan to use CESM.
Glossary for GEOS-Chem Users
Getting Started
Configuring CIME
Scenario 1: NCAR Derecho HPC cluster
Scenario 2: External HPC cluster
Downloading the model
Relevent CESM docs: Downloading CESM
```To use GEOS-Chem you should checkout CESM tag cesm2_3_alpha17e or later. This version uses CAM tag cam6_3_160 which includes GEOS-Chem v14.1.2.```
The NCAR CESM documentation will guide you through downloading CESM and populating the externals. "Externals" mean source code repositories that are separate from the CESM source code repository that you download. This is similar to how the GC-Classic initial download is mostly an empty set of directories until you run 'git submodule update --init --recursive' which checks out git submodules. CESM uses a package called manage_externals rather than git submodules and stores information about the externals in local configuration file Externals.cfg (see here for example file). All externals are checked out with command "./manage_externals/checkout_externals". The checkout is recursive, meaning any externals that have custom externals config files are also checked out. This is the case for downloading HEMCO which is specified in HEMCO_CESM/Externals_HCO.cfg (example here), and also GEOS-Chem which is specified in CAM/Externals_CAM.cfg (example here).
Creating a case (run directory)
Downloading input data
Building the model
Running the model
Logs and diagnostics
Advanced topics
Guide to the source code
Changing the source code
Using CIME tools to update case configuration
Debugging and getting help
For general CESM help please use the DiscussCESM forum linked to in the CESM Resources section of this page. For GEOS-Chem help please following support instructions provided on GEOS-Chem ReadTheDocs here. Depending on the issue you may be referred by the CESM Support Team to contact the GEOS-Chem Support Team, or vice versa.