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| | #[[Running GEOS-Chem|Running]] | | #[[Running GEOS-Chem|Running]] |
| | #[[GEOS-Chem output files|Output files]] | | #[[GEOS-Chem output files|Output files]] |
| − | #[[Guide_to_visualization_and_analysis_tools_for_GEOS-Chem|Visualizing and processing output]] | + | #[[Python tools for use with GEOS-Chem]] |
| | #[[GEOS-Chem_coding_and_debugging|Coding and debugging]] | | #[[GEOS-Chem_coding_and_debugging|Coding and debugging]] |
| | #[[GEOS-Chem_overview#Further_reading|Further reading]] | | #[[GEOS-Chem_overview#Further_reading|Further reading]] |
| | | | |
| | | | |
| − | == Overview ==
| + | This content has been migrated to the [https://geos-chem.readthedocs.io/en/latest/gcc-guide/02-build/create-rundir.html '''Create a run directory''' chapter of <tt>geos-chem.readthedocs.io</tt>]. |
| − | | + | |
| − | 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.
| + | |
| − | | + | |
| − | == 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 <tt>GCClassic</tt> 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, <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:
| + | |
| − | | + | |
| − | 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 <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 <tt>createRunDir.sh</tt> script. Type:
| + | |
| − | | + | |
| − | ./createRunDir.sh
| + | |
| − | | + | |
| − | '''4.''' You will then be prompted to supply information about the 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
| + | |
| − | | + | |
| − | :To create a run directory for the full-chemistry simulation, type <tt>1</tt> followed by the <tt>ENTER</tt> key.
| + | |
| − | | + | |
| − | '''5.''' You will then be prompted to specify whether you want to perform chemistry in the stratosphere or not:
| + | |
| − | | + | |
| − | -----------------------------------------------------------
| + | |
| − | Choose chemistry domain:
| + | |
| − | -----------------------------------------------------------
| + | |
| − | 1. Troposphere + stratosphere (Recommended)
| + | |
| − | 2. Troposphere only
| + | |
| − | | + | |
| − | :Select the recommended option: Type <tt>1</tt> and then <tt>ENTER</tt>.
| + | |
| − | | + | |
| − | '''6.''' You will then be asked to specify any additional options for the full-chemistry simulation (such as adding the RRTMG radiative transfer model, APM or TOMAS microphysics, etc.)
| + | |
| − | | + | |
| − | -----------------------------------------------------------
| + | |
| − | 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
| + | |
| − | | + | |
| − | :'''6a''': For the standard full-chemistry simulation, type <tt>1</tt> followed by <tt>ENTER</tt>.
| + | |
| − | | + | |
| − | :'''6b''': To add an option to the full-chemistry simulation, type a number between <tt>2</tt> to <tt>8</tt> and press <tt>ENTER</tt>.
| + | |
| − | | + | |
| − | '''7.''' You will then be asked to specify the meteorology type for the simulation (GEOS-FP or MERRA-2):
| + | |
| − | | + | |
| − | -----------------------------------------------------------
| + | |
| − | Choose meteorology source:
| + | |
| − | -----------------------------------------------------------
| + | |
| − | 1. MERRA-2 (Recommended)
| + | |
| − | 2. GEOS-FP
| + | |
| − | | + | |
| − | :You should use the recommended option (MERRA-2) if possible. 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
| + | |
| − | | + | |
| − | :'''8a.''' If you wish to set up a global simulation, type either <tt>1</tt> or <tt>2</tt> followed by <tt>ENTER</tt>.
| + | |
| − | | + | |
| − | :'''8b.''' 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
| + | |
| − | | + | |
| − | :Select your preferred horizontal domain, followed by <tt>ENTER</tt>.
| + | |
| − | | + | |
| − | '''9.''' You will then be prompted for the vertical dimension of the grid.
| + | |
| − | | + | |
| − | -----------------------------------------------------------
| + | |
| − | Choose number of levels:
| + | |
| − | -----------------------------------------------------------
| + | |
| − | 1. 72 (native)
| + | |
| − | 2. 47 (reduced)
| + | |
| − | | + | |
| − | :'''9a.''' For most simulations, you will want to use 72 levels. Type <tt>1</tt> followed by <tt>ENTER</tt>.
| + | |
| − | | + | |
| − | :'''9b.''' For some memory-intensive simulations (such as nested-grid simulations), you can use 47 levels. Type <tt>2</tt> followed by <tt>ENTER</tt>.
| + | |
| − | | + | |
| − | '''10.''' You will then be prompted for the folder in which you wish to create the run directory.
| + | |
| − | | + | |
| − | -----------------------------------------------------------
| + | |
| − | Enter path where the run directory will be created:
| + | |
| − | -----------------------------------------------------------
| + | |
| − | | + | |
| − | :'''10a.''' You can enter an absolute path (such as <tt>/n/home09/ryantosca/</tt> followed by <tt>ENTER</tt>).
| + | |
| − | | + | |
| − | :'''10b.''' Or you can enter a relative path (such as <tt>~/rundirs</tt> followed by <tt>ENTER</tt>). In this case you will see that the <tt>./createRunDir.sh</tt> script will expand the path to:
| + | |
| − | | + | |
| − | Expanding to: /n/home09/ryantosca/rundirs
| + | |
| − | | + | |
| − | '''11.''' The next menu will prompt you for the run directory name.
| + | |
| − | | + | |
| − | -----------------------------------------------------------
| + | |
| − | Enter run directory name, or press return to use default:
| + | |
| − |
| + | |
| − | NOTE: This will be a subfolder of the path you entered above.
| + | |
| − | -----------------------------------------------------------
| + | |
| − | | + | |
| − | :You should use the default run directory name whenever possible. Type <tt>ENTER</tt> to select the default.
| + | |
| − | | + | |
| − | :The script will display the following output:
| + | |
| − | | + | |
| − | -- Using default directory name gc_4x5_fullchem
| + | |
| − | | + | |
| − | :or if you are creating a nested grid simulation:
| + | |
| − | | + | |
| − | -- Using default directory name gc_05x0625_fullchem
| + | |
| − | | + | |
| − | :and then:
| + | |
| − |
| + | |
| − | -- This run directory has been set up for 20190701 - 20190801.
| + | |
| − | You may modify these settings in input.geos.
| + | |
| − |
| + | |
| − | -- The default frequency and duration of diagnostics is set to monthly.
| + | |
| − | You may modify these settings in HISTORY.rc and HEMCO_Config.rc.
| + | |
| − | | + | |
| − | '''12.''' The last menu will prompt you with: | + | |
| − | | + | |
| − | -----------------------------------------------------------
| + | |
| − | Do you want to track run directory changes with git? (y/n)
| + | |
| − | -----------------------------------------------------------
| + | |
| − | | + | |
| − | :Type <tt>y</tt> and then <tt>ENTER</tt>/ Then you will be able to track changes that you make to GEOS-Chem configuration files with Git. This can be a lifesaver when debugging -- you can revert to an earlier state and then start fresh.
| + | |
| − | | + | |
| − | '''13.''' The script will display the full path to the run directory. You can navigate there and then start editing the GEOS-Chem configuration files.
| + | |
| − | | + | |
| − | == Example 2: Creating a run directory for the methane simulation ==
| + | |
| − | | + | |
| − | The process of creating run directories for the GEOS-Chem specialty simulations is similar to that as listed in Example 1 above. However, the number of menus that you need to select from will likely be fewer than for the full-chemistry simulation. We'll use the methane simulation as an example.
| + | |
| − | | + | |
| − | '''1.''' Navigate to the <tt>GCClassic</tt> 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, <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:
| + | |
| − | | + | |
| − | 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 <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 <tt>createRunDir.sh</tt>. Type:
| + | |
| − | | + | |
| − | ./createRunDir.sh
| + | |
| − | | + | |
| − | '''4.''' You will then be prompted to supply information about the 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
| + | |
| − | | + | |
| − | :To select the GEOS-Chem methane specialty simulation, type <tt>3</tt> followed by <tt>ENTER</tt>.
| + | |
| − | | + | |
| − | '''5.''' You will then be asked to specify the meteorology type for the simulation (GEOS-FP or MERRA-2):
| + | |
| − | | + | |
| − | -----------------------------------------------------------
| + | |
| − | Choose meteorology source:
| + | |
| − | -----------------------------------------------------------
| + | |
| − | 1. MERRA-2 (Recommended)
| + | |
| − | 2. GEOS-FP
| + | |
| − | | + | |
| − | To accept the recommended meteorology (MERRA-2), type <tt>1</tt> followed by <tt>ENTER</tt>.
| + | |
| − | | + | |
| − | '''6.''' 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
| + | |
| − | | + | |
| − | '''6a.''' If you wish to set up global simulation, type either <tt>1</tt> or <tt>2</tt> followed by <tt>ENTER</tt>.
| + | |
| − | | + | |
| − | '''6b.''' 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
| + | |
| − | | + | |
| − | Type the number of your preferred option and then hit <tt>ENTER</tt>.
| + | |
| − | | + | |
| − | '''7.''' You will then be prompted for the vertical dimension of the grid.
| + | |
| − | | + | |
| − | -----------------------------------------------------------
| + | |
| − | Choose number of levels:
| + | |
| − | -----------------------------------------------------------
| + | |
| − | 1. 72 (native)
| + | |
| − | 2. 47 (reduced)
| + | |
| − | | + | |
| − | '''7a.''' For most simulations, you will want to use 72 levels. Type <tt>1</tt> followed by <tt>ENTER</tt>
| + | |
| − | | + | |
| − | '''7b.''' For some memory-intensive simulations (such as nested-grid simulations), you can use 47 levels. Type <tt>2</tt> followed by <tt>ENTER</tt>.
| + | |
| − | | + | |
| − | '''8.''' You will then be prompted for the folder in which you wish to create the run directory.
| + | |
| − | | + | |
| − | -----------------------------------------------------------
| + | |
| − | Enter path where the run directory will be created:
| + | |
| − | -----------------------------------------------------------
| + | |
| − | | + | |
| − | '''8a.''' You enter this an absolute path (such as <tt>/n/home09/ryantosca/</tt> followed by <tt>ENTER</tt>).
| + | |
| − | | + | |
| − | '''8b.''' Or you can enter a relative path (such as <tt>~/rundirs</tt> followed by <tt>ENTER</tt>). In this case you will see that the <tt>./createRunDir.sh</tt> script will expand the path to:
| + | |
| − | | + | |
| − | Expanding to: /n/home09/ryantosca/rundirs
| + | |
| − | | + | |
| − | '''9.''' The next menu will prompt you for the run directory name.
| + | |
| − | | + | |
| − | -----------------------------------------------------------
| + | |
| − | Enter run directory name, or press return to use default:
| + | |
| − |
| + | |
| − | NOTE: This will be a subfolder of the path you entered above.
| + | |
| − | -----------------------------------------------------------
| + | |
| − | | + | |
| − | In most cases, you should use the default run directory name. So type <tt>ENTER</tt>. The script will display the following output:
| + | |
| − | | + | |
| − | -- Using default directory name gc_4x5_CH4
| + | |
| − |
| + | |
| − | or if you are creating a nested grid simulation:
| + | |
| − | | + | |
| − | -- Using default directory name gc_05x0625_CH4
| + | |
| − | | + | |
| − | and then:
| + | |
| − |
| + | |
| − | -- This run directory has been set up for 20190701 - 20190801.
| + | |
| − | You may modify these settings in input.geos.
| + | |
| − |
| + | |
| − | -- The default frequency and duration of diagnostics is set to monthly.
| + | |
| − | You may modify these settings in HISTORY.rc and HEMCO_Config.rc.
| + | |
| − | | + | |
| − | '''10.''' The last menu will prompt you with:
| + | |
| − | | + | |
| − | -----------------------------------------------------------
| + | |
| − | Do you want to track run directory changes with git? (y/n)
| + | |
| − | -----------------------------------------------------------
| + | |
| − | | + | |
| − | Type <tt>y</tt> and then <tt>ENTER</tt>/ Then you will be able to track changes that you make to GEOS-Chem configuration files with Git. This can be a lifesaver when debugging -- you can revert to an earlier state and then start fresh.
| + | |
| − | | + | |
| − | The script will display the full path to the run directory. You can navigate there and then start editing the GEOS-Chem configuration files.
| + | |
| | | | |
| | | | |
| | ---- | | ---- |
| | '''''[[Creating GEOS-Chem run directories|Previous]] | [[Creating run directories for GEOS-Chem 12.9.3 and prior|Next]] | [[Getting Started with GEOS-Chem]]''''' | | '''''[[Creating GEOS-Chem run directories|Previous]] | [[Creating run directories for GEOS-Chem 12.9.3 and prior|Next]] | [[Getting Started with GEOS-Chem]]''''' |
