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

From Geos-chem
Jump to: navigation, search
(Example 1: Creating a run directory for a full-chemistry simulation)
Line 39: Line 39:
  
 
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.   
 
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.   
 
  
 
'''2.'''  Navigate to the <tt>run</tt> folder and get a directory listing:
 
'''2.'''  Navigate to the <tt>run</tt> folder and get a directory listing:
Line 53: Line 52:
  
 
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>.
 
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>.
 
  
 
'''3.''' Run the createRunDir.sh script and answer the prompts:
 
'''3.''' Run the createRunDir.sh script and answer the prompts:
  
Run the  <tt>/createRunDir.sh</tt> script:
+
Run the  <tt>/createRunDir.sh</tt> script by typing:
  
 
  ./createRunDir.sh
 
  ./createRunDir.sh
  
The script will start asking you to supply information about the type of run directory that you wish to create:
+
'''4.''' The script will start asking you to supply information about the type of run directory that you wish to create:
  
 
  ===========================================================
 
  ===========================================================
Line 81: Line 79:
 
   10. TransportTracers
 
   10. TransportTracers
  
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.
+
We would to create a run directory for a full-chemistry simulation, so type <tt>1</tt> followed by the <tt>ENTER</tt> key.   
 +
 
 +
'''5.''' The script will prompt you with the next menu.
  
 
  -----------------------------------------------------------
 
  -----------------------------------------------------------
Line 89: Line 89:
 
   2. Troposphere only
 
   2. Troposphere only
  
We will select the recommended option (type <tt>1</tt> and then <tt>ENTER</tt>.  The next menu will appear:
+
We will select the recommended option (type <tt>1</tt> and then <tt>ENTER</tt>.   
 +
 
 +
'''6.''' The next menu will appear:
  
 
  -----------------------------------------------------------
 
  -----------------------------------------------------------
Line 103: Line 105:
 
   8. RRTMG
 
   8. RRTMG
  
In this menu, you can select among different full-chemistry options (such as adding the RRTG
+
In this menu, you can select among different full-chemistry options, such as adding the RRTMG radiative transfer model, microphysics models (APM or TOMAS), etc.  Here we will take the standard fullchem simulation, so type <tt>1</tt> and then <tt>ENTER</tt>.
 +
 
 +
'''7.''' The next menu will ask you to specify the type of meteorology that you wish to use (GEOS-FP or MERRA-2):
 +
 
 +
-----------------------------------------------------------
 +
Choose meteorology source:
 +
-----------------------------------------------------------
 +
  1. MERRA-2 (Recommended)
 +
  2. GEOS-FP
 +
 
 +
Let's select the recommended option, so type <tt>1</tt> followed by <tt>ENTER</tt>.
 +
 
 +
'''8.''' The next menu will prompt you for the horizontal resolution that you wish to use:
 +
 
 +
-----------------------------------------------------------
 +
Choose horizontal resolution:
 +
-----------------------------------------------------------
 +
  1. 4.0  x 5.0
 +
  2. 2.0  x 2.5
 +
  3. 0.5  x 0.625
 +
 
 +
If you wish to set up global simulation, type either <tt>1</tt> or <tt>2</tt> followed by <tt>ENTER</tt>. 
 +
 
 +
If you wish to set up a nested-grid simulation, type <tt>3</tt> and hit <tt>ENTER</tt>.  Then you will be followed by a nested-grid menu:
 +
 
 +
-----------------------------------------------------------
 +
Choose horizontal grid domain:
 +
-----------------------------------------------------------
 +
  1. Global
 +
  2. Asia
 +
  3. Europe
 +
  4. North America
 +
  5. Custom
 +
 
 +
 
  
  
 +
Let's select the 4&deg; x 5&deg; option, so type <tt>1</tt> and then <tt>ENTER</tt>.
  
 +
'''8a.''' NOTE: If you want to create a nested-grid simulation instead of a global simulation, type <tt>
  
  

Revision as of 21:46, 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 by typing:

./createRunDir.sh

4. 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.

5. 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.

6. 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 RRTMG radiative transfer model, microphysics models (APM or TOMAS), etc. Here we will take the standard fullchem simulation, so type 1 and then ENTER.

7. The next menu will ask you to specify the type of meteorology that you wish to use (GEOS-FP or MERRA-2):

-----------------------------------------------------------
Choose meteorology source:
-----------------------------------------------------------
  1. MERRA-2 (Recommended)
  2. GEOS-FP 

Let's select the recommended option, so type 1 followed by ENTER.

8. The next menu will prompt you for the horizontal resolution that you wish to use:

-----------------------------------------------------------
Choose horizontal resolution:
-----------------------------------------------------------
  1. 4.0  x 5.0
  2. 2.0  x 2.5
  3. 0.5  x 0.625

If you wish to set up global simulation, type either 1 or 2 followed by ENTER.

If you wish to set up a nested-grid simulation, type 3 and hit ENTER. Then you will be followed by a nested-grid menu:

-----------------------------------------------------------
Choose horizontal grid domain:
-----------------------------------------------------------
  1. Global
  2. Asia
  3. Europe
  4. North America
  5. Custom



Let's select the 4° x 5° option, so type 1 and then ENTER.

8a. NOTE: If you want to create a nested-grid simulation instead of a global simulation, type



Previous | Next | Getting Started with GEOS-Chem