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| − | [[Image:Page is under construction.jpg]]
| + | #REDIRECT [[Unit Tester for GEOS-Chem 12]] |
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| − | This page describes the GEOS-Chem Unit Tester that corresponds to
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| − | == Overview ==
| + | |
| − | | + | |
| − | The GEOS-Chem Unit Tester contains all of the necessary Makefiles, scripts, and run directories that you need to run
| + | |
| − | | + | |
| − | | + | |
| − | | + | |
| − | is a package of scripts and Makefiles that will compile and run several GEOS-Chem with a set of standard debugging flags.
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| − | An individual '''GEOS-Chem Unit Test''' will look for computational and numerical issues in simulations for a given combination of:
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| − | | + | |
| − | # Met field type | + | |
| − | # Horizontal grid
| + | |
| − | # Simulation type
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| − | You can specify the unit tests that you wish the GEOS-Chem Unit Tester to perform in an [[#Specifying_unit_test_options_with_an_input_file|customizable input file, as described below]].
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| − | The GEOS_Chem Unit TEster
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| − | | + | |
| − | == Installing the GEOS-Chem Unit Tester ==
| + | |
| − | | + | |
| − | === Requirements ===
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| − | | + | |
| − | Most GEOS-Chem users will already have the necessary software to be able to run the GEOS-Chem Unit Test package. These are:
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| − | | + | |
| − | #A modern "Linux-like" operating system, e.g.
| + | |
| − | #*Linux (all flavors)
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| − | #*CentOS
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| − | #*Ubuntu
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| − | #*Fedora
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| − | #[http://www.gnu.org/software/bash/bash.html The <tt>bash</tt> Unix shell] (usually comes pre-installed with your OS)
| + | |
| − | #[http://www.perl.org/ The <tt>Perl</tt> programming language] (usually comes pre-installed with your OS)
| + | |
| − | #[http://www.gnu.org/software/make/ The GNU <tt>make</tt> utility] (usually comes pre-installed with your OS)
| + | |
| − | #'''IMPORTANT! You will also need [[GEOS-Chem v9-02 benchmark history#v9-02o|GEOS-Chem v9-02o]] or a later version'''.
| + | |
| − | #*Previous versions are not compatible with the GEOS-Chem Unit Tester because they use the <tt>Headers/define.h</tt> file to specify some [http://acmg.seas.harvard.edu/geos/doc/man/chapter_3.html#3.4 C-preprocessor switches].
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| − | #*In GEOS-Chem v9-02o and higher versions, all C-preprocessor switches will be set from command-line inputs to GNU Make.'''
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| − | | + | |
| − | --[[User:Bmy|Bob Y.]] 17:20, 6 September 2013 (EDT)
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| − | | + | |
| − | === Downloading the GEOS-Chem Unit Tester ===
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| − | | + | |
| − | You may download the GEOS-Chem unit tester with Git:
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| − | | + | |
| − | git clone <nowiki>https://bitbucket.org/gcst/geos-chem-unittest</nowiki> UT
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| − | git checkout master
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| − | This will download a fresh copy of the <tt>GEOS-Chem-UnitTest</tt> repository into a directory named <tt>UT</tt>, and place you in the '''master''' branch. This branch corresponds to the last publicly-released GEOS-Chem version (which as of Feb 2017 is the v11-01 public release).
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| − | ==== Reverting to an older state ====
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| − | Currently, the GEOS-Chem Unit Tester is synchronized with [[GEOS-Chem v10-01]]. If you would like to use the Unit Tester to validate an older version of GEOS-Chem, then you can use the gitk browser to open a new branch at a past commit as follows:
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| − | | + | |
| − | # Open the gitk browser by typing '''gitk &''' at the command line.
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| − | # In the top-left window of gitk, find the commit that you want to revert to. Usually this will be denoted with a yellow tag (e.g. '''v9-02-Provisional-Release''' or '''v10-01b'', etc.).
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| − | # Right click with the mouse. This will open a context menu. Select '''Create new branch'''.
| + | |
| − | # A new dialog box will pop up asking you to name the branch. Type '''OLDER_BRANCH''' and press '''OK'''.
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| − | # Close gitk and open the Git GUI by typing '''git gui &'''
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| − | # From the Git GUI dropdown menu, select '''Branch / Checkout''', and then pick '''OLDER_BRANCH'''.
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| − | That's it! We now have two branches that represent different GEOS-Chem versions.
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| − | # The '''master''' branch represents current state of the unit tester
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| − | # The '''OLDER_BRANCH''' branch represents the state of the unit tester that you checked out (synced to an older GEOS-Chem version)
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| − | --[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:48, 24 April 2017 (UTC)
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| − | | + | |
| − | === Directory structure ===
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| − | The GEOS-Chem Unit Tester adheres to the following directory structure:
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| − | {| border=1 cellspacing=0 cellpadding=5
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| − | |-bgcolor="#CCCCCC"
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| − | !width="100px"|Directory
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| − | !width="900px"|Description
| + | |
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| − | |-valign="top"
| + | |
| − | |<tt>jobs/</tt>
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| − | |Job scripts created by the GEOS-Chem Unit Test driver script <tt>gcUnitTest</tt> will be sent here.
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| − | |-valign="top"
| + | |
| − | |<tt>logs/</tt>
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| − | |Log files containing output from the GEOS-Chem Unit Test simulations will be sent here.
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| − | | + | |
| − | |-valign="top"
| + | |
| − | |<tt>perl/</tt>
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| − | |Contains the Perl scripts that are used to submit GEOS-Chem Unit Test simulations.
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| − | *The driver script is called <tt>gcUnitTest</tt>.
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| − | *The default input file for <tt>gcUnitTest</tt> is named <tt>UnitTest.input</tt>.
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| − | *Sample customized versions of <tt>UnitTest.input</tt> are stored in the <tt>perl/inputs</tt> subdirectory.
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| − | *The <tt>cleanFiles</tt> script is used to remove job scripts, log files, and output files created by GEOS-Chem.
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| − | |-valign="top"
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| − | |<tt>runs/</tt>
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| − | |Contains the various run directories. Each run directory is named according to the met field, horizontal grid, and type of simulation (<tt>4x5_standard</tt>, <tt>2x25_RnPbBe</tt>, etc).
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| − | | + | |
| − | |}
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| − | --[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 15:08, 20 December 2016 (UTC)
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| − | | + | |
| − | == Using the GEOS-Chem Unit Tester ==
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| − | === What the GEOS-Chem Unit Tester does ===
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| − | For each individual unit test (met field + horizontal grid + simulation type) that you specify in the [[#The RUNS section|RUNS section of the input file]] (more on this below), the GEOS-Chem Unit Tester will do the following:
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| − | #Run GEOS-Chem with strict debugging flags with OpenMP parallelization turned OFF
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| − | #*This is called the '''single processor''' or '''sp''' test phase.
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| − | #Run GEOS-Chem with strict debugging flags with OpenMP parallelization turned ON
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| − | #*This is called the '''multi processor''' or '''mp''' test phase.
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| − | The strict debugging flags will look for common computational and numerical issues, such as
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| − | #[http://floating-point-gui.de/ Floating-point math exceptions]: div-by-zero, invalid computations (i.e. <tt>SQRT(-1)</tt>, <tt>LOG(-1)</tt>, etc.)
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| − | #[[Common_GEOS-Chem_error_messages#Array-out-of-bounds_error|Array-out-of-bounds errors]]
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| − | #[[Passing_array_arguments_efficiently_in_GEOS-Chem|Creation of array temporaries]]
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| − | Furthermore, the Unit Tester compare the output of the '''sp''' and '''mp''' test phases. If these outputs differ, then this indicates a [[Parallelizing GEOS-Chem|parallelization error]].
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| − | --[[User:Bmy|Bob Y.]] 10:08, 25 April 2014 (EDT)
| + | |
| − | | + | |
| − | === Specifying unit test options with an input file ===
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| − | Before you can start the GEOS-Chem Unit Tester, you must first specify the options for the unit test simulations in an input file. You can specify the directory paths for your system, the location of the GEOS-Chem code directory, the submit command for your system, and the types of simulations that you want the GEOS-Chem Unit Tester to validate. The default input file is named <tt>UnitTest.input</tt>, but you can cut-n-paste this file to create as many customized input files as you need.
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| − | The <tt>UnitTest.input</tt> file looks like this. All lines beginning with a <tt>#</tt> character are treated as comments and will be ignored.
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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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| − | # !INCLUDE: UnitTest.input
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| − | #
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| − | # !DESCRIPTION: Input file that specifies debugging options for the
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| − | # GEOS-Chem unit tester.
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| − | #\\
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| − | #\\
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| − | # !REMARKS:
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| − | # To omit individual unit tests (or input settings), place a # comment
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| − | # character in the first column.
| + | |
| − | #
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| − | # For a complete explanation of how to customize the settings below for
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| − | # your installation, please see these wiki posts:
| + | |
| − | #
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| − | # <nowiki>http://wiki.geos-chem.org/GEOS-Chem_Unit_Tester#The_INPUTS_section</nowiki>
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| − | # <nowiki>http://wiki.geos-chem.org/GEOS-Chem_Unit_Tester#The_RUNS_section</nowiki>
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| − | #
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| − | # !REVISION HISTORY:
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| − | # Type 'gitk' at the prompt to browse the revision history.
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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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| − | # %%% ID tags %%%
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| − | #
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| − | VERSION : v11-01
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| − | DESCRIPTION : Tests GEOS-Chem v11-01
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| − | #
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| − | # %%% Data path and HEMCO settings %%%
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| − | #
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| − | DATA_ROOT : /n/holylfs/EXTERNAL_REPOS/GEOS-CHEM/gcgrid/data/ExtData
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| − | HEMCO_ROOT : {DATAROOT}/HEMCO
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| − | VERBOSE : 3
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| − | WARNINGS : 3
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| − | #
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| − | # %%% Code, compiler, and queue settings %%%
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| − | #
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| − | CODE_DIR : {HOME}/GC/Code.v11-01
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| − | COMPILER : ifort
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| − | MAKE_CMD : make -j4 BOUNDS=y DEBUG=y FPE=y NO_ISO=y
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| − | SUBMIT : sbatch
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| − | #
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| − | # %%% Unit tester path names %%%
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| − | #
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| − | UNIT_TEST_ROOT : {HOME}/UT
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| − | RUN_ROOT : {UTROOT}/runs
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| − | RUN_DIR : {RUNROOT}/{RUNDIR}
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| − | JOB_DIR : {UTROOT}/jobs
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| − | LOG_DIR : {UTROOT}/logs/{VERSION}
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| − | PERL_DIR : {UTROOT}/perl
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| − | #
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| − | # %%% Web and text display options %%%
| + | |
| − | #
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| − | TEMPLATE : {PERLDIR}/ut_template.html
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| − | TXT_GRID : {LOGDIR}/{VERSION}.results.txt
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| − | WEB_GRID : {LOGDIR}/{VERSION}.results.html
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| − | WEB_PUSH : NONE
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| − | #
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| − | # %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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| − | # %%% OPTIONAL SLURM COMMANDS: %%%
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| − | # %%% %%%
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| − | # %%% Set these if your system uses the SLURM scheduler. %%%
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| − | # %%% These will be used to set #SBATCH tags for the job script. %%%
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| − | # %%% Otherwise you can comment these lines out. %%%
| + | |
| − | # %%% %%%
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| − | # %%% NOTE: If you do use these SLURM commands, then also be %%%
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| − | # %%% sure to set the SUBMIT command above to "sbatch". %%%
| + | |
| − | # %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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| − | #
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| − | SLURM_CPUS : 4
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| − | SLURM_NODES : 1
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| − | SLURM_TIME : 1-12:00
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| − | SLURM_MEMORY : 30000
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| − | SLURM_PARTITION : jacob
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| − | SLURM_CONSTRAINT : intel
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| − | SLURM_MAILTYPE : END
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| − | SLURM_MAILUSER : your-email-address
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| − | SLURM_STDOUT : {LOGDIR}/{VERSION}.stdout.log
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| − | SLURM_STDERR : {LOGDIR}/{VERSION}.stderr.log
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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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| − | # MET | GRID | NEST | SIMULATION | START DATE | END DATE | EXTRA? |
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| − | #--------|-----------|------|------------|------------|--------------|--------|
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| − | # ======= Radon-Lead-Beryllium ===============================================
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| − | geosfp 4x5 - RnPbBe 2013070100 201307010020 -
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| − | merra2 4x5 - RnPbBe 2013070100 201307010020 -
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| − | merra 4x5 - RnPbBe 2006070100 200607010020 -
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| − | geos5 4x5 - RnPbBe 2006070100 200607010020 -
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| − | geos4 4x5 - RnPbBe 2006070100 200607010020 -
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| − | gcap 4x5 - RnPbBe 2005070100 200507010020 -
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| − | geosfp 2x25 - RnPbBe 2013070100 201307010020 -
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| − | merra2 2x25 - RnPbBe 2013070100 201307010020 -
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| − | geos5 2x25 - RnPbBe 2006070100 200607010020 -
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| − | # ======= Mercury ============================================================
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| − | geosfp 4x5 - Hg 2013010100 201301010020 -
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| − | merra2 4x5 - Hg 2013010100 201301010020 -
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| − | merra 4x5 - Hg 2009010100 200901010020 -
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| − | geos5 4x5 - Hg 2009010100 200901010020 -
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| − | geos4 4x5 - Hg 2006010100 200601010020 -
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| − | geosfp 2x25 - Hg 2013010100 201301010020 -
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| − | merra2 2x25 - Hg 2013010100 201301010020 -
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| − | merra 2x25 - Hg 2009010100 200901010020 -
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| − | geos5 2x25 - Hg 2009010100 200901010020 -
| + | |
| − | # geos5 05x0666 na Hg 2008010100 200801010020 -
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| − | # ======= Tagged Mercury =====================================================
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| − | geos5 4x5 - tagHg 2010010100 2010010101 -
| + | |
| − | # ======= POPs ===============================================================
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| − | geosfp 4x5 - POPs 2013070100 201307010020 -
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| − | merra2 4x5 - POPs 2013070100 201307010020 -
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| − | merra 4x5 - POPs 2006070100 200607010020 -
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| − | geos5 4x5 - POPs 2006070100 200607010020 -
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| − | geos4 4x5 - POPs 2006070100 200607010020 -
| + | |
| − | gcap 4x5 - POPs 2005070100 200507010020 -
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| − | geosfp 2x25 - POPs 2013070100 201307010020 -
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| − | merra2 2x25 - POPs 2013070100 201307010020 -
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| − | geos5 2x25 - POPs 2006070100 200607010020 -
| + | |
| − | # ======= Methane ============================================================
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| − | geosfp 4x5 - CH4 2013070100 201307010020 -
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| − | merra2 4x5 - CH4 2013070100 201307010020 -
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| − | merra 4x5 - CH4 2006070100 200607010020 -
| + | |
| − | geos5 4x5 - CH4 2006070100 200607010020 -
| + | |
| − | geos4 4x5 - CH4 2006070100 200607010020 -
| + | |
| − | geosfp 2x25 - CH4 2013070100 201307010020 -
| + | |
| − | merra2 2x25 - CH4 2013070100 201307010020 -
| + | |
| − | geos5 2x25 - CH4 2006070100 200607010020 -
| + | |
| − | merra2 05x0625 na CH4 2013070100 201307010020 -
| + | |
| − | geos5 05x0666 na CH4 2006070100 200607010020 -
| + | |
| − | # ======= Tagged O3 ==========================================================
| + | |
| − | geosfp 4x5 - tagO3 2013070100 201307010020 -
| + | |
| − | merra2 4x5 - tagO3 2013070100 201307010020 -
| + | |
| − | merra 4x5 - tagO3 2006070100 200607010020 -
| + | |
| − | geos5 4x5 - tagO3 2006070100 200607010020 -
| + | |
| − | geos4 4x5 - tagO3 2006070100 200607010020 -
| + | |
| − | geosfp 2x25 - tagO3 2013070100 201307010020 -
| + | |
| − | merra2 2x25 - tagO3 2013070100 201307010020 -
| + | |
| − | geos5 2x25 - tagO3 2006070100 200607010020 -
| + | |
| − | # ======= Tagged CO ==========================================================
| + | |
| − | geosfp 4x5 - tagCO 2013070100 201307010020 -
| + | |
| − | merra2 4x5 - tagCO 2013070100 201307010020 -
| + | |
| − | merra 4x5 - tagCO 2006070100 200607010020 -
| + | |
| − | geos5 4x5 - tagCO 2006070100 200607010020 -
| + | |
| − | # ======= Carbon Dioxide =====================================================
| + | |
| − | geosfp 2x25 - CO2 2013070100 201307010020 -
| + | |
| − | merra2 2x25 - CO2 2013070100 201307010020 -
| + | |
| − | geos5 2x25 - CO2 2006070100 200607010020 -
| + | |
| − | # ======= Offline Aerosols ===================================================
| + | |
| − | geosfp 4x5 - aerosol 2013070100 201307010020 -
| + | |
| − | merra2 4x5 - aerosol 2013070100 201307010020 -
| + | |
| − | merra 4x5 - aerosol 2006070100 200607010020 -
| + | |
| − | geos5 4x5 - aerosol 2006070100 200607010020 -
| + | |
| − | geos4 4x5 - aerosol 2006070100 200607010020 -
| + | |
| − | geosfp 2x25 - aerosol 2013070100 201307010020 -
| + | |
| − | merra2 2x25 - aerosol 2013070100 201307010020 -
| + | |
| − | geos5 2x25 - aerosol 2006070100 200607010020 -
| + | |
| − | # ======= GEOS-Chem benchmark ================================================
| + | |
| − | geosfp 4x5 - standard 2013070100 201307010020 -
| + | |
| − | merra2 4x5 - standard 2013070100 201307010020 -
| + | |
| − | geosfp 2x25 - standard 2013070100 201307010020 -
| + | |
| − | # ======= Tropchem ===========================================================
| + | |
| − | geosfp 4x5 - tropchem 2013070100 201307010020 -
| + | |
| − | merra2 4x5 - tropchem 2013070100 201307010020 -
| + | |
| − | merra 4x5 - tropchem 2006070100 200607010020 -
| + | |
| − | geos5 4x5 - tropchem 2006070100 200607010020 -
| + | |
| − | geos4 4x5 - tropchem 2006070100 200607010020 -
| + | |
| − | # gcap 4x5 - tropchem 2005070100 200507010020 -
| + | |
| − | geosfp 2x25 - tropchem 2013070100 201307010020 -
| + | |
| − | merra2 2x25 - tropchem 2013070100 201307010020 -
| + | |
| − | geos5 2x25 - tropchem 2006070100 200607010020 -
| + | |
| − | # ======= SOA (w/o SVPOA) ====================================================
| + | |
| − | geosfp 4x5 - soa 2013070100 201307010020 -
| + | |
| − | merra2 4x5 - soa 2013070100 201307010020 -
| + | |
| − | merra 4x5 - soa 2006070100 200607010020 -
| + | |
| − | geos5 4x5 - soa 2006070100 200607010020 -
| + | |
| − | geosfp 2x25 - soa 2013070100 201307010020 -
| + | |
| − | merra2 2x25 - soa 2013070100 201307010020 -
| + | |
| − | geos5 2x25 - soa 2006070100 200607010020 -
| + | |
| − | # ======= SOA (w/ SVPOA) =====================================================
| + | |
| − | geosfp 4x5 - soa_svpoa 2013070100 201307010020 -
| + | |
| − | merra2 4x5 - soa_svpoa 2013070100 201307010020 -
| + | |
| − | merra 4x5 - soa_svpoa 2006070100 200607010020 -
| + | |
| − | geos5 4x5 - soa_svpoa 2006070100 200607010020 -
| + | |
| − | geosfp 2x25 - soa_svpoa 2013070100 201307010020 -
| + | |
| − | merra2 2x25 - soa_svpoa 2013070100 201307010020 -
| + | |
| − | geos5 2x25 - soa_svpoa 2006070100 200607010020 -
| + | |
| − | # ======= Acid uptake on dust ================================================
| + | |
| − | geosfp 4x5 - aciduptake 2013070100 201307010020 -
| + | |
| − | geosfp 2x25 - aciduptake 2013070100 201307010020 -
| + | |
| − | # ======= Marine POA =========================================================
| + | |
| − | geosfp 4x5 - marinePOA 2013070100 201307010020 -
| + | |
| − | geosfp 2x25 - marinePOA 2013070100 201307010020 -
| + | |
| − | # ======= TOMAS aerosol microphysics =========================================
| + | |
| − | geosfp 4x5 - TOMAS15 2013070100 201307010020 -
| + | |
| − | geos5 4x5 - TOMAS15 2006070100 200607010020 -
| + | |
| − | geosfp 4x5 - TOMAS40 2013070100 201307010020 -
| + | |
| − | geos5 4x5 - TOMAS40 2006070100 200607010020 -
| + | |
| − | # ======= UCX strat-trop chemistry ===========================================
| + | |
| − | geosfp 4x5 - UCX 2013070100 201307010020 -
| + | |
| − | merra2 4x5 - UCX 2013070100 201307010020 -
| + | |
| − | geos5 4x5 - UCX 2006070100 200607010020 -
| + | |
| − | geosfp 2x25 - UCX 2013070100 201307010020 -
| + | |
| − | merra2 2x25 - UCX 2013070100 201307010020 -
| + | |
| − | geos5 2x25 - UCX 2006070100 200607010020 -
| + | |
| − | # ======= RRTMG online radiative transfer ====================================
| + | |
| − | geosfp 4x5 - RRTMG 2013070100 201307010040 -
| + | |
| − | merra2 4x5 - RRTMG 2013070100 201307010040 -
| + | |
| − | merra 4x5 - RRTMG 2006070100 200607010040 -
| + | |
| − | geos5 4x5 - RRTMG 2006070100 200607010040 -
| + | |
| − | # geosfp 2x25 - RRTMG 2013070100 201307010040 -
| + | |
| − | # merra2 2x25 - RRTMG 2013070100 201307010040 -
| + | |
| − | # geos5 2x25 - RRTMG 2006070100 200607010040 -
| + | |
| − | # ======= Nested model runs ==================================================
| + | |
| − | # geosfp 025x03125 ch tropchem 2013070100 201307010010 -
| + | |
| − | geosfp 025x03125 na tropchem 2013070100 201307010010 -
| + | |
| − | merra2 05x0625 as tropchem 2013070100 201307010020 -
| + | |
| − | merra2 05x0625 na tropchem 2013070100 201307010020 -
| + | |
| − | geos5 05x0666 ch tropchem 2006070100 200607010020 -
| + | |
| − | geos5 05x0666 na tropchem 2006070100 200607010020 -
| + | |
| − | !END OF RUNS:
| + | |
| − | #EOP
| + | |
| − | #------------------------------------------------------------------------------
| + | |
| − | | + | |
| − | --[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 15:59, 22 February 2017 (UTC)
| + | |
| − | | + | |
| − | ==== 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="150x"|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>DATA_ROOT</tt>
| + | |
| − | |Specifies the path for your root-level data directory.
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | |<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>VERBOSE</tt>
| + | |
| − | |Specifies the level of debug output that will be sent to the HEMCO log file. (0=no debug output; 3=max debug output)
| + | |
| − | *Recommended setting: <tt>0</tt>
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | |<tt>WARNINGS</tt>
| + | |
| − | |Specifies the level of warning messages that will be sent to the HEMCO log file. (0=no warnings; 3=max warnings)
| + | |
| − | *Recommended setting: <tt>1</tt>
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | |<tt>CODE_DIR</tt>
| + | |
| − | |Specifies the path of the source code directory.
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | |<tt>COMPILER</tt>
| + | |
| − | |Specifies the compiler type.
| + | |
| − | *Currently allowed values are <tt>ifort</tt>, <tt>gfortran</tt>, and <tt>pgi</tt>.
| + | |
| − | *<span style="color:darkorange">'''''NOTE: In [[GEOS-Chem v11-02]] and newer versions, the value of <tt>COMPILER</tt> is automatically determined from the <tt>FC</tt> Unix environment variable. Therefore, the <tt>COMPILER</tt> setting will be obsolete for the newest versions of GEOS-Chem.'''''</span>
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | |<tt>MAKE_CMD</tt>
| + | |
| − | |Specifies the make command for your system. Usually this is <tt>make</tt>, but on some systems this may be <tt>gmake</tt>. Recommended options are:
| + | |
| − | *<tt>BOUNDS=y</tt>: Turns on array-out-of-bounds checking
| + | |
| − | *<tt>DEBUG=y</tt>: Turns off optimization and enables features that will facilitate running GEOS-Chem in a debugger (if need be). Will cause GEOS-Chem to check for array temporaries. Also enables program traceback.
| + | |
| − | *<tt>NO_ISO=y</tt>: Disables the ISORROPIA aerosol thermodynamical equilibrium module, which is known to produce random numerical noise.
| + | |
| − | *<tt>FPE=y</tt>: Turns on checks for floating-point issues (div-by-zero, floating invalid, underflow, overflow, etc).
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | |<tt>SUBMIT</tt>
| + | |
| − | |Specifies the command that will send the Unit Test job to your queue system.
| + | |
| − | *If you don't have a queue system, leave this blank, and the Unit Tester will run interactively.
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | |<tt>UNIT_TEST_ROOT</tt>
| + | |
| − | |Specifies the path to the GEOS-Chem Unit Tester.
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | |<tt>RUN_ROOT</tt>
| + | |
| − | |Specifies the top-level unit test run directories.
| + | |
| − | <b>Leave this as-is.</b>
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | |<tt>RUN_DIR</tt>
| + | |
| − | |Specifies the run directory subdirectory.
| + | |
| − | *The <tt>{RUNDIR}</tt> token in <tt>RUN_DIR</tt> will be replaced with the name of a subdirectory.
| + | |
| − | <b>Leave this as-is.</b>
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | |<tt>JOB_DIR</tt>
| + | |
| − | |Specifies the directory where the unit test job script will be created.
| + | |
| − | <b>Leave this as-is.</b>
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | |<tt>LOG_DIR</tt>
| + | |
| − | |Specifies the directory where log files from this unit test simulation will be sent.
| + | |
| − | *The <tt>{VERSION}</tt> token in <tt>LOG_DIR</tt> will be replaced with the value of <tt>VERSION</tt> that you specify above. This allows the Unit Tester to send log files from different unit tests to subdirectories of <tt>LOG_DIR</tt>. This will let you preserve older log files.
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | |<tt>PERL_DIR</tt>
| + | |
| − | |Specifies the directory where the unit test Perl scripts are found.
| + | |
| − | *Leave this as-is.
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | |<tt>TEMPLATE</tt>
| + | |
| − | |Specifies the template HTML file that will be used to create a web page with unit test results.
| + | |
| − | *Leave this as-is.
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | |<tt>TXT_GRID</tt>
| + | |
| − | |Specifies the path of this summary text file
| + | |
| − | *The <tt>{LOGDIR}</tt> token in <tt>TXT_GRID</tt> will be replaced with the value of <tt>LOG_DIR</tt>. Leave this as-is.
| + | |
| − | *The <tt>{VERSION}</tt> token in <tt>TXT_GRID</tt> will be replaced with the value of <tt>VERSION</tt> that you specify above. Leave this as-is.
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | |<tt>WEB_GRID</tt>
| + | |
| − | |Specifies the name of the web page that will contain the unit test results.
| + | |
| − | *This web page is created from the template HTML file specified with the <tt>TEMPLATE</tt> option.
| + | |
| − | *The <tt>{LOGDIR}</tt> token in <tt>WEB_GRID</tt> will be replaced with the value of <tt>LOG_DIR</tt>. Leave this as-is.
| + | |
| − | *The <tt>{VERSION}</tt> token in <tt>WEB_GRID</tt> will be replaced with the value of <tt>VERSION</tt> that you specify above. Leave this as-is.
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | |<tt>WEB_PUSH</tt>
| + | |
| − | |Specifies the remote server to which the <tt>WEB_GRID</tt> web page will be uploaded. Options are:
| + | |
| − | *<tt>NONE</tt>: Do not upload the page
| + | |
| − | *<tt>user@host|directory/</tt>: Specifies the remote directory. (Example: <tt>geoschem@fas.harvard.edu|public_html/ut/</tt>)
| + | |
| − | | + | |
| − | |}
| + | |
| − | | + | |
| − | Note that you can use a symbolic link (i.e. <tt>/home/{USER}/UT/</tt> in the <tt>RUN_ROOT</tt>, <tt>RUN_DIR</tt>, <tt>JOB_DIR</tt>, <tt>LOG_DIR</tt> and <tt>PERL_DIR</tt> variables. This can help you shorten the file paths.
| + | |
| − | | + | |
| − | --[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 15:59, 22 February 2017 (UTC)
| + | |
| − | | + | |
| − | ==== The RUNS section ====
| + | |
| − | | + | |
| − | Under the <tt>!RUNS:</tt> section, you will list each of the combinations that you want the GEOS-Chem Unit Tester to validate. Simply list the following information under the proper column heading. Lines starting with <tt>#</tt> will be ignored.
| + | |
| − | | + | |
| − | # !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 4x5 - RnPbBe 2013070100 2013070101 -
| + | |
| − | geosfp 4x5 - Hg 2013070100 2013070101 -
| + | |
| − | geosfp 4x5 - POPs 2013070100 2013070101 -
| + | |
| − | geosfp 4x5 - CH4 2013070100 2013070101 -
| + | |
| − | geosfp 4x5 - tagO3 2013070100 2013070101 -
| + | |
| − | geosfp 4x5 - tagCO 2013070100 2013070101 -
| + | |
| − | geosfp 4x5 - aerosol 2013070100 2013070101 -
| + | |
| − | geosfp 4x5 - standard 2013070100 2013070101 -
| + | |
| − | geosfp 4x5 - tropchem 2013070100 2013070101 -
| + | |
| − | geosfp 4x5 - soa 2013070100 2013070101 -
| + | |
| − | geosfp 4x5 - soa_svpoa 2013070100 2013070101 -
| + | |
| − | geosfp 4x5 - aciduptake 2013070100 2013070101 -
| + | |
| − | geosfp 4x5 - marinePOA 2013070100 2013070101 -
| + | |
| − | geosfp 4x5 - TOMAS40 2013070100 2013070101 -
| + | |
| − | geosfp 4x5 - UCX 2013070100 2013070101 -
| + | |
| − | . . . etc . . .
| + | |
| − | !END OF RUNS:
| + | |
| − | | + | |
| − | Options:
| + | |
| − | | + | |
| − | ;MET: Specifies the met field type. Allowable values are:
| + | |
| − | <blockquote>
| + | |
| − | {| border=1 cellspacing=0 cellpadding=5
| + | |
| − | |-bgcolor="#CCCCCC"
| + | |
| − | !width="125px"|Value
| + | |
| − | !width="600px"|Met field type
| + | |
| − | |-
| + | |
| − | |<tt>gcap</tt>
| + | |
| − | |Selects the [[GCAP|GCAP met fields]].
| + | |
| − | |-
| + | |
| − | |<tt>geos4</tt>
| + | |
| − | |Selects the [[GMAO GEOS-4|GEOS-4 met fields]].
| + | |
| − | |-
| + | |
| − | |<tt>geos5</tt>
| + | |
| − | |Selects the [[GEOS-5|GEOS-5 met fields]].
| + | |
| − | |-
| + | |
| − | |<tt>geosfp</tt>
| + | |
| − | |Selects the [[GEOS-FP|GEOS-FP met fields]].
| + | |
| − | |-
| + | |
| − | |<tt>merra</tt>
| + | |
| − | |Selects the [[MERRA|MERRA met fields]].
| + | |
| − | |-
| + | |
| − | |<tt>merra2</tt>
| + | |
| − | |Selects the [[MERRA-2|MERRA-2 met fields]].
| + | |
| − | |}
| + | |
| − | </blockquote>
| + | |
| − | ;GRID: Specifies the horizontal grid. Allowable values are:
| + | |
| − | <blockquote>
| + | |
| − | {| border=1 cellspacing=0 cellpadding=5
| + | |
| − | |-bgcolor="#CCCCCC"
| + | |
| − | !width="125px"|Value
| + | |
| − | !width="600px"|Grid type
| + | |
| − | |-
| + | |
| − | |<tt>4x5</tt>
| + | |
| − | |Selects the [[GEOS-Chem_horizontal_grids#GMAO_4_x_5_grid|GMAO 4° x 5° horizontal grid]].
| + | |
| − | |-
| + | |
| − | |<tt>2x25</tt>
| + | |
| − | |Selects the [[GEOS-Chem_horizontal_grids#GMAO_2_x_2.5_grid|GMAO 2° x 2.5° horizontal grid]].
| + | |
| − | |-
| + | |
| − | |<tt>05x0666</tt>
| + | |
| − | |Selects the [[GEOS-Chem_horizontal_grids#GMAO_0.5_x_0.666_grid|GMAO 0.5° x 0.666° grid]] for use with GEOS-5 met fields only.<br>(You must also specify a value for <tt>NEST</tt>.)
| + | |
| − | |-
| + | |
| − | |<tt>05x0625</tt>
| + | |
| − | |Selects the [[GEOS-Chem_horizontal_grids#GMAO_0.5_x_0.625_grid|GMAO 0.5° x 0.625° grid]] for use with MERRA-2 met fields only.<br>(You must also specify a value for <tt>NEST</tt>.)
| + | |
| − | |-
| + | |
| − | |<tt>025x03125</tt>
| + | |
| − | |Selects the [[GEOS-Chem_horizontal_grids#GMAO_0.25_x_0.3125_grid|GMAO 0.25° x 0.3125° grid]] for use with GEOS-FP met fields only.<br> (You must also specify a value for <tt>NEST</tt>.)
| + | |
| − | |}
| + | |
| − | </blockquote>
| + | |
| − | ;NEST: Specifies the nested grid. May only be used if the value for <tt>GRID</tt> is <tt>05x0666</tt>, <tt>05x0625</tt>, or <tt>025x03125</tt>. Allowable values are:
| + | |
| − | <blockquote>
| + | |
| − | {| border=1 cellspacing=0 cellpadding=5
| + | |
| − | |-bgcolor="#CCCCCC"
| + | |
| − | !width="125px"|Value
| + | |
| − | !width="600px"|Nested grid option
| + | |
| − | |-
| + | |
| − | |<tt>-</tt>
| + | |
| − | |Skips the nested grid option (default). Use this for global simulations.
| + | |
| − | |-
| + | |
| − | |<tt>as</tt>
| + | |
| − | |Selects the Asia (AS) nested grid option for use with MERRA-2 met fields only.
| + | |
| − | |-
| + | |
| − | |<tt>ch</tt>
| + | |
| − | |Selects the China (CH) nested grid option for use with GEOS-5 or GEOS-FP met fields only.
| + | |
| − | |-
| + | |
| − | |<tt>eu</tt>
| + | |
| − | |Selects the Europe (EU) nested grid option.
| + | |
| − | |-
| + | |
| − | |<tt>na</tt>
| + | |
| − | |Selects the North American (NA) nested grid option.
| + | |
| − | |}
| + | |
| − | </blockquote>
| + | |
| − | ;SIMULATION: Specifies the simulation type. Allowable values are:
| + | |
| − | <blockquote>
| + | |
| − | {| border=1 cellspacing=0 cellpadding=5
| + | |
| − | |-bgcolor="#CCCCCC"
| + | |
| − | !width="125px"|Value
| + | |
| − | !width="600px"|Simulation
| + | |
| − | |-bgcolor="#CCFFFF"
| + | |
| − | !
| + | |
| − | !Full-chemistry simulations
| + | |
| − | |-
| + | |
| − | |<tt>standard</tt>
| + | |
| − | |Selects the [[GEOS-Chem_chemistry_mechanisms#Mechanisms_in_GEOS-Chem_v10-01_and_later_versions|Standard chemistry mechanism]] used in the GEOS-Chem benchmark simulations.
| + | |
| − | |-
| + | |
| − | |<tt>tropchem</tt>
| + | |
| − | |Selects the [[NOx-Ox-HC-aerosol|The NOx-Ox-HC-Aer-Br tropospheric chemistry simulation]].
| + | |
| − | |-
| + | |
| − | |<tt>soa</tt>
| + | |
| − | |Selects the [[Secondary organic aerosols]] simulation, without semi-volatile POA.
| + | |
| − | |-
| + | |
| − | |<tt>soa_svpoa</tt>
| + | |
| − | |Selects the [[Secondary organic aerosols]] simulation, with semi-volatile POA.
| + | |
| − | |-
| + | |
| − | |<tt>aciduptake</tt>
| + | |
| − | |Selects the [[GEOS-Chem_chemistry_mechanisms#Mechanisms_in_GEOS-Chem_v10-01_and_later_versions|Standard chemistry simulation]], with [[Mineral_dust_aerosols#Surface_chemistry_on_dust|acid uptake on dust aerosols]] turned on.
| + | |
| − | |-
| + | |
| − | |<tt>marinePOA</tt>
| + | |
| − | |Selects the [[GEOS-Chem_chemistry_mechanisms#Mechanisms_in_GEOS-Chem_v10-01_and_later_versions|Standard chemistry simulation]], with [[Aerosol_emissions#Online_emission_of_marine_primary_organic_aerosol_.28POA.29|marine primary organic aerosols]] turned on.
| + | |
| − | |-
| + | |
| − | |<tt>UCX</tt>
| + | |
| − | |Selects the [[UCX chemistry mechanism]]: combined stratospheric and tropospheric chemistry
| + | |
| − | |-
| + | |
| − | |<tt>RRTMG</tt>
| + | |
| − | |Selects the [[NOx-Ox-HC-aerosol|The NOx-Ox-HC-Aer-Br tropospheric chemistry simulation]], with [[Coupling GEOS-Chem with RRTMG|RRTMG]] turned on.
| + | |
| − | |-bgcolor="#CCFFFF"
| + | |
| − | !
| + | |
| − | !Specialty simulations
| + | |
| − | |-
| + | |
| − | |<tt>RnPbBe</tt>
| + | |
| − | |Selects the [[Rn-Pb-Be simulation|Radon-Lead-Beryllium]] simulation.
| + | |
| − | |-
| + | |
| − | |<tt>Hg</tt>
| + | |
| − | |Selects the [[Mercury]] simulation.
| + | |
| − | |-
| + | |
| − | |<tt>tagHg</tt>
| + | |
| − | |Selects the [[Mercury|Tagged mercury]] simulation.
| + | |
| − | |-
| + | |
| − | |<tt>POPs</tt>
| + | |
| − | |Selects the [[POPs simulation|Persistent Organic Pollutants (POPs) simulation]].
| + | |
| − | |-
| + | |
| − | |<tt>CH4</tt>
| + | |
| − | |Selects the [[CH4 simulation]].
| + | |
| − | |-
| + | |
| − | |<tt>tagCO</tt>
| + | |
| − | |Selects the [[Tagged CO simulation]].
| + | |
| − | |-
| + | |
| − | |<tt>tagO3</tt>
| + | |
| − | |Selects the [[Tagged O3 simulation|Simple tagged O3 simulation]] (w/ 2 tracers: Total O3 and Stratospheric O3).
| + | |
| − | |-
| + | |
| − | |<tt>CO2</tt>
| + | |
| − | |Selects the [[CO2 simulation]].
| + | |
| − | |-
| + | |
| − | |<tt>TOMAS15</tt>
| + | |
| − | |Selects the [[TOMAS aerosol microphysics]] simulation with 15 size bins.
| + | |
| − | |-
| + | |
| − | |<tt>TOMAS40</tt>
| + | |
| − | |Selects the [[TOMAS aerosol microphysics]] simulation with 40 size bins.
| + | |
| − | |}
| + | |
| − | </blockquote>
| + | |
| − | ;START DATE: Specifies the start date (YYYYMMDD) and hour (hh) of the unit test.
| + | |
| − | ;END DATE: Specifies the ending date (YYYYMMDD), hour (hh), and minutes (mm) of the unit test.
| + | |
| − | :*In most cases, a 1-hour simulation is sufficient to detect bugs.
| + | |
| − | :*For unit tests at 2° x 2.5° resolution or higher, you can end the simulation after one timestep, which is less than an hour.
| + | |
| − | ;EXTRA?: Specifies any simulation-specific Makefile options that need to be set at compile time for a particular simulation. Typical values are:
| + | |
| − | <blockquote>
| + | |
| − | {| border=1 cellspacing=0 cellpadding=5
| + | |
| − | |-bgcolor="#CCCCCC"
| + | |
| − | !width="125px"|Value
| + | |
| − | !width="600px"|Met field type
| + | |
| − | |-
| + | |
| − | |<tt>-</tt>
| + | |
| − | |Skips using an extra Makefile command (default).
| + | |
| − | |}
| + | |
| − | </blockquote>
| + | |
| − | | + | |
| − | Further notes about the <tt>!RUNS</tt> section:
| + | |
| − | | + | |
| − | #We typically run from <tt>2005070100</tt> to <tt>2005070101</tt> for [[GCAP]] met fields.
| + | |
| − | #We typically run from <tt>2006070100</tt> to <tt>2006070101</tt> for [[GMAO GEOS-4|GEOS-4]], [[GEOS-5]] and [[MERRA]] met fields.
| + | |
| − | #We typically run from <tt>2013070100</tt> to <tt>2013070101</tt> for [[GEOS-FP]] and [[MERRA-2]] met fields.
| + | |
| − | #The actual year for the met fields does not matter so much for the unit tests. The unit tests runs the same simulation twice (with and without parallelization) and then tests for identical results.
| + | |
| − | | + | |
| − | --[[User:Bmy|Bob Y.]] 11:05, 25 April 2014 (EDT)<br>--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 15:59, 22 February 2017 (UTC)
| + | |
| − | | + | |
| − | === Running the GEOS-Chem Unit Tester ===
| + | |
| − | | + | |
| − | Once you have [[#Specifying unit test options with an input file|added your desired options to the input file]], you may then proceed to start the GEOS-Chem Unit Tester. At the Unix prompt, type:
| + | |
| − | | + | |
| − | cd perl
| + | |
| − | ./gcUnitTest FILENAME
| + | |
| − | | + | |
| − | where <tt>FILENAME</tt> is the name the input file (e.g. <tt>UnitTest.input</tt>) that you have just edited. The settings in the input file will be used in the Unit Test simulations. If <tt>FILENAME</tt> is omitted, then the <tt>gcUnitTest</tt> script will use <tt>UnitTest.input</tt> by default.
| + | |
| − | | + | |
| − | You will usually want the Unit Test simulations to run in a queue on your computational cluster. For example, you can set up a Unit Test job to run overnight. The GEOS-Chem Unit Tester will compile and run the code for each of the types of simulations that you specified in the input file. The Unit Tester will compile and run GEOS-Chem twice for each type of simulation (once with OpenMP parallelizaton turned off, and again with OpenMP parallelization turned on). Then the Unit tester will check to see if the output files from both simulations are identical.
| + | |
| − | | + | |
| − | [[#Log files created by the Unit Tester|Log-file output generated by the GEOS-Chem Unit Tester]] is sent to the <tt>logs/{VERSION}</tt> directory, where <tt>{VERSION}</tt> denotes the version tag that you assigned in the input file. (This allows you to preserve log file output from several previous Unit Test simulations.)
| + | |
| − | | + | |
| − | --[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:05, 24 April 2017 (UTC)
| + | |
| − | | + | |
| − | == Examining the results ==
| + | |
| − | | + | |
| − | === Output files generated by the GEOS-Chem Unit Tester ===
| + | |
| − | | + | |
| − | The GEOS-Chem Unit Tester will run GEOS-Chem simulations in the subdirectories of the <tt>runs/</tt> directory. Each individual subdirectory of <tt>runs/</tt> corresponds to a particular unit test, or combination of met field + horizontal grid + simulation type. Some example run directory names are:
| + | |
| − | | + | |
| − | runs/geos5_4x5_tropchem # Run dir for unit test w/ GEOS-5 met, 4x5 grid, tropospheric-chemistry simulation
| + | |
| − | runs/geosfp_2x25_CO2 # Run dir for unit test w/ GEOS-FP met, 2x25 grid, CO2 simulation
| + | |
| − | runs/merra_4x5_RnPbBe # Run dir for unit test w/ MERRA met, 4x5 grid, and Rn-Pb-Be simulation
| + | |
| − | etc.
| + | |
| − | | + | |
| − | etc. In each of these run directories, GEOS-Chem will create several output files containing tracer concentrations and diagnostic quantities. These files are:
| + | |
| − | | + | |
| − | {| border=1 cellspacing=0 cellpadding=5
| + | |
| − | |- bgcolor="#CCCCCC"
| + | |
| − | !width="200px"|File
| + | |
| − | !width="800px"|Description
| + | |
| − | |-valign="top"
| + | |
| − | |<tt>trac.avg.*.sp</tt>
| + | |
| − | |Diagnostic output file (aka <tt>ctm.bpch</tt>) containing averaged diagnostic quantities from the single-processor test.
| + | |
| − | |-valign="top"
| + | |
| − | |<tt>trac.avg.*.mp</tt>
| + | |
| − | |Diagnostic output file (aka <tt>ctm.bpch</tt>) containing averaged diagnostic quantities from the multi-processor test.
| + | |
| − | |-valign="top"
| + | |
| − | |<tt>GEOSChem_restart.*.sp</tt>
| + | |
| − | |Restart file containing instantaneous tracer concentrations at the end of the single-processor test.
| + | |
| − | |-valign="top"
| + | |
| − | |<tt>GEOSChem_restart.*.mp</tt>
| + | |
| − | |Restart file containing instantaneous tracer concentrations at the end of the multi-processor test.
| + | |
| − | |-valign="top"
| + | |
| − | |<tt>HEMCO_restart.*.sp</tt>
| + | |
| − | |Restart file generated by HEMCO at the end of the single processor test.
| + | |
| − | |-valign="top"
| + | |
| − | |<tt>HEMCO_restart.*.mp</tt>
| + | |
| − | |Restart file generated by HEMCO at the end of the multi-processor test
| + | |
| − | |}
| + | |
| − | | + | |
| − | The GEOS-Chem Unit Tester will then [[#Interpreting results generated by the GEOS-Chem Unit Tester|examine each of these files]] to determine if the unit test succeeded or not.
| + | |
| − | | + | |
| − | In addition, HEMCO will save out log files in each run directory. These are not examined by the GEOS-Chem unit tester, but can be manually viewed in order to determine why particular unit test failed.
| + | |
| − | | + | |
| − | {| border=1 cellspacing=0 cellpadding=5
| + | |
| − | |- bgcolor="#CCCCCC"
| + | |
| − | !width="200px"|File
| + | |
| − | !width="800px"|Description
| + | |
| − | |-valign="top"
| + | |
| − | |<tt>HEMCO.log.sp</tt>
| + | |
| − | |HEMCO log file generated by the single-processor test.
| + | |
| − | *Contains detailed information about the creation of HEMCO diagnostic containers and file I/O processes.
| + | |
| − | *Useful for debugging.
| + | |
| − | |-valign="top"
| + | |
| − | |<tt>HEMCO.log.mp</tt>
| + | |
| − | |HEMCO log file generated by the multi-processor test.
| + | |
| − | *Contains detailed information about the creation of HEMCO diagnostic containers and file I/O processes.
| + | |
| − | *Useful for debugging.
| + | |
| − | |}
| + | |
| − | | + | |
| − | --[[User:Bmy|Bob Y.]] 14:26, 18 March 2015 (EDT)
| + | |
| − | | + | |
| − | === Log files created by the GEOS-Chem Unit Tester ===
| + | |
| − | | + | |
| − | The GEOS-Chem Unit Tester will also create a series of log files in the <tt>logs/{VERSION}</tt> directory, where <tt>{VERSION}</tt> is specifed in the The [[#The INPUTS section|<tt>!INPUTS</tt> section]] of the unit test input file. These log files are:
| + | |
| − | | + | |
| − | {| border=1 cellspacing=0 cellpadding=5
| + | |
| − | |-bgcolor="#CCCCCC" valign="top"
| + | |
| − | !width="400px"|File
| + | |
| − | !width="550px"|Description
| + | |
| − | !width="200px"|Notes
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | |<tt>{VERSION}.stderr.log</tt><br>(SLURM scheduler)<br><br><tt>job.{VERSION}.o*</tt><br>(GridEngine scheduler)
| + | |
| − | |File containing the Unix <tt>stderr</tt> output. All error and warning messages will get sent to this file. This is created if you run the Unit Tester in the Oracle Grid Engine queue system.
| + | |
| − | |You normally won't have to look at this file, unless a particular simulation dies unexpectedly. The output contained can be very useful in determining where the error ocurrred.
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | |<tt>{VERSION}.stdout.log</tt>
| + | |
| − | |File containing the Unix <tt>stdout</tt> output.
| + | |
| − | |In most cases you will not need to look at this file.
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | |<tt>{VERSION}.results.log</tt>
| + | |
| − | |Log file containing the results from each individual unit test simulation that you ran.
| + | |
| − | [[#Interpreting results generated by the GEOS-Chem Unit Tester |More information on this file]] is contained below.
| + | |
| − | |
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | |<tt>{VERSION}.results.html</tt>
| + | |
| − | |Web page (HTML) containing a graphical representation of the unit test results.
| + | |
| − | [[#Web page with graphical output|More information on this file]] is contained below.
| + | |
| − | |
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | |<tt>{VERSION}.results.txt</tt>
| + | |
| − | |Text file containing a table representation of the unit test results.
| + | |
| − | [[#You can now request a summary of unit test results in plain text format|More information on this file]] is contained below.
| + | |
| − | |
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | |<tt>{VERSION}.{MET}_{GRID}_{SIM}.log.sp</tt><br>(Global simulations)<br><br><tt>{VERSION}.{MET}_{GRID}_{SIM}_{NEST}.log.sp</tt><br>(Nested-grid simulations)
| + | |
| − | |GEOS-Chem log file output from the single-processor test phase of the unit test for the given met field, grid, simulation type (and, if applicable, nested-grid region).
| + | |
| − | |
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | |<tt>{VERSION}.{MET}_{GRID}_{SIM}.log.mp</tt><br>(Global simulations)<br><br><tt>{VERSION}.{MET}_{GRID}_{SIM}_{NEST}.log.mp</tt><br>(Nested-grid simulations)
| + | |
| − | |GEOS-Chem log file output from the multi-processor test phase of the unit test for the given met field, grid, simulation type (and, if applicable, nested-grid region).
| + | |
| − | |
| + | |
| − | | + | |
| − | | + | |
| − | |}
| + | |
| − | | + | |
| − | --[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:20, 24 April 2017 (UTC)
| + | |
| − | | + | |
| − | === Interpreting results generated by the GEOS-Chem Unit Tester ===
| + | |
| − | | + | |
| − | To determine whether or not the Unit Tests were successful, check the following [[#Log files created by the GEOS-Chem Unit Tester|log files]]:
| + | |
| − | | + | |
| − | #<tt>{VERSION}.results.log</tt> (The "results" file)
| + | |
| − | #The <tt>stderr</tt> file:
| + | |
| − | #*<tt>{VERSION}.stderr.log</tt> (SLURM scheduler)
| + | |
| − | #*<tt>job.{VERSION}.o*</tt> (Grid Engine scheduler).
| + | |
| − | | + | |
| − | The <tt>{VERSION}.results.log</tt> file will contain printout similar to the following. Looking at this file will tell you if the output from the '''sp''' and '''mp''' test phases of each unit test simulation were identical to each other, or if they differed.
| + | |
| − | | + | |
| − | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
| + | |
| − | %%%
| + | |
| − | %%% GEOS-CHEM UNIT TEST RESULTS FOR VERSION: v10-01e
| + | |
| − | %%% job sent to queue @ 2014/10/23 11:50:45
| + | |
| − | %%%
| + | |
| − | %%% DESCRIPTION: Tests v10-01e -- HEMCO emissions
| + | |
| − | %%%
| + | |
| − | %%% This is the main log file, which shows output from
| + | |
| − | %%% each individual phase of the unit test sequence.
| + | |
| − | %%%
| + | |
| − | %%% Log files from individual unit-test runs are also
| + | |
| − | %%% stored in this same directory.
| + | |
| − | %%%
| + | |
| − | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
| + | |
| − | ###############################################################################
| + | |
| − | ### VALIDATION OF GEOS-CHEM OUTPUT FILES
| + | |
| − | ### In directory: geosfp_4x5_standard
| + | |
| − | ###
| + | |
| − | ### File 1 : trac_avg.geosfp_4x5_standard.201307010000.sp
| + | |
| − | ### File 2 : trac_avg.geosfp_4x5_standard.201307010000.mp
| + | |
| − | ### Sizes : IDENTICAL (347020492 and 347020492)
| + | |
| − | ### Checksums : IDENTICAL (3903897761 and 3903897761)
| + | |
| − | ### Diffs : IDENTICAL
| + | |
| − | ###
| + | |
| − | ### File 1 : GEOSChem_restart.201307010200.nc.sp
| + | |
| − | ### File 2 : GEOSChem_restart.201307010200.nc.mp
| + | |
| − | ### Sizes : IDENTICAL (125832842 and 125832842)
| + | |
| − | ### Checksums : IDENTICAL (3907029337 and 3907029337)
| + | |
| − | ### Diffs : IDENTICAL
| + | |
| − | ###
| + | |
| − | ### File 1 : HEMCO_restart.201307010200.nc.mp
| + | |
| − | ### File 2 : HEMCO_restart.201307010200.nc.sp
| + | |
| − | ### Sizes : IDENTICAL (118525 and 118525)
| + | |
| − | ### Checksums : IDENTICAL (378999821 and 378999821)
| + | |
| − | ### Diffs : IDENTICAL
| + | |
| − | ###############################################################################
| + | |
| − |
| + | |
| − | ... etc ...
| + | |
| − |
| + | |
| − | ###############################################################################
| + | |
| − | ### VALIDATION OF GEOS-CHEM OUTPUT FILES
| + | |
| − | ### In directory: geosfp_4x5_POPs
| + | |
| − | ###
| + | |
| − | ### File 1 : trac_avg.geosfp_4x5_POPs.201307010000.sp
| + | |
| − | ### File 2 : trac_avg.geosfp_4x5_POPs.201307010000.mp
| + | |
| − | ### Sizes : IDENTICAL (28256020 and 28256020)
| + | |
| − | ### Checksums : IDENTICAL (560324576 and 560324576)
| + | |
| − | ### Diffs : IDENTICAL
| + | |
| − | ###
| + | |
| − | ### File 1 : GEOSChem_restart.201307010020.nc.sp
| + | |
| − | ### File 2 : GEOSChem_restart.201307010020.nc.mp
| + | |
| − | ### Sizes : IDENTICAL (1868497 and 1868497)
| + | |
| − | ### Checksums : IDENTICAL (241223905 and 241223905)
| + | |
| − | ### Diffs : IDENTICAL
| + | |
| − | ###
| + | |
| − | ### File 1 : HEMCO_restart.201307010020.nc.sp
| + | |
| − | ### File 2 : HEMCO_restart.201307010020.nc.mp
| + | |
| − | ### Sizes : IDENTICAL (20558 and 20558)
| + | |
| − | ### Checksums : IDENTICAL (804171793 and 804171793)
| + | |
| − | ### Diffs : IDENTICAL
| + | |
| − | ###############################################################################
| + | |
| − |
| + | |
| − | ... etc ...
| + | |
| − |
| + | |
| − | If the unit halted with an error prematurely, then you will also have to look at the stderr log file.
| + | |
| − | | + | |
| − | Here is a quick table that you can use to interpret the results of each unit test (i.e. combination of met field + horizontal grid + simulation type) that you selected:
| + | |
| − | | + | |
| − | {| border=1 cellspacing=0 cellpadding=5
| + | |
| − | |- bgcolor="#CCCCCC" valign="top"
| + | |
| − | !width="50px"|Case
| + | |
| − | !width="500px"|Description
| + | |
| − | !width="550px"|Interpretation
| + | |
| − | |-valign="top"
| + | |
| − | |1
| + | |
| − | |Unit test did not halt prematurely with any errors.<br>In the <tt>{VERSION}.results.log</tt> file we see:
| + | |
| − | | + | |
| − | *<tt>trac.avg.*.sp</tt> and <tt>trac_avg.*.mp</tt> are IDENTICAL
| + | |
| − | *<tt>GEOSChem_restart.*.sp</tt> and <tt>GEOSChem_restart.*.mp</tt> are IDENTICAL
| + | |
| − | *<tt>HEMCO_restart.*.sp</tt> and <tt>HEMCO_restart.*.mp</tt> are IDENTICAL
| + | |
| − | |
| + | |
| − | *The single processor (sp) test phase produced identical output to the multi-processor (mp) test phase. Likewise, all of the emissions diagnostics saved to the HEMCO restart file (e.g. soil NOx restart-file quantities) are identical. Therefore we can consider this unit test successful.
| + | |
| − | |-valign="top"
| + | |
| − | |2
| + | |
| − | |Unit test did not halt prematurely with any errors.<br>In the <tt>{VERSION}.results.log</tt> file we see:
| + | |
| − | | + | |
| − | *<tt>trac.avg.*.sp</tt> and <tt>trac_avg.*.mp</tt> are DIFFERENT
| + | |
| − | *<tt>GEOSChem_restart.*.sp</tt> and <tt>GEOSChem_restart.*.mp</tt> are IDENTICAL
| + | |
| − | *<tt>HEMCO_restart.*.sp</tt> and <tt>HEMCO_restart.*.mp</tt> are IDENTICAL
| + | |
| − | |
| + | |
| − | *Because the restart files are identical, we can say that the single-processor (sp) test phase yielded identical output to the multi-processor (mp) test phase as far as the tracers are concerned. This indicates that the chemistry is being performed properly.
| + | |
| − | *Because the <tt>trac.avg*</tt> files are DIFFERENT, we can say that there is a numerical issue in one of the archived diagnostics that merits further investigation. In many instances, this can be caused by a parallelization error where GEOS-Chem diagnostics are being archived. It may be that a particular variable needs was not declared <tt>!$OMP+PRIVATE</tt> in a parallel DO-loop.
| + | |
| − | |-valign="top"
| + | |
| − | |3
| + | |
| − | |Unit test did not halt prematurely with any errors.<br>In the <tt>{VERSION}.results.log</tt> file we see:
| + | |
| − | | + | |
| − | *<tt>trac.avg.*.sp</tt> and <tt>trac_avg.*.mp</tt> are DIFFERENT
| + | |
| − | *<tt>GEOSChem_restart.*.sp</tt> and <tt>GEOSChem_restart.*.mp</tt> are DIFFERENT
| + | |
| − | *<tt>HEMCO_restart.*.sp</tt> and <tt>HEMCO_restart.*.mp</tt> are DIFFERENT
| + | |
| − | |
| + | |
| − | *The multi processor (mp) test phase could not reproduce the results obtained by the single processor (sp) test phase. Therefore, this unit test is not successful. Further debugging will be needed to reveal the source of the discrepancy.
| + | |
| − | *In some cases you will see that the <tt>Checksums</tt> and/or <tt>Diffs</tt> lines in the log file may say <tt>FILE NOT FOUND</tt>. This indicates that the unit test died before the output files could be created.
| + | |
| − | |-valign="top"
| + | |
| − | |4
| + | |
| − | |Unit test halted with an error.<br>In the <tt>stderr</tt> output we see the error output similar to this:
| + | |
| − | | + | |
| − | > forrtl: error (65): floating invalid
| + | |
| − | Image PC Routine Line Source
| + | |
| − |
| + | |
| − | geos 00000000004703B1 Unknown Unknown Unknown
| + | |
| − | geos 000000000040325C MAIN__ 12 main.F
| + | |
| − | geos 000000000040319C Unknown Unknown geos
| + | |
| − | libc.so.6 00000037B2A21A05 Unknown Unknown Unknown
| + | |
| − | geos 0000000000403099 Unknown Unknown Unknown
| + | |
| − | |
| + | |
| − | *The '''floating invalid error''' indicates that a division by zero or other illegal computation (such as <tt>SQRT(-1)</tt>, <tt>LOG(0)</tt>, etc.) has occurred. You can use the error trace stack to find the line of code that caused the error.
| + | |
| − | |-valign="top"
| + | |
| − | |5
| + | |
| − | |Unit test halted with an error.<br>In the <tt>stderr</tt> output we see the error output similar to this:
| + | |
| − | | + | |
| − | > main.F(12): error #5561: Subscript #1 of the array ARRAY has
| + | |
| − | value 4 which is greater than the upper bound of 3
| + | |
| − | ARRAY(4) = 4.0
| + | |
| − | |
| + | |
| − | *This output indicates that an [[Common_GEOS-Chem_error_messages#Array-out-of-bounds_error|'''array-out-of-bounds error''']] has occurred. For example, we were trying to access <tt>ARRAY(4)</tt>, but <tt>ARRAY</tt> may be declared with less than 4 elements. This type of error can actually overwrite another variable—whichever variable happens to be stored next to ARRAY in the computer memory—with junk data. This can cause GEOS-Chem to die with an error in a very different location from where the array-out-of-bounds error actually occurred.
| + | |
| − | |-valign="top"
| + | |
| − | |6
| + | |
| − | |Unit tester did not halt prematurely with any errors, but we noticed the following warning message in the <tt>stderr</tt> output:
| + | |
| − | | + | |
| − | > forrtl: warning (402): fort: (1): In call to MY_ROUTINE,
| + | |
| − | an array temporary was created for argument #1
| + | |
| − | |
| + | |
| − | *This message indicates the presence of an [[Passing array arguments efficiently in GEOS-Chem|'''array temporary''']]. When GEOS-Chem is passing data to subroutine <tt>MY_ROUTINE</tt>, it has to make a duplicate copy of the data before passing to the subroutine. This can cause GEOS-Chem to execute more slowly, as the creation of the array temporary is wasteful both CPU cycles and memory.
| + | |
| − | | + | |
| − | |}
| + | |
| − | | + | |
| − | --[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:43, 24 April 2017 (UTC)
| + | |
| − | | + | |
| − | === Web page with graphical output ===
| + | |
| − | | + | |
| − | The GEOS-Chem Unit Tester will also create a web page that summarizes the results in an easy-to-read table. The name of the web page is specified with the <tt>WEB_GRID</tt> option in [[#The INPUTS section|the <tt>!INPUTS:</tt> section]] of the unit test input file. The web page will contain output similar to this example:
| + | |
| − | | + | |
| − | | + | |
| − | <blockquote>
| + | |
| − | <big><big><big><strong>GEOS-Chem Unit Test Results</strong></big></big></big>
| + | |
| − | <br /><br />
| + | |
| − | | + | |
| − | <table border="0" cellspacing="0" cellpadding="5">
| + | |
| − | <tr>
| + | |
| − | <td><big><strong>Version:</strong></big></td>
| + | |
| − | <td><big><strong>v10-01e</strong></big></td>
| + | |
| − | </tr>
| + | |
| − | <tr>
| + | |
| − | <td><big><strong>Date Submitted:</strong></big></td>
| + | |
| − | <td><big><strong>2014/10/28 12:08:16</strong></big></td>
| + | |
| − | </tr>
| + | |
| − | <tr>
| + | |
| − | <td><big><strong>Description:</strong></big></td>
| + | |
| − | <td><big><strong>Tests v10-01e -- HEMCO emissions</strong></big></td>
| + | |
| − | </tr>
| + | |
| − | </table>
| + | |
| − | | + | |
| − | <br />
| + | |
| − | | + | |
| − | <table border="1" cellspacing="0" cellpadding="5" bordercolor="#000000">
| + | |
| − | | + | |
| − | <!-- 4x5 -->
| + | |
| − | <tr>
| + | |
| − | <th scope="col" bgcolor="#CCCCCC" width="150">4° x 5° Unit Tests</th>
| + | |
| − | <th scope="col" bgcolor="#CCCCCC" width="55">UCX</th>
| + | |
| − | <th scope="col" bgcolor="#CCCCCC" width="55">Trop-<br />chem</th>
| + | |
| − | <th scope="col" bgcolor="#CCCCCC" width="55">SOA</th>
| + | |
| − | <th scope="col" bgcolor="#CCCCCC" width="55">SOA w/ SVPOA</th>
| + | |
| − | <th scope="col" bgcolor="#CCCCCC" width="55">Rn-<br>Pb-Be</th>
| + | |
| − | <th scope="col" bgcolor="#CCCCCC" width="55">Hg</th>
| + | |
| − | <th scope="col" bgcolor="#CCCCCC" width="55">POPs</th>
| + | |
| − | <th scope="col" bgcolor="#CCCCCC" width="55">TagCO</th>
| + | |
| − | <th scope="col" bgcolor="#CCCCCC" width="55">TagO3</th>
| + | |
| − | <th scope="col" bgcolor="#CCCCCC" width="55">CH4</th>
| + | |
| − | <th scope="col" bgcolor="#CCCCCC" width="55">CO2</th>
| + | |
| − | <th scope="col" bgcolor="#CCCCCC" width="55">Aer-<br>osols</th>
| + | |
| − | <th scope="col" bgcolor="#CCCCCC" width="55">TOMAS<br />40</th>
| + | |
| − | </tr>
| + | |
| − | <tr>
| + | |
| − | <td>GEOS-FP @ 4° x 5°</td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | </tr>
| + | |
| − | <tr>
| + | |
| − | <td>MERRA @ 4° x 5°</td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | </tr>
| + | |
| − | <tr>
| + | |
| − | <td>GEOS-5 @ 4° x 5°</td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | </tr>
| + | |
| − | <tr>
| + | |
| − | <td>GEOS-4 @ 4° x 5°</td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | </tr>
| + | |
| − | <tr>
| + | |
| − | <td>GCAP @ 4° x 5°</td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | </tr>
| + | |
| − | <tr>
| + | |
| − | <th scope="col" bgcolor="#CCCCCC" width="150">2° x 2.5° Unit Tests</th>
| + | |
| − | <th scope="col" bgcolor="#CCCCCC" width="55">UCX</th>
| + | |
| − | <th scope="col" bgcolor="#CCCCCC" width="55">Trop-<br />chem</th>
| + | |
| − | <th scope="col" bgcolor="#CCCCCC" width="55">SOA</th>
| + | |
| − | <th scope="col" bgcolor="#CCCCCC" width="55">SOA w/ SVPOA</th>
| + | |
| − | <th scope="col" bgcolor="#CCCCCC" width="55">Rn-<br>Pb-Be</th>
| + | |
| − | <th scope="col" bgcolor="#CCCCCC" width="55">Hg</th>
| + | |
| − | <th scope="col" bgcolor="#CCCCCC" width="55">POPs</th>
| + | |
| − | <th scope="col" bgcolor="#CCCCCC" width="55">TagCO</th>
| + | |
| − | <th scope="col" bgcolor="#CCCCCC" width="55">TagO3</th>
| + | |
| − | <th scope="col" bgcolor="#CCCCCC" width="55">CH4</th>
| + | |
| − | <th scope="col" bgcolor="#CCCCCC" width="55">CO2</th>
| + | |
| − | <th scope="col" bgcolor="#CCCCCC" width="55">Aer-<br>osols</th>
| + | |
| − | <th scope="col" bgcolor="#CCCCCC" width="55">TOMAS<br />40</th>
| + | |
| − | </tr>
| + | |
| − | <tr>
| + | |
| − | <td>GEOS-FP @ 2° x 2.5°</td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | </tr>
| + | |
| − | <tr>
| + | |
| − | <td>GEOS-5 @ 2° x 2.5°</td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#00FF00"> </td>
| + | |
| − | <td bgcolor="#FFFFFF"> </td>
| + | |
| − | </tr>
| + | |
| − | </table>
| + | |
| − | | + | |
| − | | + | |
| − | <br/>
| + | |
| − | <h3>LEGEND</h3>
| + | |
| − | | + | |
| − | <table border="0" cellspacing="0" cellpadding="10">
| + | |
| − | <tr>
| + | |
| − | <td bgcolor="#00FF00" width="25" class="legend"> </td>
| + | |
| − | <td>The unit test was successful.</td>
| + | |
| − | </tr>
| + | |
| − | <tr>
| + | |
| − | <td bgcolor="#FFFF00" class="legend"> </td>
| + | |
| − | <td>Further investigation is necessary (e.g. The restart files were
| + | |
| − | identical but the diagnostic output differed).</td>
| + | |
| − | </tr>
| + | |
| − | <tr>
| + | |
| − | <td bgcolor="#FF0000" class="legend"> </td>
| + | |
| − | <td>The unit test failed.</td>
| + | |
| − | </tr>
| + | |
| − | <tr>
| + | |
| − | <td bgcolor="#FFFFFF" class="legendlast"> </td>
| + | |
| − | <td>A unit test was not performed for this combination of
| + | |
| − | met field, horizontal grid, and simulation type.</td>
| + | |
| − | </tr>
| + | |
| − | | + | |
| − | </table>
| + | |
| − | | + | |
| − | </blockquote>
| + | |
| − | | + | |
| − | NOTES:
| + | |
| − | #As you can see, each unit test is assigned a color (red, yellow, or green) to denote if the test was successful or not. This lets you easily scan the results at a single glance.
| + | |
| − | #This web page can be pushed to a remote server where it can be viewed online. You can specify the directory where the page can be pushed with the the <tt>WEB_PUSH</tt> option in [[#The INPUTS section|the <tt>!INPUTS:</tt> section]] of the unit test input file.
| + | |
| − | #We usually do not perform every possible unit test indicated on the grid above, for the following reasons:
| + | |
| − | #*In order to save time, we typically perform most unit tests at 4° x 5° resolution, with a few selected unit tests at 2° x 2.5° resolution. This is usually sufficient to detect most bugs and numerical issues.
| + | |
| − | #*We usually have to run the the high-resolution nested grid unit tests (0.5° x 0.666° or 0.25° x 0.3125°) separately from the global 4° x 5° and 2° x 2.5° simulations. The nested-grid simulations require much more memory and thus must be submitted to our high-memory computational queue.
| + | |
| − | #*We typically focus on GEOS-Chem simulations driven by the GMAO met fields. For this reason we usually only perform a single unit test for GCAP (the 4° x 5° full-chemistry simulation).
| + | |
| − | | + | |
| − | --[[User:Bmy|Bob Y.]] 15:01, 30 October 2014 (EDT)
| + | |
| − | | + | |
| − | == Cleaning old files ==
| + | |
| − | | + | |
| − | To clean all of the files created by the unit tester (job scripts, logs, bpch files), type:
| + | |
| − | | + | |
| − | cd perl
| + | |
| − | ./cleanFiles
| + | |
| − | | + | |
| − | --[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:44, 24 April 2017 (UTC)
| + | |
| − | | + | |
| − | == Generating GEOS-Chem run directories ==
| + | |
| − | | + | |
| − | The GEOS-Chem Unit Tester contains several run directories for many different types of GEOS-Chem simulations. You can use the script <tt>gcCopyRunDirs</tt> (located in the <tt>perl/</tt> directory) to create fresh copies of these run directories that you can use for your own GEOS-Chem simulations. Please see our [[Creating GEOS-Chem run directories|''Creating GEOS-Chem run directories'' wiki page]].
| + | |
| − | | + | |
| − | --[[User:Bmy|Bob Y.]] 14:31, 18 March 2015 (EDT)
| + | |
| − | | + | |
| − | == Updates for GEOS-Chem v11-01 ==
| + | |
| − | | + | |
| − | The following features were introduced in the GEOS-Chem Unit Tester for [[GEOS-Chem v11-01]].
| + | |
| − | | + | |
| − | === The GEOS-Chem-UnitTest repository for v11-01 is now on bitbucket.org ===
| + | |
| − | | + | |
| − | By [[#We removed the Restart files from the GEOS-Chem-UnitTest repository|removing the restart files from the unit tester repository]], we were able to condense the size of the Git repository from over 10GB down to about 200 MB. This allowed us to move the <tt>GEOS-Chem-UnitTest</tt> Git repository from <tt>git://git.as.harvard.edu</tt> to <tt>https://bitbucket.org/gcst/GEOS-Chem-UnitTest</tt>. This move was necessitated by technical considerations.
| + | |
| − | | + | |
| − | --[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:38, 18 December 2015 (UTC)
| + | |
| − | | + | |
| − | === You can now create difference tests with the unit tester ===
| + | |
| − | | + | |
| − | Lizzie Lundgren ([[GCST]]) added the capability to generate difference test directories from the unit tester. The script <tt>gcCreateDiffTest</tt> will generate a difference test directory based on the specifications in the file <tt>DiffTest.input</tt>.
| + | |
| − | | + | |
| − | To create a difference test directory, make sure you are in the <tt>perl/</tt> folder, then type:
| + | |
| − | | + | |
| − | ./gcCreateDiffTest DiffTest.input
| + | |
| − | | + | |
| − | This feature is present in the GEOS-Chem Unit Tester corresponding to [[GEOS-Chem v11-01]].
| + | |
| − | | + | |
| − | --[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:38, 18 December 2015 (UTC)
| + | |
| − | | + | |
| − | === You can now specify the unit test root directory ===
| + | |
| − | | + | |
| − | The unit tester corresponding to [[GEOS-Chem v10-01]] and earlier versions always assumed that the root folder would be placed into a user's home folder. For example, a typical <tt>UnitTest.input</tt> file would have these settings:
| + | |
| − | | + | |
| − | RUN_ROOT : {HOME}/UT/runs
| + | |
| − | RUN_DIR : {RUNROOT}/{RUNDIR}
| + | |
| − | JOB_DIR : {HOME}/UT/jobs
| + | |
| − | LOG_DIR : {HOME}/UT/logs/{VERSION}
| + | |
| − | PERL_DIR : {HOME}/UT/perl
| + | |
| − | | + | |
| − | where the <tt>{HOME}</tt> token would be replaced with the user's home folder (i.e. the value specified by the <tt>$home</tt> environment variable.)
| + | |
| − | | + | |
| − | But on many computer systems, it is necessary to install the unit tester onto a scratch disk instead of a home folder. Scratch disks are often mounted onto fast networks (such as Infiniband) and have much more disk space available than a home folder. We have therefore modified the unit tester corresponding to [[GEOS-Chem v11-01]] so that you may specify the unit test root directory independently of your home folder.
| + | |
| − | | + | |
| − | The new <tt>UNIT_TEST_ROOT</tt> tag lets you specify the location of the unit tester's root directory. If your unit tester is installed on a scratch disk, then make sure these lines are in your <tt>UnitTest.input</tt>:
| + | |
| − | | + | |
| − | <span style="color:green">UNIT_TEST_ROOT : /fast/scratch/disk/UT</span>
| + | |
| − | RUN_ROOT : {UTHOME}/runs
| + | |
| − | RUN_DIR : {RUNROOT}/{RUNDIR}
| + | |
| − | JOB_DIR : {UTHOME}/jobs
| + | |
| − | LOG_DIR : {UTHOME}/logs/{VERSION}
| + | |
| − | PERL_DIR : {UTHOME}/perl
| + | |
| − | | + | |
| − | NOTE: The <tt>{UTHOME}</tt> token in the will be replaced by the value assinged to <tt>UNIT_TEST_ROOT</tt>.
| + | |
| − | | + | |
| − | On the other hand, if your unit tester is installed into your home directory, then add these lines:
| + | |
| − | | + | |
| − | <span style="color:green">UNIT_TEST_ROOT : {HOME}/UT</span>
| + | |
| − | RUN_ROOT : {UTHOME}/runs
| + | |
| − | RUN_DIR : {RUNROOT}/{RUNDIR}
| + | |
| − | JOB_DIR : {UTHOME}/jobs
| + | |
| − | LOG_DIR : {UTHOME}/logs/{VERSION}
| + | |
| − | PERL_DIR : {UTHOME}/perl
| + | |
| − | | + | |
| − | Note that only the line in <span style="color:green">GREEN</span> has to specify the root folder of the unit tester.
| + | |
| − | | + | |
| − | --[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:19, 18 December 2015 (UTC)
| + | |
| − | | + | |
| − | === You can now submit unit tests to the SLURM scheduler ===
| + | |
| − | | + | |
| − | We modified the <tt>UnitTest.input</tt> file so that you can specify parameters for submitting the unit test job using the [http://slurm.schedmd.com/ SLURM scheduler]. The following optional settings are now present in [[#The_INPUTS_section|the <tt>INPUTS:</tt> section]]:
| + | |
| − | | + | |
| − | #
| + | |
| − | # !INPUTS:
| + | |
| − | #
| + | |
| − | VERSION : v11-01
| + | |
| − | ... etc ...
| + | |
| − | LOG_DIR : {HOME}/UT/logs/{VERSION}
| + | |
| − | ... etc ...
| + | |
| − | SUBMIT : sbatch
| + | |
| − | ... etc ...
| + | |
| − | #
| + | |
| − | # %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
| + | |
| − | # %%% OPTIONAL SLURM COMMANDS: %%%
| + | |
| − | # %%% %%%
| + | |
| − | # %%% Set these if your system uses the SLURM scheduler. %%%
| + | |
| − | # %%% These will be used to set #SBATCH tags for the job script. %%%
| + | |
| − | # %%% Otherwise you can comment these lines out. %%%
| + | |
| − | # %%% %%%
| + | |
| − | # %%% NOTE: If you do use these SLURM commands, then also be %%%
| + | |
| − | # %%% sure to set the SUBMIT command above to "sbatch". %%%
| + | |
| − | # %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
| + | |
| − | #
| + | |
| − | SLURM_CPUS : 4
| + | |
| − | SLURM_NODES : 1
| + | |
| − | SLURM_TIME : 1-00:00
| + | |
| − | SLURM_MEM : 7000
| + | |
| − | SLURM_PARTITION : general
| + | |
| − | SLURM_CONSTRAINT : intel
| + | |
| − | SLURM_MAILTYPE : ALL
| + | |
| − | SLURM_MAILUSER : person@email.somewhere.edu
| + | |
| − | SLURM_STDOUT : {LOGDIR}/{VERSION}.stdout.log
| + | |
| − | SLURM_STDERR : {LOGDIR}/{VERSION}.stderr.log
| + | |
| − | | + | |
| − | These settings are then used to add the appropriate <tt>#SBATCH</tt> tags at the top of the Unit test job script:
| + | |
| − | | + | |
| − | #!/bin/bash
| + | |
| − |
| + | |
| − | #SBATCH -n 4
| + | |
| − | #SBATCH -N 1
| + | |
| − | #SBATCH -t 1-00:00
| + | |
| − | #SBATCH --mem=7000
| + | |
| − | #SBATCH -p general
| + | |
| − | #SBATCH --constraint=intel
| + | |
| − | #SBATCH --mail-user=person@email.somewhere.edu
| + | |
| − | #SBATCH --mail-type=ALL
| + | |
| − | #SBATCH -o /home/person/UT/logs/v11-01/v11-01.stdout.log
| + | |
| − | #SBATCH -e /home/person/UT/logs/v11-01/v11-01.stderr.log
| + | |
| − | export OMP_NUM_THREADS=4
| + | |
| − |
| + | |
| − | ###############################################################################
| + | |
| − | # Job script for unit test: v11-01
| + | |
| − | # Tests v11-01
| + | |
| − | ###############################################################################
| + | |
| − | | + | |
| − | --[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 18:58, 18 December 2015 (UTC)
| + | |
| − | | + | |
| − | === You can now request a summary of unit test results in plain text format ===
| + | |
| − | | + | |
| − | On some computer systems, a job running in the computational queues does not have access to the internet. This would prevent the GEOS-Chem Unit Tester from being able to push a summary of unit test results in HTML format (e.g <tt>v11-01.results.html</tt>) to a web server while the unit tests are still running.
| + | |
| − | | + | |
| − | We have therefore modified the Unit Tester so that it can create a plain text file containing the unit test results. You can tail this file while the unit tests are running in order to see the status of the jobs (i.e. use Unix command <tt>tail -f</tt>).
| + | |
| − | | + | |
| − | You specify the path of this summary text file with the <tt>TXT_GRID</tt> option in the <tt>UnitTest.input</tt> file:
| + | |
| − | | + | |
| − | #
| + | |
| − | # !INPUTS:
| + | |
| − | #
| + | |
| − | VERSION : v11-01
| + | |
| − | ... etc ...
| + | |
| − | WEB_GRID : NONE
| + | |
| − | TXT_GRID : {LOGDIR}/{VERSION}.results.txt
| + | |
| − | WEB_PUSH : NONE
| + | |
| − | | + | |
| − | In this case, we are telling the Unit Tester that we want to disable creating the HTML web page, and also want to disable pushing both text and HTML output to a web server. The Unit Tester will place a file named <tt>v11-01.results.txt</tt> in the log directory, which contains output similar to this:
| + | |
| − | | + | |
| − | GEOS-Chem Unit Test : RESULT
| + | |
| − | ------------------------------------------
| + | |
| − | geosfp_4x5_RnPbBe : GREEN
| + | |
| − | merra_4x5_RnPbBe : GREEN
| + | |
| − | ... etc ...
| + | |
| − | | + | |
| − | As with the HTML web page format:
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| − | * GREEN means that the unit test passed
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| − | * YELLOW means that the unit test passed, but that the diagnostic output differed
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| − | * RED means that the unit test failed
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| − | --[[User:Bmy|Bob Y.]] ([[User talk:Bmy|talk]]) 23:30, 23 June 2015 (UTC)
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| − | === You can now check for mass conservation ===
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| − | We have now modified [[GEOS-Chem v11-01]] and the GEOS-Chem Unit Tester so that you can run a mass conservation test (based on the 2° x 2.5° CO2 simulation). For more information, please see [[GEOS-Chem_v11-01#Added_a_test_for_mass_conservation|this post on our ''GEOS-Chem v11-01'' wiki page]].
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| − | --[[User:Bmy|Bob Y.]] ([[User talk:Bmy|talk]]) 22:26, 24 June 2015 (UTC)
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| − | === You can now generate run directories for timing tests ===
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| − | With the the Unit Tester for v11-01, you may now create one or more run directories for 7-model-day timing tests. This will allow you to quickly evaluate the performance of GEOS-Chem on your system. For more information, please see [[Timing tests with GEOS-Chem v11-01|our ''Timing tests with GEOS-Chem v11-01'' wiki page]].
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| − | --[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:51, 19 December 2016 (UTC)
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