Difference between revisions of "GEOS-Chem basics"

Revision as of 22:07, 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.

Overview

GEOS-Chem requirements

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:

Unix resources

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

--Bob Yantosca (talk) 20:11, 19 September 2017 (UTC)

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:

• Compiling GEOS-Chem
• Guide to compilers for GEOS-Chem

--Bob Yantosca (talk) 19:40, 19 December 2016 (UTC)

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.

--Bob Yantosca (talk) 17:28, 21 June 2019 (UTC)

Fortran resources

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.

--Bob Yantosca (talk) 14:58, 14 June 2019 (UTC)

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).

--Bob Yantosca (talk) 15:58, 13 June 2019 (UTC)

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.

--Melissa Sulprizio (talk) 13:56, 12 June 2019 (UTC)

The GEOS-Chem shared data directories

For more information, please see our Downloading GEOS-Chem data directories wiki page.

--Bob Yantosca (talk) 15:15, 14 June 2019 (UTC)

Restart files

You will need a restart file before you can start your GEOS-Chem simulation. A restart file contains the initial conditions for a GEOS-Chem simulation. There are two restart files for GEOS-Chem:

1. GEOS-Chem restart file containing instantaneous species concentrations (Required)
2. HEMCO restart file containing values needed for some of the HEMCO extensions (Optional)

When you run a GEOS-Chem simulation, it will write new GEOS-Chem restart files at the intervals you specify in HISTORY.rc. New HEMCO restart files are written with frequency configured in HEMCO_Config.rc if HEMCO is used in your simulation.

You can read more about restart files at the GEOS-Chem restart files wiki page.

--Melissa Sulprizio (talk) 12:21, 16 July 2019 (UTC)

Visualization packages

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.

--Bob Yantosca (talk) 16:59, 14 June 2019 (UTC)

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.

--Bob Yantosca (talk) 22:08, 11 January 2019 (UTC)

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.

Logistics

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.

--Bob Yantosca (talk) 22:08, 11 January 2019 (UTC)

GEOS-Chem tutorials

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:
  • Working with GEOS-Chem
  • High-performance GEOS-Chem (GCHP)
  • WRF-GC: GEOS-Chem in WRF
  • GEOS-Chem on the AWS Cloud
  • GEOS-Chem in Earth System Models
  • GEOS-Chem nested model
  • GEOS-Chem adjoint model; Handout

--Melissa Sulprizio (talk) 14:12, 12 June 2019 (UTC)

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?

--Melissa Sulprizio (talk) 14:12, 12 June 2019 (UTC)