Difference between revisions of "Creating run directories for GEOS-Chem 13.0.0 and later"

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== Overview ==
 
== Overview ==
Content to be added
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We have greatly simplified run directory creation in [[GEOS-Chem 13.0.0]] and later versions.  You no longer need to download the separate [[GEOS-Chem Unit Tester]] repository any longer, but can create run directories from a script in the GEOS-Chem source code itself.
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We have
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== Example 1: Creating a run directory for a full-chemistry simulation ==
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Let us walk through the process of creating a run directory for a global GEOS-Chem full-chemistry simulation.
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'''1.''' Navigate to the <tt>GCClassic</tt> superproject folder and get a directory listing:
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cd /path/to/your/GCClassic
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ls -CF
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You should see this output:
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CMakeLists.txt  LICENSE  run@  src/
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As mentioned previously, <tt>run@</tt> is a symbolic link.  It actually points to the to the <tt>src/GEOS-Chem/run/GCClassic</tt> folder.  This folder contains several scripts and template files for run directory creation. 
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'''2.'''  Navigate to the <tt>run</tt> folder and get a directory listing:
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cd run
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ls -CF
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and you should see this output:
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archiveRun.sh*    gitignore                  HISTORY.rc.templates/  runScriptSamples/
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createRunDir.sh*  HEMCO_Config.rc.templates/  input.geos.templates/
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getRunInfo*      HEMCO_Diagn.rc.templates/  README
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You can see several folders (highlighted in the directory display with <tt>/</tt>) and a few executable scripts (highlighted with <tt>*</tt>).  The script we are interested in is <tt>createRunDir.sh</tt>.
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'''3.''' Run the createRunDir.sh script and answer the prompts:
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Run the  <tt>/createRunDir.sh</tt> script:
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./createRunDir.sh
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The script will start asking you to supply information about the type of run directory that you wish to create:
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===========================================================
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GEOS-CHEM RUN DIRECTORY CREATION
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===========================================================
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-----------------------------------------------------------
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Choose simulation type:
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-----------------------------------------------------------
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    1. Full chemistry
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    2. Aerosols only
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    3. CH4
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    4. CO2
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    5. Hg
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    6. POPs
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    7. Tagged CH4
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    8. Tagged CO
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    9. Tagged O3
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  10. TransportTracers
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We would to create a run directory for a full-chemistry simulation, so type <tt>1</tt> followed by the <tt>ENTER</tt> key.  The script will prompt you with the next menu.
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-----------------------------------------------------------
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Choose chemistry domain:
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-----------------------------------------------------------
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  1. Troposphere + stratosphere (Recommended)
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  2. Troposphere only
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We will select the recommended option (type <tt>1</tt> and then <tt>ENTER</tt>.  The next menu will appear:
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-----------------------------------------------------------
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Choose additional simulation option:
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-----------------------------------------------------------
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  1. Standard
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  2. Benchmark
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  3. Complex SOA
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  4. Marine POA
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  5. Acid uptake on dust
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  6. TOMAS
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  7. APM
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  8. RRTMG
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In this menu, you can select among different full-chemistry options (such as adding the RRTG
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----
 
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'''''[[Creating run directories for GEOS-Chem|Previous]] | [[Creating run directories for GEOS-Chem 12.9.3 and prior|Next]] | [[Getting Started with GEOS-Chem]]'''''
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'''''[[Creating GEOS-Chem run directories|Previous]] | [[Creating run directories for GEOS-Chem 12.9.3 and prior|Next]] | [[Getting Started with GEOS-Chem]]'''''

Revision as of 21:35, 7 December 2020

Previous | Next | Getting Started with GEOS-Chem

  1. Minimum system requirements
  2. Installing required software
  3. Configuring your computational environment
  4. Downloading source code
  5. Downloading data directories
  6. Creating GEOS-Chem run directories
  7. Configuring runs
  8. Compiling
  9. Running
  10. Output files
  11. Visualizing and processing output
  12. Coding and debugging
  13. Further reading


Overview

We have greatly simplified run directory creation in GEOS-Chem 13.0.0 and later versions. You no longer need to download the separate GEOS-Chem Unit Tester repository any longer, but can create run directories from a script in the GEOS-Chem source code itself.

We have


Example 1: Creating a run directory for a full-chemistry simulation

Let us walk through the process of creating a run directory for a global GEOS-Chem full-chemistry simulation.

1. Navigate to the GCClassic superproject folder and get a directory listing:

cd /path/to/your/GCClassic
ls -CF

You should see this output:

CMakeLists.txt  LICENSE  run@  src/

As mentioned previously, run@ is a symbolic link. It actually points to the to the src/GEOS-Chem/run/GCClassic folder. This folder contains several scripts and template files for run directory creation.


2. Navigate to the run folder and get a directory listing:

cd run
ls -CF

and you should see this output:

archiveRun.sh*    gitignore                   HISTORY.rc.templates/  runScriptSamples/
createRunDir.sh*  HEMCO_Config.rc.templates/  input.geos.templates/
getRunInfo*       HEMCO_Diagn.rc.templates/   README

You can see several folders (highlighted in the directory display with /) and a few executable scripts (highlighted with *). The script we are interested in is createRunDir.sh.


3. Run the createRunDir.sh script and answer the prompts:

Run the /createRunDir.sh script:

./createRunDir.sh

The script will start asking you to supply information about the type of run directory that you wish to create:

===========================================================
GEOS-CHEM RUN DIRECTORY CREATION
===========================================================

-----------------------------------------------------------
Choose simulation type:
-----------------------------------------------------------
   1. Full chemistry
   2. Aerosols only
   3. CH4
   4. CO2
   5. Hg
   6. POPs
   7. Tagged CH4
   8. Tagged CO
   9. Tagged O3
  10. TransportTracers

We would to create a run directory for a full-chemistry simulation, so type 1 followed by the ENTER key. The script will prompt you with the next menu.

-----------------------------------------------------------
Choose chemistry domain:
-----------------------------------------------------------
  1. Troposphere + stratosphere (Recommended)
  2. Troposphere only

We will select the recommended option (type 1 and then ENTER. The next menu will appear:

-----------------------------------------------------------
Choose additional simulation option:
-----------------------------------------------------------
  1. Standard
  2. Benchmark
  3. Complex SOA
  4. Marine POA
  5. Acid uptake on dust
  6. TOMAS
  7. APM
  8. RRTMG

In this menu, you can select among different full-chemistry options (such as adding the RRTG





Previous | Next | Getting Started with GEOS-Chem