Difference between revisions of "Obtaining a GCHP Run Directory"

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(→‎Simulation type)
(→‎Step 1: Create Run Directory)
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During the course of script execution you will be asked a series of questions:
 
During the course of script execution you will be asked a series of questions:
  
−
=== ExtData directory path ===
+
==== ExtData directory path ====
  
 
The first time you create a GCHP run directory on your system you will be prompted for a path to GEOS-Chem shared data directories. The path should include the name of your <code>ExtData</code> directory and should not contain symbolic links. The path you enter will be stored in file <code>.geoschem/config</code> in your home directory as environment variable <code>GC_DATA_ROOT</code>. If that file does not already exist it will be created for you. When creating additional run directories you will only be prompted again if the file is missing or if the path within it is not valid.
 
The first time you create a GCHP run directory on your system you will be prompted for a path to GEOS-Chem shared data directories. The path should include the name of your <code>ExtData</code> directory and should not contain symbolic links. The path you enter will be stored in file <code>.geoschem/config</code> in your home directory as environment variable <code>GC_DATA_ROOT</code>. If that file does not already exist it will be created for you. When creating additional run directories you will only be prompted again if the file is missing or if the path within it is not valid.
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  -----------------------------------------------------------
 
  -----------------------------------------------------------
  
−
===Simulation type===
+
====Simulation type====
  
 
Enter the integer number that is next to the simulation type you want to use.
 
Enter the integer number that is next to the simulation type you want to use.
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   8. RRTMG
 
   8. RRTMG
  
−
===Meteorology source===
+
====Meteorology source====
  
−
Next, choose which meteorology source you would like to use.
+
Enter the integer number that is next to the input meteorology source you would like to use.
  
 +
-----------------------------------------------------------
 
  Choose meteorology source:
 
  Choose meteorology source:
−
   1. MERRA2 (recommended)
+
-----------------------------------------------------------
 +
   1. MERRA2 (Recommended)
 
   2. GEOS-FP
 
   2. GEOS-FP
  
−
Currently GCHP supports GEOS-FP and MERRA2 data only. Input data resolution is 0.25x0.325 for GEOS-FP and 0.5x0.625 for MERRA2 by default. Unlike GEOS-Chem Classic, GCHP input meteorology data does not need to be the same grid type or grid resolution as the grid and resolution you run at.
+
====Run directory path====
  
−
===Storage location===
+
Enter the target path where the run directory will be stored. You will be prompted to enter a new path if the one you enter does not exist.
−
 
+
−
Next, enter the target path where you want your run directory to be stored.
+
  
 +
-----------------------------------------------------------
 
  Enter path where the run directory will be created:
 
  Enter path where the run directory will be created:
 +
-----------------------------------------------------------
  
−
Do not include symbolic links in the path. Choose your path wisely to keep your runs organized.
+
====Run directory name====
  
−
===Run directory name===
+
Enter the run directory name, or accept the default. You will be prompted for a new name if a run directory of the same name already exists at the target path.
−
 
+
−
You will then be prompted to enter a run directory name if you did not pass one as an optional argument when calling the script. You are given the option to simply press return and use the default run directory name of format <code>gchp_{simulation_type}</code>. Here is an example of what you will see if using the default name for the standard full chemistry simulation:
+
  
 +
-----------------------------------------------------------
 
  Enter run directory name, or press return to use default:
 
  Enter run directory name, or press return to use default:
−
   
+
  -----------------------------------------------------------
−
+
−
Using default directory name gchp_standard
+
  
−
===Run directory version control===
+
====Run directory version control====
  
−
Finally, you will be asked if you want to track run directory changes with git version control. This feature is useful if you plan on making feature updates to GEOS-Chem that involve changes to the run directory, such as adding emissions or turning components on or off. With version control you can keep track of exactly what you changed relative to the original settings.
+
Enter whether you would like your run directory tracked with git version control. With version control you can keep track of exactly what you changed relative to the original settings.
−
 
+
−
This is what you will see if you use to put your run directory under version control with git:
+
  
 +
-----------------------------------------------------------
 
  Do you want to track run directory changes with git? (y/n)
 
  Do you want to track run directory changes with git? (y/n)
−
  y
+
  -----------------------------------------------------------
−
Initialized empty Git repository in /n/home/user003/gchp_standard/.git/
+
−
 
+
−
We strongly recommend using this feature if you plan on submitting an update for inclusion in the standard model since you can copy changes directly from your version history to <tt>GCHP/Run</tt>, and then commit those changes with your source code updates. If you forked the repository you can then push to your fork and do a pull request to send us your updates.
+
  
 
== Step 2: Set Environment ==
 
== Step 2: Set Environment ==

Revision as of 19:05, 20 October 2020

Previous | Next | Getting Started with GCHP | GCHP Main Page

  1. Hardware and Software Requirements
  2. Downloading Source Code and Data Directories
  3. Obtaining a Run Directory
  4. Setting Up the GCHP Environment
  5. Compiling
  6. Running GCHP: Basics
  7. Running GCHP: Configuration
  8. Output Data
  9. Developing GCHP
  10. Run Configuration Files


Step 1: Create Run Directory

Navigate to the run/ subdirectory of the source code and create a run directory using shell script createRunDir.sh. 

$ cd ~/GCHPctm/run
$ ./createRunDir.sh

During the course of script execution you will be asked a series of questions:

ExtData directory path

The first time you create a GCHP run directory on your system you will be prompted for a path to GEOS-Chem shared data directories. The path should include the name of your ExtData directory and should not contain symbolic links. The path you enter will be stored in file .geoschem/config in your home directory as environment variable GC_DATA_ROOT. If that file does not already exist it will be created for you. When creating additional run directories you will only be prompted again if the file is missing or if the path within it is not valid. 

-----------------------------------------------------------
Enter path for ExtData:
-----------------------------------------------------------

Simulation type

Enter the integer number that is next to the simulation type you want to use. 

-----------------------------------------------------------
Choose simulation type:
-----------------------------------------------------------
  1. Full chemistry
  2. TransportTracers

If creating a full chemistry run directory you will be given additional options. Enter the integer number that is next to the simulation option you want to run. 

-----------------------------------------------------------
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

Meteorology source

Enter the integer number that is next to the input meteorology source you would like to use. 

-----------------------------------------------------------
Choose meteorology source:
-----------------------------------------------------------
 1. MERRA2 (Recommended)
 2. GEOS-FP

Run directory path

Enter the target path where the run directory will be stored. You will be prompted to enter a new path if the one you enter does not exist. 

-----------------------------------------------------------
Enter path where the run directory will be created:
-----------------------------------------------------------

Run directory name

Enter the run directory name, or accept the default. You will be prompted for a new name if a run directory of the same name already exists at the target path. 

-----------------------------------------------------------
Enter run directory name, or press return to use default:
-----------------------------------------------------------

Run directory version control

Enter whether you would like your run directory tracked with git version control. With version control you can keep track of exactly what you changed relative to the original settings. 

-----------------------------------------------------------
Do you want to track run directory changes with git? (y/n)
-----------------------------------------------------------

Step 2: Set Environment

Set the gchp.env symbolic link to your GCHP environment file using shell script setEnvironment. 

cd /home/gchp_fullchem
./setEnvironment /home/envs/gchp_ifort19_openmpi4.env

Tips:

  • You can keep your environment file anywhere on your system for reuse across multiple run directories.
  • Always source gchp.env prior to building and running GCHP.
  • Include source gchp.env at the top of your run scripts.

Additional information

A new run directory should be created for each different version of GEOS-Chem you use. Version information per run directory is located in file rundir.version.

Previous | Next | Getting Started with GCHP | GCHP Main Page

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