GEOS-Chem unit tester for v11-02
The GEOS-Chem Unit Tester is a package of scripts and Makefiles that will compile and run several GEOS-Chem with a set of standard debugging flags. An individual GEOS-Chem Unit Test will look for computational and numerical issues in simulations for a given combination of:
- Met field type
- Horizontal grid
- Simulation type
You can specify the unit tests that you wish the GEOS-Chem Unit Tester to perform in an customizable input file, as described below.
Contents
- 1 Installing the GEOS-Chem Unit Tester
- 2 Using the GEOS-Chem Unit Tester
- 3 Examining the results
- 4 Cleaning old files
- 5 Generating GEOS-Chem run directories
- 6 Updates for GEOS-Chem v11-01
- 6.1 We removed the Restart files from the GEOS-Chem-UnitTest repository
- 6.2 The GEOS-Chem-UnitTest repository for v11-01 is now on bitbucket.org
- 6.3 You can now create difference tests with the unit tester
- 6.4 You can now specify the unit test root directory
- 6.5 You can now submit unit tests to the SLURM scheduler
- 6.6 You can now request a summary of unit test results in plain text format
- 6.7 You can now check for mass conservation
- 6.8 You can now generate run directories for timing tests
Installing the GEOS-Chem Unit Tester
Requirements
Most GEOS-Chem users will already have the necessary software to be able to run the GEOS-Chem Unit Test package. These are:
- A modern "Linux-like" operating system, e.g.
- Linux (all flavors)
- CentOS
- Ubuntu
- Fedora
- The bash Unix shell (usually comes pre-installed with your OS)
- The Perl programming language (usually comes pre-installed with your OS)
- The GNU make utility (usually comes pre-installed with your OS)
- IMPORTANT! You will also need GEOS-Chem v9-02o or a later version.
- Previous versions are not compatible with the GEOS-Chem Unit Tester because they use the Headers/define.h file to specify some C-preprocessor switches.
- In GEOS-Chem v9-02o and higher versions, all C-preprocessor switches will be set from command-line inputs to GNU Make.
--Bob Y. 17:20, 6 September 2013 (EDT)
Downloading the GEOS-Chem Unit Tester
You may download the GEOS-Chem unit tester with Git:
git clone https://bitbucket.org/gcst/geos-chem-unittest UT git checkout master
This will download a fresh copy of the GEOS-Chem-UnitTest repository into a directory named UT, 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).
Reverting to an older state
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:
- Open the gitk browser by typing gitk & at the command line.
- 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.).
- 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.
- Close gitk and open the Git GUI by typing git gui &
- From the Git GUI dropdown menu, select Branch / Checkout, and then pick OLDER_BRANCH.
That's it! We now have two branches that represent different GEOS-Chem versions.
- The master branch represents current state of the unit tester
- The OLDER_BRANCH branch represents the state of the unit tester that you checked out (synced to an older GEOS-Chem version)
--Bob Yantosca (talk) 19:48, 24 April 2017 (UTC)
Directory structure
The GEOS-Chem Unit Tester adheres to the following directory structure:
| Directory | Description |
|---|---|
| jobs/ | Job scripts created by the GEOS-Chem Unit Test driver script gcUnitTest will be sent here. |
| logs/ | Log files containing output from the GEOS-Chem Unit Test simulations will be sent here. |
| perl/ | Contains the Perl scripts that are used to submit GEOS-Chem Unit Test simulations.
|
| runs/ | Contains the various run directories. Each run directory is named according to the met field, horizontal grid, and type of simulation (4x5_standard, 2x25_RnPbBe, etc). |
--Bob Yantosca (talk) 15:08, 20 December 2016 (UTC)
Using the GEOS-Chem Unit Tester
What the GEOS-Chem Unit Tester does
For each individual unit test (met field + horizontal grid + simulation type) that you specify in the RUNS section of the input file (more on this below), the GEOS-Chem Unit Tester will do the following:
- Run GEOS-Chem with strict debugging flags with OpenMP parallelization turned OFF
- This is called the single processor or sp test phase.
- Run GEOS-Chem with strict debugging flags with OpenMP parallelization turned ON
- This is called the multi processor or mp test phase.
The strict debugging flags will look for common computational and numerical issues, such as
- Floating-point math exceptions: div-by-zero, invalid computations (i.e. SQRT(-1), LOG(-1), etc.)
- Array-out-of-bounds errors
- Creation of array temporaries
Furthermore, the Unit Tester compare the output of the sp and mp test phases. If these outputs differ, then this indicates a parallelization error.
--Bob Y. 10:08, 25 April 2014 (EDT)
Specifying unit test options with an input file
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 UnitTest.input, but you can cut-n-paste this file to create as many customized input files as you need.
The UnitTest.input file looks like this. All lines beginning with a # character are treated as comments and will be ignored.
#------------------------------------------------------------------------------
# GEOS-Chem Global Chemical Transport Model !
#------------------------------------------------------------------------------
#BOP
#
# !INCLUDE: UnitTest.input
#
# !DESCRIPTION: Input file that specifies debugging options for the
# GEOS-Chem unit tester.
#\\
#\\
# !REMARKS:
# To omit individual unit tests (or input settings), place a # comment
# character in the first column.
#
# For a complete explanation of how to customize the settings below for
# your installation, please see these wiki posts:
#
# http://wiki.geos-chem.org/GEOS-Chem_Unit_Tester#The_INPUTS_section
# http://wiki.geos-chem.org/GEOS-Chem_Unit_Tester#The_RUNS_section
#
# !REVISION HISTORY:
# Type 'gitk' at the prompt to browse the revision history.
#EOP
#------------------------------------------------------------------------------
#
# !INPUTS:
#
# %%% ID tags %%%
#
VERSION : v11-01
DESCRIPTION : Tests GEOS-Chem v11-01
#
# %%% Data path and HEMCO settings %%%
#
DATA_ROOT : /n/holylfs/EXTERNAL_REPOS/GEOS-CHEM/gcgrid/data/ExtData
HEMCO_ROOT : {DATAROOT}/HEMCO
VERBOSE : 3
WARNINGS : 3
#
# %%% Code, compiler, and queue settings %%%
#
CODE_DIR : {HOME}/GC/Code.v11-01
COMPILER : ifort
MAKE_CMD : make -j4 BOUNDS=y DEBUG=y FPE=y NO_ISO=y
SUBMIT : sbatch
#
# %%% Unit tester path names %%%
#
UNIT_TEST_ROOT : {HOME}/UT
RUN_ROOT : {UTROOT}/runs
RUN_DIR : {RUNROOT}/{RUNDIR}
JOB_DIR : {UTROOT}/jobs
LOG_DIR : {UTROOT}/logs/{VERSION}
PERL_DIR : {UTROOT}/perl
#
# %%% Web and text display options %%%
#
TEMPLATE : {PERLDIR}/ut_template.html
TXT_GRID : {LOGDIR}/{VERSION}.results.txt
WEB_GRID : {LOGDIR}/{VERSION}.results.html
WEB_PUSH : NONE
#
# %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# %%% 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 : 1-12:00
SLURM_MEMORY : 30000
SLURM_PARTITION : jacob
SLURM_CONSTRAINT : intel
SLURM_MAILTYPE : END
SLURM_MAILUSER : your-email-address
SLURM_STDOUT : {LOGDIR}/{VERSION}.stdout.log
SLURM_STDERR : {LOGDIR}/{VERSION}.stderr.log
#
# !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? |
#--------|-----------|------|------------|------------|--------------|--------|
# ======= Radon-Lead-Beryllium ===============================================
geosfp 4x5 - RnPbBe 2013070100 201307010020 -
merra2 4x5 - RnPbBe 2013070100 201307010020 -
merra 4x5 - RnPbBe 2006070100 200607010020 -
geos5 4x5 - RnPbBe 2006070100 200607010020 -
geos4 4x5 - RnPbBe 2006070100 200607010020 -
gcap 4x5 - RnPbBe 2005070100 200507010020 -
geosfp 2x25 - RnPbBe 2013070100 201307010020 -
merra2 2x25 - RnPbBe 2013070100 201307010020 -
geos5 2x25 - RnPbBe 2006070100 200607010020 -
# ======= Mercury ============================================================
geosfp 4x5 - Hg 2013010100 201301010020 -
merra2 4x5 - Hg 2013010100 201301010020 -
merra 4x5 - Hg 2009010100 200901010020 -
geos5 4x5 - Hg 2009010100 200901010020 -
geos4 4x5 - Hg 2006010100 200601010020 -
geosfp 2x25 - Hg 2013010100 201301010020 -
merra2 2x25 - Hg 2013010100 201301010020 -
merra 2x25 - Hg 2009010100 200901010020 -
geos5 2x25 - Hg 2009010100 200901010020 -
# geos5 05x0666 na Hg 2008010100 200801010020 -
# ======= Tagged Mercury =====================================================
geos5 4x5 - tagHg 2010010100 2010010101 -
# ======= POPs ===============================================================
geosfp 4x5 - POPs 2013070100 201307010020 -
merra2 4x5 - POPs 2013070100 201307010020 -
merra 4x5 - POPs 2006070100 200607010020 -
geos5 4x5 - POPs 2006070100 200607010020 -
geos4 4x5 - POPs 2006070100 200607010020 -
gcap 4x5 - POPs 2005070100 200507010020 -
geosfp 2x25 - POPs 2013070100 201307010020 -
merra2 2x25 - POPs 2013070100 201307010020 -
geos5 2x25 - POPs 2006070100 200607010020 -
# ======= Methane ============================================================
geosfp 4x5 - CH4 2013070100 201307010020 -
merra2 4x5 - CH4 2013070100 201307010020 -
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
#------------------------------------------------------------------------------
--Melissa Sulprizio (talk) 15:59, 22 February 2017 (UTC)
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. |
| DATA_ROOT | Specifies the path for your root-level data directory. |
| HEMCO_ROOT | Specifies the top-level path for the HEMCO data directory tree.
|
| VERBOSE | Specifies the level of debug output that will be sent to the HEMCO log file. (0=no debug output; 3=max debug output)
|
| WARNINGS | Specifies the level of warning messages that will be sent to the HEMCO log file. (0=no warnings; 3=max warnings)
|
| CODE_DIR | Specifies the path of the source code directory. |
| COMPILER | Specifies the compiler type.
|
| MAKE_CMD | Specifies the make command for your system. Usually this is make, but on some systems this may be gmake. Recommended options are:
|
| SUBMIT | Specifies the command that will send the Unit Test job to your queue system.
|
| UNIT_TEST_ROOT | Specifies the path to the GEOS-Chem Unit Tester. |
| RUN_ROOT | Specifies the top-level unit test run directories.
Leave this as-is. |
| RUN_DIR | Specifies the run directory subdirectory.
Leave this as-is. |
| JOB_DIR | Specifies the directory where the unit test job script will be created.
Leave this as-is. |
| LOG_DIR | Specifies the directory where log files from this unit test simulation will be sent.
|
| PERL_DIR | Specifies the directory where the unit test Perl scripts are found.
|
| TEMPLATE | Specifies the template HTML file that will be used to create a web page with unit test results.
|
| TXT_GRID | Specifies the path of this summary text file
|
| WEB_GRID | Specifies the name of the web page that will contain the unit test results.
|
| WEB_PUSH | Specifies the remote server to which the WEB_GRID web page will be uploaded. Options are:
|
Note that you can use a symbolic link (i.e. /home/{USER}/UT/ in the RUN_ROOT, RUN_DIR, JOB_DIR, LOG_DIR and PERL_DIR variables. This can help you shorten the file paths.
--Melissa Sulprizio (talk) 15:59, 22 February 2017 (UTC)
The RUNS section
Under the !RUNS: 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 # 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:
Value Met field type gcap Selects the GCAP met fields. geos4 Selects the GEOS-4 met fields. geos5 Selects the GEOS-5 met fields. geosfp Selects the GEOS-FP met fields. merra Selects the MERRA met fields. merra2 Selects the MERRA-2 met fields.
- GRID
- Specifies the horizontal grid. Allowable values are:
Value Grid type 4x5 Selects the GMAO 4° x 5° horizontal grid. 2x25 Selects the GMAO 2° x 2.5° horizontal grid. 05x0666 Selects the GMAO 0.5° x 0.666° grid for use with GEOS-5 met fields only.
(You must also specify a value for NEST.)05x0625 Selects the GMAO 0.5° x 0.625° grid for use with MERRA-2 met fields only.
(You must also specify a value for NEST.)025x03125 Selects the GMAO 0.25° x 0.3125° grid for use with GEOS-FP met fields only.
(You must also specify a value for NEST.)
- NEST
- Specifies the nested grid. May only be used if the value for GRID is 05x0666, 05x0625, or 025x03125. Allowable values are:
Value Nested grid option - Skips the nested grid option (default). Use this for global simulations. as Selects the Asia (AS) nested grid option for use with MERRA-2 met fields only. ch Selects the China (CH) nested grid option for use with GEOS-5 or GEOS-FP met fields only. eu Selects the Europe (EU) nested grid option. na Selects the North American (NA) nested grid option.
- SIMULATION
- Specifies the simulation type. Allowable values are:
Value Simulation Full-chemistry simulations standard Selects the Standard chemistry mechanism used in the GEOS-Chem benchmark simulations. tropchem Selects the The NOx-Ox-HC-Aer-Br tropospheric chemistry simulation. soa Selects the Secondary organic aerosols simulation, without semi-volatile POA. soa_svpoa Selects the Secondary organic aerosols simulation, with semi-volatile POA. aciduptake Selects the Standard chemistry simulation, with acid uptake on dust aerosols turned on. marinePOA Selects the Standard chemistry simulation, with marine primary organic aerosols turned on. UCX Selects the UCX chemistry mechanism: combined stratospheric and tropospheric chemistry RRTMG Selects the The NOx-Ox-HC-Aer-Br tropospheric chemistry simulation, with RRTMG turned on. Specialty simulations RnPbBe Selects the Radon-Lead-Beryllium simulation. Hg Selects the Mercury simulation. tagHg Selects the Tagged mercury simulation. POPs Selects the Persistent Organic Pollutants (POPs) simulation. CH4 Selects the CH4 simulation. tagCO Selects the Tagged CO simulation. tagO3 Selects the Simple tagged O3 simulation (w/ 2 tracers: Total O3 and Stratospheric O3). CO2 Selects the CO2 simulation. TOMAS15 Selects the TOMAS aerosol microphysics simulation with 15 size bins. TOMAS40 Selects the TOMAS aerosol microphysics simulation with 40 size bins.
- 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:
Value Met field type - Skips using an extra Makefile command (default).
Further notes about the !RUNS section:
- We typically run from 2005070100 to 2005070101 for GCAP met fields.
- We typically run from 2006070100 to 2006070101 for GEOS-4, GEOS-5 and MERRA met fields.
- We typically run from 2013070100 to 2013070101 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.
--Bob Y. 11:05, 25 April 2014 (EDT)
--Melissa Sulprizio (talk) 15:59, 22 February 2017 (UTC)
Running the GEOS-Chem Unit Tester
Once you have 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 FILENAME is the name the input file (e.g. UnitTest.input) that you have just edited. The settings in the input file will be used in the Unit Test simulations. If FILENAME is omitted, then the gcUnitTest script will use UnitTest.input 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-file output generated by the GEOS-Chem Unit Tester is sent to the logs/{VERSION} directory, where {VERSION} 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.)
--Bob Yantosca (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 runs/ directory. Each individual subdirectory of runs/ 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:
| File | Description |
|---|---|
| trac.avg.*.sp | Diagnostic output file (aka ctm.bpch) containing averaged diagnostic quantities from the single-processor test. |
| trac.avg.*.mp | Diagnostic output file (aka ctm.bpch) containing averaged diagnostic quantities from the multi-processor test. |
| GEOSChem_restart.*.sp | Restart file containing instantaneous tracer concentrations at the end of the single-processor test. |
| GEOSChem_restart.*.mp | Restart file containing instantaneous tracer concentrations at the end of the multi-processor test. |
| HEMCO_restart.*.sp | Restart file generated by HEMCO at the end of the single processor test. |
| HEMCO_restart.*.mp | Restart file generated by HEMCO at the end of the multi-processor test |
The GEOS-Chem Unit Tester will then 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.
| File | Description |
|---|---|
| HEMCO.log.sp | HEMCO log file generated by the single-processor test.
|
| HEMCO.log.mp | HEMCO log file generated by the multi-processor test.
|
--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 logs/{VERSION} directory, where {VERSION} is specifed in the The !INPUTS section of the unit test input file. These log files are:
| File | Description | Notes |
|---|---|---|
| {VERSION}.stderr.log (SLURM scheduler) job.{VERSION}.o* (GridEngine scheduler) |
File containing the Unix stderr 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. |
| {VERSION}.stdout.log | File containing the Unix stdout output. | In most cases you will not need to look at this file. |
| {VERSION}.results.log | Log file containing the results from each individual unit test simulation that you ran.
More information on this file is contained below. |
|
| {VERSION}.results.html | Web page (HTML) containing a graphical representation of the unit test results.
More information on this file is contained below. |
|
| {VERSION}.results.txt | Text file containing a table representation of the unit test results.
More information on this file is contained below. |
|
| {VERSION}.{MET}_{GRID}_{SIM}.log.sp (Global simulations) {VERSION}.{MET}_{GRID}_{SIM}_{NEST}.log.sp (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). | |
| {VERSION}.{MET}_{GRID}_{SIM}.log.mp (Global simulations) {VERSION}.{MET}_{GRID}_{SIM}_{NEST}.log.mp (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). |
|
--Bob Yantosca (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:
- {VERSION}.results.log (The "results" file)
- The stderr file:
- {VERSION}.stderr.log (SLURM scheduler)
- job.{VERSION}.o* (Grid Engine scheduler).
The {VERSION}.results.log 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:
| Case | Description | Interpretation |
|---|---|---|
| 1 | Unit test did not halt prematurely with any errors. In the {VERSION}.results.log file we see:
|
|
| 2 | Unit test did not halt prematurely with any errors. In the {VERSION}.results.log file we see:
|
|
| 3 | Unit test did not halt prematurely with any errors. In the {VERSION}.results.log file we see:
|
|
| 4 | Unit test halted with an error. In the stderr 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
|
|
| 5 | Unit test halted with an error. In the stderr 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
|
|
| 6 | Unit tester did not halt prematurely with any errors, but we noticed the following warning message in the stderr output:
> forrtl: warning (402): fort: (1): In call to MY_ROUTINE, an array temporary was created for argument #1 |
|
--Bob Yantosca (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 WEB_GRID option in the !INPUTS: section of the unit test input file. The web page will contain output similar to this example:
GEOS-Chem Unit Test Results
Version: v10-01e Date Submitted: 2014/10/28 12:08:16 Description: Tests v10-01e -- HEMCO emissions
4° x 5° Unit Tests UCX Trop-
chemSOA SOA w/ SVPOA Rn-
Pb-BeHg POPs TagCO TagO3 CH4 CO2 Aer-
osolsTOMAS
40GEOS-FP @ 4° x 5° MERRA @ 4° x 5° GEOS-5 @ 4° x 5° GEOS-4 @ 4° x 5° GCAP @ 4° x 5° 2° x 2.5° Unit Tests UCX Trop-
chemSOA SOA w/ SVPOA Rn-
Pb-BeHg POPs TagCO TagO3 CH4 CO2 Aer-
osolsTOMAS
40GEOS-FP @ 2° x 2.5° GEOS-5 @ 2° x 2.5°
LEGEND
The unit test was successful. Further investigation is necessary (e.g. The restart files were identical but the diagnostic output differed). The unit test failed. A unit test was not performed for this combination of met field, horizontal grid, and simulation type.
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 WEB_PUSH option in the !INPUTS: 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).
--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
--Bob Yantosca (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 gcCopyRunDirs (located in the perl/ 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 wiki page.
--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.
We removed the Restart files from the GEOS-Chem-UnitTest repository
Melissa Sulprizio wrote:
We now store the tracer restart files in directory {DATA_ROOT}/GC_RESTARTS/. The ocean restart files for the Hg simulations have also been moved to that directory. Users can download GC_RESTARTS using the wget utility. They can choose to download the entire directory or only the resolutions/simulation types that they need.
The path to the input restart file is now hardwired in the input.geos.template files. For users that create run directories using gcCopyRunDirs, they may use the initial_trac_restart file specified to start their simulation, but it is recommended that they spin up a more representative restart file and modify the line for the input restart file in input.geos accordingly.
--Bob Yantosca (talk) 19:38, 18 December 2015 (UTC)
The GEOS-Chem-UnitTest repository for v11-01 is now on bitbucket.org
By 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 GEOS-Chem-UnitTest Git repository from git://git.as.harvard.edu to https://bitbucket.org/gcst/GEOS-Chem-UnitTest. This move was necessitated by technical considerations.
--Bob Yantosca (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 gcCreateDiffTest will generate a difference test directory based on the specifications in the file DiffTest.input.
To create a difference test directory, make sure you are in the perl/ folder, then type:
./gcCreateDiffTest DiffTest.input
This feature is present in the GEOS-Chem Unit Tester corresponding to GEOS-Chem v11-01.
--Bob Yantosca (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 UnitTest.input 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 {HOME} token would be replaced with the user's home folder (i.e. the value specified by the $home 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 UNIT_TEST_ROOT 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 UnitTest.input:
UNIT_TEST_ROOT : /fast/scratch/disk/UT
RUN_ROOT : {UTHOME}/runs
RUN_DIR : {RUNROOT}/{RUNDIR}
JOB_DIR : {UTHOME}/jobs
LOG_DIR : {UTHOME}/logs/{VERSION}
PERL_DIR : {UTHOME}/perl
NOTE: The {UTHOME} token in the will be replaced by the value assinged to UNIT_TEST_ROOT.
On the other hand, if your unit tester is installed into your home directory, then add these lines:
UNIT_TEST_ROOT : {HOME}/UT
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 GREEN has to specify the root folder of the unit tester.
--Bob Yantosca (talk) 19:19, 18 December 2015 (UTC)
You can now submit unit tests to the SLURM scheduler
We modified the UnitTest.input file so that you can specify parameters for submitting the unit test job using the SLURM scheduler. The following optional settings are now present in the INPUTS: 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 #SBATCH 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 ###############################################################################
--Bob Yantosca (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 v11-01.results.html) 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 tail -f).
You specify the path of this summary text file with the TXT_GRID option in the UnitTest.input 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 v11-01.results.txt 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:
- GREEN means that the unit test passed
- YELLOW means that the unit test passed, but that the diagnostic output differed
- RED means that the unit test failed
--Bob Y. (talk) 23:30, 23 June 2015 (UTC)
You can now check for mass conservation
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 this post on our GEOS-Chem v11-01 wiki page.
--Bob Y. (talk) 22:26, 24 June 2015 (UTC)
You can now generate run directories for timing tests
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 our Timing tests with GEOS-Chem v11-01 wiki page.
--Bob Yantosca (talk) 19:51, 19 December 2016 (UTC)
