View source for 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.  

== Downloading the GEOS-Chem Unit Tester ==

First, make sure that your system [[Debugging_with_the_GEOS-Chem_unit_tester#Requirements|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-Release 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 <tt>UT</tt> for short.  

The option

 -b v10-01-Release

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]].

''NOTE: The Git clone process may take a few of minutes to complete, depending on your connection speed.''

--[[User:Bmy|Bob Y.]] 12:25, 1 May 2015 (EDT)

== Available run directories ==

=== Benchmark run directory ===

The [[GEOS-Chem Unit Tester]] includes a run directory called '''geosfp_4x5_benchmark.''' As of May 2015, the standard [http://acmg.seas.harvard.edu/geos/geos_benchmark.html GEOS-Chem benchmark simulation] utilizes the [[GEOS-FP]] met fields ([http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_4x5 4&deg; x 5 &deg;], [http://acmg.seas.harvard.edu/geos/doc/man/appendix_3.html#GEOS-5_native 72 levels]) with the [[#UCX chemistry mechanism|UCX tropospheric-stratospheric chemistry mechanism]] and [[Secondary organic aerosols|secondary organic aerosols]] included. 

To reproduce our latest [[GEOS-Chem_v10-01_benchmark_history#1-month_benchmark_v10-01-public-release_with_SOA_on|1-month benchmark simulation for v10-01]], you can edit the <tt>CopyRunDirs.input</tt> file so that the following line is uncommented under <tt>RUNS</tt>:

  geosfp   4x5         -      benchmark    2013070100   2013080100   UCX=y

Make sure to check the start and end date so that your simulation will run for July 2013. You can then create the GEOS-Chem benchmark run directory by typing <tt>gcCopyRunDirs</tt>. Navigate to your the newly created <tt>geosfp_4x5_benchmark</tt> run directory. To compile and run your benchmark simulation, type:

 make -j4 mp

To compile only, type:

 make -j4 mpbuild

That will create a <tt>geos.mp</tt> executable file that you can use to submit your GEOS-Chem benchmark simulation to a queue system.

'''''NOTE: If you are compiling GEOS-Chem within the code directory, and not within a run directory created from the GEOS-Chem Unit Tester, you will need to pass the <tt>UCX=y</tt> option in your <tt>make</tt> command.'''''

--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 19:38, 23 June 2015 (UTC)

=== Other run directories ===

Run directories are provided for a combination of met field, grid, and simulation type and are named accordingly (e.g. geosfp_4x5_UCX). For more details on the simulation types, please see our [[GEOS-Chem chemistry mechanisms|''GEOS-Chem chemistry mechanism'' wiki page]].

The following table summarizes the run directories that are available in the [[GEOS-Chem Unit Tester]]. Please choose the run directory or run directories that are most relevant for your research.

{| border=1 cellspacing=0 cellpadding=5
|-bgcolor="#CCCCCC"
!width="100px"|Met field
!width="175px"|Grid
!width="100px"|[[NOx-Ox-HC-aerosol|NOx-Ox-<br>HC-aerosol]]
!width="100px"|[[UCX chemistry mechanism|UCX]]
!width="100px"|[[Coupling GEOS-Chem with RRTMG|RRTMG]]
!width="100px"|[[Secondary organic aerosols|soa]]
!width="100px"|[[Secondary organic aerosols#SOA simulation with semi-volatile POA|soa_svpoa]]
!width="100px"|[[Rn-Pb-Be simulation|RnPbBe]]
!width="100px"|[[Mercury|Hg]]
!width="100px"|[[POPs simulation|POPs]]
!width="100px"|[[Tagged CO simulation|tagCO]]
!width="100px"|[[Tagged O3 simulation|tagO3]]
!width="100px"|[[CH4 simulation|CH4]]
!width="100px"|[[CO2 simulation|CO2]]
!width="100px"|[[Aerosol-only simulation|aerosol]]
!width="100px"|[[TOMAS aerosol microphysics|TOMAS40]]

|-valign="top"
|[[GEOS-FP|geosfp]]
|[http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_4x5 4x5]
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 

|-valign="top"
|[[GEOS-FP|geosfp]]
|[http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_2x25 2x25]
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|

|-valign="top"
|[[GEOS-FP|geosfp]]
|[http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_025_CH 025x03125<br>CH]
|bgcolor="#00FF00"| 
|
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|-valign="top"
|[[GEOS-FP|geosfp]]
|[http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_025_NA 025x03125<br>NA]
|bgcolor="#00FF00"| 
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|-bgcolor="#CCCCCC" height="10px"
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|-valign="top"
|[[GEOS-5|geos5]]
|[http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_4x5 4x5]
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 

|-valign="top"
|[[GEOS-5|geos5]]
|[http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_2x25 2x25]
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|

|-valign="top"
|[[GEOS-5|geos5]]
|[http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_05_CH 05x0666<br>CH]
|bgcolor="#00FF00"| 
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|-valign="top"
|[[GEOS-5|geos5]]
|[http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_05_NA 05x0666<br>NA]
|bgcolor="#00FF00"| 
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|bgcolor="#00FF00"| 
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|bgcolor="#00FF00"| 
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|-bgcolor="#CCCCCC"
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|-valign="top"
|[[MERRA|merra]]
|[http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_4x5 4x5]
|bgcolor="#00FF00"| 
|
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|
|bgcolor="#00FF00"| 
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|-valign="top"
|[[MERRA|merra]]
|[http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_2x25 2x25]
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|-bgcolor="#CCCCCC" height="10px"
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|-valign="top"
|[[GEOS-4|geos4]]
|[http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_4x5 4x5]
|bgcolor="#00FF00"| 
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|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
|bgcolor="#00FF00"| 
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|-bgcolor="#CCCCCC" height="10px"
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|-valign="top"
|[[GCAP|gcap]]
|[http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GCAP_4x5 4x5]
|bgcolor="#00FF00"| 
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|bgcolor="#00FF00"| 
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|bgcolor="#00FF00"| 
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|}

'''LEGEND'''
{| border=1 cellspacing=0 cellpadding=5
|-valign="top"
|width="75px" bgcolor="#00FF00"|
|width="250px"|Run directory is available

|-valign="top"
|bgcolor="#FFFF00"|
|Run directory is in need of updating

|-valign="top"
|bgcolor="#FF0000"|
|Run directory is obsolete  

|-valign="top"
|
|Run directory is not available

|}

--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 17:36, 26 May 2015 (UTC)

== Editing the CopyRunDirs.input file ==

Once you have downloaded the GEOS-Chem Unit Tester to your disk space, switch to the <tt>perl/</tt> directory:

 cd UT/perl

In this directory there is a Perl script named <tt>gcCopyRunDirs</tt> that you will use to generate fresh copies of GEOS-Chem run directories.  This script uses an input file named <tt>CopyRunDirs.input</tt>, which is also located in the <tt>perl</tt> directory.  

Your <tt>CopyRunDirs.input</tt> 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
 #  VERBOSE     : HEMCO verbose level  (0=no output, 3=max output)
 #  WARNINGS    : HEMCO warnings level (0=no warnings, 3=max warnings)
 #
 # !REVISION HISTORY:
 #  18 Mar 2015 - R. Yantosca - Initial version
 #  19 Mar 2015 - E. Lundgren - Simplify content for only copying run dirs
 #EOP
 #------------------------------------------------------------------------------
 #
 # !INPUTS:
 #
    VERSION     : v10-01
    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
    VERBOSE     : 0
    WARNINGS    : 1
 #
 # !RUNS:
 #  Specify the debugging runs that you want to perform below.
 #  Here we provide a few examples, but you may copy additional entries from
 #  UnitTest.input and modify the dates as needed. You can deactivate copying
 #  run certain directories by commenting them out with "#".
 #
 #--------|-----------|------|------------|------------|------------|---------|
 # MET    | GRID      | NEST | SIMULATION | START DATE | END DATE   | EXTRA?  |
 #--------|-----------|------|------------|------------|------------|---------|
   geosfp   4x5         -      fullchem     2013070100   2013070101   -
   geosfp   4x5         -      soa          2013070100   2013070101   -
   geosfp   4x5         -      soa_svpoa    2013070100   2013070101   -
   geosfp   4x5         -      UCX          2013070100   2013070101   UCX=y
   geosfp   4x5         -      RRTMG        2013070100   2013070101   RRTMG=y
   geosfp   4x5         -      RnPbBe       2013070100   2013070101   -
   geosfp   4x5         -      Hg           2013070100   2013070101   -
   geosfp   4x5         -      POPs         2013070100   2013070101   -
   geosfp   4x5         -      CH4          2013070100   2013070101   -
   geosfp   4x5         -      tagO3        2013070100   2013070101   -
   geosfp   4x5         -      tagCO        2013070100   2013070101   -
   geosfp   2x25        -      CO2          2013070100   201307010030 -
   geosfp   4x5         -      aerosol      2013070100   2013070101   - 
   geosfp   025x03125   ch     fullchem     2013070100   201307010010 -
   geosfp   025x03125   na     fullchem     2013070100   201307010010 -
 !END OF RUNS:
 #EOP
 #------------------------------------------------------------------------------

''NOTE: Lines starting with a <tt>#</tt> character will be treated as comments.''

The <tt>CopyRunDirs.input</tt> file has a layout that is very similar to the [[Debugging_with_the_GEOS-Chem_unit_tester#Specifying_unit_test_options_with_an_input_file|GEOS-Chem Unit Tester input files]] (<tt>UnitTest.input</tt> located within this directory). Like the GEOS-Chem Unit Tester input files, <tt>CopyRunDirs.input</tt> is composed of an <tt>INPUTS</tt> section and a <tt>RUNS</tt> section, which are described below.

=== Section 1: INPUTS ===

Under the <tt>INPUTS</tt> section, you can customize the directory paths and other options for your system. Each configurable input is described in the table below.

{| border=1 cellspacing=0 cellpadding=5 
|-bgcolor="#CCCCCC"
!width="100px"|Option
!width="825px"|Description

|-valign="top"
|<tt>VERSION</tt>
|An ID tag that will be added to all log files and output files.

|-valign="top"
|<tt>DESCRIPTION</tt>
|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.

|-valign="top"
|<tt>COPY_PATH</tt>
|Specifies the root directory on your disk server where copies of the GEOS-Chem run directories will be created.

|-valign="top"
|<tt>DATA_ROOT</tt>
|Specifies the path for your root-level data directory.  

|-valign="top"http://wiki.seas.harvard.edu/geos-chem/skins//common/images/button_nowiki.png
|<tt>HEMCO_ROOT</tt>
|Specifies the top-level path for the [[HEMCO data directories|HEMCO data directory tree]].
*The <tt>{DATAROOT}</tt> token in <tt>HEMCO_ROOT</tt> will be replaced with the value you specify for <tt>RUN_ROOT</tt> option.  
<b>Leave this as-is.</b>

|-valign="top"
|<tt>RUN_ROOT</tt>
|Specifies the top-level unit test run directories.  
<b>Leave this as-is.</b>

|-valign="top"
|<tt>PERL_DIR</tt>
|Specifies the directory where the unit test Perl scripts are found.
<b>Leave this as-is.</b>

|-valign="top"
|<tt>COPY_CMD</tt>
|Specifies the command used to copy run directories from the GEOS-Chem Unit Tester to <tt>COPY_PATH</tt>.
*The default setting is <tt>cp -rfL</tt>.  This will create a new copy of the directory, even if the prior copy exists. 
*The <tt>-L</tt> option to the <tt>cp</tt> will create "hard" copies of files that are symbolic links.  This command may differ slightly depending on the flavor of your Unix-based Operating system.

|-valign="top"
|<tt>VERBOSE</tt>
|Specifies the level of debug output that will be sent to the HEMCO log file. (0=no debug output; 3=max debug output)
*Recommended setting: <tt>0</tt>

|-valign="top"
|<tt>WARNINGS</tt>
|Specifies the level of warning messages that will be sent to the HEMCO log file. (0=no warnings; 3=max warnings)
*Recommended setting: <tt>1</tt>

|}

--[[User:Bmy|Bob Y.]] ([[User talk:Bmy|talk]]) 22:38, 19 May 2015 (UTC)

=== Section 2: RUNS ===

The layout of the <tt>RUNS</tt> section is identical to the <tt>RUNS</tt> section in the GEOS-Chem Unit Tester input file. This enables copying and pasting simulation settings text from <tt>UnitTest.input</tt> into <tt>CopyRunDirs.input</tt>.

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   4x5         -      fullchem     2013070100   2013070101   -

will tell the <tt>gcCopyRunDirs</tt> script to create a run directory for a GEOS-Chem simulation using:

*[[GEOS-FP]] met fields
*On the [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_4x5 4&deg; x 5&deg; GEOS-Chem horizontal grid]
*For the [[NOx-Ox-HC-aerosol|GEOS-Chem standard full-chemistry 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 <tt>input.geos</tt> file that is read during a GEOS-Chem simulation. Once the run directory is created, you may edit these dates within the <tt>input.geos</tt> file. Note, however, that time ranges must remain within the time range covered by the <tt>MET</tt> field you are using. You can check the <tt>MET</tt> field temporal coverage on the [http://wiki.seas.harvard.edu/geos-chem/index.php/Overview_of_GMAO_met_data_products; GMAO met data products wiki page]. Also note that we recommend using the restart files to spin up GEOS-Chem for at least one year prior to your simulation start date. You may use the resulting output restart files as initial values for your simulation.  

You can add as many entries to the <tt>RUNS</tt> section as you wish. Simply comment out the lines containing runs you may wish to copy in the future.

== Generating a GEOS-Chem Run Directory ==

Once you have edited the <tt>CopyRunDirs.input</tt> script to your liking, you can use that to generate fresh copies of GEOS-Chem run directories.  Make sure you are in the <tt>perl</tt> directory, and then type:

 gcCopyRunDirs

If you do not pass a file name to <tt>gcCopyRunDirs</tt>, then the <tt>gcCopyRunDirs</tt> script will use the <tt>CopyRunDirs.input</tt> file that you just created.  

If you wish, you can create many customized copies of <tt>CopyRunDirs.input</tt>.  For example, suppose you edit <tt>CopyRunDirs.input</tt> to generate a full-chemistry run directory. You can then save it as a separate file and use it explicitly with <tt>gcCopyRunDirs</tt>.

 cp CopyRunDirs.input CopyRunDirs.fullchem   # Input file set up to only copy the full-chemistry run directories
  
 gcCopyRunDirs CopyRunDirs.Hg                 

Executing <tt>gcCopyRunDirs</tt> will create a new GEOS-Chem run directory corresponding to each entry that you specified in the input file <tt>RUNS</tt>.  Each run directory will be created as a subdirectory of <tt>COPY_PATH</tt> that you specified in the input file <tt>INPUTS</tt> section.

Let's examine the contents of a sample <tt>geosfp_4x5_fullchem</tt> run directory.  Issue the following commands:

 cd ~/GC/rundirs/geosfp_4x5_fullchem  # Change to geosfp_4x5_fullchem 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 mpayer mpayer     7862 2015-04-03 15:19 FJX_j2j.dat
 -rw-r--r-- 1 mpayer mpayer    44808 2015-04-03 15:19 FJX_spec.dat
 -rw-r--r-- 1 mpayer mpayer   186359 2015-04-03 15:19 HEMCO_Config.rc
 -rw-r--r-- 1 mpayer mpayer     4872 2015-04-03 15:19 Makefile
 -rw-r--r-- 1 mpayer mpayer      783 2015-04-03 15:19 README
 -rw-r--r-- 1 mpayer mpayer      610 2015-04-03 15:19 chemga.dat
 -rw-r--r-- 1 mpayer mpayer    42186 2015-04-03 15:19 dust.dat
 -rwxr-xr-x 1 mpayer mpayer     1458 2015-04-03 15:19 getEnd.pl*
 -rwxr-xr-x 1 mpayer mpayer     1374 2015-04-03 15:19 getStart.pl*
 -rw-r--r-- 1 mpayer mpayer   199632 2015-04-03 15:19 globchem.dat
 -rw-r--r-- 1 mpayer mpayer   401972 2015-04-03 15:19 initial_hemco_rst.geosfp_4x5_fullchem.nc
 -rw-r--r-- 1 mpayer mpayer 41110480 2015-04-03 15:19 initial_trac_rst.geosfp_4x5_fullchem
 -rw-r--r-- 1 mpayer mpayer    15913 2015-04-03 15:19 input.geos
 -rw-r--r-- 1 mpayer mpayer    26194 2015-04-03 15:19 jv_spec_mie.dat
 -rw-r--r-- 1 mpayer mpayer      905 2015-04-03 15:19 mglob.dat
 -rw-r--r-- 1 mpayer mpayer    42185 2015-04-03 15:19 org.dat
 -rw-r--r-- 1 mpayer mpayer    42185 2015-04-03 15:19 so4.dat
 -rw-r--r-- 1 mpayer mpayer    42186 2015-04-03 15:19 soot.dat
 -rw-r--r-- 1 mpayer mpayer    42185 2015-04-03 15:19 ssa.dat
 -rw-r--r-- 1 mpayer mpayer    42185 2015-04-03 15:19 ssc.dat
 -rwxr-xr-x 1 mpayer mpayer     7303 2015-04-03 15:19 validate*

''NOTE: Run directories for other simulations may contain other files not pictured here.''

The <tt>input.geos</tt> and <tt>HEMCO_Config.rc</tt> files have been customized for this particular simulation.  They were created from the corresponding template files <tt>input.geos.template</tt> and <tt>HEMCO_Config.template</tt> in the Unit Tester.

The Perl script <tt>getRunInfo</tt> is used by the Makefile to extract information about the simulation from <tt>input.geos</tt>.

--[[User:Lizzie Lundgren|Lizzie Lundgren]] 10:50, 15 April 2015 (EDT)

== Tips and tricks for creating run directories ==

*In each run directory, we provide a GEOS-Chem restart file that you can use to initialize your simulation. However, it is highly recommended that you not use these restart files for any of your production runs. Rather, you will want to generate your own restart file by spinning up the model for at least a year.

* You can create a run directory for the [[GEOS-Chem_nested_grid_simulations|nested grid simulations]] from a 4&deg; x 5&deg; or 2&deg; x 2.5&deg; run directory by following these steps:
*# Modify the <tt>input.geos</tt> file for the nested grid simulation. Complete instructions can be found on [[Setting_up_GEOS-Chem_nested_grid_simulations|this wiki page]].
*# Regrid the restart file(s) using the [http://acmg.seas.harvard.edu/gamap/doc/by_category/Regridding.html GAMAP regridding routines]. For example, [http://acmg.seas.harvard.edu/gamap/doc/by_category/Regridding.html#REGRIDH_RESTART REGRIDH_RESTART] can be used to regrid the tracer restart file from one horizontal resolution to another. You can then use [http://acmg.seas.harvard.edu/gamap/doc/by_alphabet/gamap_c.html#CREATE_NESTED CREATE_NESTED] to crop the restart file to your nested domain (CH, EU, or NA).

* You can create a [[MERRA]] run directory from a [[GEOS-5]] or [[GEOS-FP]] run directory, since all three met fields have the same horizontal and vertical resolution. Gabriele Curci found found that the following procedure can be used to create a MERRA run directory from a GEOS-FP run directory (using a <tt>geosfp_4x5_UCX</tt> run directory as an example).
*#[[#Generating_a_GEOS-Chem_Run_Directory|Create a run directory]] for GEOS-FP using <tt>gcCopyRunDirs</tt>
*#Type <tt>cp -R geosfp_4x5_UCX merra_4x5_UCX</tt>
*#Type <tt>cd merra_4x5_UCX</tt>
*#Type <tt>rename geosfp merra *</tt>
*#Open <tt>input.geos</tt> in a text editor and change all the occurrences of "geosfp" to "merra"
*#Type <tt>make superclean</tt>
*#Type <tt>make distclean in the Code dir</tt>
*#[[#Compiling_and_Running_GEOS-Chem|Compile and run]]

* If you would like to run a simulation and the run directory is not available in the Unit Tester, you can follow these steps:
*# Modify the <tt>input.geos</tt> file for your simulation type following the relevant checklist in [http://acmg.seas.harvard.edu/geos/doc/man/contents.html# Chapter 6 of the GEOS-Chem Manual].
*# Create a "fake" restart file using GAMAP routine [http://acmg.seas.harvard.edu/gamap/doc/by_alphabet/gamap_m.html#MAKE_RESTART MAKE_RESTART].
*# Alternatively, you can send an email to the relevant [http://acmg.seas.harvard.edu/geos/geos_working_groups.html Working Group] to see if another member can provide you with a run directory or restart file.

*The [[GEOS-Chem Unit Tester]] can be used to create run directories for [[GEOS-Chem v10-01]] and later versions. If you wish to download a run directory for an older version of GEOS-Chem, you can follow [http://acmg.seas.harvard.edu/geos/doc/archive/man.v9-02/chapter_2.html#DownRun these instructions].

--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 18:42, 26 August 2015 (UTC)

== Compiling and Running GEOS-Chem ==

Once you have created one or more GEOS-Chem run directories, you may use them for your GEOS-Chem simulations.  First, double-check that the settings in the <tt>input.geos</tt> and <tt>HEMCO_Config.rc</tt> files are correct for the simulation that you are trying to run. See the [http://manual.geos-chem.org/ GEOS-Chem Manual] for more information about setting simulation options.

Next, open the Makefile in a text editor and define the variables CODE_DIR, LOG_DIR, and VERSION specific to your simulation. CODE_DIR is the path to the GEOS-Chem source code you wish to use. LOG_DIR is the path to which you wish to send your log files. VERSION is text you wish to include as a prefix in your output log filename. You can also pass any of these three variables manually to the make command, overwriting the definitions stored in the Makefile. 

To start a GEOS-Chem simulation, type the following commands. (We'll use the example of the <tt>geosfp_4x5_fullchem</tt> simulation, from the previous sections.)

 make -j4 TRACEBACK=y mp

The above command turns on traceback for debugging and invokes the <tt>mp</tt> target in the Makefile. This compiles the source code at path CODE_DIR with [[Parallelizing_GEOS-Chem|OpenMP parallelization]] and then runs the resultant GEOS-Chem executable using the simulation settings in the configuration files. The suffix <tt>.mp</tt> is included in each output filename to indicate that you enabled OpenMP parallelization for your GEOS-Chem run. 

There are many other targets you may use with make. For example, you can use target <tt>sp</tt> to compile and run code using a single processor rather than multiple processors. This is useful for generating a baseline from which you can diagnose and debug parallelization errors. Output files will have a <tt>.sp</tt> rather than <tt>.mp</tt> suffix to distinguish them from the OpenMP parallelized run output. Alternatively, you can build GEOS-Chem source code without running a simulation (<tt>mpbuild</tt> or <tt>spbuild</tt>) or run a simulation without rebuilding (<tt>mprun</tt> or <tt>sprun</tt>). There are also several housekeeping targets that clean the run directory (e.g. <tt>mpdataclean</tt>, <tt>mpexeclean</tt>, <tt>mplogclean</tt>, and <tt>mpclean</tt>) and the source code (e.g. <tt>realclean</tt>). 

See the <tt>Makefile</tt> for all make options and the [[GEOS-Chem_Makefile_Structure|GEOS-Chem Makefile Structure wiki page]] wiki page for more information about compiling GEOS-Chem and using the run directory Makefile.

--[[User:Lizzie Lundgren|Lizzie Lundgren]] 13:12, 15 April 2015 (EDT)

== 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 full-chemistry simulation example, the following files are output:

{| border=1 cellspacing=0 cellpadding=5 
|-bgcolor="#CCCCCC"
!width="350px"|File
!width="750px"|Description

|-valign="top"
|<tt>trac_avg.geosfp_4x5_fullchem.YYYYMMDDhh.mp</tt> or<br><tt>trac_avg.geosfp_4x5_fullchem.YYYYMMDDhh.sp</tt>
|Diagnostic output file that contains time-averaged output for diagnostics enabled in <tt>input.geos</tt>.

<b>Data in this file are in [http://acmg.seas.harvard.edu/gamap/doc/Chapter_6.html#6.2 "binary punch" format] and may be viewed and manipulated using [http://acmg.seas.harvard.edu/gamap GAMAP].</b>

|-valign="top"
|<tt>trac_rst.geosfp_4x5_fullchem.YYYYMMDDhhmm.mp</tt> or<br><tt>trac_rst.geosfp_4x5_fullchem.YYYYMMDDhhmm.sp</tt>
|Tracer restart file that contains instantaneous tracer concentrations at simulation end time. This file saves instantaneous concentrations of all transported tracers (listed in the [http://acmg.seas.harvard.edu/geos/doc/man/chapter_5.html#TracerMenu Tracer Menu] of <tt>input.geos</tt>) on all levels and may be used to initialize another GEOS-Chem simulation. 

<b>Data in this file are in [http://acmg.seas.harvard.edu/gamap/doc/Chapter_6.html#6.2 "binary punch" format] and may be viewed and manipulated using [http://acmg.seas.harvard.edu/gamap/ GAMAP].</b>

|-valign="top"
|<tt>HEMCO_restart.YYYYMMDDhh.nc.mp</tt> or<br><tt>HEMCO_restart.YYYYMMDDhh.nc.sp</tt>
|HEMCO restart file containing several quantities tracked by HEMCO for use in initializing another GEOS-Chem simulation. This file includes data used to calculate [[Hudman_et_al_2012_soil_NOx_emissions_algorithm|soil NOx emissions]], [[Ship_emissions#PARANOX_ship_plume_model|PARANOX ship plume chemistry]], and [[MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions|MEGAN biogenic emissions]].

<b>Data in this file are in [http://www.unidata.ucar.edu/software/netcdf/docs/faq.html#whatisit netcdf format].</b>

|-valign="top"
|<tt>v10-01.geosfp_4x5_fullchem.mp</tt> or<br><tt>v10-01.geosfp_4x5_fullchem.sp</tt>
|GEOS-Chem simulation log file.

<b>Open this file in a text editor to diagnose compile and run errors.</b>

|-valign="top"
|<tt>HEMCO.log.mp</tt> or<br><tt>HEMCO.log.sp</tt>
|HEMCO log file containing detailed information about the emissions read from disk into HEMCO.

<b>Open this file in a text editor to diagnose HEMCO errors.</b>

|-valign="top"
|<tt>smv2.log</tt>
|SMVGEAR II log file containing information about reactions and species used by the ND65 prod-loss diagnostic. This file is only produced when SMVGEAR, and thus it will not be created for the [[GEOS-Chem_chemistry_mechanisms#Specialty_simulations|specialty simulations]].

<b>Open this file in a text editor to see if SMVGEAR read the [http://acmg.seas.harvard.edu/geos/doc/man/chapter_5.html#Globchem <tt>globchem.dat</tt>] file properly.</b>

|-valign="top"
|<tt>diaginfo.dat</tt>
|File generated by GEOS-Chem that contains diagnostic quantities for use with [http://acmg.seas.harvard.edu/gamap/ GAMAP].

|-valign="top"
|<tt>tracerinfo.dat</tt>
|File generated by GEOS-Chem that contains tracer name metadata for use with [http://acmg.seas.harvard.edu/gamap/ GAMAP].
|}


Additional files may be created by GEOS-Chem, depending on your simulation type and the options specified in the <tt>input.geos</tt> file. Other optional GEOS-Chem output files include:

{| border=1 cellspacing=0 cellpadding=5 
|-bgcolor="#CCCCCC"
!width="350px"|File
!width="750px"|Description

|-valign="top"
|<tt>spec_rst.geosfp_4x5_fullchem.YYYYMMDDhh</tt>
|Species restart file that contains instantaneous species concentrations at simulation end time. This file saves instantaneous concentrations of all chemical species (listed in [http://acmg.seas.harvard.edu/geos/doc/man/chapter_5.html#Globchem <tt>globchem.dat</tt>]) on all levels and may be used to initialize another GEOS-Chem simulation. 

NOTE: If you are going to be running a very long GEOS–Chem simulation and must split your simulation into several stages (i.e. in order to stay within the computational time limits of your system), then you should set LSVCSPEC to T in the [http://acmg.seas.harvard.edu/geos/doc/man/chapter_5.html#ChemMenu Chemistry Menu] of <tt>input.geos</tt>. That will make sure that the chemical species concentrations are preserved when the next run stage starts. Otherwise, GEOS-Chem use the default species concentrations specified in globchem.dat at the beginning of each run.

<b>Data in this file are in [http://acmg.seas.harvard.edu/gamap/doc/Chapter_6.html#6.2 "binary punch" format] and may be viewed and manipulated using [http://acmg.seas.harvard.edu/gamap/ GAMAP].</b>

|-valign="top"
|<tt>stations.YYYYMMDDhh</tt>
|Diagnostic output file that contains ND48 station timeseries output as specified in <tt>input.geos</tt>.

<b>Data in this file are in [http://acmg.seas.harvard.edu/gamap/doc/Chapter_6.html#6.2 "binary punch" format] and may be viewed and manipulated using [http://acmg.seas.harvard.edu/gamap/ GAMAP]. For more information on working with ND48 timeseries output, see our [http://acmg.seas.harvard.edu/gamap/doc/timeseries_brief_tutorial.pdf timeseries tutorial].</b>

|-valign="top"
|<tt>tsYYYYMMDDhh.bpch</tt>
|Diagnostic output file that contains ND49 instantaneous timeseries output as specified in <tt>input.geos</tt>.

<b>Data in this file are in [http://acmg.seas.harvard.edu/gamap/doc/Chapter_6.html#6.2 "binary punch" format] and may be viewed and manipulated using [http://acmg.seas.harvard.edu/gamap/ GAMAP]. For more information on working with ND49 timeseries output, see our [http://acmg.seas.harvard.edu/gamap/doc/timeseries_brief_tutorial.pdf timeseries tutorial].</b>

|-valign="top"
|<tt>ts_24hr_avg.YYYYMMDDhh.bpch</tt>
|Diagnostic output file that contains ND50 24-hour average timeseries output as specified in <tt>input.geos</tt>.

<b>Data in this file are in [http://acmg.seas.harvard.edu/gamap/doc/Chapter_6.html#6.2 "binary punch" format] and may be viewed and manipulated using [http://acmg.seas.harvard.edu/gamap/ GAMAP].</b>

|-valign="top"
|<tt>ts_satellite.YYYYMMDDhh.bpch</tt>
|Diagnostic output file that contains ND51 local-time-average (satellite) timeseries output as specified in <tt>input.geos</tt>.

<b>Data in this file are in [http://acmg.seas.harvard.edu/gamap/doc/Chapter_6.html#6.2 "binary punch" format] and may be viewed and manipulated using [http://acmg.seas.harvard.edu/gamap/ GAMAP].</b>

|-valign="top"
|<tt>paranox_ts.YYYYMMDDhh.bpch</tt>
|Diagnostic output file that contains ND63 ship timeseries output as specified in <tt>input.geos</tt>.

<b>Data in this file are in [http://acmg.seas.harvard.edu/gamap/doc/Chapter_6.html#6.2 "binary punch" format] and may be viewed and manipulated using [http://acmg.seas.harvard.edu/gamap/ GAMAP].</b>

|-valign="top"
|<tt>ocean_rst.YYYYMMDDhhmm.nc</tt>
|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|mercury simulation]]. 

<b>Data in this file are in the in [http://www.unidata.ucar.edu/software/netcdf/docs/faq.html#whatisit netcdf format].</b>

|-valign="top"
|<tt>plane.log.YYYYMMDD</tt?>
|Diagnostic output file containing planeflight information scheduled via the [http://acmg.seas.harvard.edu/geos/doc/man/chapter_5.html#Planeflight <tt>Planeflight.dat</tt>] file. This diagnostic is turned on in the Planeflight Menu of <tt>input.geos</tt>.

<b>The data in this text file can be read and plotted using GAMAP routines [http://acmg.seas.harvard.edu/gamap/doc/by_alphabet/gamap_c.html#CTM_READ_PLANEFLIGHT <tt>CTM_READ_PLANEFLIGHT</tt>] and [http://acmg.seas.harvard.edu/gamap/doc/by_alphabet/gamap_p.html#PLANE_PLOT <tt>PLANE_PLOT</tt>].

|}

--[[User:Melissa Payer|Melissa Sulprizio]] 15:42, 3 April 2015 (EDT)