GEOS–Chem v9–01–02 Online User's Guide

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2. Installation

2.1 What you need to download before you can run GEOS–Chem

When setting up GEOS–Chem on your system, you will need install the following components:

  1. The GEOS–Chem source code directory. This is the directory where the Fortran-90 source code files (i.e. *.F, *.F90 files) and Makefiles reside. Your Fortran compiler will create an executable from these source code files.

  2. A GEOS–Chem run directory. Here is where you will run the compiled GEOS–Chem executable. Each run directory contains:

    You may find a complete description of the run directory contents in Chapter 5.

  3. The GEOS–Chem shared data directories. This is the directory tree where the following types of data are stored:

    You may find a detailed description of the GEOS–Chem shared data directories in Chapter 4.

The GEOS–Chem source code and run directories are small enough to download directly to your own disk space in your Unix account. You can download these with the Git version control software, as described in Chapter 2.2 and Chapter 2.3.

On the other hand, the GEOS–Chem shared data directories contain many large files that probably cannot all fit into your own personal disk quota. Therefore, you (or your sysadmin) should download the shared data directories to a common disk space where all GEOS–Chem users in your group can access them. The volume of data contained in the shared data directories precludes using Git; you must instead download these files via FTP, wget, or similar file transfer programs.

2.2 Downloading the GEOS–Chem Source Code

The GEOS–Chem "standard" source code is kept in a Git repository at Harvard:

git://git.as.harvard.edu/bmy/GEOS-Chem/

All official releases of the GEOS–Chem "standard" code shall originate from this repository.

You can download the directory containing the latest GEOS–Chem source code version by means of the git clone command. Type:

git clone git://git.as.harvard.edu/bmy/GEOS-Chem/ Code.v9-01-02

This will create an exact copy (or "clone") of the official GEOS–Chem repository to your local disk space, in a directory named Code.v9-01-02. (You can choose a different name than Code.v9-01-02 if you wish.)

NOTE: When you clone, you will always get the most recent state of the repository. (i.e. the latest GEOS–Chem version or "bug fix" patch). If, you wish to download an older version of GEOS–Chem (say v8–03–01) with Git, please follow these instructions.

Please see Chapter 3 for instructions on how to compile the GEOS–Chem source code into an executable file.

2.3 Downloading the GEOS–Chem run directories

As mentioned above, the GEOS–Chem run directory is where you will run the compiled executable file (see Chapter 3). The run directory contains several input files that you can modify in order to select the various options for your GEOS–Chem simulation.

We have compiled a collection of GEOS–Chem run directories, grouped by meteorological data type, horizontal resolution, and simulation type. These run directories are stored as individual Git repositories. This allows you to only download the particular run directories that you need.

You can use the Git clone command to download the run directories to your local disk space. The command will take the form:

git clone git://git.as.harvard.edu/bmy/GEOS-Chem-rundirs/DIR-OPTION LOCAL-DIR-NAME

LOCAL-DIR-NAME is the name you chose for your local directory to contain GEOS–Chem

DIR-OPTION may be one of the following:

DIR_OPTION
0.5 x 0.666 GEOS–5 simlulations
Description
0.5x0.666/NA 0.5 x 0.666 GEOS–5 offline nested grid simulation for North America

DIR_OPTION
2 x 2.5 GEOS–4 simlulations
Description
2x2.5/geos4/CO2_run 2 x 2.5 GEOS–4 offline CO2 simulation
2x2.5/geos4/SOA 2 x 2.5 GEOS–4 fullchem w/ SOA simulation
2x2.5/geos4/dicarbonyls 2 x 2.5 GEOS–4 fullchem w/ dicarbonyls option
2x2.5/geos4/isoprene 2 x 2.5 GEOS–4 fullchem w/ Caltech isoprene scheme
2x2.5/geos4/standard 2 x 2.5 GEOS–4 fullchem standard (43 tracers)

DIR_OPTION
2 x 2.5 GEOS–5 simulations
Description
2x2.5/geos5/CO2_run 2 x 2.5 GEOS–5 offline CO2 simulation
2x2.5/geos5/Hg 2 x 2.5 GEOS–5 offline Hg simulation
2x2.5/geos5/SOA 2 x 2.5 GEOS–5 fullchem w/ SOA simulation
2x2.5/geos5/dicarbonyls 2 x 2.5 GEOS–5 fullchem w/ dicarbonyls option
2x2.5/geos5/isoprene 2 x 2.5 GEOS–5 fullchem w/ Caltech isoprene scheme
2x2.5/geos5/standard 2 x 2.5 GEOS–5 fullchem standard (43 tracers)

DIR_OPTION
4 x 5 GEOS–4 simulations
Description
4x5/geos4/CO2_run 4 x 5 GEOS–4 offline CO2 simulation
4x5/geos4/SOA 4 x 5 GEOS–4 fullchem w/ SOA simulation
4x5/geos4/dicarbonyls 4 x 5 GEOS–4 fullchem w/ dicarbonyls option
4x5/geos4/isoprene 4 x 5 GEOS–4 fullchem w/ Caltech isoprene scheme
4x5/geos4/standard 4 x 5 GEOS–4 fullchem standard (43 tracers)

DIR_OPTION
4 x 5 GEOS–5 simulations
Description
4x5/geos5/APM 4 x 5 GEOS–5 fullchem w/ APM aerosol microphysics option
4x5/geos5/Hg 4 x 5 GEOS–5 offline Hg simulation
4x5/geos5/Hg_GTMM 4 x 5 GEOS–5 offline Hg simulation with GTMM option
4x5/geos5/SOA 4 x 5 GEOS–5 fullchem w/ SOA simulation
4x5/geos5/dicarbonyls 4 x 5 GEOS–5 fullchem w/ dicarbonyls option
4x5/geos5/isoprene 4 x 5 GEOS–5 fullchem w/ Caltech isoprene scheme
4x5/geos5/standard 4 x 5 GEOS–5 fullchem standard (43 tracers)

DIR_OPTION
4 x 5 MERRA simulations
Description
4x5/merra/Hg_GTMM 4 x 5 MERRA offline Hg simulation with GTMM option
4x5/merra/SOA 4 x 5 MERRA fullchem w/ SOA simulation
4x5/merra/dicarbonyls 4 x 5 MERRA fullchem w/ dicarbonyls option
4x5/merra/isoprene 4 x 5 MERRA fullchem w/ Caltech isoprene scheme
4x5/merra/standard 4 x 5 MERRA fullchem standard (43 tracers)

DIR_OPTION
1-month benchmark results
Description
benchmark_1mon/v9-01-02

Run directories used for the 4 x 5 GEOS–5 and MERRA 1-month benchmark simulations for GEOS–Chem v9–01–02. These run directories contain the following types of files:

  1. Initial conditions (a.k.a. restart files)
  2. Input files used to select the various GEOS–Chem options
  3. Output files from the simulation
  4. IDL plotting code for creating the validation plots
  5. Validation plots in PostScript format

NOTE: We shall create a new 1-month benchmark Git repository for each new GEOS–Chem version. This will help to keep the size of the repository manageable and will facilitate downloading via Git file transfer.

benchmark_1mon/prior

Run directories used for the 4 x 5 GEOS–5 benchmarks for GEOS–Chem versions v8–03–01, v8–03–02, and v9–01–01.

Please note:

2.4 Downloading the GEOS–Chem shared data directories

The GEOS–Chem shared data directories contain the various met fields, emissions, and other data that GEOS–Chem will read in during the course of a simulation. You must download the shared data directories via FTP or a similar utility (e.g. wget, FireFTP, SecureFX, etc.) The large volume of data makes it impossible to track this directory structure with Git.

If there are several GEOS–Chem users in your research group, then chances are someone (perhaps your sysadmin) has already downloaded the GEOS–Chem shared directory structure to a common disk space on your servers. Nevertheless, you should still check to make sure that the most recent subdirectories are present. See Chapter 4 for complete details about the contents of the GEOS–Chem shared data directories.

2.4.1 Data archives

There are currently two data archives from which you may download the GEOS–Chem shared data directories:

  1. Harvard archive (ftp.as.harvard.edu)
  2. Dalhousie archive (rain.ucis.dal.ca)

The Dalhousie archive is not as comprehensive as the Harvard archive. However, the Dalhousie archive stores data files for the various nested grids and global 1° x 1.25° grids that are not available on the Harvard archive.

For those of you who are interested in using GEOS–Chem with the GCAP data, please contact Loretta Mickley for more information.

2.4.2 Downloading instructions

We recommend that you use the GNU wget utility to download the GEOS–Chem shared data directories. Wget will allow you to download the directories and subdirectories in one fell swoop. The wget commands take the form of:

wget -r -nH "ftp://ftp.as.harvard.edu/gcgrid/geos-chem/data/DIRECTORY_NAME/"

where DIRECTORY_NAME is the name of the directory you want to download. Please see our wiki page on how to download data with wget for more information.

You can also download the shared data directories via anonymous FTP:

ftp ftp.as.harvard.edu
cd gcgrid/geos-chem/data/GEOS_0.5x0.666_CH
cd gcgrid/geos-chem/data/GEOS_0.5x0.666_NA
cd gcgrid/geos-chem/data/GEOS_1x1
cd gcgrid/geos-chem/data/GEOS_2x2.5
cd gcgrid/geos-chem/data/GEOS_4x5
cd gcgrid/gcap/GCAP_4x5

However, for those of you in the Atmospheric Chemistry Modeling Group at Harvard, you do not need to download this data, as it is already stored on the group's internal filesystem, in directories:

/as/group/geos/data/GEOS_0.5x0.666_CH
/as/group/geos/data/GEOS_0.5x0.666_CH
/as/group/geos/data/GEOS_1x1
/as/group/geos/data/GEOS_2x2.5
/as/group/geos/data/GEOS_4x5
/as/group/gcap/data/GCAP_4x5

If you wish to download data from the Dalhousie data archive, use this command:

wget -r -nH "ftp://rain.ucis.dal.ca/DIRECTORY_NAME/"

Please see the following links for more information:

  1. Chapter 4: GEOS–Chem data directories
  2. GEOS–Chem wiki: Downloading GEOS–Chem data directories
  3. GEOS–Chem wiki: Using wget to download data

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