Difference between revisions of "Downloading data with the GEOS-Chem dry-run option"

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(Executing GEOS-Chem in dry-run mode)
(Executing GEOS-Chem in dry-run mode)
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Follow these steps to perform a GEOS-Chem dry-run:
 
Follow these steps to perform a GEOS-Chem dry-run:
  
'''(1)''' Create a run directory for the type of GEOS-Chem simulation that you wish to perform (e.g. <tt>geosfp_4x5_standard</tt>, <tt>merra2_2x25_tropchem</tt>, etc..  For detailed instructions, please see our [[Creating_GEOS-Chem_run_directories|our ''Creating run directories'' chapter]].
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#<p>'''Create a run directory''' for the type of GEOS-Chem simulation that you wish to perform (e.g. <tt>geosfp_4x5_standard</tt>, <tt>merra2_2x25_tropchem</tt>, etc..  For detailed instructions, please see our [[Creating_GEOS-Chem_run_directories|our ''Creating run directories'' chapter]].</p>
 
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#<p>Change to the run directory (e.g. <tt>cd geosfp_4x5_standard</tt>, etc.) and '''compile GEOS-Chem''' as you normally would.  For detailed instructions, please see our [[Compiling GEOS-Chem|our ''Compiling'' chapter]].</p>
'''(2)''' Change to the run directory (e.g. <tt>cd geosfp_4x5_standard</tt>, etc.) and compile GEOS-Chem as you normally would.  For detailed instructions, please see our [[Compiling GEOS-Chem|our ''Compiling'' chapter]].
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#<p>Check to see if these settings in [[The input.geos file#Simulation|the SIMULATION MENU of <tt>input.geos</tt> file]] are as you expect:</p>
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#*<tt>Start YYYYMMDD and hhmmss</tt>
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#*<tt>End  YYYYMMDD and hhmsss</tt>
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#*<tt>Root data directory</tt>
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#*<tt>Simulation name</tt>
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#<p>Check to see if these settings in [[The input.geos file#Grid|the GRID MENU of <tt>input.geos</tt> file]] are as you expect:</p>
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#*<tt>Grid resolution</tt>
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#<p>Check to see if these settings in the SECTION SETTINGS of the HEMCO_Config.rc file are as you expect
  
 
== Downloading data from dry-run output ==
 
== Downloading data from dry-run output ==

Revision as of 16:25, 6 January 2020

Previous | Next | Getting Started with GEOS-Chem

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


Overview

The GEOS-Chem dry-run option will be available in GEOS-Chem 12.7.0 and later versions. This version should be released by mid-to-late January 2020 (pending successful benchmarking).

What is a GEOS-Chem dry-run?

A "dry-run" is a is a GEOS-Chem "Classic" simulation that steps through time, but does not perform computations or read data files from disk. Instead, a dry-run simulation prints a list of all data files that a regular GEOS-Chem simulation would have read. The dry-run output also denotes whether each data file was found on disk, or if it is missing.

Why should I perform a GEOS-Chem dry-run?

A GEOS-Chem dry-run is a good way for you to check if you have properly configured your computational environment. This is especially important if you are porting GEOS-Chem to run on a new computer system, or on the AWS cloud.

For example:

Problem encountered in dry-run What this can indicate
GEOS-Chem "Classic" does not compile
  • Your system does not have a supported compiler
  • Your system is missing one or more required software libraries
  • You have invalid settings in your Unix startup scripts (e.g. .bashrc, etc.)
GEOS-Chem "Classic" compiles but does not run
  • Your GEOS-Chem configuration files (input.geos, HEMCO_Config.rc, etc.) contain errors
  • You have invalid settings in your Unix startup scripts (e.g. .bashrc, etc.)

Once you have can successfully finished a GEOS-Chem dry-run, you can have confidence that GEOS-Chem can run on your system.

More importantly, output from the GEOS-Chem dry-run simulation can be used to download required met field and emissions data for a GEOS-Chem simulation (see next section).

What can I do with the output of a GEOS-Chem dry-run?

When you run GEOS-Chem in dry-run mode, you must pipe the output to a log file (as you would do for any other GEOS-Chem simulation). The log file containing dry-run output looks similar to a regular GEOS-Chem log file, but will also contain text such as:

...
HEMCO: Opening /path/to/ExtData/HEMCO/EDGARv43/v2016-11/EDGAR_v43.BC.POW.0.1x0.1.nc
...
HEMCO: REQUIRED FILE NOT FOUND /path/to/ExtData/HEMCO/EDGARv43/v2016-11/EDGAR_v43.BC.POW.0.1x0.1.nc
...

NOTE: /path/to/ExtData denotes the full pathname of the ExtData folder. This is the root of the directory tree containing all GEOS-Chem met fields and emissions data. This will of course be different on each system.

This text lets you know if GEOS-Chem was able to find each input file on disk or not. This information can be parsed by a Python script (download_data.py, which is included in each run directory) to produce:

  1. A unique list of required data files (with all duplicates removed). This can be useful for documentation purposes.
  2. A bash script that will download all MISSING data files from one of the GEOS-Chem data repositories:
    • Compute Canada repository
    • Amazon Web Services s3://gcgrid repository

In the following sections, we will describe the commands that are needed to execute a complete GEOS-chem dry-run workflow.

Which GEOS-Chem simulations can execute in dry-run mode?

Any of the supported GEOS-Chem "Classic" simulations (e.g. standard, benchmark, complexSOA, CH4, TransportTracers, etc.) can be executed in dry-run mode.

As of this writing (Jan 2020), GCHP cannot execute in dry-run mode. Dry-run functionality may be added in the future, but this will require modifications to the NASA MAPL software library. Because GCHP uses the same data files as GEOS-Chem "Classic", you can use a GEOS-Chem "Classic" dry-run to facilitate downloading met fields and emissions data for a GCHP simulation.

Executing GEOS-Chem in dry-run mode

Follow these steps to perform a GEOS-Chem dry-run:

  1. Create a run directory for the type of GEOS-Chem simulation that you wish to perform (e.g. geosfp_4x5_standard, merra2_2x25_tropchem, etc.. For detailed instructions, please see our our Creating run directories chapter.

  2. Change to the run directory (e.g. cd geosfp_4x5_standard, etc.) and compile GEOS-Chem as you normally would. For detailed instructions, please see our our Compiling chapter.

  3. Check to see if these settings in the SIMULATION MENU of input.geos file are as you expect:

    • Start YYYYMMDD and hhmmss
    • End YYYYMMDD and hhmsss
    • Root data directory
    • Simulation name
  4. Check to see if these settings in the GRID MENU of input.geos file are as you expect:

    • Grid resolution
  5. Check to see if these settings in the SECTION SETTINGS of the HEMCO_Config.rc file are as you expect

Downloading data from dry-run output

Further reading

  1. A
  2. B



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