Difference between revisions of "Creating GEOS-Chem run directories"

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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. 
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__FORCETOC__
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'''''[[Downloading_data_from_Amazon_Web_Services_cloud_storage|Previous]] | [[GEOS-Chem configuration files|Next]] | [[Getting Started with GEOS-Chem]]'''''
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#[[Minimum system requirements for GEOS-Chem|Minimum system requirements (and software installation)]]
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#[[Configuring your computational environment]]
 +
#[[Downloading GEOS-Chem source code|Downloading source code]]
 +
#[[Downloading GEOS-Chem data directories|Downloading data directories]]
 +
#<span style="color:blue">'''Creating run directories'''</span>
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#[[GEOS-Chem configuration files|Configuring runs]]
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#[[Compiling GEOS-Chem|Compiling]]
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#[[Running GEOS-Chem|Running]]
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#[[GEOS-Chem output files|Output files]]
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#[[Python tools for use with GEOS-Chem]]
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#[[GEOS-Chem_coding_and_debugging|Coding and debugging]]
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#[[GEOS-Chem_overview#Further_reading|Further reading]]
  
== 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.)
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The method that you will use to download run directories changed in [[GEOS-Chem 13.0.0]].   
  
Next, clone the [[GEOS-Chem Unit Tester]] package with the command:
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== For GEOS-Chem 13.0.0 and later versions ==
  
git clone -b v10-01-Release git://git.as.harvard.edu/bmy/GEOS-Chem-UnitTest UT
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This content has been migrated to the [https://geos-chem.readthedocs.io/en/latest/gcc-guide/02-build/create-rundir.html '''Create a run directory''' chapter of <tt>geos-chem.readthedocs.io</tt>.]
  
This will create a copy of the GEOS-Chem Unit Tester package in a directory named <tt>UT</tt> for short.
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== For GEOS-Chem 12.9.3 and prior versions ==
  
The option
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<span style="color:red"><big><strong>NOTE: The GEOS-Chem Unit Tester was retired for GEOS-Chem 13.0.0 and later versions.<br>
 +
This content is now outdated, but we will preserve it here for reference.</strong></big></span>
 +
----
  
  -b v10-01-Release
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First, make sure that your system [[Unit_Tester_for_GEOS-Chem_12#Requirements|has these software packages installed]]. (Most of these come standard with your Unix-based operating system.)
  
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]].
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Next, clone the [[GEOS-Chem Unit Tester]] package with these commands:
  
''NOTE: The Git clone process may take a few of minutes to complete, depending on your connection speed.''
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git clone <nowiki>https://github.com/geoschem/geos-chem-unittest</nowiki> UT
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cd UT
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git checkout master
  
--[[User:Bmy|Bob Y.]] 12:25, 1 May 2015 (EDT)
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This will download a fresh copy of the <tt>GEOS-Chem-UnitTest</tt> repository into a directory named <tt>UT</tt>, and place you in the '''master''' branch.  The '''master''' branch always corresponds to the last benchmarked GEOS-Chem version.
  
== Available run directories ==
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If you would like to check out the Unit Tester that corresponds to a specific numbered GEOS-Chem version you can type one of the following commands:
  
=== Benchmark run directory ===
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git checkout 12.0.0
 +
git checkout v11-02-rc
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git checkout v11-02e
  
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.  
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etc.
  
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>:
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''NOTE: The Git clone process may take a few minutes to complete depending on your connection speed.''
  
  geosfp  4x5        -     benchmark    2013070100  2013080100  UCX=y
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--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 21:10, 21 June 2018 (UTC)
  
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:
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== Available run directories ==
  
make -j4 mp
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=== Benchmark run directory ===
  
To compile only, type:
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The [[GEOS-Chem Unit Tester]] includes a run directory called '''4x5_standard''' (GEOS-Chem v11-01 and later) or '''4x5_benchmark''' (GEOS-Chem v10-01). The standard [http://acmg.seas.harvard.edu/geos/geos_benchmark.html GEOS-Chem benchmark simulation] utilizes the [[GEOS-FP]] met fields ([[GEOS-Chem_horizontal_grids#GMAO_4_x_5_grid|4&deg; x 5 &deg;]], [[GEOS-Chem_vertical_grids#72-layer_vertical_grid|72 levels]]) with the [[#UCX chemistry mechanism|UCX tropospheric-stratospheric chemistry mechanism]] and [[Secondary organic aerosols|secondary organic aerosols]] included.
  
make -j4 mpbuild
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To reproduce our latest 1-month benchmark simulation, you can edit the <tt>CopyRunDirs.input</tt> file so that the following line is uncommented under <tt>RUNS</tt>:
  
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.
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  geosfp  4x5        -     benchmark     2016070100  2016080100  -
  
'''''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.'''''
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Make sure to check the start and end date so that your simulation will run for July 2016. 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 the GEOS-Chem source code, type:
  
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 19:38, 23 June 2015 (UTC)
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make -j4 build
  
=== Other run directories ===
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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.
  
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]].
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For older versions of GEOS-Chem, the compile command was formerly
  
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.
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make -j4 mpbuild
  
{| border=1 cellspacing=0 cellpadding=5
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=== Other run directories ===
|-bgcolor="#CCCCCC"
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!width="100px"|Met field
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!width="175px"|Grid
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!width="100px"|[[NOx-Ox-HC-aerosol|NOx-Ox-<br>HC-aerosol]]
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!width="100px"|[[UCX chemistry mechanism|UCX]]
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!width="100px"|[[Coupling GEOS-Chem with RRTMG|RRTMG]]
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!width="100px"|[[Secondary organic aerosols|soa]]
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!width="100px"|[[Secondary organic aerosols#SOA simulation with semi-volatile POA|soa_svpoa]]
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!width="100px"|[[Rn-Pb-Be simulation|RnPbBe]]
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!width="100px"|[[Mercury|Hg]]
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!width="100px"|[[POPs simulation|POPs]]
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!width="100px"|[[Tagged CO simulation|tagCO]]
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!width="100px"|[[Tagged O3 simulation|tagO3]]
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!width="100px"|[[CH4 simulation|CH4]]
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!width="100px"|[[CO2 simulation|CO2]]
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!width="100px"|[[Aerosol-only simulation|aerosol]]
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!width="100px"|[[TOMAS aerosol microphysics|TOMAS40]]
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|-valign="top"
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|[[GEOS-FP|geosfp]]
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|[http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_4x5 4x5]
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|-valign="top"
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|[[GEOS-FP|geosfp]]
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|[http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_2x25 2x25]
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|
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|-valign="top"
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|[[GEOS-FP|geosfp]]
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|[http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_025_CH 025x03125<br>CH]
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|bgcolor="#00FF00"|
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|-valign="top"
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|[[GEOS-FP|geosfp]]
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|[http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_025_NA 025x03125<br>NA]
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|bgcolor="#00FF00"|
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|-bgcolor="#CCCCCC" height="10px"
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|-valign="top"
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|[[GEOS-5|geos5]]
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|[http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_4x5 4x5]
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|-valign="top"
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|[[GEOS-5|geos5]]
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|[http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_2x25 2x25]
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|
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|-valign="top"
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|[[GEOS-5|geos5]]
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|[http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_05_CH 05x0666<br>CH]
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|bgcolor="#00FF00"|
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|-valign="top"
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|[[GEOS-5|geos5]]
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|[http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_05_NA 05x0666<br>NA]
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|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"
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|[[MERRA|merra]]
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|[http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_4x5 4x5]
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|-valign="top"
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|[[MERRA|merra]]
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|[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"
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|[[GEOS-4|geos4]]
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|[http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_4x5 4x5]
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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|-bgcolor="#CCCCCC" height="10px"
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|-valign="top"
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|[[GCAP|gcap]]
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|[http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GCAP_4x5 4x5]
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|bgcolor="#00FF00"|
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|bgcolor="#00FF00"|
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'''LEGEND'''
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{| border=1 cellspacing=0 cellpadding=5
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|-valign="top"
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|width="75px" bgcolor="#00FF00"|
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|width="250px"|Run directory is available
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|-valign="top"
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|bgcolor="#FFFF00"|
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|Run directory is in need of updating
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|-valign="top"
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|bgcolor="#FF0000"|
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|Run directory is obsolete 
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|-valign="top"
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|
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|Run directory is not available
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|}
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--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 17:36, 26 May 2015 (UTC)
+
Run directories are provided for a combination of met field, grid, and simulation type and are named accordingly. For more details on the simulation types, please see our [[GEOS-Chem chemistry mechanisms|''GEOS-Chem chemistry mechanism'' wiki page]].
  
 
== Editing the CopyRunDirs.input file ==
 
== Editing the CopyRunDirs.input file ==
Line 389: Line 80:
  
 
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.   
 
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.   
 +
 +
<span style="color:red">'''IMPORTANT:''' The <tt>CopyRunDirs.input</tt> file that comes with the Unit Tester provides only a small sample of the possible run directories that you can create. You can add as many entries to the <tt>RUNS</tt> section as you wish. See the <tt>UnitTest.input</tt> file for a complete list of all possible run directories that you can add to <tt>CopyRunDirs.input</tt>.</span>
  
 
Your <tt>CopyRunDirs.input</tt> file will look something like this:
 
Your <tt>CopyRunDirs.input</tt> file will look something like this:
Line 401: Line 94:
 
  #\\
 
  #\\
 
  #\\
 
  #\\
  # !REMARKS:
+
  # !REMARKS:
  #  Customize the run directory for your system by specifying these values:
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  #  For a complete description of how to customize the settings in the
  #  -------------------------------------------------------------------
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  #  INPUTS and RUNS sections, see the following wiki posts:
#  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
+
  #  wiki.geos-chem.org/Creating_GEOS-Chem_run_directories#Section_1:_INPUTS
  # COPY_PATH   : Local path where run directory will be copied to
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  #   wiki.geos-chem.org/Creating_GEOS-Chem_run_directories#Section_2:_RUNS
#  DATA_ROOT  : Root GEOS-Chem data directory
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# HEMCO_ROOT  : Root directory where HEMCO emissions data files are stored
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  # RUN_ROOT    : Unit test run directories are subdirectories of RUN_ROOT
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#  RUN_DIR    : Individual unit test run directory path
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#  PERL_DIR    : Unit Test perl script directory (i.e. this directory)
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# COPY_CMD    : Unix copy command with optional tags
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#  VERBOSE    : HEMCO verbose level  (0=no output, 3=max output)
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#  WARNINGS    : HEMCO warnings level (0=no warnings, 3=max warnings)
+
 
  #
 
  #
  # !REVISION HISTORY:
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  # !REVISION HISTORY:  
 
  #  18 Mar 2015 - R. Yantosca - Initial version
 
  #  18 Mar 2015 - R. Yantosca - Initial version
 
  #  19 Mar 2015 - E. Lundgren - Simplify content for only copying run dirs
 
  #  19 Mar 2015 - E. Lundgren - Simplify content for only copying run dirs
 +
#  19 May 2015 - R. Yantosca - Now can specify VERBOSE and WARNINGS options
 
  #EOP
 
  #EOP
 
  #------------------------------------------------------------------------------
 
  #------------------------------------------------------------------------------
Line 424: Line 110:
 
  # !INPUTS:
 
  # !INPUTS:
 
  #
 
  #
     VERSION     : v10-01
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# %%% ID tags %%%
     DESCRIPTION : Create run directory from UnitTest
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#
     COPY_PATH  : /home/{USER}/GC/rundirs
+
     VERSION       : v11-01
    DATA_ROOT  : /as/data/geos/ExtData
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     DESCRIPTION   : Create run directory from UnitTest
     HEMCO_ROOT : {DATAROOT}/HEMCO
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#
     RUN_ROOT    : /home/{USER}/UT/runs
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# %%% Data path and HEMCO settings %%%
     RUN_DIR     : {RUNROOT}/{RUNDIR}
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#
     PERL_DIR   : /home/{USER}/UT/perl
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     DATA_ROOT      : /n/holylfs/EXTERNAL_REPOS/GEOS-CHEM/gcgrid/data/ExtData
     COPY_CMD   : cp -rfL
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     HEMCO_ROOT     : {DATAROOT}/HEMCO
    VERBOSE    : 0
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     VERBOSE        : 0
    WARNINGS    : 1
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    WARNINGS      : 1
 +
#
 +
# %%% Unit tester path names %%%
 +
#
 +
    UNIT_TEST_ROOT : {HOME}/UT
 +
    RUN_ROOT      : {UTROOT}/runs
 +
     RUN_DIR       : {RUNROOT}/{RUNDIR}
 +
     PERL_DIR       : {UTROOT}/perl
 +
#
 +
# %%% Target directory and copy command %%%
 +
#
 +
    COPY_PATH      : {HOME}/GC/rundirs
 +
     COPY_CMD       : cp -rfL
 
  #
 
  #
 
  # !RUNS:
 
  # !RUNS:
  #  Specify the debugging runs that you want to perform below.
+
  #  Specify the runs directories that you want to copy below.
 
  #  Here we provide a few examples, but you may copy additional entries from
 
  #  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
 
  #  UnitTest.input and modify the dates as needed. You can deactivate copying
Line 445: Line 143:
 
  # MET    | GRID      | NEST | SIMULATION | START DATE | END DATE  | EXTRA?  |
 
  # MET    | GRID      | NEST | SIMULATION | START DATE | END DATE  | EXTRA?  |
 
  #--------|-----------|------|------------|------------|------------|---------|
 
  #--------|-----------|------|------------|------------|------------|---------|
   geosfp  4x5        -      fullchem     2013070100  2013070101   -
+
   geosfp  4x5        -      standard     2013070100  2013080100   -
   geosfp  4x5        -      soa          2013070100  2013070101  -
+
# geosfp  4x5        -      gc_timing   2013070100  2013070800  -
  geosfp  4x5        -      soa_svpoa    2013070100  2013070101  -
+
# geosfp  4x5        -      tropchem    2013070100  2013070101  -
  geosfp  4x5        -      UCX          2013070100  2013070101  UCX=y
+
# geosfp  4x5        -      soa          2013070100  2013070101  -
  geosfp  4x5        -      RRTMG        2013070100  2013070101  RRTMG=y
+
# geosfp  4x5        -      soa_svpoa    2013070100  2013070101  -
  geosfp  4x5        -      RnPbBe      2013070100  2013070101  -
+
# geosfp  4x5        -      aciduptake  2013070100  2013070101  -
  geosfp  4x5        -      Hg          2013070100   2013070101   -
+
# geosfp  4x5        -      UCX          2013070100  2013070101  -
  geosfp  4x5        -      POPs        2013070100  2013070101  -
+
# geosfp  4x5        -      RRTMG        2013070100  2013070101  -
  geosfp  4x5        -      CH4          2013070100  2013070101  -
+
# geosfp  4x5        -      RnPbBe      2013070100  2013070101  -
  geosfp  4x5        -      tagO3        2013070100  2013070101  -
+
# geosfp  4x5        -      Hg          2013010100   2013010101   -
  geosfp  4x5        -      tagCO        2013070100  2013070101  -
+
# geosfp  4x5        -      POPs        2013070100  2013070101  -
  geosfp  2x25        -      CO2          2013070100  201307010030 -
+
# geosfp  4x5        -      TOMAS40      2013070100  2013070101  -
  geosfp  4x5        -      aerosol      2013070100  2013070101  -  
+
# geosfp  4x5        -      CH4          2013070100  2013070101  -
  geosfp  025x03125  ch    fullchem     2013070100  201307010010 -
+
# geosfp  4x5        -      tagO3        2013070100  2013070101  -
  geosfp  025x03125  na    fullchem     2013070100  201307010010 -
+
# geosfp  4x5        -      tagCO        2013070100  2013070101  -
 +
# geosfp  2x25        -      CO2          2013070100  201307010030 -
 +
# geosfp  4x5        -      aerosol      2013070100  2013070101  -  
 +
# geosfp  025x03125  ch    tropchem     2013070100  201307010010 -
 +
# geosfp  025x03125  na    tropchem     2013070100  201307010010 -
 +
# gchp    4x5        -      tropchem    2013070100  2013070101  -
 
  !END OF RUNS:
 
  !END OF RUNS:
 
  #EOP
 
  #EOP
Line 484: Line 187:
 
|<tt>DESCRIPTION</tt>
 
|<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.
 
|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"
 
|-valign="top"
Line 493: Line 192:
 
|Specifies the path for your root-level data directory.   
 
|Specifies the path for your root-level data directory.   
  
|-valign="top"http://wiki.seas.harvard.edu/geos-chem/skins//common/images/button_nowiki.png
+
|-valign="top"
 
|<tt>HEMCO_ROOT</tt>
 
|<tt>HEMCO_ROOT</tt>
 
|Specifies the top-level path for the [[HEMCO data directories|HEMCO data directory tree]].
 
|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.   
 
*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>
 
<b>Leave this as-is.</b>
 +
 +
|-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>
 +
 +
|-valign="top"
 +
|<tt>UNIT_TEST_ROOT</tt>
 +
|Specifies the path to the GEOS-Chem Unit Tester.
  
 
|-valign="top"
 
|-valign="top"
 
|<tt>RUN_ROOT</tt>
 
|<tt>RUN_ROOT</tt>
 
|Specifies the top-level unit test run directories.   
 
|Specifies the top-level unit test run directories.   
 +
<b>Leave this as-is.</b>
 +
 +
|-valign="top"
 +
|<tt>RUN_DIR</tt>
 +
|Specifies the run directory subdirectory.
 
<b>Leave this as-is.</b>
 
<b>Leave this as-is.</b>
  
Line 508: Line 226:
 
|Specifies the directory where the unit test Perl scripts are found.
 
|Specifies the directory where the unit test Perl scripts are found.
 
<b>Leave this as-is.</b>
 
<b>Leave this as-is.</b>
 +
 +
|-valign="top"
 +
|<tt>COPY_PATH</tt>
 +
|Specifies the directory on your disk server where copies of the GEOS-Chem run directories will be created.
  
 
|-valign="top"
 
|-valign="top"
Line 514: Line 236:
 
*The default setting is <tt>cp -rfL</tt>.  This will create a new copy of the directory, even if the prior copy exists.  
 
*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.
 
*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 ===
 
=== Section 2: RUNS ===
Line 543: Line 253:
 
  # MET    | GRID      | NEST | SIMULATION | START DATE | END DATE  | EXTRA?  |
 
  # MET    | GRID      | NEST | SIMULATION | START DATE | END DATE  | EXTRA?  |
 
  #--------|-----------|------|------------|------------|------------|---------|
 
  #--------|-----------|------|------------|------------|------------|---------|
   geosfp  4x5        -      fullchem     2013070100  2013070101   -
+
   geosfp  4x5        -      standard     2013070100  2013080100   -
  
will tell the <tt>gcCopyRunDirs</tt> script to create a run directory for a GEOS-Chem simulation using:
+
will tell the <tt>gcCopyRunDirs</tt> script to create a run directory for a GEOS-Chem simulation with the following settings:
  
*[[GEOS-FP]] met fields
+
*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]
+
*On the [[GEOS-Chem_horizontal_grids#GMAO_4_x_5_grid|4&deg; x 5&deg; GEOS-Chem horizontal grid]]
 
*For the [[NOx-Ox-HC-aerosol|GEOS-Chem standard full-chemistry simulation]]
 
*For the [[NOx-Ox-HC-aerosol|GEOS-Chem standard full-chemistry simulation]]
 
*Starting at 00:00 GMT on 2013/07/01
 
*Starting at 00:00 GMT on 2013/07/01
*Ending at 01:00 GMT on 2013/07/01
+
*Ending at 00:00 GMT on 2013/08/01
  
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.
+
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 [[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.
+
You can add as many entries to the RUNS section as you wish. See the <tt>UnitTest.input</tt> file for a complete list of all possible run directories entries that you can add to <tt>CopyRunDirs.input</tt>.
  
== Generating a GEOS-Chem run directory ==
+
== 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:
 
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
+
  ./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 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 modified.   
  
 
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>.
 
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>.
Line 569: Line 279:
 
  cp CopyRunDirs.input CopyRunDirs.fullchem  # Input file set up to only copy the full-chemistry run directories
 
  cp CopyRunDirs.input CopyRunDirs.fullchem  # Input file set up to only copy the full-chemistry run directories
 
    
 
    
  gcCopyRunDirs CopyRunDirs.Hg               
+
  ./gcCopyRunDirs CopyRunDirs.fullchem           
  
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.
+
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> section.  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:
+
Let's examine the contents of a sample <tt>geosfp_4x5_standard</tt> run directory.  Navigate to your newly created run directory and tssue 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
 
  make fileclean                      # Remove any files left over from previous unit test runs
 
   
 
   
  ls -l                               # Get detailed directory listing
+
  ls -1                               # Get directory listing
  
 
And you will see this directory listing:
 
And you will see this directory listing:
  
  -rw-r--r-- 1 mpayer mpayer    7862 2015-04-03 15:19 FJX_j2j.dat
+
  benchmark.run
  -rw-r--r-- 1 mpayer mpayer    44808 2015-04-03 15:19 FJX_spec.dat
+
  GEOSChem.Restart.20160701_0000z.nc4
-rw-r--r-- 1 mpayer mpayer  186359 2015-04-03 15:19 HEMCO_Config.rc
+
  getRunInfo
-rw-r--r-- 1 mpayer mpayer    4872 2015-04-03 15:19 Makefile
+
  HEMCO_Config.rc
-rw-r--r-- 1 mpayer mpayer      783 2015-04-03 15:19 README
+
  HEMCO_Diagn.rc
-rw-r--r-- 1 mpayer mpayer      610 2015-04-03 15:19 chemga.dat
+
  HISTORY.rc
  -rw-r--r-- 1 mpayer mpayer    42186 2015-04-03 15:19 dust.dat
+
  input.geos
  -rwxr-xr-x 1 mpayer mpayer    1458 2015-04-03 15:19 getEnd.pl*
+
  Makefile
  -rwxr-xr-x 1 mpayer mpayer    1374 2015-04-03 15:19 getStart.pl*
+
  output/
  -rw-r--r-- 1 mpayer mpayer  199632 2015-04-03 15:19 globchem.dat
+
  README
  -rw-r--r-- 1 mpayer mpayer  401972 2015-04-03 15:19 initial_hemco_rst.geosfp_4x5_fullchem.nc
+
  validate
-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.''
 
''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 <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>. HEMCO and tracer restart files are also included in every run directory but care must be taken when using them. See the section below for more information about restart files.
  
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 probably 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)
+
----
 +
'''''[[Downloading_data_from_Amazon_Web_Services_cloud_storage|Previous]] | [[GEOS-Chem configuration files|Next]] | [[Getting Started with GEOS-Chem]]'''''

Revision as of 18:36, 10 August 2022

Previous | Next | Getting Started with GEOS-Chem

  1. Minimum system requirements (and software installation)
  2. Configuring your computational environment
  3. Downloading source code
  4. Downloading data directories
  5. Creating run directories
  6. Configuring runs
  7. Compiling
  8. Running
  9. Output files
  10. Python tools for use with GEOS-Chem
  11. Coding and debugging
  12. Further reading


The method that you will use to download run directories changed in GEOS-Chem 13.0.0.

For GEOS-Chem 13.0.0 and later versions

This content has been migrated to the Create a run directory chapter of geos-chem.readthedocs.io.

For GEOS-Chem 12.9.3 and prior versions

NOTE: The GEOS-Chem Unit Tester was retired for GEOS-Chem 13.0.0 and later versions.
This content is now outdated, but we will preserve it here for reference.


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 these commands:

git clone https://github.com/geoschem/geos-chem-unittest UT
cd UT
git checkout master

This will download a fresh copy of the GEOS-Chem-UnitTest repository into a directory named UT, and place you in the master branch. The master branch always corresponds to the last benchmarked GEOS-Chem version.

If you would like to check out the Unit Tester that corresponds to a specific numbered GEOS-Chem version you can type one of the following commands:

git checkout 12.0.0
git checkout v11-02-rc
git checkout v11-02e

etc.

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

--Bob Yantosca (talk) 21:10, 21 June 2018 (UTC)

Available run directories

Benchmark run directory

The GEOS-Chem Unit Tester includes a run directory called 4x5_standard (GEOS-Chem v11-01 and later) or 4x5_benchmark (GEOS-Chem v10-01). The standard GEOS-Chem benchmark simulation utilizes the GEOS-FP met fields (4° x 5 °, 72 levels) with the UCX tropospheric-stratospheric chemistry mechanism and secondary organic aerosols included.

To reproduce our latest 1-month benchmark simulation, you can edit the CopyRunDirs.input file so that the following line is uncommented under RUNS:

 geosfp   4x5         -      benchmark     2016070100   2016080100   -

Make sure to check the start and end date so that your simulation will run for July 2016. You can then create the GEOS-Chem benchmark run directory by typing ./gcCopyRunDirs. Navigate to your the newly created geosfp_4x5_benchmark run directory. To compile the GEOS-Chem source code, type:

make -j4 build

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

For older versions of GEOS-Chem, the compile command was formerly

make -j4 mpbuild

Other run directories

Run directories are provided for a combination of met field, grid, and simulation type and are named accordingly. For more details on the simulation types, please see our GEOS-Chem chemistry mechanism wiki page.

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.

IMPORTANT: The CopyRunDirs.input file that comes with the Unit Tester provides only a small sample of the possible run directories that you can create. You can add as many entries to the RUNS section as you wish. See the UnitTest.input file for a complete list of all possible run directories that you can add to CopyRunDirs.input.

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:
#  For a complete description of how to customize the settings in the
#  INPUTS and RUNS sections, see the following wiki posts:
#
#   wiki.geos-chem.org/Creating_GEOS-Chem_run_directories#Section_1:_INPUTS
#   wiki.geos-chem.org/Creating_GEOS-Chem_run_directories#Section_2:_RUNS
#
# !REVISION HISTORY: 
#  18 Mar 2015 - R. Yantosca - Initial version
#  19 Mar 2015 - E. Lundgren - Simplify content for only copying run dirs
#  19 May 2015 - R. Yantosca - Now can specify VERBOSE and WARNINGS options
#EOP
#------------------------------------------------------------------------------
#
# !INPUTS:
#
# %%% ID tags %%%
#
   VERSION        : v11-01
   DESCRIPTION    : Create run directory from UnitTest
#
# %%% Data path and HEMCO settings %%%
#
   DATA_ROOT      : /n/holylfs/EXTERNAL_REPOS/GEOS-CHEM/gcgrid/data/ExtData
   HEMCO_ROOT     : {DATAROOT}/HEMCO
   VERBOSE        : 0
   WARNINGS       : 1
#
# %%% Unit tester path names %%%
#
   UNIT_TEST_ROOT : {HOME}/UT
   RUN_ROOT       : {UTROOT}/runs
   RUN_DIR        : {RUNROOT}/{RUNDIR}
   PERL_DIR       : {UTROOT}/perl
#
# %%% Target directory and copy command %%%
# 
   COPY_PATH      : {HOME}/GC/rundirs
   COPY_CMD       : cp -rfL
#
# !RUNS:
#  Specify the runs directories that you want to copy 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         -      standard     2013070100   2013080100   -
# geosfp   4x5         -      gc_timing    2013070100   2013070800   -
# geosfp   4x5         -      tropchem     2013070100   2013070101   -
# geosfp   4x5         -      soa          2013070100   2013070101   -
# geosfp   4x5         -      soa_svpoa    2013070100   2013070101   -
# geosfp   4x5         -      aciduptake   2013070100   2013070101   -
# geosfp   4x5         -      UCX          2013070100   2013070101   -
# geosfp   4x5         -      RRTMG        2013070100   2013070101   -
# geosfp   4x5         -      RnPbBe       2013070100   2013070101   -
# geosfp   4x5         -      Hg           2013010100   2013010101   -
# geosfp   4x5         -      POPs         2013070100   2013070101   -
# geosfp   4x5         -      TOMAS40      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     tropchem     2013070100   201307010010 -
# geosfp   025x03125   na     tropchem     2013070100   201307010010 -
# gchp     4x5         -      tropchem     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 (UnitTest.input located within this directory). 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. Each configurable input is described in the table below.

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.
DATA_ROOT Specifies the path for your root-level data directory.
HEMCO_ROOT Specifies the top-level path for the HEMCO data directory tree.
  • The {DATAROOT} token in HEMCO_ROOT will be replaced with the value you specify for RUN_ROOT option.

Leave this as-is.

VERBOSE 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: 0
WARNINGS Specifies the level of warning messages that will be sent to the HEMCO log file. (0=no warnings; 3=max warnings)
  • Recommended setting: 1
UNIT_TEST_ROOT Specifies the path to the GEOS-Chem Unit Tester.
RUN_ROOT Specifies the top-level unit test run directories.

Leave this as-is.

RUN_DIR Specifies the run directory subdirectory.

Leave this as-is.

PERL_DIR Specifies the directory where the unit test Perl scripts are found.

Leave this as-is.

COPY_PATH Specifies the directory on your disk server where copies of the GEOS-Chem run directories will be created.
COPY_CMD Specifies the command used to copy run directories from the GEOS-Chem Unit Tester to COPY_PATH.
  • The default setting is cp -rfL. This will create a new copy of the directory, even if the prior copy exists.
  • The -L option to the cp 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.

Section 2: RUNS

The layout of the RUNS section is identical to the RUNS section in the GEOS-Chem Unit Tester input file. This enables copying and pasting simulation settings text from UnitTest.input 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   4x5         -      standard     2013070100   2013080100   -

will tell the gcCopyRunDirs script to create a run directory for a GEOS-Chem simulation with the following settings:

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 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 RUNS section as you wish. See the UnitTest.input file for a complete list of all possible run directories entries that you can add to CopyRunDirs.input.

Generating a GEOS-Chem 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 modified.

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

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

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

Let's examine the contents of a sample geosfp_4x5_standard run directory. Navigate to your newly created run directory and tssue the following commands:

make fileclean                       # Remove any files left over from previous unit test runs

ls -1                                # Get directory listing

And you will see this directory listing:

benchmark.run
GEOSChem.Restart.20160701_0000z.nc4
getRunInfo
HEMCO_Config.rc
HEMCO_Diagn.rc
HISTORY.rc
input.geos
Makefile
output/
README
validate

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 in the Unit Tester. The Perl script getRunInfo is used by the Makefile to extract information about the simulation from input.geos. HEMCO and tracer restart files are also included in every run directory but care must be taken when using them. See the section below for more information about restart files.



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