Difference between revisions of "Creating GEOS-Chem run directories"

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(Downloading the GEOS-Chem unit tester)
(Editing the CopyRunDirs.input file)
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== Editing the CopyRunDirs.input file ==
 
== Editing the CopyRunDirs.input file ==
 +
 +
Once you have [[#Downloading the GEOS-Chem unit tester|downloaded the GEOS-Chem Unit Tester]] to your disk space, switch to the <tt>perl/</tt> directory:
 +
 +
    cd UT/perl
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 +
and then look for the file named <tt>CopyRunDirs.input</tt>.  This file will look similar to this:
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 +
#------------------------------------------------------------------------------
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#                  GEOS-Chem Global Chemical Transport Model                  !
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#------------------------------------------------------------------------------
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#BOP
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#
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# !DESCRIPTION: Input file that specifies configuration for creating and
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#  copying a run directory from the UnitTester.
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#\\
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#\\
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# !REMARKS: 
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#  Customize the run directory for your system by specifying these values:
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#  -------------------------------------------------------------------
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#  VERSION    : A tag used to identify this Unit Test (e.g. v10-01h)
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#  DESCRIPTION : A short description of this file's run dir copy configuration
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#  COPY_PATH  : Local path where run directory will be copied to
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#  DATA_ROOT  : Root GEOS-Chem data directory
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#  HEMCO_ROOT  : Root directory where HEMCO emissions data files are stored
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#  RUN_ROOT    : Unit test run directories are subdirectories of RUN_ROOT
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#  RUN_DIR    : Individual unit test run directory path
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#  PERL_DIR    : Unit Test perl script directory (i.e. this directory)
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#  COPY_CMD    : Unix copy command with optional tags
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#
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# !REVISION HISTORY:
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#  18 Mar 2015 - R. Yantosca - Initial version
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#  19 Mar 2015 - E. Lundgren - Simplify content for only copying run dirs
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#EOP
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#------------------------------------------------------------------------------
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#
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# !INPUTS:
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#
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    VERSION    : v10-01h
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    DESCRIPTION : Create run directory from UnitTest
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    COPY_PATH  : /home/{USER}/GC/rundirs
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    DATA_ROOT  : /as/data/geos/ExtData
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    HEMCO_ROOT  : {DATAROOT}/HEMCO
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    RUN_ROOT    : /home/{USER}/UT/runs
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    RUN_DIR    : {RUNROOT}/{RUNDIR}
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    PERL_DIR    : /home/{USER}/UT/perl
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    COPY_CMD    : cp -rfL
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#
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# !RUNS:
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#  Specify the debugging runs that you want to perform below.
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#  You can deactivate runs by commenting them out with "#".
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#
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#--------|-----------|------|------------|------------|------------|---------|
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# MET    | GRID      | NEST | SIMULATION | START DATE | END DATE  | EXTRA?  |
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#--------|-----------|------|------------|------------|------------|---------|
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  geosfp  2x25        -      Hg          2013070100  2013070101  -
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  geos5    2x25        -      Hg          2005070100  2005070101  -
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  geosfp  4x5        -      fullchem    2013070100  2013070101  -
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  geos4    4x5        -      Hg          2005070100  2005070101  -
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  geos4    4x5        -      CH4          2005070100  2005070101  -
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  geosfp  4x5        -      Hg          2013070100  2013070101  -
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  geosfp  4x5        -      POPs        2013070100  2013070101  -
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!END OF RUNS:
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#EOP
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#------------------------------------------------------------------------------
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 +
The <tt>CopyRunDirs.input</tt> file has a layout that is very similar to the [[Debugging_with_the_GEOS-Chem_unit_tester#Specifying_unit_test_options_with_an_input_file|GEOS-Chem Unit Testerinput files]].  Like these files, <tt>CopyRunDirs.input</tt> is composed of an [[#The_INPUTS_section|</tt>!INPUTS</tt>]] section and a [[#The_RUNS_section|</tt>!RUNS</tt>]] section.

Revision as of 17:57, 19 March 2015

NOTE: Page under construction

You can use the GEOS-Chem Unit Tester package to generate fresh copies of run directories for your GEOS-Chem simulations. On this page we

Downloading the GEOS-Chem unit tester

First, make sure that your system has these software packages installed. (Most of these come standard with your Unix-based operating system.)

Next, clone the GEOS-Chem unit tester package with the command:

   git clone -b v10-01-public git://git.as.harvard.edu/bmy/GEOS-Chem-UnitTest UT

This will create a copy of the GEOS-Chem Unit Tester package in a directory named UT for short.

The option

   -b v10-01-public

specifies which branch of the GEOS-Chem Unit Tester that you would like to download. Branches in the GEOS-Chem unit tester correspond to each internal version of GEOS-Chem (i.e. the states of the code for which we run 1-month benchmark simulations), as well as the publicly-released versions. Most likely, you will want to download the v10-01-public branch of the GEOS-Chem Unit Tester, which corresponds to the public release of GEOS-Chem v10-01.

--Bob Y. 13:36, 19 March 2015 (EDT)

Editing the CopyRunDirs.input file

Once you have downloaded the GEOS-Chem Unit Tester to your disk space, switch to the perl/ directory:

   cd UT/perl

and then look for the file named CopyRunDirs.input. This file will look similar to this:

#------------------------------------------------------------------------------
#                  GEOS-Chem Global Chemical Transport Model                  !
#------------------------------------------------------------------------------
#BOP
#
# !DESCRIPTION: Input file that specifies configuration for creating and
#  copying a run directory from the UnitTester. 
#\\
#\\
# !REMARKS:  
#  Customize the run directory for your system by specifying these values:
#  -------------------------------------------------------------------
#  VERSION     : A tag used to identify this Unit Test (e.g. v10-01h)
#  DESCRIPTION : A short description of this file's run dir copy configuration
#  COPY_PATH   : Local path where run directory will be copied to
#  DATA_ROOT   : Root GEOS-Chem data directory
#  HEMCO_ROOT  : Root directory where HEMCO emissions data files are stored 
#  RUN_ROOT    : Unit test run directories are subdirectories of RUN_ROOT
#  RUN_DIR     : Individual unit test run directory path
#  PERL_DIR    : Unit Test perl script directory (i.e. this directory)
#  COPY_CMD    : Unix copy command with optional tags
#
# !REVISION HISTORY:
#  18 Mar 2015 - R. Yantosca - Initial version
#  19 Mar 2015 - E. Lundgren - Simplify content for only copying run dirs
#EOP
#------------------------------------------------------------------------------
#
# !INPUTS:
#
   VERSION     : v10-01h
   DESCRIPTION : Create run directory from UnitTest
   COPY_PATH   : /home/{USER}/GC/rundirs
   DATA_ROOT   : /as/data/geos/ExtData
   HEMCO_ROOT  : {DATAROOT}/HEMCO
   RUN_ROOT    : /home/{USER}/UT/runs
   RUN_DIR     : {RUNROOT}/{RUNDIR}
   PERL_DIR    : /home/{USER}/UT/perl
   COPY_CMD    : cp -rfL
#
# !RUNS:
#  Specify the debugging runs that you want to perform below.
#  You can deactivate runs by commenting them out with "#".
#
#--------|-----------|------|------------|------------|------------|---------|
# MET    | GRID      | NEST | SIMULATION | START DATE | END DATE   | EXTRA?  |
#--------|-----------|------|------------|------------|------------|---------|
  geosfp   2x25        -      Hg           2013070100   2013070101   -
  geos5    2x25        -      Hg           2005070100   2005070101   -
  geosfp   4x5         -      fullchem     2013070100   2013070101   -
  geos4    4x5         -      Hg           2005070100   2005070101   -
  geos4    4x5         -      CH4          2005070100   2005070101   -
  geosfp   4x5         -      Hg           2013070100   2013070101   -
  geosfp   4x5         -      POPs         2013070100   2013070101   -
!END OF RUNS:
#EOP
#------------------------------------------------------------------------------

The CopyRunDirs.input file has a layout that is very similar to the GEOS-Chem Unit Testerinput files. Like these files, CopyRunDirs.input is composed of an </tt>!INPUTS</tt> section and a </tt>!RUNS</tt> section.