Difference between revisions of "Obtaining a GCHP Run Directory"

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(Step 2: Set Up the Run Directory)
 
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<span style="color:crimson;font-size:120%">'''The GCHP documentation has moved to https://gchp.readthedocs.io/.''' The GCHP documentation on http://wiki.seas.harvard.edu/ will stay online for several months, but it is outdated and no longer active!</span>
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__FORCETOC__
 
__FORCETOC__
'''''[[Downloading_GCHP|Previous]] | [[Setting_Up_the_GCHP_Environment|Next]] | [[Getting_Started_With_GCHP|Getting Started with GCHP]]'''''
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'''''[[Compiling_GCHP|Previous]] | [[Running_GCHP:_Basics|Next]] | [[Getting Started with GCHP]] | [[GCHP Main Page]]'''''
 
#[[GCHP_Hardware_and_Software_Requirements|Hardware and Software Requirements]]
 
#[[GCHP_Hardware_and_Software_Requirements|Hardware and Software Requirements]]
#[[Downloading_GCHP|Downloading Source Code]]
 
#<span style="color:blue">'''Obtaining a Run Directory'''</span>
 
 
#[[Setting_Up_the_GCHP_Environment|Setting Up the GCHP Environment]]
 
#[[Setting_Up_the_GCHP_Environment|Setting Up the GCHP Environment]]
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#[[Downloading_GCHP|Downloading Source Code and Data Directories]]
 
#[[Compiling_GCHP|Compiling]]
 
#[[Compiling_GCHP|Compiling]]
#[[GCHP_Basic_Example_Run|Basic Example Run]]
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#<span style="color:blue">'''Obtaining a Run Directory'''</span>
#[[GCHP_Run_Configuration_Files|Run Configuration Files]]
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#[[Running_GCHP:_Basics|Running GCHP: Basics]]
#[[Running_GCHP|Advanced Run Examples]]
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#[[Running_GCHP:_Configuration|Running GCHP: Configuration]]
#[[GEOS-Chem_HP_Output_Data|Output Data]]
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#[[GCHP_Output_Data|Output Data]]
 
#[[Developing_GCHP|Developing GCHP]]
 
#[[Developing_GCHP|Developing GCHP]]
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#[[GCHP_Run_Configuration_Files|Run Configuration Files]]
 
<br>
 
<br>
  
== Overview ==
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==Create Run Directory==
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GCHP run directories are created from within the source code. A new run directory should be created for each different version of GEOS-Chem you use. Git version information is logged to file <code>rundir.version</code> within the run directory upon creation.
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To create a run directory, navigate to the <code>run/</code> subdirectory of the source code and execute shell script <code>createRunDir.sh</code>.
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$ cd ~/GCHPctm/run
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$ ./createRunDir.sh
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During the course of script execution you will be asked a series of questions:
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==== Enter ExtData directory path ====
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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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-----------------------------------------------------------
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Enter path for ExtData:
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-----------------------------------------------------------
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====Choose simulation type====
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Enter the integer number that is next to the simulation type you want to use.
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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. TransportTracers
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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.
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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
 +
 
 +
====Choose meteorology source====
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Enter the integer number that is next to the input meteorology source you would like to use.
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 +
-----------------------------------------------------------
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Choose meteorology source:
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-----------------------------------------------------------
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  1. MERRA2 (Recommended)
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  2. GEOS-FP
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====Enter run directory path====
  
The procedure for acquiring a GCHP run directory is the same as acquiring a GEOS-Chem Classic run directory. Once you have your run directory you must set your source code directory path prior to moving onto the next steps of setting up your environment, compiling, and running.
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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.
  
==Step 1: Create Run Directory==
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-----------------------------------------------------------
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Enter path where the run directory will be created:
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-----------------------------------------------------------
  
You can create a GCHP run directory using the [[GEOS-Chem Unit Tester]]. From your primary GCHP directory (e.g. <tt>/mypath/GCHP</tt>), download a clean copy the development version of the GEOS-Chem Unit Tester on Github:
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====Enter run directory name====
  
git clone git@github.com:geoschem/geos-chem-unittest.git UT
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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.
  
There are three run directories available for GCHP: the radon-lead-beryllium simulation, the standard full chemistry simulation, and the benchmarking simulation which incorporates both simple and complex SOA for validation. The default settings for all run directories are a 72-level simulation using 0.25x0.3125 GEOS-FP meteorology and internal c24 cubed sphere grid resolution (roughly equivalent to 4x5). Please note that unlike GEOS-Chem Classic there are not separate run directories for different grid resolutions.
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-----------------------------------------------------------
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Enter run directory name, or press return to use default:
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-----------------------------------------------------------
  
Example steps for creating a standard full-chemistry run directory called <tt>gchp_standard</tt>:
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====Put run directory under version control (optional)====
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#Change directories into <tt>/mypath/GCHP/UT/perl</tt>
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#Open <tt>CopyRunDirs.input</tt> in a text editor and make the following changes:
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##Update <tt>DATA_ROOT</tt> to point to the [[GEOS-Chem_basics#The_GEOS-Chem_shared_data_directories|GEOS-Chem shared data directories]] on your system. The default settings are compatible with the Harvard Odyssey compute cluster.
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##Change variable <tt>UNIT_TEST_ROOT</tt> to match the directory to which you cloned the unit tester (e.g. <tt>/mypath/UT</tt>)
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##Change variable <tt>COPY_PATH</tt> to be the target directory where you want to store your run directories (e.g. <tt>/mypath/GCHP/rundirs</tt>)
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##Uncomment the lines for the GCHP run directories you would like to download (search for gchp_standard)
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##Make sure all other run directory options are commented out
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#Run the following perl script to create the run directory <tt>/mypath/GCHP/rundirs/gchp_standard</tt>:
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    ./gcCopyRunDirs CopyRunDirs.input
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See the [[Creating_GEOS-Chem_run_directories|''Creating GEOS-Chem run directories'' wiki page]] for more information.
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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 useful for trouble-shooting as well as tracking run directory feature changes you wish to migrate back to the standard model.
  
==Step 2: Set Up the Run Directory==
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-----------------------------------------------------------
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Do you want to track run directory changes with git? (y/n)
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-----------------------------------------------------------
  
Symbolic links to restart files, input data, and tile files for mapping between lat-lon and cubed sphere grids are automatically included in the run directory and do not require additional setup. However, you should check that the links were properly set by ensuring none are broken symbolic links.
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== Set Environment ==
  
Then manually set a symbolic link to your source code directory. A utility bash script included in the run directory called <tt>setCodeDir</tt> will do this for you. Execute it as follows:
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Set the <code>gchp.env</code> symbolic link to the same GCHP environment file you used for building the executable. This generically named symbolic link exists for convenience for inclusion in reusable scripts to automate build and run. To set it, use shell script <code>setEnvironment</code>.
  
  ./setCodeDir /path/to/code
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cd /home/gchp_fullchem
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  ./setEnvironment /home/envs/gchp_ifort19_openmpi4.env
  
Note that there should not be any symbolic links within the path that you pass to setCodeDir as this will cause a compile error within ESMF.
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'''Tips:'''
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*You can keep your environment file anywhere on your system for reuse across multiple run directories.
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*Always source <code>gchp.env</code> prior to building and running GCHP. It is included by default in all example run scripts.
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*Check CMake file <tt>CMakeCache.txt</tt> when in doubt about what environment was used to build the executable.
  
 
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'''''[[Downloading_GCHP|Previous]] | [[Setting_Up_the_GCHP_Environment|Next]] | [[GEOS-Chem_HP|GCHP Home]]'''''
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'''''[[Compiling_GCHP|Previous]] | [[Running_GCHP:_Basics|Next]] | [[Getting Started with GCHP]] | [[GCHP Main Page]]'''''

Latest revision as of 15:40, 8 December 2020


The GCHP documentation has moved to https://gchp.readthedocs.io/. The GCHP documentation on http://wiki.seas.harvard.edu/ will stay online for several months, but it is outdated and no longer active!



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

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


Create Run Directory

GCHP run directories are created from within the source code. A new run directory should be created for each different version of GEOS-Chem you use. Git version information is logged to file rundir.version within the run directory upon creation.

To create a run directory, navigate to the run/ subdirectory of the source code and execute shell script createRunDir.sh.

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

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

Enter 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:
-----------------------------------------------------------

Choose 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

Choose 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

Enter 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:
-----------------------------------------------------------

Enter 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:
-----------------------------------------------------------

Put run directory under version control (optional)

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 useful for trouble-shooting as well as tracking run directory feature changes you wish to migrate back to the standard model.

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

Set Environment

Set the gchp.env symbolic link to the same GCHP environment file you used for building the executable. This generically named symbolic link exists for convenience for inclusion in reusable scripts to automate build and run. To set it, use 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. It is included by default in all example run scripts.
  • Check CMake file CMakeCache.txt when in doubt about what environment was used to build the executable.

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