Difference between revisions of "Creating GEOS-Chem run directories"
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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|< | + | 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. |
+ | |||
+ | === The INPUTS section === | ||
+ | |||
+ | Under the <tt>!INPUTS:</tt> section, you can customize the directory paths and other options for your system. [[#Specifying options in the input file|As seen above]], most of these inputs are self-explanatory. | ||
+ | |||
+ | {| border=1 cellspacing=0 cellpadding=5 | ||
+ | |-bgcolor="#CCCCCC" | ||
+ | !width="100px"|Option | ||
+ | !width="825px"|DescriptionMet field type | ||
+ | |||
+ | |-valign="top" | ||
+ | |<tt>VERSION</tt> | ||
+ | |An ID tag that will be added to all log files and output files. | ||
+ | |||
+ | |-valign="top" | ||
+ | |<tt>DESCRIPTION</tt> | ||
+ | |A short (1-sentence) description of what features are being validated by this unit test. | ||
+ | |||
+ | |-valign="top" | ||
+ | |<tt>COPY_PATH</tt> | ||
+ | |Specifies the root directory on your disk server where copies of the GEOS-Chem run directories will be created. | ||
+ | |||
+ | |-valign="top" | ||
+ | |<tt>DATA_ROOT</tt> | ||
+ | |Specifies the path for your root-level data directory. | ||
+ | |||
+ | |-valign="top"http://wiki.seas.harvard.edu/geos-chem/skins//common/images/button_nowiki.png | ||
+ | |<tt>HEMCO_ROOT</tt> | ||
+ | |Specifies the top-level path for the [[HEMCO data directories|HEMCO data directory tree]]. | ||
+ | *The <tt>{DATAROOT}</tt> token in <tt>HEMCO_ROOT</tt> will be replaced with the value you specify for <tt>RUN_ROOT</tt> option. Leave this as-is. | ||
+ | |||
+ | |-valign="top" | ||
+ | |<tt>RUN_ROOT</tt> | ||
+ | |Specifies the top-level unit test run directories. Leave this as-is. | ||
+ | |||
+ | |-valign="top" | ||
+ | |<tt>PERL_DIR</tt> | ||
+ | |Specifies the directory where the unit test Perl scripts are found. | ||
+ | *Leave this as-is. | ||
+ | |||
+ | |-valign="top" | ||
+ | |<tt>COPY_CMD</tt> | ||
+ | |Specifies the command used to copy run directories from the GEOS-Chem Unit Tester to <tt>COPY_PATH</tt>. | ||
+ | *The default setting is <tt>cp -rfL</tt>. This will create a new copy of the directory, even if the prior copy exists. | ||
+ | *The <tt>-L</tt> option to the <tt>cp</tt> will create "hard" copies of files that are linked to other files. | ||
+ | |||
+ | |} | ||
+ | |||
+ | --[[User:Bmy|Bob Y.]] 14:03, 19 March 2015 (EDT) | ||
+ | |||
+ | === The RUNS section === |
Revision as of 18:03, 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
Contents
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 !INPUTS section and a </tt>!RUNS</tt> section.
The INPUTS section
Under the !INPUTS: section, you can customize the directory paths and other options for your system. As seen above, most of these inputs are self-explanatory.
Option | DescriptionMet field type |
---|---|
VERSION | An ID tag that will be added to all log files and output files. |
DESCRIPTION | A short (1-sentence) description of what features are being validated by this unit test. |
COPY_PATH | Specifies the root directory on your disk server where copies of the GEOS-Chem run directories will be created. |
DATA_ROOT | Specifies the path for your root-level data directory. |
HEMCO_ROOT | Specifies the top-level path for the HEMCO data directory tree.
|
RUN_ROOT | Specifies the top-level unit test run directories. Leave this as-is. |
PERL_DIR | Specifies the directory where the unit test Perl scripts are found.
|
COPY_CMD | Specifies the command used to copy run directories from the GEOS-Chem Unit Tester to COPY_PATH.
|
--Bob Y. 14:03, 19 March 2015 (EDT)