GEOS-Chem v10-01 Online User's Guide

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2. Installation

2.1 Requirements

When first setting up GEOS-Chem on your system, after checking that you meet the basic computer requirements outlined in Chapter 1.2 you will need to install the following components :

  1. GEOS-Chem Source Code Directory

  2. GEOS-Chem Run Directory

  3. GEOS-Chem Shared Data Directories.

  4. NetCDF Library Installation

The GEOS-Chem source code directory and run directories are small enough to download directly to your own disk space in your Unix account. You can download these with Git version control software, as described below in Sections 2.2 and 2.3. Please see the version control with Git wiki page for information about installing Git.

The GEOS-Chem shared data directories, on the other hand, contain many large files that probably cannot all fit into your own personal disk quota. Therefore, we recommend that you or your system administrator download the shared data directories to a common disk space where all GEOS-Chem users in your group can access them. Information about downloading shared data directories is in Section 2.4.

Most of the data files read by GEOS-Chem v10-01 are now in COARDS-compliant netCDF format. As part of our High-Performance Computing (HPC) GEOS-Chem project, we are in the process of converting the remaining binary data files to netCDF format. This will facilitate running GEOS-Chem in (HPC) environments, such as our efforts to interface GEOS-Chem with the NASA GEOS-5 GCM. Instructions on obtaining compatible netCDF libraries for use with GEOS-Chem v10-01 are in Section 2.5.

2.2 Downloading GEOS-Chem Source Code Directory

The GEOS-Chem source code directory contains the Makefile and Fortran-90 source code files (i.e. *.F, *.F90 files). Compiling the source code with a Fortran compiler creates the GEOS-Chem executable geos.

The GEOS-Chem "standard" source code directory is kept in the following Git repository at Harvard University:


All official releases of the GEOS-Chem "standard" code shall originate from this repository. You can download the latest official GEOS-Chem release by means of the git clone command by typing the following at the command line:

git clone git:// Code.v10-01

This will create an exact copy (or "clone") of the official GEOS-Chem repository to your local disk space in a directory named Code.v10-01. Using Code.v10-01 as your local repository name is optional and you may specify a different directory name if you wish. Note that you will always get the most recent state of the repository, meaning the latest GEOS-Chem version or "bug fix" patch.

For detailed information about Git and downloading the GEOS-Chem source code, please visit the following wiki resources:

If you wish to download an earlier version of GEOS-Chem using Git, such as v9-02 for example, please see the Using Git with GEOS-Chem wiki page section on reverting to an older state of code.

2.3 Downloading GEOS-Chem Run Directories

There is a unique run directory for every combination of GEOS-Chem simulation type, grid resolution, meteorological data source, and nested region. Each run directory contains the following:

A collection of GEOS-Chem run directories are stored in the GEOS-Chem Unit Tester. You can create fresh copies of any of these GEOS-Chem run directories for your own use by using the gcCopyRunDirs perl script and the CopyRunDirs.input configuration file within the Unit Tester perl directory.

For detailed information about downloading the GEOS-Chem Unit Tester using Git, please see the Debugging with the GEOS-Chem Unit Tester wiki page. Quick links to relevant subsections of this wiki page are as follows:

For detailed instructions on creating fresh copies of run directories for your GEOS-Chem simulations, please see the Creating GEOS-Chem run directories wiki page. Quick links to relevant subsections of this wiki page are included below:

Our 1-month benchmark run directories for GEOS-Chem v10-01 and later versions are also available. You may download them via anonymous FTP from:

2.4 Downloading GEOS-Chem Shared Data Directories

The GEOS-Chem shared data directories contain the various met fields, emission inventories, scale factors, and other data that GEOS-Chem reads in during the course of a simulation.

Because of the large volume of data, you must download the shared data directories via FTP or a similar utility such as wget, FireFTP, or SecureFX. Tracking the shared data directory structure with Git is impossible due to its size. See the Minimum system requirements for GEOS-Chem wiki page for information on typical disk space requirements for GEOS-Chem.

If your research group consists of several GEOS-Chem users, it is possible that you already have access to the GEOS-Chem shared directory structure on common disk space on your servers. If this is the case you should check that you have the most recent data directories and subdirectories prior to using GEOS-Chem v10-01.

For detailed instructions on downloading the shared data directories, please see the following wiki page subsections:

Important Note! In GEOS-Chem v10-01, all shared data directories are now subdirectories of a single root directory called ExtData. If downloading the shared data directories for the first time, you (or your sysadmin/IT staff) must set up the ExtData directory prior to running GEOS-Chem v10-01. If you have previously downloaded the GEOS-Chem shared data directories, you can simply add symbolic links from ExtData to the existing data directories.

Please see the Setting up the ExtData directory wiki page for detailed instructions on setting up your shared data directories so that they are compatible with GEOS-Chem v10-01.

2.5 Installing netCDF with the GEOS-Chem-Libraries Package

GEOS-Chem v10-01 requires that you have a netCDF library installation on your your computer system. On many modern computer systems, you can load pre-compiled libraries and software packages (such as netCDF, HDF5, IDL ifort compiler, etc.) with the module command. Check with your sysadmin or IT staff if module is already installed on your system. If it is, we recommend that you use module to load a version of the netCDF libraries into your computing environment.

In order to facilitate building the netCDF library, the GEOS-Chem Support Team has constructed the GEOS-Chem-Libraries installer package. You (or your IT staff) can use the installer package to build a copy of the netCDF libraries if your computer system does not already have netCDF libraries installed.

For detailed instructions on how to use the GEOS-Chem-Libraries installer program, please see the Installing libraries for GEOS-Chem wiki page. Here you will find an overview of the individual library files that are generated and the commands used to link to them.

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