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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.
| + | __FORCETOC__ |
| | + | '''''[[Downloading_data_from_Amazon_Web_Services_cloud_storage|Previous]] | [[Creating run directories for GEOS-Chem 13.0.0 and later|Next]] | [[Getting Started with GEOS-Chem]]''''' |
| | + | #[[Minimum system requirements for GEOS-Chem|Minimum system requirements]] |
| | + | #[[Installing required software]] |
| | + | #[[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> |
| | + | #*[[Creating run directories for GEOS-Chem 13.0.0 and later|... for GEOS-Chem 13.0.0 and later versions]] |
| | + | #*[[Creating run directories for GEOS-Chem 12.9.3 and prior|... for GEOS-Chem 12.9.3 and prior versions]] |
| | + | #[[GEOS-Chem configuration files|Configuring runs]] |
| | + | #[[Compiling GEOS-Chem|Compiling]] |
| | + | #[[Running GEOS-Chem|Running]] |
| | + | #[[GEOS-Chem output files|Output files]] |
| | + | #[[Python tools for use with GEOS-Chem]] |
| | + | #[[GEOS-Chem_coding_and_debugging|Coding and debugging]] |
| | + | #[[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.)
| + | == Overview == |
| | | | |
| − | Next, clone the [[GEOS-Chem Unit Tester]] package with the command:
| + | The method that you will use to download run directories changed in [[GEOS-Chem 13.0.0]]. Detailed instructions for downloading GEOS-Chem source code may be found in the links below: |
| − | | + | |
| − | git clone <nowiki>https://bitbucket.org/gcst/geos-chem-unittest</nowiki> UT
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| − | 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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| − | ''NOTE: The Git clone process may take a few minutes to complete depending on your connection speed.''
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| − | --[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 15:12, 20 December 2016 (UTC)
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| − | == Available run directories ==
| + | |
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| − | === Benchmark run directory ===
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| − | The [[GEOS-Chem Unit Tester]] includes a run directory called '''4x5_standard''' (GEOS-Chem v11-01 and later) or '''geosfp_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° x 5 °]], [[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.
| + | |
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| − | To reproduce our latest [[GEOS-Chem_v11-01_benchmark_history#v11-01k|1-month benchmark simulation for v11-01]], you can edit the <tt>CopyRunDirs.input</tt> file so that the following line is uncommented under <tt>RUNS</tt>:
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| − | geosfp 4x5 - standard 2013070100 2013080100 -
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| − | 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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| − | make -j4 mp
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| − | To compile only, type:
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| − | make -j4 mpbuild
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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.
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| − | <span style="color:darkorange">'''''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.'''''</span>
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| − | --[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 19:38, 23 June 2015 (UTC)
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| − | === Other run directories ===
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| − | 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]].
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| − | The following table summarizes the run directories that are available in the [[GEOS-Chem Unit Tester]]. Please choose the run directories that are most relevant for your research.
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| − | {| border=1 cellspacing=0 cellpadding=5
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| − | |-bgcolor="#CCCCCC"
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| − | !width="100px"|Met field(s)
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| − | !width="200px"|Grid
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| − | !width="100px"|[[GEOS-Chem_chemistry_mechanisms#Mechanisms_in_GEOS-Chem_v10-01_and_later_versions|Standard]]
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| − | !width="100px"|[[NOx-Ox-HC-aerosol|Tropchem]]
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| − | !width="100px"|[[UCX chemistry mechanism|UCX]]
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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"|[[Mineral_dust_aerosols#Surface_chemistry_on_dust|AcidUptake]]
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| − | !width="100px"|[[Aerosol_emissions#Online_emission_of_marine_primary_organic_aerosol_.28POA.29|MarinePOA]]
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| − | !width="100px"|[[Coupling GEOS-Chem with RRTMG|RRTMG]]
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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"|[[Mercury|tagHg]]
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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|TOMAS15]]
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| − | !width="100px"|[[TOMAS aerosol microphysics|TOMAS40]]
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| − | |-valign="top"
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| − | |[[GEOS-FP]]<br>[[GEOS-5]]<br>[[MERRA]]<br>[[MERRA-2]]
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| − | |[[GEOS-Chem_horizontal_grids#GMAO_4_x_5_grid|4x5]]
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| − | |[[GEOS-FP]]<br>[[GEOS-5]]<br>[[MERRA]]<br>[[MERRA-2]]
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| − | |[[GEOS-Chem_horizontal_grids#GMAO_2_x_2.5_grid|2x2.5]]
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| − | |bgcolor="#00FF00"|
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| − | |bgcolor="#00FF00"|
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| − | |bgcolor="#00FF00"|
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| − | !colspan="21"|Nested grid simulations:
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| − | |-valign="top"
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| − | |[[GEOS-FP]]
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| − | |[[GEOS-Chem_horizontal_grids#0.25_x_0.3125_CH_nested_grid|025x03125<br>CH]]
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| − | |[[GEOS-FP]]
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| − | |[[GEOS-Chem_horizontal_grids#0.25_x_0.3125_NA_nested_grid|025x03125<br>NA]]
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| − | |[[GEOS-5]]
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| − | |[[GEOS-Chem_horizontal_grids#0.5_x_0.666_CH_nested_grid|05x0666<br>CH]]
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| − | |[[GEOS-5]]
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| − | |[[GEOS-Chem_horizontal_grids#0.5_x_0.666_NA_nested_grid|05x0666<br>NA]]
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| − | !colspan="21"|Other:
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| − | |-valign="top"
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| − | |[[GMAO_GEOS-4|GEOS-4]]
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| − | |[[GEOS-Chem_horizontal_grids#GMAO_4_x_5_grid|4x5]]
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| − | |[[GCAP]]
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| − | |[[GEOS-Chem_horizontal_grids#GMAO_4_x_5_grid|4x5]]
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| − | |}
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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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| − | |Run directory is not available
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| − | |}
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| − | --[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 20:10, 8 December 2016 (UTC)
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| − | == Editing the CopyRunDirs.input file ==
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| − | | + | |
| − | Once you have downloaded the GEOS-Chem Unit Tester to your disk space, switch to the <tt>perl/</tt> directory:
| + | |
| − | | + | |
| − | cd UT/perl
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| − | | + | |
| − | 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.
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| − | 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
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| − | # copying a run directory from the UnitTester.
| + | |
| − | #\\
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| − | #\\
| + | |
| − | # !REMARKS:
| + | |
| − | # For a complete description of how to customize the settings in the
| + | |
| − | # INPUTS and RUNS sections, see the following wiki posts:
| + | |
| − | #
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| − | # 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
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| − | #------------------------------------------------------------------------------
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| − | #
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| − | # !INPUTS:
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| − | #
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| − | # %%% ID tags %%%
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| − | #
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| − | VERSION : v11-01
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| − | DESCRIPTION : Create run directory from UnitTest
| + | |
| − | #
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| − | # %%% Data path and HEMCO settings %%%
| + | |
| − | #
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| − | DATA_ROOT : /n/holylfs/EXTERNAL_REPOS/GEOS-CHEM/gcgrid/data/ExtData
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| − | HEMCO_ROOT : {DATAROOT}/HEMCO
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| − | VERBOSE : 0
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| − | WARNINGS : 1
| + | |
| − | #
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| − | # %%% Unit tester path names %%%
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| − | #
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| − | UNIT_TEST_ROOT : {HOME}/UT
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| − | RUN_ROOT : {UTROOT}/runs
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| − | RUN_DIR : {RUNROOT}/{RUNDIR}
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| − | PERL_DIR : {UTROOT}/perl
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| − | #
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| − | # %%% Target directory and copy command %%%
| + | |
| − | #
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| − | COPY_PATH : {HOME}/GC/rundirs
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| − | COPY_CMD : cp -rfL
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| − | #
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| − | # !RUNS:
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| − | # 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 "#".
| + | |
| − | #
| + | |
| − | #--------|-----------|------|------------|------------|------------|---------|
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| − | # MET | GRID | NEST | SIMULATION | START DATE | END DATE | EXTRA? |
| + | |
| − | #--------|-----------|------|------------|------------|------------|---------|
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| − | geosfp 4x5 - standard 2013070100 2013080100 -
| + | |
| − | # geosfp 4x5 - gc_timing 2013070100 2013070800 -
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| − | # geosfp 4x5 - tropchem 2013070100 2013070101 -
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| − | # geosfp 4x5 - soa 2013070100 2013070101 -
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| − | # 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 -
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| − | # geosfp 4x5 - Hg 2013010100 2013010101 -
| + | |
| − | # geosfp 4x5 - POPs 2013070100 2013070101 -
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| − | # 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 -
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| − | # geosfp 025x03125 na tropchem 2013070100 201307010010 -
| + | |
| − | # gchp 4x5 - tropchem 2013070100 2013070101 -
| + | |
| − | !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 | | {| border=1 cellspacing=0 cellpadding=5 |
| − | |-bgcolor="#CCCCCC" | + | |- bgcolor="#CCCCCC" |
| − | !width="100px"|Option | + | !width="300px"|If you are using |
| − | !width="825px"|Description | + | !width="500px"|Then please read this chapter |
| | | | |
| | |-valign="top" | | |-valign="top" |
| − | |<tt>VERSION</tt> | + | |[[GEOS-Chem 13.0.0]] or later |
| − | |An ID tag that will be added to all log files and output files. | + | |''[[Creating run directories for GEOS-Chem 13.0.0 and later]]'' |
| | | | |
| | |-valign="top" | | |-valign="top" |
| − | |<tt>DESCRIPTION</tt> | + | |[[GEOS-Chem 12#12.9.3|GEOS-Chem 12.9.3]] or earlier |
| − | |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.
| + | |''[[Creating run directories for GEOS-Chem 12.9.3 and prior]]'' |
| − | | + | |
| − | |-valign="top"
| + | |
| − | |<tt>DATA_ROOT</tt>
| + | |
| − | |Specifies the path for your root-level data directory.
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | |<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>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"
| + | |
| − | |<tt>RUN_ROOT</tt>
| + | |
| − | |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>
| + | |
| − | | + | |
| − | |-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_PATH</tt>
| + | |
| − | |Specifies the directory on your disk server where copies of the GEOS-Chem run directories will be created.
| + | |
| − | | + | |
| − | |-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.
| + | |
| | | | |
| | |} | | |} |
| | | | |
| − | === 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 - standard 2013070100 2013080100 -
| |
| − |
| |
| − | will tell the <tt>gcCopyRunDirs</tt> script to create a run directory for a GEOS-Chem simulation with the following settings:
| |
| − |
| |
| − | *Using [[GEOS-FP]] met fields
| |
| − | *On the [[GEOS-Chem_horizontal_grids#GMAO_4_x_5_grid|4° x 5° GEOS-Chem horizontal grid]]
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| − | *For the [[NOx-Ox-HC-aerosol|GEOS-Chem standard full-chemistry simulation]]
| |
| − | *Starting at 00:00 GMT on 2013/07/01
| |
| − | *Ending at 00:00 GMT on 2013/08/01
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| − |
| |
| − | 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.'''
| |
| − |
| |
| − | <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>
| |
| − |
| |
| − | == 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
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| − |
| |
| − | 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.
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| − |
| |
| − | 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
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| − |
| |
| − | gcCopyRunDirs CopyRunDirs.Hg
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| − |
| |
| − | 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_standard</tt> 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
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| − |
| |
| − | ls -1 # Get directory listing
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| − |
| |
| − | And you will see this directory listing:
| |
| − |
| |
| − | brc.dat
| |
| − | dust.dat
| |
| − | FJX_j2j.dat
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| − | FJX_spec.dat
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| − | getRunInfo
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| − | h2so4.dat
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| − | HEMCO_Config.rc
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| − | HEMCO_restart.201307010000.nc
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| − | input.geos
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| − | jv_spec_mie.dat
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| − | Makefile
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| − | org.dat
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| − | output/
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| − | README
| |
| − | so4.dat
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| − | soot.dat
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| − | ssa.dat
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| − | ssc.dat
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| − | v11-01.run
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| − | validate
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| − |
| |
| − | ''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>. 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.
| |
| − |
| |
| − | == Important Notes About Restart Files ==
| |
| − |
| |
| − | Please see [[GEOS-Chem_basics#Restart_files|this post on the ''GEOS-Chem basics'' wiki page]] for more information about how to obtain sample restart files for your simulations.
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| − |
| |
| − | == Tips and tricks for creating run directories ==
| |
| − |
| |
| − | * You can create a run directory for the [[GEOS-Chem_nested_grid_simulations|nested grid simulations]] from a 4° x 5° or 2° x 2.5° 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).
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| − |
| |
| − | * 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.
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| − |
| |
| − | *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].
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| − |
| |
| − | --[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 18:42, 26 August 2015 (UTC)
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| − |
| |
| − | == Compiling GEOS-Chem ==
| |
| − |
| |
| − | Starting in v11-01, you can now compile GEOS-Chem directory from the run directory. See 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.
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| − |
| |
| − | --[[User:Lizzie Lundgren|Lizzie Lundgren]] ([[User talk:Lizzie Lundgren|talk]]) 15:07, 1 February 2017 (UTC)
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| − |
| |
| − | == GEOS-Chem Output Files ==
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| − |
| |
| − | 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 more information, see our [[GEOS-Chem Output Files|''GEOS-Chem Output Files'' wiki page]].
| |
| | | | |
| − | --[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 22:25, 5 February 2016 (UTC) | + | ---- |
| | + | '''''[[Downloading_data_from_Amazon_Web_Services_cloud_storage|Previous]] | [[Creating run directories for GEOS-Chem 13.0.0 and later|Next]] | [[Getting Started with GEOS-Chem]]''''' |
