Creating GEOS-Chem run directories
On this page we show you how to use the GEOS-Chem Unit Tester to generate and use fresh copies of run directories for your GEOS-Chem simulations.
Contents
Downloading the GEOS-Chem Unit Tester
First, make sure that your system has these software packages installed. (Most of these come standard with your Unix-based operating system.)
Next, clone the GEOS-Chem unit tester package with the command:
git clone -b v10-01-public git://git.as.harvard.edu/bmy/GEOS-Chem-UnitTest UT
This will create a copy of the GEOS-Chem Unit Tester package in a directory named UT for short.
The option
-b v10-01-public
specifies which branch of the GEOS-Chem Unit Tester that you would like to download. Branches in the GEOS-Chem unit tester correspond to each internal version of GEOS-Chem (i.e. the states of the code for which we run 1-month benchmark simulations), as well as the publicly-released versions. Most likely, you will want to download the v10-01-public branch of the GEOS-Chem Unit Tester, which corresponds to the public release of GEOS-Chem v10-01.
--Bob Y. 13:36, 19 March 2015 (EDT)
Editing the CopyRunDirs.input file
Once you have downloaded the GEOS-Chem Unit Tester to your disk space, switch to the perl/ directory:
cd UT/perl
In this directory there is a Perl script named gcCopyRunDirs that you will use to generate fresh copies of GEOS-Chem run directories. This script uses an input file named CopyRunDirs.input, which is also located in the perl directory.
Your CopyRunDirs.input file will look something like this:
#------------------------------------------------------------------------------
# GEOS-Chem Global Chemical Transport Model !
#------------------------------------------------------------------------------
#BOP
#
# !DESCRIPTION: Input file that specifies configuration for creating and
# copying a run directory from the UnitTester.
#\\
#\\
# !REMARKS:
# Customize the run directory for your system by specifying these values:
# -------------------------------------------------------------------
# VERSION : A tag used to identify this Unit Test (e.g. v10-01h)
# DESCRIPTION : A short description of this file's run dir copy configuration
# COPY_PATH : Local path where run directory will be copied to
# DATA_ROOT : Root GEOS-Chem data directory
# HEMCO_ROOT : Root directory where HEMCO emissions data files are stored
# RUN_ROOT : Unit test run directories are subdirectories of RUN_ROOT
# RUN_DIR : Individual unit test run directory path
# PERL_DIR : Unit Test perl script directory (i.e. this directory)
# COPY_CMD : Unix copy command with optional tags
#
# !REVISION HISTORY:
# 18 Mar 2015 - R. Yantosca - Initial version
# 19 Mar 2015 - E. Lundgren - Simplify content for only copying run dirs
#EOP
#------------------------------------------------------------------------------
#
# !INPUTS:
#
VERSION : v10-01h
DESCRIPTION : Create run directory from UnitTest
COPY_PATH : /home/{USER}/GC/rundirs
DATA_ROOT : /as/data/geos/ExtData
HEMCO_ROOT : {DATAROOT}/HEMCO
RUN_ROOT : /home/{USER}/UT/runs
RUN_DIR : {RUNROOT}/{RUNDIR}
PERL_DIR : /home/{USER}/UT/perl
COPY_CMD : cp -rfL
#
# !RUNS:
# Specify the debugging runs that you want to perform below.
# You can deactivate runs by commenting them out with "#".
#
#--------|-----------|------|------------|------------|------------|---------|
# MET | GRID | NEST | SIMULATION | START DATE | END DATE | EXTRA? |
#--------|-----------|------|------------|------------|------------|---------|
geosfp 2x25 - Hg 2013070100 2013070101 -
geos5 2x25 - Hg 2005070100 2005070101 -
geosfp 4x5 - fullchem 2013070100 2013070101 -
geos4 4x5 - Hg 2005070100 2005070101 -
geos4 4x5 - CH4 2005070100 2005070101 -
geosfp 4x5 - Hg 2013070100 2013070101 -
geosfp 4x5 - POPs 2013070100 2013070101 -
!END OF RUNS:
#EOP
#------------------------------------------------------------------------------
NOTE: Lines starting with a # character will be treated as comments.
The CopyRunDirs.input file has a layout that is very similar to the GEOS-Chem Unit Tester input files. (These are the files named UnitTest.input, etc.) Like the GEOS-Chem Unit Tester input files, CopyRunDirs.input is composed of an !INPUTS section and a !RUNS section, which are described below.
Section 1: INPUTS
Under the !INPUTS: section, you can customize the directory paths and other options for your system. As seen above, most of these inputs are self-explanatory.
| Option | Description |
|---|---|
| VERSION | An ID tag that will be added to all log files and output files. |
| DESCRIPTION | A short (1-sentence) description of the purpose of this specific file (optional). This may be used to differentiate different input files, such as if you pre-configure several for future re-use. |
| COPY_PATH | Specifies the root directory on your disk server where copies of the GEOS-Chem run directories will be created. |
| DATA_ROOT | Specifies the path for your root-level data directory. |
| HEMCO_ROOT | Specifies the top-level path for the HEMCO data directory tree.
Leave this as-is. |
| RUN_ROOT | Specifies the top-level unit test run directories.
Leave this as-is. |
| PERL_DIR | Specifies the directory where the unit test Perl scripts are found.
Leave this as-is. |
| COPY_CMD | Specifies the command used to copy run directories from the GEOS-Chem Unit Tester to COPY_PATH.
|
--Bob Y. 14:20, 19 March 2015 (EDT)
Section 2: RUNS
The layout of the !RUNS section is identical to The !RUNS section in the GEOS-Chem Unit Tester input files. This allows you to copy and paste text from one or more GEOS-Chem Unit Tester input files into CopyRunDirs.input.
For example, the following line:
# # !RUNS: # Specify the debugging runs that you want to perform below. # You can deactivate runs by commenting them out with "#". # #--------|-----------|------|------------|------------|------------|---------| # MET | GRID | NEST | SIMULATION | START DATE | END DATE | EXTRA? | #--------|-----------|------|------------|------------|------------|---------| geosfp 2x25 - Hg 2013070100 2013070101 -
will tell the gcCopyRunDirs script to create a run directory for a GEOS-Chem simulation using:
- GEOS-FP met fields
- On the 2° x 2.5° GEOS-Chem horizontal grid
- For the GEOS-Chem Hg specialty simulation
- Starting at 00:00 GMT on 2013/07/01
- Ending at 01:00 GMT on 2013/07/01
The date range will be used to initialize the input.geos file that is read during a GEOS-Chem simulation. Once the run directory is created, you may edit these dates within the input.geos file. Note, however, that time ranges must remain within the time range covered by the MET field you are using. You can check the MET field temporal coverage on the GMAO met data products wiki page. Also note that the restart files automatically generated for the run directory correspond only to the original date specified in the CopyRunDirs.input file. Restart files for a later dates must be generated by running a simulation that ends on that date.
You can add as many entries to the !RUNS section as you wish. Simply cut and paste from one of the existing GEOS-Chem Unit Test input files (e.g. UnitTest.input within UT/perl).
Generating a Run Directory
Once you have edited the CopyRunDirs.input script to your liking, you can use that to generate fresh copies of GEOS-Chem run directories. Make sure you are in the perl directory, and then type:
gcCopyRunDirs
If you do not pass a file name to gcCopyRunDirs, then the gcCopyRunDirs script will use the CopyRunDirs.input file that you just created.
If you wish, you can create many customized copies of CopyRunDirs.input. For example, suppose you edit CopyRunDirs.input to generate a mercury run directory. You can then save it as a separate file and use it explicitly with gcCopyRunDirs.
cp CopyRunDirs.input CopyRunDirs.Hg # Input file set up to only copy the Hg run directories gcCopyRunDirs CopyRunDirs.Hg
Executing gcCopyRunDirs will create a new GEOS-Chem run directory corresponding to each entry that you specified in the CopyRunDirs.* file. Each run directory will be created as a subdirectory of !COPY_PATH.
Let's examine the contents of a sample geosfp_2x25_Hg run directory. Issue the following commands:
cd ~/GC/rundirs/geosfp_2x25_Hg # Change to geosfp_2x25_Hg run dir make fileclean # Remove any files left over from previous unit test runs ls -l # Get detailed directory listing
And you will see this directory listing:
-rw-r--r-- 1 bmy bmy 17137 2015-03-18 16:18 HEMCO_Config.rc -rw-r--r-- 1 bmy bmy 17116 2015-03-18 16:18 HEMCO_Config.template -rw-r--r-- 1 bmy bmy 4568 2015-03-18 16:18 Makefile -rwxr-xr-x 1 bmy bmy 1458 2015-03-18 16:18 getEnd.pl* -rwxr-xr-x 1 bmy bmy 1374 2015-03-18 16:18 getStart.pl* -rw-r--r-- 1 bmy bmy 7391476 2015-03-18 16:18 initial_trac_rst.geosfp_2x25_Hg -rw-r--r-- 1 bmy bmy 12082 2015-03-18 16:20 input.geos -rw-r--r-- 1 bmy bmy 12060 2015-03-18 16:18 input.geos.template -rw-r--r-- 1 bmy bmy 210712 2015-03-18 16:18 ocean_rst.geosfp_2x25_Hg.201307010000
NOTE: Run directories for other simulations may contain other files not pictured here.
The input.geos and HEMCO_Config.rc files have been customized for this particular simulation. They were created from the corresponding template files input.geos.template and HEMCO_Config.template. The template files are otherwise not used.
The Perl scripts getStart.pl and getEnd.pl pass the starting and ending dates of the simulation, as specified in the input.geos file, to the Makefile.
--Bob Y. 14:24, 19 March 2015 (EDT)
Compiling and Running GEOS-Chem
Once you have created one or more GEOS-Chem run directories, you can use them for your GEOS-Chem simulations. First, doublecheck that the settings in the input.geos and HEMCO_Config.rc files are correct for the simulation that you are trying to run. See the GEOS-Chem Manual for more information about setting simulation options.
To start a GEOS-Chem simulation, type the following commands. (We'll use the example of the geos5_2x25_Hg simulation, from the previous sections.)
make -j4 CODE_DIR=~/GC/Code.v10-01 VERSION=v10-01 MET=geosfp GRID=2x25 TRACEBACK=y mp
The above command specifies: (1) the location of the code to compile (CODE_DIR), (2) a version tag to use as a prefix in our data output file (VERSION), (3) the met field to use (MET), (4) the grid resolution to use (GRID), and (5) whether to show traceback for debugging (TRACEBACK). The MET and GRID values must match those for your run directory. If you wish, you can omit the VERSION option. If you do not include VERSION, it will automatically be set to GC..
The final command mp is a makefile target defined in the file 'Makefile' within the run directory. In our example, mp indicates that our code will be compiled and then run with OpenMP parallelization. You can also specify sp to compile and run code using a single processor. This will result in output files having the .sp rather than .mp suffix. See the Makefile for other make options and Section 3.6.2 of the GEOS-Chem Manual for more information about Makefiles.
GEOS-Chem Output Files
Once the GEOS-Chem simulation is complete, you will see several new files in the run directory. Some of these are generated for all simulations while others may be simulation-dependent. For the case of our mercury simulation example, the following files are output:
| File | Description |
|---|---|
| trac_avg.geosfp_2x25_Hg.YYYYMMDDhh.mp | Diagnostic output file that contains time-averaged output for diagnostics enabled in input.geos. Data in this file are in "binary punch" format and may be viewed and manipulated using GAMAP. |
| trac_rst.geosfp_2x25_Hg.YYYYMMDDhhmm.mp | Tracer restart file that contains instantaneous tracer concentrations at simulation end time. This file may be used to initialize another GEOS-Chem simulation. Data in this file are in "binary punch" format and may be viewed and manipulated using GAMAP. |
| HEMCO_restart.YYYYMMDDhh.nc | HEMCO restart file containing several quantities tracked by HEMCO for use in initializing another GEOS-Chem simulation. Data in this file are in netcdf format. |
| ocean_rst.YYYYMMDDhhmm.nc | Ocean mercury restart file containing several quantities pertaining to the ocean mercury module saved at the end of the GEOS-Chem simulation. Like the tracer restart file, this file may be used to initialize another GEOS-Chem mercury simulation. Data in this file are in the in netcdf format. |
| v10-01.geosfp_2x25_Hg.mp | GEOS-Chem simulation log file. Look at this file to diagnose compile and run errors. |
| HEMCO.log.mp | HEMCO log file containing detailed information about the emissions read from disk into HEMCO. Look at this file to diagnose HEMCO errors. |
| diaginfo.dat | File generated by GEOS-Chem that contains diagnostic quantities for use with GAMAP. |
| tracerinfo.dat | File generated by GEOS-Chem that contains tracer name metadata for use with GAMAP. |
--Lizzie Lundgren 16:38, 23 March 2015 (EDT)
