Difference between revisions of "GEOS-Chem basics"
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== Restart files ==
== Restart files ==
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== Visualization packages ==
== Visualization packages ==
Revision as of 22:08, 9 August 2022
The GEOS-Chem Support Team has created this page to assist new GEOS-Chem users to download and run GEOS-Chem on their computer systems.
- 1 Overview
- 2 Unix resources
- 3 The GNU Make utility
- 4 The Git source code management system
- 5 Fortran resources
- 6 The netCDF library
- 7 The GEOS-Chem source code
- 8 The GEOS-Chem shared data directories
- 9 Restart files
- 10 Visualization packages
- 11 The GEOS-Chem website
- 12 The GEOS-Chem wiki
- 13 GEOS-Chem tutorials
- 14 For more information
This information has been migrated to geos-chem.readthedocs.io.
GEOS-Chem documentation and support
We have compiled a list of resources that will help you get started with GEOS-Chem:
|The GEOS-Chem website (geos-chem.org)||The main GEOS-Chem website, which links to many other resources.|
|The GEOS-Chem wiki (wiki.geos-chem.org)||The GEOS-Chem wiki (i.e. this wiki).|
|GEOS-Chem user manuals||User manuals for GEOS-Chem Classic, GCHP, HEMCO, and related software.|
|The GEOS-Chem FAQ||Answers to the most commonly-asked questions about GEOS-Chem.|
|GEOS-Chem tutorial presentations||Several online tutorial presentations about how to use GEOS-Chem|
|GEOS-Chem licensing||Information about the public license under which GEOS-Chem (and related software) are distributed.|
GEOS-Chem is designed to run on computers with the Unix operating system. There is no single version of Unix; rather, Unix comes packaged in several different distributions. Many modern computer clusters use CentOS, which is an open-source Unix implementation. Other systems may use a proprietary Unix distribution, such as Red Hat Enterprise. GEOS-Chem will perform in the same way regardless of the specific Unix implementation on your system.
If you require assistance setting up or customizing your Unix login environment, please contact your local IT staff. The GEOS-Chem Support Team can only provide support for GEOS-Chem-related issues.
You can now run GEOS-Chem on the Amazon Web Services cloud infrastructure. See our cloud computing tutorial (cloud.geos-chem.org) for more details.
IMPORTANT! Please make sure that your computer system meets the minimum system requirements for memory and disk space in order to run GEOS-Chem.
Common Unix commands
The resources below cover many common Unix commands. You will find these useful, particularly if you have never worked on a Unix machine before.
- Summary of Unix commands (PDF doc)
- A Brief Introduction to Unix (by Corey Satten)
- The 15 Essential Unix commands (by Pete Freitag)
Unix shells and shell scripting
One of the nice features of Unix is that you can highly customize your environment. You can also write scripts to perform several commands (such as copying files or running programs) sequentially. This will save you the trouble of having to type the same commands over and over at the command-line prompt.
There are several Unix shells that you can use, but we recommend using bash. Here are some resources that you can use to learn more about the bash shell:
- What is the .bashrc file on SuperUser
- The Bash Shell Startup Files from Beyond Linux from Scratch
- LinuxCommand.org—interactive tutorial
- How to use the Unix alias command
- Bash Guide for Beginners
- Advanced Bash scripting
- Bash programming—Introduction How-To
The GNU Make utility
The GNU Make utility is used to compile GEOS-Chem—that is, to create an executable file from source code. GNU Make usually comes pre-packaged with your Unix distribution (e.g. CentOS, Linux, Ubuntu, Fedora, etc.), so you will probably not need to install it yourself.
GEOS-Chem contains several Makefiles. A Makefile contains several commands in the GNU Make language direct how the Fortran compiler will build GEOS-Chem. Makefiles determine the sequence in which individual files are compiled, as well as the options that will be activated.
Unless you are going to be adding a significant amount of new code into GEOS-Chem, you will probably not need to know the nitty-gritty details of how to create or modify Makefiles. But if you do have to change an existing Makefile, you can contact the GEOS-Chem Support Team, who will be happy to assist you.
If you are interested in learning more about the GNU Make utility, we invite you to consult the following resources:
- The GNU Make manual
- GNU Make in detail for beginners at OpenSource.com
- Using Make and writing makefiles at Swarthmore U.
- Make at wikibooks.org
- Managing projects with GNU Make by O'Reilly
For specific information about compiling GEOS-Chem, see:
The Git source code management system
Please see our Guide to using Git with GEOS-Chem for more information about how to use Git with GEOS-Chem.
Please see our Guide to compilers for GEOS-Chem wiki page for more information about the compilers that you can use to build GEOS-Chem, as well as some Fortran-language resources.
The netCDF library
Please see our Guide to netCDF in GEOS-Chem for more information about how to install netCDF on your system (or check if it is already installed).
The GEOS-Chem source code
The GEOS-Chem model source code is kept in a publicly-accessible Git repository. You must compile the source code into an executable file with one of the supported Fortran compilers. The compilation is managed by the GNU Make utility, which reads the various GEOS-Chem makefiles to produce the executable with the desired options.
For more information and detailed downloading instructions, please see our Downloading GEOS-Chem source code wiki page.
For more information, please see our Downloading GEOS-Chem data directories wiki page.
This content has been migrated to the Restart files chapter of geos-chem.readthedocs.io.
Please see our Guide to visualization and analysis tools for GEOS-Chem for information about software packages that you can use to analyze or plot GEOS-Chem output.
The GEOS-Chem website
The GEOS-Chem website is located at geos-chem.org.
From this website you may:
- Read a welcome letter which outlines user responsibilities
- Access GEOS-Chem-related publications
- View online presentations from GEOS-Chem user meetings
- See a list of who is using GEOS-Chem at other institutions
- Obtain information about the GAMAP visualization package
Also, please take a minute to read the GEOS-Chem overview page. This document outlines the responsibilities for all GEOS-Chem users.
The GEOS-Chem wiki
The GEOS-Chem wiki (i.e. this wiki) is located at: wiki.geos-chem.org.
The wiki has many features that are designed to facilitate communication between GEOS-Chem users and developers. The Main Page of the wiki contains links to several commonly-read pages. If you can't find your desired topic, the best way to search for information on the wiki is by using the Search Box located in the upper right corner of each wiki page.
We encourage all GEOS-Chem code developers and users to check the wiki frequently, as this is the place where the latest information about GEOS-Chem will be posted. The wiki is designed to be a two-way street of communication. Users should feel free to add content to the wiki pages that are most closely related to their research.
In particular, the GEOS-Chem Support Team has begun an effort to make sure that all 3rd-party code and data that is submitted into GEOS-Chem has a corresponding wiki page. This will ensure that all information can be shared transparently.
All GEOS-Chem wiki posts can be read by anyone. However, to add or modify wiki pages, you will need to register for a wiki account. Simply click on the "Log In/Create Account" link at the top right of your browser window. The GEOS-Chem support team will confirm your account request (this is an anti-spamming measure).
The best way to find information on the GEOS-Chem wiki is to use the Search Box located in the upper right corner of each wiki page. You can also let the GEOS-Chem wiki inform you of recent updates to the site via RSS. Click here to find out how.
Please see the following GEOS-Chem tutorials:
- GEOS-Chem video tutorials (youtube.geos-chem.org)
- Using GEOS-Chem on the Amazon Web Services Cloud computing environment (cloud.geos-chem.org)
- GEOS-Chem Python Tutorial
- IGC9 model clinics:
For more information
You can find much more information about GEOS-Chem on our website and wiki. We invite you to consult the following resources:
- Getting Started with GEOS-Chem
- Getting Started with GCHP
- The HEMCO User's Guide
- GEOS-Chem Guides
- Frequently asked questions about GEOS-Chem
- What should I do if my GEOS-Chem simulation dies with an error?
- Is there a comprehensive list of bugs and when they were fixed?
- Do you have any debugging tips?
- How can I contact the GEOS-Chem Support Team for assistance? What should I include in my request?