Welcome to the UFS Weather Model User’s Guide¶
Introduction¶
The Unified Forecast System (UFS) Weather Model (WM) is a prognostic model that can be used for short- and medium-range research and operational forecasts, as exemplified by its use in the operational Global Forecast System (GFS) of the National Oceanic and Atmospheric Administration (NOAA). The UFS WM v2.0.0 is the latest public release of this software and represents a snapshot of a continuously evolving system undergoing open development. More information about the UFS can be found on the UFS Community Portal at https://ufscommunity.org/.
Key architectural elements of the UFS WM, along with links to external detailed documentation for those elements, are listed below:
The Finite-Volume Cubed-Sphere (FV3) dynamical core is the computational part of an atmospheric model that solves the equations of fluid motion.
The Flexible Modeling System (FMS), is a software framework for supporting the efficient development, construction, execution, and scientific interpretation of atmospheric, oceanic, and climate system models. It is used for functions such as parallelization.
The Common-Community Physics Package (CCPP), provides a framework and library of physics schemes, or parameterizations, that support interoperable atmospheric physics. Atmospheric physics is a set of numerical methods approximating the effects of small-scale processes such as clouds, turbulence, radiation, and their interactions.
Stochastic physics schemes apply randomized perturbations to the physical tendencies, or physical parameters, of a model in order to compensate for model uncertainty. They include the Stochastic Kinetic Backscatter Scheme (SKEBS), the Stochastically Perturbed Parameterization Tendencies (SPPT) scheme, the perturbed boundary layer humidity (SHUM) scheme, the Stochastically Perturbed Parameterizations (SPP) scheme, Land Surface Model SPP (LSM-SPP), and the cellular automata method (Bengtsson et al. [BDT+20]).
The libraries needed to build the system, such as:
The build system used to compile the code and generate the executable.
The regression tests used to maintain software integrity as innovations are added.
The UFS Weather Model is currently included in two UFS Application releases: The UFS Short-Range Weather (SRW) Application v2.0.0 release (June 2022) and the UFS Medium Range Weather Application (MRW) v1.1.0 release (October 2020). These UFS Apps also contain pre- and post-processing components, a comprehensive build system, and workflows for configuration and execution of the application. The SRW App v2.0.0 documentation and details can be found here. The MRW App v1.1.0 documentation and details can be found here.
The UFS WM code is portable and can be used with Linux or Mac operating systems and with Intel or GNU compilers. It has been tested on a variety of platforms widely used by atmospheric scientists, such as the NOAA Research Hera system, the National Center for Atmospheric Research (NCAR) Cheyenne system, the National Science Foundation Stampede system, and Mac laptops.
Note
At this time, the following aspects are unsupported: configurations in which a mediator is used to couple the atmospheric model to models of other earth domains (such as ocean, ice, and waves), horizontal resolutions other than the supported ones, different number or placement of vertical levels, the cellular automata stochastic scheme, and the use of different file formats for input and output. It is expected that the UFS WM supported capabilities will be expanded in future releases.
Those wishing to contribute development to the UFS WM should become familiar with the procedures for running the model as a standalone component and for executing the regression tests described in the UFS WM GitHub wiki to make sure no inadvertent changes to the results have been introduced during the development process.
Support for the UFS WM is provided through the UFS Forum by the Developmental Testbed Center (DTC) and other groups involved in UFS development, such as NOAA’s Environmental Modeling Center (EMC), NOAA research laboratories (GFDL, NSSL, ESRL, and AOML), and NCAR. UFS users and developers are encouraged not only to post questions, but also to help address questions posted by other members of the community.
This WM User’s Guide is organized as follows:
Chapter 2 (Code Overview) provides a description of the various code repositories from which source code is pulled and an overview of the directory structure.
Chapter 3 (Building and Running the WM) explains how to use the WM without an application.
Chapter 4 (Data: Input, Model Configuration, and Output Files) lists the model inputs and outputs and has a description of the key files.
Chapter 5 (Configuration Parameters) lists the purpose and valid values for various configuration parameters.
Chapter 6 (Automated Testing) describes UFS WM automated testing options.
Chapter 7 (FAQ) lists frequently asked questions and answers.
Finally, Chapters 8 and 9 contain a list of acronyms and a glossary, respectively.
- BDT+20
L. Bengtsson, J. Dias, S. Tulich, M. Gehne, and J. Bao. A stochastic parameterization of organized tropical convection using cellular automata for global forecasts in noaa's unified forecast system. Journal of Advances in Modeling Earth Systems, 2020. URL: https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2020MS002260.
Code Overview¶
UFS Weather Model Hierarchical Repository Structure¶
The UFS Weather Model (WM) repository supports the UFS short- and medium-range weather applications (SRW / MRW Apps). The WM repository contains atmosphere, ocean, sea ice, and wave components, as well as some infrastructure components. Each of these subcomponents has its own repository. All the repositories are currently located in GitHub with public access to the broad community. Table 2.1 describes the list of repositories that comprises the UFS WM.
Repository Description |
Authoritative repository URL |
|---|---|
Umbrella repository for the UFS Weather Model |
|
Framework to connect the CCPP library to a host model |
|
CCPP library of physical parameterizations |
|
Umbrella repository for the physics and dynamics of the atmospheric model (FV3) |
|
FV3 dynamical core |
|
Stochastic physics pattern generator |
|
Modular Ocean Model (MOM6) |
|
HYbrid Coordinate Ocean Model (HYCOM) |
|
Los Alamos sea ice model (CICE6) |
|
NOAA/NCEP WAVEWATCH III Model (WW3) |
|
The Goddard Chemistry Aerosol Radiation and Transport (GOCART) |
|
NUOPC Community Mediator for Earth Prediction Systems (CMEPS) |
|
Community Data Models for Earth Prediction Systems (CDEPS) |
|
Air Quality Model (AQM) |
In the table, the left column contains a description of each repository, and the right column shows the component repositories which are pointing to (or will point to) the authoritative repositories. The UFS WM currently uses Git submodules to manage the sub-components.
Directory Structure¶
The umbrella repository for the UFS Weather Model is named ufs-weather-model. Under this repository reside a number of submodules that are nested in specific directories under the parent repository’s working directory. When the ufs-weather-model repository is cloned, the basic directory structure will be similar to the example below. Files and some directories have been removed for brevity. Directories in parentheses will appear only after a submodule update (git submodule update --init --recursive).
ufs-weather-model/
├── build.sh -------- script for building the WM
├── cmake -------- cmake configuration files
├── CMakeLists.txt
├── CMakeModules
├── doc -------- User Guide files
├── driver
├── FV3 -------- UFSAtm atmosphere model
│ ├── (atmos_cubed_sphere) -------- FV3 dynamical core
│ │ ├── (docs)
│ │ ├── (driver)
│ │ ├── (model)
│ │ └── (tools)
│ ├── (ccpp) -------- Common Community Physics Package
│ │ ├── (config)
│ │ ├── (driver)
│ │ ├── (framework) -------- CCPP framework
│ │ ├── (physics) -------- CCPP compliant physics schemes
│ │ └── (suites) -------- CCPP physics suite definition files (SDFs)
│ ├── (cpl) -------- Coupling field data structures
│ ├── (io) -------- UFSAtm write grid comp code
│ └── (stochastic_physics) -------- Wrapper for stochastic physics
│
├── stochastic_physics -------- stochastic physics pattern generator
├── AQM
│ └── (src)
│ ├── (model)
│ └── (CMAQ) --------- EPA AQ Model
├── CICE-interface
│ └── CICE --------- CICE6 sea ice model
│ ├── (icepack) --------- Sea ice column physics
│ └── (cicecore/drivers/nuopc/cmeps) --------- NUOPC CICE6 cap
├── GOCART
│ └── (ESMF) --------- GOCART model
├── HYCOM-interface
│ └── HYCOM --------- HYCOM ocean model
│ └── (NUOPC) --------- NUOPC HYCOM cap
├── MOM6-interface
│ └── MOM6
│ ├── (src) --------- MOM6 ocean model
│ └── (config_source/drivers/nuopc_cap) --------- NUOPC MOM6 cap
├── WW3
│ └── (model) --------- WW3 model
│ └── (esmf) --------- NUOPC WW3 cap
├── CDEPS-interface
│ └── CDEPS
│ ├── (datm) --------- CDEPS DATM
│ └── (docn) --------- CDEPS DOCN
├── CMEPS-interface
│ └── CMEPS
│ └── (cesm) --------- CMEPS CESM
├── modulefiles -------- system module files for supported HPC systems
└── tests -------- regression test infrastructure
└── parm
└── tests
└── fv3_conf
The physics subdirectory in the gfsphysics directory is not used or supported
as part of this release (all physics is available through the CCPP using
the repository described in Table 2.1).
Building and Running the UFS Weather Model¶
Supported Platforms & Compilers¶
Before running the Weather Model (WM), users should determine which of the levels of support is applicable to their system. Generally, Level 1 & 2 systems are restricted to those with access through NOAA and its affiliates. These systems are named (e.g., Hera, Orion, Cheyenne). Level 3 & 4 systems include certain personal computers or non-NOAA-affiliated HPC systems. The prerequisite software libraries for building the WM already exist on Level 1/preconfigured systems, so users may skip directly downloading the code. On other systems, users will need to build the prerequisite libraries using HPC-Stack.
Prerequisite Libraries¶
The UFS Weather Model (WM) requires a number of libraries for it to compile. The WM uses two categories of libraries, which are available as a bundle via HPC-Stack:
NCEP libraries (NCEPLIBS): These are libraries developed for use with NOAA weather models. Most have an NCEPLIBS prefix in the repository (e.g., NCEPLIBS-bacio). Select tools from the UFS Utilities repository (UFS_UTILS) are also included in this category. A list of the bundled libraries tested with this WM release is available in the top-level
READMEof the NCEPLIBS repository (be sure to look at the tag in that repository that matches the tag on the most recent WM release).Third-party libraries (NCEPLIBS-external): These are libraries that were developed external to the UFS Weather Model. They are general software packages that are also used by other community models. Building these libraries is optional if users can point to existing builds of these libraries on their system instead. A list of the external libraries tested with this WM release is in the top-level
READMEof the NCEPLIBS-external repository. Again, be sure to look at the tag in that repository that matches the tag on this WM release.
Note
Documentation is available for installing HPC-Stack. One of these software stacks (or the libraries they contain) must be installed before running the Weather Model.
For users who do need to build the prerequisite libraries, it is a good idea to check the platform- and compiler-specific
README files in the doc directory of the NCEPLIBS-external repository
first to see if their system or one similar to it is included. These files have detailed
instructions for building NCEPLIBS-external, NCEPLIBS, and the UFS Weather Model. They may be all the
documentation you need. Be sure to use the tag that corresponds to this version of the WM, and define a
WORK directory path before you get started.
If your platform is not included in these platform- and compiler-specific README files, there is a more
generic set of instructions in the README file at the top level of the NCEPLIBS-external repository and at the top level of the NCEPLIBS repository. It may still be a good idea to look at some of the platform-
and compiler-specific README files as a guide. Again, be sure to use the tag that corresponds to this version of the WM.
The top-level README in the NCEPLIBS-external repository includes a troubleshooting section that may be helpful.
You can also get expert help through a user support forum set up specifically for issues related to build dependencies.
Downloading the Weather Model Code¶
To clone the develop branch of the ufs-weather-model repository and update its submodules, execute the following commands:
git clone https://github.com/ufs-community/ufs-weather-model.git ufs-weather-model
cd ufs-weather-model
git submodule update --init --recursive
Compiling the model will take place within the ufs-weather-model directory you just created.
Building the Weather Model¶
Loading the Required Modules¶
Modulefiles for pre-configured platforms
are located in modulefiles/ufs_<platform>.<compiler>. For example, to load the modules from the ufs-weather-model
directory on Hera:
module use modulefiles
module load ufs_hera.intel
Note that loading this module file will also set the CMake environment variables shown in Table 3.1.
EnvironmentVariable |
Description |
Hera Intel Value |
|---|---|---|
CMAKE_C_COMPILER |
Name of C compiler |
mpiicc |
CMAKE_CXX_COMPILER |
Name of C++ compiler |
mpiicpc |
CMAKE_Fortran_COMPILER |
Name of Fortran compiler |
mpiifort |
CMAKE_Platform |
String containing platform and compiler name |
hera.intel |
If you are not running on one of the pre-configured platforms, you will need to set the environment variables manually. For example, in a bash shell, a command in the following form will set the C compiler environment variable:
export CMAKE_C_COMPILER=</path/to/C/compiler>
Setting the CMAKE_FLAGS and CCPP_SUITES Environment Variables¶
The UFS Weather Model can be built in one of twelve configurations (cf. Table 4.1).
The CMAKE_FLAGS environment variable specifies which configuration to build.
Additionally, users must select the CCPP suite(s) by setting the CCPP_SUITES environment variable at
build time in order to have one or more CCPP physics suites available at runtime. Multiple suites can be set.
Additional environment variables, such as -D32BIT=ON, can be set if the user chooses. These options are documented
in Section 5.1.3.
The following examples assume a bash shell.
ATM Configurations¶
Standalone ATM
For the ufs-weather-model ATM configuration (standalone ATM):
export CMAKE_FLAGS="-DAPP=ATM -DCCPP_SUITES=FV3_GFS_v16"
ATMW
For the ufs-weather-model ATMW configuration (standalone ATM coupled to WW3):
export CMAKE_FLAGS="-DAPP=ATMW -DCCPP_SUITES=FV3_GFS_v16"
ATMAERO
For the ufs-weather-model ATMAERO configuration (standalone ATM coupled to GOCART):
export CMAKE_FLAGS="-DAPP=ATMAERO -DCCPP_SUITES=FV3_GFS_v17_p8"
ATMAQ
For the ufs-weather-model ATMAQ configuration (standalone ATM coupled to CMAQ):
export CMAKE_FLAGS="-DAPP=ATMAQ -DCCPP_SUITES=FV3_GFS_v15p2"
S2S Configurations¶
S2S
For the ufs-weather-model S2S configuration (coupled atm/ice/ocean):
export CMAKE_FLAGS="-DAPP=S2S -DCCPP_SUITES=FV3_GFS_v17_coupled_p8"
To turn on debugging flags, add -DDEBUG=ON flag after -DAPP=S2S. Users can allow verbose build messages by running:
export BUILD_VERBOSE=1
To receive atmosphere-ocean fluxes from the CMEPS mediator, add the argument -DCMEPS_AOFLUX=ON.
For example:
export CMAKE_FLAGS="-DAPP=S2S -DCCPP_SUITES=FV3_GFS_v17_coupled_p8_sfcocn -DCMEPS_AOFLUX=ON"
S2SA
For the ufs-weather-model S2SA configuration (atm/ice/ocean/aerosols):
export CMAKE_FLAGS="-DAPP=S2SA -DCCPP_SUITES=FV3_GFS_2017_coupled,FV3_GFS_v15p2_coupled,FV3_GFS_v16_coupled,FV3_GFS_v16_coupled_noahmp"
S2SW
For the ufs-weather-model S2SW configuration (atm/ice/ocean/wave):
export CMAKE_FLAGS="-DAPP=S2SW -DCCPP_SUITES=FV3_GFS_v17_coupled_p8"
S2SWA
For the ufs-weather-model S2SWA configuration (atm/ice/ocean/wave/aerosols):
export CMAKE_FLAGS="-DAPP=S2SWA -DCCPP_SUITES=FV3_GFS_v17_coupled_p8,FV3_GFS_cpld_rasmgshocnsstnoahmp_ugwp"
NG-GODAS Configuration¶
For the ufs-weather-model NG-GODAS configuration (atm/ocean/ice/data assimilation):
export CMAKE_FLAGS="-DAPP=NG-GODAS"
HAFS Configurations¶
HAFS
For the ufs-weather-model HAFS configuration (atm/ocean) in 32 bit:
export CMAKE_FLAGS="-DAPP=HAFS -D32BIT=ON -DCCPP_SUITES=FV3_HAFS_v0_gfdlmp_tedmf_nonsst,FV3_HAFS_v0_gfdlmp_tedmf"
HAFSW
For the ufs-weather-model HAFSW configuration (atm/ocean/wave) in 32-bit with moving nest:
export CMAKE_FLAGS="-DAPP=HAFSW -D32BIT=ON -DMOVING_NEST=ON -DCCPP_SUITES=FV3_HAFS_v0_gfdlmp_tedmf,FV3_HAFS_v0_gfdlmp_tedmf_nonsst,FV3_HAFS_v0_thompson_tedmf_gfdlsf"
HAFS-ALL
For the ufs-weather-model HAFS-ALL configuration (data/atm/ocean/wave) in 32 bit:
export CMAKE_FLAGS="-DAPP=HAFS-ALL -D32BIT=ON -DCCPP_SUITES=FV3_HAFS_v0_gfdlmp_tedmf,FV3_HAFS_v0_gfdlmp_tedmf_nonsst"
Building the Model¶
The UFS Weather Model uses the CMake build system. There is a build script called build.sh in the
top-level directory of the WM repository that configures the build environment and runs the make
command. This script also checks that all necessary environment variables have been set.
If any of the environment variables have not been set, the build.sh script will exit with a message similar to:
./build.sh: line 11: CMAKE_Platform: Please set the CMAKE_Platform environment variable, e.g. [macosx.gnu|linux.gnu|linux.intel|hera.intel|...]
The WM can be built by running the following command from the ufs-weather-model directory:
./build.sh
Once build.sh is finished, you should see the executable, named ufs_model, in the ufs-weather-model/build/ directory.
If it is desired to build in a different directory, specify the BUILD_DIR environment variable: e.g. export BUILD_DIR=test_cpld
will build in the ufs-weather-model/test_cpld directory instead.
Expert help is available through a user support forum set up specifically for issues related to the Weather Model.
Running the Model¶
Attention
Although the following discussions are general, users may not be able to execute the script successfully “as is” unless they are on a Tier-1 platform.
Using the Regression Test Script¶
Users can run a number of preconfigured regression test cases using the regression test script
rt.sh in the tests directory. This script is the top-level script
that calls lower-level scripts to build specified WM configurations, set up environments, and run tests.
On Tier-1 platforms, users can run
regression tests by (1) editing the rt.conf file and (2) executing:
./rt.sh -l rt.conf
Users may need to add additional command line arguments or change information in the rt.sh file as well.
This information is provided in Section 3.5.1.2 below.
The rt.conf File¶
Each line in the PSV (Pipe-separated values) file rt.conf contains four columns of information.
The first column specifies whether to build a test (COMPILE) or run a test (RUN).
The second column specifies either configuration information for building a test or
the name of a test to run.
Thus, the second column in a COMPILE line will list the application to build (e.g., APP=S2S),
the CCPP suite to use (e.g., SUITES=FV3_GFS_2017_coupled), and additional build options
(e.g., DEBUG=Y) as needed. On a RUN line, the second column will contain a test name
(e.g., control_p8). The test name should match the name of one of the test files in the
tests/tests directory or, if the user is adding a new test, the name of the new test file.
The third column of rt.conf relates to the platform;
if blank, the test can run on any WM Tier-1 platform.
The fourth column deals with baseline creation
(see information on -c option below for more),
and fv3 means that the test will be included during baseline creation.
The order of lines in rt.conf matters
since rt.sh processes them sequentially; a RUN line should be preceeded
by a COMPILE line that builds the model used in the test. The following
rt.conf file excerpt builds the standalone ATM model in 32-bit mode and then runs the
control test:
COMPILE | -DAPP=ATM -DCCPP_SUITES=FV3_GFS_v16 -D32BIT=ON | | fv3
RUN | control | | fv3
The rt.conf file includes a large number of tests. If the user wants to run
only specific tests, s/he can either (1) comment out the tests to be skipped (using the # prefix)
or (2) create a new file (e.g., my_rt.conf) and execute ./rt.sh -l my_rt.conf.
The rt.sh File¶
This section contains additional information on command line options and troubleshooting for the rt.sh file.
Optional Arguments¶
To display detailed information on how to use rt.sh, users can simply run ./rt.sh, which will output the following options:
./rt.sh -c | -f | -l | -m | -k | -r | -e | -h
-c: create baseline
-f: use rt.conf
-l: use instead of rt.conf
-m: compare against new baseline results
-k: keep run directory
-r: use Rocoto workflow manager
-e: use ecFlow workflow manager
-h: display help (same as ./rt.sh)
When running a large number (10’s or 100’s) of tests, the -e or -r options can significantly
decrease testing time by using a workflow manager (ecFlow or Rocoto, respectively) to queue the jobs
according to dependencies and run them concurrently.
The -n option can be used to run a single test; for example, ./rt.sh -n control
will build the ATM model and run the control test.
The -c option is used to create a baseline. New baslines are needed when code changes lead
to result changes and therefore deviate from existing baselines on a bit-for-bit basis.
Troubleshooting¶
Users may need to adjust certain information in the rt.sh file, such as
the 'Machine' and 'Account' variables ($ACCNR and $MACHINE_ID), for the tests to run
correctly. If there is a problem with these or other variables (e.g., file paths), the output should indicate where:
+ echo 'Machine: ' hera.intel ' Account: ' nems
Machine: hera.intel Account: nems
+ mkdir -p /scratch1/NCEPDEV/stmp4/First.Last
mkdir: cannot create directory ‘/scratch1/NCEPDEV/stmp4/First.Last’: Permission denied
++ echo 'rt.sh error on line 370'
rt.sh error on line 370
Then, users can adjust the information in rt.sh accordingly.
Log Files¶
The regression test generates a number of log files. The summary log file
RegressionTests_<machine>.<compiler>.log in the tests directory compares
the results of the test against the baseline for a given platform and
reports the outcome:
'Missing file'results when the expected files from the simulation are not found and typically occurs when the simulation did not run to completion;
'OK'means that the simulation results are bit-for-bit identical to those of the baseline;
'NOT OK'when the results are not bit-for-bit identical; and
'Missing baseline'when there is no baseline data to compare against.
More detailed log files are located in the tests/log_<machine>.<compiler>/ directory.
The run directory path, which corresponds to the value of RUNDIR in the run_<test-name> file,
is particularly useful. $RUNDIR is a self-contained (i.e., sandboxed)
directory with the executable file, initial conditions, model configuration files,
environment setup scripts and a batch job submission script. The user can run the test
by cd-ing into $RUNDIR and invoking the command:
sbatch job_card
This can be particularly useful for debugging and testing code changes. Note that
$RUNDIR is automatically deleted at the end of a successful regression test;
specifying the -k option retains the $RUNDIR, e.g. ./rt.sh -l rt.conf -k.
Inside the $RUNDIR directory are a number of model configuration files (input.nml,
model_configure, nems.configure) and other application
dependent files (e.g., ice_in for the Subseasonal-to-Seasonal application).
These model configuration files are
generated by rt.sh from the template files in the tests/parm directory.
Specific values used to fill in the template files are test-dependent and
are set in two stages. First, default values are specified in tests/default_vars.sh, and
the default values are overriden if necessary by values specified in a test file
tests/tests/<test-name>. For example, the variable DT_ATMOS is initially assigned 1800
in the function export_fv3 of the script default_vars.sh, but the test file
tests/tests/control overrides this setting by reassigning 720 to the variable.
The files fv3_run and job_card also reside in the $RUNDIR directory.
These files are generated from the template files in the tests/fv3_conf
directory. job_card is a platform-specific batch job submission script, while
fv3_run prepares the initial conditions for the test by copying relevant data from the
input data directory of a given platform to the $RUNDIR directory.
Table 3.2 summarizes the subdirectories discussed above.
Name |
Description |
|---|---|
tests/ |
Regression test root directory. Contains rt-related scripts and the summary log file |
tests/tests/ |
Contains specific test files |
tests/parm/ |
Contains templates for model configuration files |
tests/fv3_conf/ |
Contains templates for setting up initial conditions and a batch job |
tests/log_*/ |
Contains fine-grained log files |
Creating a New Test¶
When a developer needs to create a new test for his/her implementation, the
first step would be to identify a test in the tests/tests directory that can
be used as a basis and to examine the variables defined in the test file. As
mentioned above, some of the variables may be overrides for those defined in
default_vars.sh. Others may be new variables that are needed specifically
for that test. Default variables and their values are defined in the export_fv3
function of the default_vars.sh script for ATM configurations, the export_cpl
function for S2S configurations, and the export_datm function for the NG-GODAS configuration.
Also, the names of template files for model configuration and initial conditions
can be identified via variables INPUT_NML, NEMS_CONFIGURE and FV3_RUN
by running grep -n INPUT_NML * inside the tests and tests/tests directories.
Using the Operational Requirement Test Script¶
The operational requirement test script opnReqTest in the tests directory can be used to run
tests in place of rt.sh. Given the name of a test, opnReqTest carries out a suite of test cases.
Each test case addresses an aspect of the requirements that new operational implementations
should satisfy. These requirements are shown in Table 3.3.
For the following discussions on opnReqTest, the user should note the distinction between
'test name' and 'test case'. Examples of test names are control, cpld_control
and regional_control which are all found in the tests/tests directory, whereas
test case refers to any one of thr, mpi, dcp, rst, bit and dbg.
Case |
Description |
|---|---|
thr |
Varying the number of threads produces the same results |
mpi |
Varying the number of MPI tasks produces the same results |
dcp |
Varying the decomposition (i.e. tile layout of FV3) produces the same results |
rst |
Restarting produces the same results |
bit |
Model can be compiled in double/single precision and run to completion |
dbg |
Model can be compiled and run to completion in debug mode |
The operational requirement testing uses the same testing framework as the regression
tests, so it is recommened that the user first read Section 3.5.1.
All the files in the subdirectories shown in Table 3.2 are relevant to the
operational requirement test. The only difference is that the opnReqTest script replaces rt.sh.
The tests/opnReqTests directory contains
opnReqTest-specific lower-level scripts used to set up run configurations.
On Tier-1 platforms, tests can be run by invoking
./opnReqTest -n <test-name>
For example, ./opnReqTest -n control performs all six test cases
listed in Table 3.3 for the control
test. At the end of the run, a log file OpnReqTests_<machine>.<compiler>.log
is generated in the tests directory, which informs the user whether each test case
passed or failed. The user can choose to run a specific test case by invoking
./opnReqTest -n <test-name> -c <test-case>
where <test-case> is one or
more comma-separated values selected from thr, mpi, dcp, rst,
bit, dbg. For example, ./opnReqTest -n control -c thr,rst runs the
control test and checks the reproducibility of threading and restart.
The user can see different command line options available to opnReqTest by
executing ./opnReqTest -h, which produces the following results:
Usage: opnReqTest -n <test-name> [ -c <test-case> ] [-b] [-d] [-e] [-k] [-h] [-x] [-z]
-n specify <test-name>
-c specify <test-case>
defaults to all test-cases: thr,mpi,dcp,rst,bit,dbg,fhz
comma-separated list of any combination of std,thr,mpi,dcp,rst,bit,dbg,fhz
-b test reproducibility for bit; compare against baseline
-d test reproducibility for dbg; compare against baseline
-s test reproducibility for std; compare against baseline
-e use ecFlow workflow manager
-k keep run directory
-h display this help and exit
-x skip compile
-z skip run
Frequently used options are -e to use the ecFlow
workflow manager, and -k to keep the $RUNDIR. Not that the Rocoto workflow manager
is not used operationally and therefore is not an option.
As discussed in Section 3.5.1.3, the variables and
values used to configure model parameters and to set up initial conditions in the
$RUNDIR directory are set up in two stages. First, tests/default_vars.sh
define default values; then a specific test file in the tests/tests subdirectory
either overrides the default values or creates new variables if required by the test.
The regression test treats the different test cases shown in
Table 3.3 as different tests. Therefore, each
test case requires a test file in the tests/tests subdirectory. Examples include
control_2threads, control_decomp, control_restart and control_debug,
which are just variations of the control test to check various reproducibilities.
There are two potential issues with this approach. First, if several different
variations of a given test were created and included in the rt.conf file,
there would be too many tests to run. Second, if a new test is added by the user, s/he
will also have to create these variations. The idea behind the operational requirement test is to
automatically configure and run these variations, or test cases, given a test file.
For example, ./opnReqTest -n control will run all six test cases in
Table 3.3 based on a single control test file.
Similarly, if the user adds a new test new_test, then ./opnReqTest -n new_test will
run all test cases. This is done by the operational requirement test script opnReqTest by adding a third
stage of variable overrides. The related scripts can be found in the tests/opnReqTests
directory.
Data: Input, Model Configuration, and Output Files¶
The UFS Weather Model can be run in one of several configurations, from a single component atmospheric model to a fully coupled model with multiple earth system components (e.g., atmosphere, ocean, sea-ice and mediator). Currently the supported configurations are:
Configuration Name |
Description |
|---|---|
ATM |
Standalone UFSAtm |
ATMW |
UFSAtm coupled to WW3 |
ATMAERO |
UFSAtm coupled to GOCART |
ATMAQ |
UFSAtm coupled to CMAQ |
S2S |
Coupled UFSATM-MOM6-CICE6-CMEPS |
S2SA |
Coupled UFSATM-MOM6-CICE6-GOCART-CMEPS |
S2SW |
Coupled UFSATM-MOM6-CICE6-WW3-CMEPS |
S2SWA |
Coupled UFSATM-MOM6-CICE6-WW3-GOCART-CMEPS |
NG-GODAS |
Coupled CDEPS-DATM-MOM6-CICE6-CMEPS |
HAFS |
Coupled UFSATM-HYCOM-CMEPS |
HAFSW |
Coupled UFSATM-HYCOM-WW3-CMEPS |
HAFS-ALL |
Coupled CDEPS-UFSATM-HYCOM-WW3-CMEPS |
Each of the component models for a given configuration requires specific input files, and each component model outputs a particular set of files. Each configuration requires a set of model configuration files, as well. This chapter describes the input and output files involved with each component model. It also discusses the various configuration files involved in running the model. Users will need to view the input file requirements for each component model involved in the configuration they are running. For example, users running the S2S configuration would need to gather input data required for the ATM, MOM6, and CICE6 component models. Then, they would need to alter certain model configuration files to reflect the ufs-weather-model configuration they plan to run.
Input files¶
There are three types of files needed to execute a run:
Static datasets (fix files containing climatological information)
Files that depend on grid resolution and initial/boundary conditions
Model configuration files (such as namelists)
Information on the first two types of file appears in detail below for each component model. Information on Model Configuration files can be viewed in Section 4.2.
ATM¶
Static Datasets (i.e., fix files)¶
The static input files for global configurations are listed and described in Table 4.2. Similar files are used for a regional grid but are grid-specific and generated by pre-processing utilities (e.g., UFS_UTILS).
Filename |
Description |
|---|---|
aerosol.dat |
External aerosols data file |
CFSR.SEAICE.1982.2012.monthly.clim.grb |
CFS reanalysis of monthly sea ice climatology |
co2historicaldata_YYYY.txt |
Monthly CO2 in PPMV data for year YYYY |
global_albedo4.1x1.grb |
Four albedo fields for seasonal mean climatology: 2 for strong zenith angle dependent (visible and near IR) and 2 for weak zenith angle dependent |
global_glacier.2x2.grb |
Glacier points, permanent/extreme features |
global_h2oprdlos.f77 |
Coefficients for the parameterization of photochemical production and loss of water (H2O) |
global_maxice.2x2.grb |
Maximum ice extent, permanent/extreme features |
global_mxsnoalb.uariz.t126.384.190.rg.grb |
Climatological maximum snow albedo |
global_o3prdlos.f77 |
Monthly mean ozone coefficients |
global_shdmax.0.144x0.144.grb |
Climatological maximum vegetation cover |
global_shdmin.0.144x0.144.grb |
Climatological minimum vegetation cover |
global_slope.1x1.grb |
Climatological slope type |
global_snoclim.1.875.grb |
Climatological snow depth |
global_snowfree_albedo.bosu.t126.384.190.rg.grb |
Climatological snowfree albedo |
global_soilmgldas.t126.384.190.grb |
Climatological soil moisture |
global_soiltype.statsgo.t126.384.190.rg.grb |
Soil type from the STATSGO dataset |
global_tg3clim.2.6x1.5.grb |
Climatological deep soil temperature |
global_vegfrac.0.144.decpercent.grb |
Climatological vegetation fraction |
global_vegtype.igbp.t126.384.190.rg.grb |
Climatological vegetation type |
global_zorclim.1x1.grb |
Climatological surface roughness |
RTGSST.1982.2012.monthly.clim.grb |
Monthly, climatological, real-time global sea surface temperature |
seaice_newland.grb |
High resolution land mask |
sfc_emissivity_idx.txt |
External surface emissivity data table |
solarconstant_noaa_an.txt |
External solar constant data table |
Grid Description and Initial Condition Files¶
The input files containing grid information and the initial conditions for global configurations are listed and described in Table 4.3. The input files for a limited area model (LAM) configuration, including grid information and initial and lateral boundary conditions, are listed and described in Table 4.4. Note that the regional grid is referred to as Tile 7 here, and it is generated by several pre-processing utilities.
Filename |
Description |
Date-dependent |
|---|---|---|
Cxx_grid.tile[1-6].nc |
Cxx grid information for tiles 1-6, where ‘xx’ is the grid number |
|
gfs_ctrl.nc |
NCEP NGGPS tracers, ak, and bk |
✔ |
gfs_data.tile[1-6].nc |
Initial condition fields (ps, u, v, u, z, t, q, O3). May include spfo3, spfo, spf02 if multiple gases are used |
✔ |
oro_data.tile[1-6].nc |
Model terrain (topographic/orographic information) for grid tiles 1-6 |
|
sfc_ctrl.nc |
Control parameters for surface input: forecast hour, date, number of soil levels |
|
sfc_data.tile[1-6].nc |
Surface properties for grid tiles 1-6 |
✔ |
Filename |
Description |
Date-dependent |
|---|---|---|
Cxx_grid.tile7.nc |
Cxx grid information for tile 7, where ‘xx’ is the grid number |
|
gfs_ctrl.nc |
NCEP NGGPS tracers, ak, and bk |
✔ |
gfs_bndy.tile7.HHH.nc |
Lateral boundary conditions at hour HHH |
✔ |
gfs_data.tile7.nc |
Initial condition fields (ps, u, v, u, z, t, q, O3). May include spfo3, spfo, spf02 if multiple gases are used |
✔ |
oro_data.tile7.nc |
Model terrain (topographic/orographic information) for grid tile 7 |
|
sfc_ctrl.nc |
Control parameters for surface input: forecast hour, date, number of soil levels |
|
sfc_data.tile7.nc |
Surface properties for grid tile 7 |
✔ |
MOM6¶
Static Datasets (i.e., fix files)¶
The static input files for global configurations are listed and described in Table 4.5.
Filename |
Description |
Used in resolution |
|---|---|---|
runoff.daitren.clim.1440x1080.v20180328.nc |
climatological runoff |
0.25 |
runoff.daitren.clim.720x576.v20180328.nc |
climatological runoff |
0.50 |
seawifs-clim-1997-2010.1440x1080.v20180328.nc |
climatological chlorophyll concentration in sea water |
0.25 |
seawifs-clim-1997-2010.720x576.v20180328.nc |
climatological chlorophyll concentration in sea water |
0.50 |
seawifs_1998-2006_smoothed_2X.nc |
climatological chlorophyll concentration in sea water |
1.00 |
tidal_amplitude.v20140616.nc |
climatological tide amplitude |
0.25 |
tidal_amplitude.nc |
climatological tide amplitude |
0.50, 1.00 |
geothermal_davies2013_v1.nc |
climatological geothermal heat flow |
0.50, 0.25 |
KH_background_2d.nc |
climatological 2-d background harmonic viscosities |
1.00 |
Grid description and initial condition files¶
The input files containing grid information and the initial conditions for global configurations are listed and described in Table 4.6.
Filename |
Description |
Valid RES options |
Date-dependent |
|---|---|---|---|
ocean_hgrid.nc |
horizonal grid information |
1.00, 0.50, 0.25 |
|
ocean_mosaic.nc |
specify horizonal starting and ending points index |
1.00, 0.50, 0.25 |
|
ocean_topog.nc |
ocean topography |
1.00, 0.50, 0.25 |
|
ocean_mask.nc |
lans/sea mask |
1.00, 0.50, 0.25 |
|
hycom1_75_800m.nc |
vertical coordinate level thickness |
1.00, 0.50, 0.25 |
|
layer_coord.nc |
vertical layer target potential density |
1.00, 0.50, 0.25 |
|
All_edits.nc |
specify grid points where topography are manually modified to adjust throughflow strength for narrow channels |
0.25 |
|
topo_edits_011818.nc |
specify grid points where topography are manually modified to adjust throughflow strength for narrow channels |
1.00 |
|
MOM_channels_global_025 |
specifies restricted channel widths |
0.50, 0.25 |
|
MOM_channel_SPEAR |
specifies restricted channel widths |
1.00 |
|
interpolate_zgrid_40L.nc |
specify target depth for output |
1.00, 0.50, 0.25 |
|
MOM.res*nc |
ocean initial conditions (from CPC ocean DA) |
0.25 |
✔ |
MOM6_IC_TS.nc |
ocean temperature and salinity initial conditions (from CFSR) |
1.00, 0.50, 0.25 |
✔ |
HYCOM¶
Static Datasets (i.e., fix files)¶
Static input files have been created for several regional domains. These domains are listed and described in Table 4.7.
Identifier |
Description |
|---|---|
hat10 |
Hurricane North Atlantic (1/12 degree) |
hep20 |
Hurricane Eastern North Pacific (1/12 degree) |
hwp30 |
Hurricane Western North Pacific (1/12 degree) |
hcp70 |
Hurricane Central North Pacific (1/12 degree) |
Static input files are listed and described in Table 4.8. Several datasets contain both dot-a (.a) and dot-b (.b) files. Dot-a files contain data written as 32-bit IEEE real values (idm*jdm) and dot-b files contain plain text metadata for each field in the dot-a file.
Filename |
Description |
Domain |
|---|---|---|
Model input parameters |
||
patch.input |
Tile description |
|
ports.input |
Open boundary cells |
|
forcing.chl.(a,b) |
Chlorophyll (monthly climatology) |
hat10, hep20, hwp30, hcp70 |
forcing.rivers.(a,b) |
River discharge (monthly climatology) |
hat10, hep20, hwp30, hcp70 |
iso.sigma.(a,b) |
Fixed sigma thickness |
hat10, hep20, hwp30, hcp70 |
regional.depth.(a,b) |
Total depth of ocean |
hat10, hep20, hwp30, hcp70 |
regional.grid.(a,b) |
Grid information for HYCOM “C” grid |
hat10, hep20, hwp30, hcp70 |
relax.rmu.(a,b) |
Open boundary nudging value |
hat10, hep20, hwp30, hcp70 |
relax.ssh.(a,b) |
Surface height nudging value (monthly climatology) |
hat10, hep20, hwp30, hcp70 |
tbaric.(a,b) |
Thermobaricity correction |
hat10, hep20, hwp30, hcp70 |
thkdf4.(a,b) |
Diffusion velocity (m/s) for Laplacian thickness diffusivity |
hat10, hep20, hwp30, hcp70 |
veldf2.(a,b) |
Diffusion velocity (m/s) for biharmonic momentum dissipation |
hat10, hep20, hwp30, hcp70 |
veldf4.(a,b) |
Diffusion velocity (m/s) for Laplacian momentum dissipation |
hat10, hep20, hwp30, hcp70 |
Grid Description and Initial Condition Files¶
The input files containing time dependent configuration and forcing data are listed and described in Table 4.9. These files are generated for specific regional domains (see Table 4.7) during ocean prep. When uncoupled, the the forcing data drives the ocean model. When coupled, the forcing data is used to fill in unmapped grid cells. Several datasets contain both dot-a (.a) and dot-b (.b) files. Dot-a files contain data written as 32-bit IEEE real values (idm*jdm) and dot-b files contain plain text metadata for each field in the dot-a file.
Filename |
Description |
Domain |
Date-dependent |
|---|---|---|---|
limits |
Model begin and end time (since HYCOM epoch) |
✔ |
|
forcing.airtmp.(a,b) |
GFS forcing data for 2m air temperature |
hat10, hep20, hwp30, hcp70 |
✔ |
forcing.mslprs.(a,b) |
GFS forcing data for mean sea level pressure (symlink) |
hat10, hep20, hwp30, hcp70 |
✔ |
forcing.precip.(a,b) |
GFS forcing data for precipitation rate |
hat10, hep20, hwp30, hcp70 |
✔ |
forcing.presur.(a,b) |
GFS forcing data for mean sea level pressure |
hat10, hep20, hwp30, hcp70 |
✔ |
forcing.radflx.(a,b) |
GFS forcing data for total radiation flux |
hat10, hep20, hwp30, hcp70 |
✔ |
forcing.shwflx.(a,b) |
GFS forcing data for net downward shortwave radiation flux |
hat10, hep20, hwp30, hcp70 |
✔ |
forcing.surtmp.(a,b) |
GFS forcing data for surface temperature |
hat10, hep20, hwp30, hcp70 |
✔ |
forcing.tauewd.(a,b) |
GFS forcing data for eastward momentum flux |
hat10, hep20, hwp30, hcp70 |
✔ |
forcing.taunwd.(a,b) |
GFS forcing data for northward momentum flux |
hat10, hep20, hwp30, hcp70 |
✔ |
forcing.vapmix.(a,b) |
GFS forcing data for 2m vapor mixing ratio |
hat10, hep20, hwp30, hcp70 |
✔ |
forcing.wndspd.(a,b) |
GFS forcing data for 10m wind speed |
hat10, hep20, hwp30, hcp70 |
✔ |
restart_in.(a,b) |
Restart file for ocean state variables |
hat10, hep20, hwp30, hcp70 |
✔ |
CICE6¶
Static Datasets (i.e., fix files)¶
No fix files are required for CICE6.
Grid Description and Initial Condition Files¶
The input files containing grid information and the initial conditions for global configurations are listed and described in Table 4.10.
Filename |
Description |
Valid RES options |
Date-dependent |
|---|---|---|---|
cice_model_RES.res_YYYYMMDDHH.nc |
cice model IC or restart file |
1.00, 0.50, 0.25 |
✔ |
grid_cice_NEMS_mxRES.nc |
cice model grid at resolution RES |
100, 050, 025 |
|
kmtu_cice_NEMS_mxRES.nc |
cice model land mask at resolution RES |
100, 050, 025 |
WW3¶
Static Datasets (i.e., fix files)¶
No fix files are required for WW3.
Grid Description and Initial Condition Files¶
The files for global configurations are listed and described in Table 4.11 for GFSv16 setup and Table 4.12 for single grid configurations. The model definitions for wave grid(s) including spectral and directional resolutions, time steps, numerical scheme and parallelization algorithm, the physics parameters, boundary conditions and grid definitions are stored in binary mod_def files. The aforementioned parameters are defined in ww3_grid.inp.<grd> and the ww3_grid executables generates the binary mod_def.<grd> files.
The WW3 version number in mod_def.<grd> files must be consistent with version of the code in ufs-weather-model. createmoddefs/creategridfiles.sh can be used in order to generate the mod_def.<grd> files, using ww3_grid.inp.<grd>, using the WW3 version in ufs-weather-model. In order to do it, the path to the location of the ufs-weather-model (UFSMODELDIR), the path to generated mod_def.<grd> outputs (OUTDIR), the path to input ww3_grid.inp.<grd> files (SRCDIR) and the path to the working directory for log files (WORKDIR) should be defined.
Filename |
Description |
Spatial Resolution |
nFreq |
nDir |
|---|---|---|---|---|
mod_def.aoc_9km |
Antarctic Ocean PolarStereo [50N 90N] |
9km |
50 |
36 |
mod_def.gnh_10m |
Global mid core [15S 52N] |
10 min |
50 |
36 |
mod_def.gsh_15m |
southern ocean [79.5S 10.5S] |
15 min |
50 |
36 |
mod_def.glo_15mxt |
Global 1/4 extended grid [90S 90S] |
15 min |
36 |
24 |
mod_def.points |
GFSv16-wave spectral grid point output |
na |
na |
na |
rmp_src_to_dst_conserv_002_001.nc |
Conservative remapping gsh_15m to gnh_10m |
na |
na |
na |
rmp_src_to_dst_conserv_003_001.nc |
Conservative remapping aoc_9km to gnh_10m |
na |
na |
na |
Filename |
Description |
Spatial Resolution |
nFreq |
nDir |
|---|---|---|---|---|
mod_def.ant_9km |
Regional polar stereo antarctic grid [90S 50S] |
9km |
36 |
24 |
mod_def.glo_10m |
Global grid [80S 80N] |
10 min |
36 |
24 |
mod_def.glo_30m |
Global grid [80S 80N] |
30 min |
36 |
36 |
mod_def.glo_1deg |
Global grid [85S 85N] |
1 degree |
25 |
24 |
mod_def.glo_2deg |
Global grid [85S 85N] |
2 degree |
20 |
18 |
mod_def.glo_5deg |
Global grid [85S 85N] |
5 degree |
18 |
12 |
mod_def.glo_gwes_30m |
Global NAWES 30 min wave grid [80S 80N] |
30 min |
36 |
36 |
mod_def.natl_6m |
Regional North Atlantic Basin [1.5N 45.5N; 98W 8W] |
6 min |
50 |
36 |
Coupled regional configurations require forcing files to fill regions that cannot be interpolated from the atmospheric component. For a list of forcing files used to fill unmapped data points see Table 4.13.
Filename |
Description |
Resolution |
|---|---|---|
wind.natl_6m |
Interpolated wind data from GFS |
6 min |
The model driver input (ww3_multi.inp) includes the input, model and output grids definition, the starting and ending times for the entire model run and output types and intervals. The ww3_multi.inp.IN template is located under tests/parm/ directory. The inputs are described hereinafter:
NMGRIDS |
Number of wave model grids |
|---|---|
NFGRIDS |
Number of grids defining input fields |
FUNIPNT |
Flag for using unified point output file. |
IOSRV |
Output server type |
FPNTPROC |
Flag for dedicated process for unified point output |
FGRDPROC |
Flag for grids sharing dedicated output processes |
If there are input data grids defined ( NFGRIDS > 0 ) then these grids are defined first (CPLILINE,
WINDLINE, ICELINE, CURRLINE). These grids are defined as if they are wave model grids using the
file mod_def.<grd>. Each grid is defined on a separate input line with <grd>, with nine input flags identifying
$ the presence of 1) water levels 2) currents 3) winds 4) ice
$ 5) momentum 6) air density and 7-9) assimilation data.
The UNIPOINTS defines the name of this grid for all point output, which gathers the output spectral grid in a unified point output file.
The WW3GRIDLINE defines actual wave model grids using 13 parameters to be
read from a single line in the file for each. It includes (1) its own input grid mod_def.<grd>, (2-10)
forcing grid ids, (3) rank number, (12) group number and (13-14) fraction of communicator (processes) used for this grid.
RUN_BEG and RUN_END define the starting and end times, FLAGMASKCOMP and FLAGMASKOUT are flags for masking at printout time (default F F), followed by the gridded and point outputs start time (OUT_BEG), interval (DTFLD and DTPNT) and end time (OUT_END). The restart outputs start time, interval and end time are define by RST_BEG, DTRST, RST_END respectively.
The OUTPARS_WAV defines gridded output fields. The GOFILETYPE, POFILETYPE and RSTTYPE are gridded, point and restart output types respectively.
No initial condition files are required for WW3.
Mesh Generation¶
For coupled applications using the CMEPS mediator, an ESMF Mesh file describing the WW3 domain is required. For regional and sub-global domains, the mesh can be created using a two-step procedure.
Generate a SCRIP format file for the domain
Generate the ESMF Mesh.
In each case, the SCRIP file needs to be checked that it contains the right start and end latitudes and longitudes to match the mod_def file being used.
For the HAFS regional domain, the following commands can be used:
ncremap -g hafswav.SCRIP.nc -G latlon=441,901#snwe=1.45,45.55,-98.05,-7.95#lat_typ=uni#lat_drc=s2n
ESMF_Scrip2Unstruct hafswav.SCRIP.nc mesh.hafs.nc 0
For the sub-global 1-deg domain extending from latitude 85.0S:
ncremap -g glo_1deg.SCRIP.nc -G latlon=171,360#snwe=-85.5,85.5,-0.5,359.5#lat_typ=uni#lat_drc=s2n
ESMF_Scrip2Unstruct glo_1deg.SCRIP.nc mesh.glo_1deg.nc 0
For the sub-global 1/2-deg domain extending from latitude 80.0S:
ncremap -g gwes_30m.SCRIP.nc -G latlon=321,720#snwe=-80.25,80.25,-0.25,359.75#lat_typ=uni#lat_drc=s2n
ESMF_Scrip2Unstruct gwes_30m.SCRIP.nc mesh.gwes_30m.nc 0
For the tripole grid, the mesh file is generated as part of the cpld_gridgen utility in
UFS_UTILS.
CDEPS¶
Static Datasets (i.e., fix files)¶
No fix files are required for CDEPS.
Grid Description and Initial Condition Files¶
The input files containing grid information and the time-varying forcing files for global configurations are listed and described in Table 4.15 and Table 4.16.
Data Atmosphere
Filename |
Description |
Date-dependent |
|---|---|---|
cfsr_mesh.nc |
ESMF mesh file for CFSR data source |
|
gefs_mesh.nc |
ESMF mesh file for GEFS data source |
|
TL639_200618_ESMFmesh.nc |
ESMF mesh file for ERA5 data source |
|
cfsr.YYYYMMM.nc |
CFSR forcing file for year YYYY and month MM |
✔ |
gefs.YYYYMMM.nc |
GEFS forcing file for year YYYY and month MM |
✔ |
ERA5.TL639.YYYY.MM.nc |
ERA5 forcing file for year YYYY and month MM |
✔ |
Data Ocean
Filename |
Description |
Date-dependent |
|---|---|---|
TX025_210327_ESMFmesh_py.nc |
ESMF mesh file for OISST data source |
|
sst.day.mean.YYYY.nc |
OISST forcing file for year YYYY |
✔ |
Filename |
Description |
Date-dependent |
|---|---|---|
hat10_210129_ESMFmesh_py.nc |
ESMF mesh file for MOM6 data source |
|
GHRSST_mesh.nc |
ESMF mesh file for GHRSST data source |
|
hycom_YYYYMM_surf_nolev.nc |
MOM6 forcing file for year YYYY and month MM |
✔ |
ghrsst_YYYYMMDD.nc |
GHRSST forcing file for year YYYY, month MM and day DD |
✔ |
GOCART¶
Static Datasets (i.e., fix files)¶
The static input files for GOCART configurations are listed and described in Table 4.18.
Filename |
Description |
|---|---|
AERO.rc |
Atmospheric Model Configuration Parameters |
AERO_ExtData.rc |
Model Inputs related to aerosol emissions |
AERO_HISTORY.rc |
Create History List for Output |
AGCM.rc |
Atmospheric Model Configuration Parameters |
CA2G_instance_CA.bc.rc |
Resource file for Black Carbon parameters |
CA2G_instance_CA.br.rc |
Resource file for Brown Carbon parameters |
CA2G_instance_CA.oc.rc |
Resource file for Organic Carbon parameters |
CAP.rc |
Meteorological fields imported from atmospheric model (CAP_imports) & Prognostic Tracers Table (CAP_exports) |
DU2G_instance_DU.rc |
Resource file for Dust parameters |
GOCART2G_GridComp.rc |
The basic properties of the GOCART2G Grid Components |
NI2G_instance_NI.rc |
Resource file for Nitrate parameters |
SS2G_instance_SS.rc |
Resource file for Sea Salt parameters |
SU2G_instance_SU.rc |
Resource file for Sulfur parameters |
GOCART inputs defined in AERO_ExtData are listed and described in Table 4.19.
Filename |
Description |
|---|---|
ExtData/dust |
FENGSHA input files |
ExtData/QFED |
QFED biomass burning emissions |
ExtData/CEDS |
Anthropogenic emissions |
ExtData/MERRA2 |
DMS concentration |
ExtData/PIESA/sfc |
Aviation emissions |
ExtData/PIESA/L127 |
H2O2, OH and NO3 mixing ratios |
ExtData/MEGAN_OFFLINE_BVOC |
VOCs MEGAN biogenic emissions |
ExtData/monochromatic |
Aerosol monochromatic optics files |
ExtData/optics |
Aerosol radiation bands optic files for RRTMG |
ExtData/volcanic |
SO2 volcanic pointwise sources |
The static input files when using climatology (MERRA2) are listed and described in Table 4.20.
Filename |
Description |
|---|---|
merra2.aerclim.2003-2014.m$(month).nc |
MERRA2 aerosol climatology mixing ratio |
Optics_BC.dat |
BC optical look-up table for MERRA2 |
Optics_DU.dat |
DUST optical look-up table for MERRA2 |
Optics_OC.dat |
OC optical look-up table for MERRA2 |
Optics_SS.dat |
Sea Salt optical look-up table for MERRA2 |
Optics_SU.dat |
Sulfate optical look-up table for MERRA2 |
Grid Description and Initial Condition Files¶
Running GOCART in UFS does not require aerosol initial conditions, as aerosol models can always start from scratch (cold start). However, this approach does require more than two weeks of model spin-up to obtain reasonable aerosol simulation results. Therefore, the most popular method is to take previous aerosol simulation results. The result is not necessarily from the same model; it could be from a climatology result, such as MERRA2, or from a different model but with the same aerosol species and bin/size distribution.
The aerosol initial input currently read by GOCART is the same format as the UFSAtm initial input data format of gfs_data_tile[1-6].nc in Table 4.3, so the aerosol initial conditions should be combined with the meteorological initial conditions as one initial input file. There are many tools available for this purpose. The UFS_UTILS preprocessing utilities provide a solution for this within the Global Workflow.
AQM (CMAQ)¶
Static Datasets (i.e., fix files)¶
The static input files for AQM configurations are listed and described in Table 4.21.
Filename |
Description |
|---|---|
AQM.rc |
NOAA Air Quality Model Parameters |
AQM inputs defined in aqm.rc are listed and described in Table 4.22.
Filename |
Description |
|---|---|
AE_cb6r3_ae6_aq.nml |
AE Matrix NML |
GC_cb6r3_ae6_aq.nml |
GC Matrix NML |
NR_cb6r3_ae6_aq.nml |
NR Matrix NML |
Species_Table_TR_0.nml |
TR Matrix NML |
CSQY_DATA_cb6r3_ae6_aq |
CSQY Data |
PHOT_OPTICS.dat |
Optics Data |
omi_cmaq_2015_361X179.dat |
OMI data |
NEXUS/NEXUS_Expt.nc |
Emissions File |
BEIS_RRFScmaq_C775.ncf |
Biogenic File |
gspro_biogenics_1mar2017.txt |
Biogenic Speciation File |
Hourly_Emissions_regrid_rrfs_13km_20190801_t12z_h72.nc |
File Emissions File |
Model configuration files¶
The configuration files used by the UFS Weather Model are listed here and described below:
diag_table
field_table
model_configure
nems.configure
suite_[suite_name].xml(used only at build time)
datm.streams(used by CDEPS)
datm_in(used by CDEPS)
blkdat.input(used by HYCOM)
While the input.nml file is also a configuration file used by the UFS Weather Model, it is described in
Section 4.2.9. The run-time configuration of model output fields is controlled by the combination of diag_table and model_configure, and is described in detail in Section 4.3.
diag_table file¶
There are three sections in file diag_table: Header (Global), File, and Field. These are described below.
Header Description
The Header section must reside in the first two lines of the diag_table file and contain the title and date
of the experiment (see example below). The title must be a Fortran character string. The base date is the
reference time used for the time units, and must be greater than or equal to the model start time. The base date
consists of six space-separated integers in the following format: year month day hour minute second. Here is an example:
20161003.00Z.C96.64bit.non-mono
2016 10 03 00 0 0
File Description
The File Description lines are used to specify the name of the file(s) to which the output will be written. They
contain one or more sets of six required and five optional fields (optional fields are denoted by square brackets
[ ]). The lines containing File Descriptions can be intermixed with the lines containing Field Descriptions as
long as files are defined before fields that are to be written to them. File entries have the following format:
"file_name", output_freq, "output_freq_units", file_format, "time_axis_units", "time_axis_name"
[, new_file_freq, "new_file_freq_units"[, "start_time"[, file_duration, "file_duration_units"]]]
These file line entries are described in Table 4.23.
File Entry |
Variable Type |
Description |
|---|---|---|
file_name |
CHARACTER(len=128) |
Output file name without the trailing “.nc” |
output_freq |
INTEGER |
The period between records in the file_name:
> 0 output frequency in output_freq_units.
= 0 output frequency every time step (output_freq_units is ignored)
=-1 output at end of run only (output_freq_units is ignored)
|
output_freq_units |
CHARACTER(len=10) |
The units in which output_freq is given. Valid values are “years”, “months”, “days”, “minutes”, “hours”, or “seconds”. |
file_format |
INTEGER |
Currently only the netCDF file format is supported. = 1 netCDF |
time_axis_units |
CHARACTER(len=10) |
The units to use for the time-axis in the file. Valid values are “years”, “months”, “days”, “minutes”, “hours”, or “seconds”. |
time_axis_name |
CHARACTER(len=128) |
Axis name for the output file time axis. The character string must contain the string ‘time’. (mixed upper and lowercase allowed.) |
new_file_freq |
INTEGER, OPTIONAL |
Frequency for closing the existing file, and creating a new file in new_file_freq_units. |
new_file_freq_units |
CHARACTER(len=10), OPTIONAL |
Time units for creating a new file: either years, months, days, minutes, hours, or seconds. NOTE: If the new_file_freq field is present, then this field must also be present. |
start_time |
CHARACTER(len=25), OPTIONAL |
Time to start the file for the first time. The format of this string is the same as the global date. NOTE: The new_file_freq and the new_file_freq_units fields must be present to use this field. |
file_duration |
INTEGER, OPTIONAL |
How long file should receive data after start time in file_duration_units. This optional field can only be used if the start_time field is present. If this field is absent, then the file duration will be equal to the frequency for creating new files. NOTE: The file_duration_units field must also be present if this field is present. |
file_duration_units |
CHARACTER(len=10), OPTIONAL |
File duration units. Can be either years, months, days, minutes, hours, or seconds. NOTE: If the file_duration field is present, then this field must also be present. |
Field Description
The field section of the diag_table specifies the fields to be output at run time. Only fields registered
with register_diag_field(), which is an API in the FMS diag_manager routine, can be used in the diag_table.
Registration of diagnostic fields is done using the following syntax
diag_id = register_diag_field(module_name, diag_name, axes, ...)
in file FV3/atmos_cubed_sphere/tools/fv_diagnostics.F90. As an example, the sea level pressure is registered as:
id_slp = register_diag_field (trim(field), 'slp', axes(1:2), & Time, 'sea-level pressure', 'mb', missing_value=missing_value, range=slprange )
All data written out by diag_manager is controlled via the diag_table. A line in the field section of the
diag_table file contains eight variables with the following format:
"module_name", "field_name", "output_name", "file_name", "time_sampling", "reduction_method", "regional_section", packing
These field section entries are described in Table 4.24.
Field Entry |
Variable Type |
Description |
|---|---|---|
module_name |
CHARACTER(len=128) |
Module that contains the field_name variable. (e.g. dynamic, gfs_phys, gfs_sfc) |
field_name |
CHARACTER(len=128) |
The name of the variable as registered in the model. |
output_name |
CHARACTER(len=128) |
Name of the field as written in file_name. |
file_name |
CHARACTER(len=128) |
Name of the file where the field is to be written. |
time_sampling |
CHARACTER(len=50) |
Currently not used. Please use the string “all”. |
reduction_method |
CHARACTER(len=50) |
The data reduction method to perform prior to writing data to disk. Current supported option is .false.. See |
regional_section |
CHARACTER(len=50) |
Bounds of the regional section to capture. Current supported option is “none”. See |
packing |
INTEGER |
Fortran number KIND of the data written. Valid values: 1=double precision, 2=float, 4=packed 16-bit integers, 8=packed 1-byte (not tested). |
Comments can be added to the diag_table using the hash symbol (#).
A brief example of the diag_table is shown below. "..." denotes where lines have been removed.
20161003.00Z.C96.64bit.non-mono
2016 10 03 00 0 0
"grid_spec", -1, "months", 1, "days", "time"
"atmos_4xdaily", 6, "hours", 1, "days", "time"
"atmos_static" -1, "hours", 1, "hours", "time"
"fv3_history", 0, "hours", 1, "hours", "time"
"fv3_history2d", 0, "hours", 1, "hours", "time"
#
#=======================
# ATMOSPHERE DIAGNOSTICS
#=======================
###
# grid_spec
###
"dynamics", "grid_lon", "grid_lon", "grid_spec", "all", .false., "none", 2,
"dynamics", "grid_lat", "grid_lat", "grid_spec", "all", .false., "none", 2,
"dynamics", "grid_lont", "grid_lont", "grid_spec", "all", .false., "none", 2,
"dynamics", "grid_latt", "grid_latt", "grid_spec", "all", .false., "none", 2,
"dynamics", "area", "area", "grid_spec", "all", .false., "none", 2,
###
# 4x daily output
###
"dynamics", "slp", "slp", "atmos_4xdaily", "all", .false., "none", 2
"dynamics", "vort850", "vort850", "atmos_4xdaily", "all", .false., "none", 2
"dynamics", "vort200", "vort200", "atmos_4xdaily", "all", .false., "none", 2
"dynamics", "us", "us", "atmos_4xdaily", "all", .false., "none", 2
"dynamics", "u1000", "u1000", "atmos_4xdaily", "all", .false., "none", 2
"dynamics", "u850", "u850", "atmos_4xdaily", "all", .false., "none", 2
"dynamics", "u700", "u700", "atmos_4xdaily", "all", .false., "none", 2
"dynamics", "u500", "u500", "atmos_4xdaily", "all", .false., "none", 2
"dynamics", "u200", "u200", "atmos_4xdaily", "all", .false., "none", 2
"dynamics", "u100", "u100", "atmos_4xdaily", "all", .false., "none", 2
"dynamics", "u50", "u50", "atmos_4xdaily", "all", .false., "none", 2
"dynamics", "u10", "u10", "atmos_4xdaily", "all", .false., "none", 2
...
###
# gfs static data
###
"dynamics", "pk", "pk", "atmos_static", "all", .false., "none", 2
"dynamics", "bk", "bk", "atmos_static", "all", .false., "none", 2
"dynamics", "hyam", "hyam", "atmos_static", "all", .false., "none", 2
"dynamics", "hybm", "hybm", "atmos_static", "all", .false., "none", 2
"dynamics", "zsurf", "zsurf", "atmos_static", "all", .false., "none", 2
###
# FV3 variables needed for NGGPS evaluation
###
"gfs_dyn", "ucomp", "ugrd", "fv3_history", "all", .false., "none", 2
"gfs_dyn", "vcomp", "vgrd", "fv3_history", "all", .false., "none", 2
"gfs_dyn", "sphum", "spfh", "fv3_history", "all", .false., "none", 2
"gfs_dyn", "temp", "tmp", "fv3_history", "all", .false., "none", 2
...
"gfs_phys", "ALBDO_ave", "albdo_ave", "fv3_history2d", "all", .false., "none", 2
"gfs_phys", "cnvprcp_ave", "cprat_ave", "fv3_history2d", "all", .false., "none", 2
"gfs_phys", "cnvprcpb_ave", "cpratb_ave","fv3_history2d", "all", .false., "none", 2
"gfs_phys", "totprcp_ave", "prate_ave", "fv3_history2d", "all", .false., "none", 2
...
"gfs_sfc", "crain", "crain", "fv3_history2d", "all", .false., "none", 2
"gfs_sfc", "tprcp", "tprcp", "fv3_history2d", "all", .false., "none", 2
"gfs_sfc", "hgtsfc", "orog", "fv3_history2d", "all", .false., "none", 2
"gfs_sfc", "weasd", "weasd", "fv3_history2d", "all", .false., "none", 2
"gfs_sfc", "f10m", "f10m", "fv3_history2d", "all", .false., "none", 2
...
More information on the content of this file can be found in FMS/diag_manager/diag_table.F90.
Note
None of the lines in the diag_table can span multiple lines.
field_table file¶
The FMS field and tracer managers are used to manage tracers and specify tracer options. All tracers
advected by the model must be registered in an ASCII table called field_table. The field table consists
of entries in the following format:
- The first line of an entry should consist of three quoted strings:
The first quoted string will tell the field manager what type of field it is. The string
"TRACER"is used to declare a field entry.The second quoted string will tell the field manager which model the field is being applied to. The supported type at present is
"atmos_mod"for the atmosphere model.The third quoted string should be a unique tracer name that the model will recognize.
The second and following lines are called methods. These lines can consist of two or three quoted strings.
The first string will be an identifier that the querying module will ask for. The second string will be a name
that the querying module can use to set up values for the module. The third string, if present, can supply
parameters to the calling module that can be parsed and used to further modify values.
An entry is ended with a forward slash (/) as the final character in a row. Comments can be inserted in the field table by adding a hash symbol (#) as the first character in the line.
Below is an example of a field table entry for the tracer called "sphum":
# added by FRE: sphum must be present in atmos
# specific humidity for moist runs
"TRACER", "atmos_mod", "sphum"
"longname", "specific humidity"
"units", "kg/kg"
"profile_type", "fixed", "surface_value=3.e-6" /
In this case, methods applied to this tracer include setting the long name to “specific humidity”, the units to “kg/kg”. Finally a field named “profile_type” will be given a child field called “fixed”, and that field will be given a field called “surface_value” with a real value of 3.E-6. The “profile_type” options are listed in Table 4.25. If the profile type is “fixed” then the tracer field values are set equal to the surface value. If the profile type is “profile” then the top/bottom of model and surface values are read and an exponential profile is calculated, with the profile being dependent on the number of levels in the component model.
Method Type |
Method Name |
Method Control |
|---|---|---|
profile_type |
fixed |
surface_value = X |
profile_type |
profile |
surface_value = X, top_value = Y (atmosphere) |
For the case of
"profile_type","profile","surface_value = 1e-12, top_value = 1e-15"
in a 15 layer model this would return values of surf_value = 1e-12 and multiplier = 0.6309573, i.e 1e-15 = 1e-12*(0.6309573^15).
A method is a way to allow a component module to alter the parameters it needs for various tracers. In essence,
this is a way to modify a default value. A namelist can supply default parameters for all tracers and a method, as
supplied through the field table, will allow the user to modify the default parameters on an individual tracer basis.
The lines in this file can be coded quite flexibly. Due to this flexibility, a number of restrictions are required.
See FMS/field_manager/field_manager.F90 for more information.
model_configure file¶
This file contains settings and configurations for the NUOPC/ESMF main component, including the simulation
start time, the processor layout/configuration, and the I/O selections. Table 4.26
shows the following parameters that can be set in model_configure at run-time.
Parameter |
Meaning |
Type |
Default Value |
|---|---|---|---|
print_esmf |
flag for ESMF PET files |
logical |
.true. |
start_year |
start year of model integration |
integer |
2019 |
start_month |
start month of model integration |
integer |
09 |
start_day |
start day of model integration |
integer |
12 |
start_hour |
start hour of model integration |
integer |
00 |
start_minute |
start minute of model integration |
integer |
0 |
start_second |
start second of model integration |
integer |
0 |
nhours_fcst |
total forecast length |
integer |
48 |
dt_atmos |
atmosphere time step in second |
integer |
1800 (for C96) |
output_1st_tstep_rst |
output first time step history file after restart |
logical |
.false. |
restart_interval |
frequency to output restart file or forecast hours to write out restart file |
integer |
0 (0: write restart file at the end of integration; 12, -1: write out restart every 12 hours; 12 24 write out restart files at fh=12 and 24) |
quilting |
flag to turn on quilt |
logical |
.true. |
write_groups |
total number of groups |
integer |
2 |
write_tasks_per_group |
total number of write tasks in each write group |
integer |
6 |
output_history |
flag to output history files |
logical |
.true. |
num_files |
number of output files |
integer |
2 |
filename_base |
file name base for the output files |
character(255) |
‘atm’ ‘sfc’ |
output_grid |
output grid |
character(255) |
gaussian_grid |
output_file |
output file format |
character(255) |
netcdf |
imo |
i-dimension for output grid |
integer |
384 |
jmo |
j-dimension for output grid |
integer |
190 |
nfhout |
history file output frequency |
integer |
3 |
nfhmax_hf |
forecast length of high history file |
integer |
0 (0:no high frequency output) |
nfhout_hf |
high history file output frequency |
integer |
1 |
nsout |
output frequency of number of time step |
integer |
-1 (negative: turn off the option, 1: output history file at every time step) |
output_fh |
history file output forecast hours or history file output frequency if the second elelment is -1 |
real |
-1 (negative: turn off the option, otherwise overwritten nfhout/nfhout_fh; 6 -1: output every 6 hoursr; 6 9: output history files at fh=6 and 9. Note: output_fh can only take 1032 characters) |
Table 4.27 shows the following parameters in model_configure that
are not usually changed.
Parameter |
Meaning |
Type |
Default Value |
|---|---|---|---|
calendar |
type of calendar year |
character(*) |
‘gregorian’ |
fhrot |
forecast hour at restart for nems/earth grid component clock in coupled model |
integer |
0 |
write_dopost |
flag to do post on write grid component |
logical |
.true. |
write_nsflip |
flag to flip the latitudes from S to N to N to S on output domain |
logical |
.false. |
ideflate |
lossless compression level |
integer |
1 (0:no compression, range 1-9) |
nbits |
lossy compression level |
integer |
14 (0: lossless, range 1-32) |
iau_offset |
IAU offset lengdth |
integer |
0 |
nems.configure file¶
This file contains information about the various NEMS components and their run sequence. The active components for a particular model configuration are given in the EARTH_component_list. For each active component, the model name and compute tasks assigned to the component are given. A specific component might also require additional configuration information to be present. The runSeq describes the order and time intervals over which one or more component models integrate in time. Additional attributes, if present, provide additional configuration of the model components when coupled with the CMEPS mediator.
For the ATM application, since it consists of a single component, the nems.configure is simple and does not need to be changed.
A sample of the file contents is shown below:
EARTH_component_list: ATM
ATM_model: fv3
runSeq::
ATM
::
For the fully coupled S2SW application, a sample nems.configure is shown below :
# EARTH #
EARTH_component_list: MED ATM OCN ICE WAV
EARTH_attributes::
Verbosity = 0
::
# MED #
MED_model: cmeps
MED_petlist_bounds: 0 143
::
# ATM #
ATM_model: fv3
ATM_petlist_bounds: 0 149
ATM_attributes::
::
# OCN #
OCN_model: mom6
OCN_petlist_bounds: 150 179
OCN_attributes::
mesh_ocn = mesh.mx100.nc
::
# ICE #
ICE_model: cice6
ICE_petlist_bounds: 180 191
ICE_attributes::
mesh_ice = mesh.mx100.nc
::
# WAV #
WAV_model: ww3
WAV_petlist_bounds: 192 395
WAV_attributes::
::
# CMEPS warm run sequence
runSeq::
@3600
MED med_phases_prep_ocn_avg
MED -> OCN :remapMethod=redist
OCN -> WAV
WAV -> OCN :srcMaskValues=1
OCN
@900
MED med_phases_prep_atm
MED med_phases_prep_ice
MED -> ATM :remapMethod=redist
MED -> ICE :remapMethod=redist
WAV -> ATM :srcMaskValues=1
ATM -> WAV
ICE -> WAV
ATM
ICE
WAV
ATM -> MED :remapMethod=redist
MED med_phases_post_atm
ICE -> MED :remapMethod=redist
MED med_phases_post_ice
MED med_phases_prep_ocn_accum
@
OCN -> MED :remapMethod=redist
MED med_phases_post_ocn
MED med_phases_restart_write
@
::
# CMEPS variables
::
MED_attributes::
ATM_model = fv3
ICE_model = cice6
OCN_model = mom6
history_n = 1
history_option = nhours
history_ymd = -999
coupling_mode = nems_orig
::
ALLCOMP_attributes::
ScalarFieldCount = 2
ScalarFieldIdxGridNX = 1
ScalarFieldIdxGridNY = 2
ScalarFieldName = cpl_scalars
start_type = startup
restart_dir = RESTART/
case_name = ufs.cpld
restart_n = 24
restart_option = nhours
restart_ymd = -999
dbug_flag = 0
use_coldstart = false
use_mommesh = true
::
For the coupled NG_GODAS application, a sample nems.configure is shown below :
# EARTH #
EARTH_component_list: MED ATM OCN ICE
EARTH_attributes::
Verbosity = 0
::
# MED #
MED_model: cmeps
MED_petlist_bounds: 0 11
Verbosity = 5
dbug_flag = 5
::
# ATM #
ATM_model: datm
ATM_petlist_bounds: 0 11
ATM_attributes::
Verbosity = 0
DumpFields = false
mesh_atm = DATM_INPUT/cfsr_mesh.nc
diro = "."
logfile = atm.log
stop_n = 24
stop_option = nhours
stop_ymd = -999
write_restart_at_endofrun = .true.
::
# OCN #
OCN_model: mom6
OCN_petlist_bounds: 12 27
OCN_attributes::
Verbosity = 0
DumpFields = false
ProfileMemory = false
OverwriteSlice = true
mesh_ocn = mesh.mx100.nc
::
# ICE #
ICE_model: cice6
ICE_petlist_bounds: 28 39
ICE_attributes::
Verbosity = 0
DumpFields = false
ProfileMemory = false
OverwriteSlice = true
mesh_ice = mesh.mx100.nc
stop_n = 12
stop_option = nhours
stop_ymd = -999
::
# CMEPS concurrent warm run sequence
runSeq::
@3600
MED med_phases_prep_ocn_avg
MED -> OCN :remapMethod=redist
OCN
@900
MED med_phases_prep_ice
MED -> ICE :remapMethod=redist
ATM
ICE
ATM -> MED :remapMethod=redist
MED med_phases_post_atm
ICE -> MED :remapMethod=redist
MED med_phases_post_ice
MED med_phases_aofluxes_run
MED med_phases_prep_ocn_accum
@
OCN -> MED :remapMethod=redist
MED med_phases_post_ocn
MED med_phases_restart_write
@
::
# CMEPS variables
DRIVER_attributes::
mediator_read_restart = false
::
MED_attributes::
ATM_model = datm
ICE_model = cice6
OCN_model = mom6
history_n = 1
history_option = nhours
history_ymd = -999
coupling_mode = nems_orig_data
::
ALLCOMP_attributes::
ScalarFieldCount = 3
ScalarFieldIdxGridNX = 1
ScalarFieldIdxGridNY = 2
ScalarFieldIdxNextSwCday = 3
ScalarFieldName = cpl_scalars
start_type = startup
restart_dir = RESTART/
case_name = DATM_CFSR
restart_n = 12
restart_option = nhours
restart_ymd = -999
dbug_flag = 0
use_coldstart = false
use_mommesh = true
coldair_outbreak_mod = .false.
flds_wiso = .false.
flux_convergence = 0.0
flux_max_iteration = 2
ocn_surface_flux_scheme = 0
orb_eccen = 1.e36
orb_iyear = 2000
orb_iyear_align = 2000
orb_mode = fixed_year
orb_mvelp = 1.e36
orb_obliq = 1.e36
::
For the coupled HAFS application, a sample nems.configure is shown below :
# EARTH #
EARTH_component_list: ATM OCN MED
# MED #
MED_model: cmeps
MED_petlist_bounds: 1340 1399
MED_attributes::
coupling_mode = hafs
system_type = ufs
normalization = none
merge_type = copy
ATM_model = fv3
OCN_model = hycom
history_ymd = -999
ScalarFieldCount = 0
ScalarFieldIdxGridNX = 0
ScalarFieldIdxGridNY = 0
ScalarFieldName = cpl_scalars
::
# ATM #
ATM_model: fv3
ATM_petlist_bounds: 0000 1339
ATM_attributes::
Verbosity = 1
Diagnostic = 0
::
# OCN #
OCN_model: hycom
OCN_petlist_bounds: 1340 1399
OCN_attributes::
Verbosity = 1
Diagnostic = 0
cdf_impexp_freq = 3
cpl_hour = 0
cpl_min = 0
cpl_sec = 360
base_dtg = 2020082512
merge_import = .true.
skip_first_import = .true.
hycom_arche_output = .false.
hyc_esmf_exp_output = .true.
hyc_esmf_imp_output = .true.
import_diagnostics = .false.
import_setting = flexible
hyc_impexp_file = nems.configure
espc_show_impexp_minmax = .true.
ocean_start_dtg = 43702.50000
start_hour = 0
start_min = 0
start_sec = 0
end_hour = 12
end_min = 0
end_sec = 0
::
DRIVER_attributes::
start_type = startup
::
ALLCOMP_attributes::
mediator_read_restart = false
::
# CMEPS cold run sequence
runSeq::
@360
ATM -> MED :remapMethod=redist
MED med_phases_post_atm
OCN -> MED :remapMethod=redist
MED med_phases_post_ocn
MED med_phases_prep_atm
MED med_phases_prep_ocn_accum
MED med_phases_prep_ocn_avg
MED -> ATM :remapMethod=redist
MED -> OCN :remapMethod=redist
ATM
OCN
@
::
# HYCOM field coupling configuration (location set by hyc_impexp_file)
ocn_export_fields::
'sst' 'sea_surface_temperature' 'K'
'mask' 'ocean_mask' '1'
::
ocn_import_fields::
'taux10' 'mean_zonal_moment_flx_atm' 'N_m-2'
'tauy10' 'mean_merid_moment_flx_atm' 'N_m-2'
'prcp' 'mean_prec_rate' 'kg_m-2_s-1'
'swflxd' 'mean_net_sw_flx' 'W_m-2'
'lwflxd' 'mean_net_lw_flx' 'W_m-2'
'mslprs' 'inst_pres_height_surface' 'Pa'
'sensflx' 'mean_sensi_heat_flx' 'W_m-2'
'latflx' 'mean_laten_heat_flx' 'W_m-2'
::
For more HAFS, HAFSW, and HAFS-ALL configurations please see the following nems.configure templates.
For the coupled GOCART in S2SAW application, a sample nems.configure is shown below :
# EARTH #
EARTH_component_list: MED ATM CHM OCN ICE WAV
EARTH_attributes::
Verbosity = 0
::
# MED #
MED_model: cmeps
MED_petlist_bounds: 0 287
::
# ATM #
ATM_model: fv3
ATM_petlist_bounds: 0 311
ATM_attributes::
Verbosity = 0
DumpFields = false
ProfileMemory = false
OverwriteSlice = true
::
# CHM #
CHM_model: gocart
CHM_petlist_bounds: 0 287
CHM_attributes::
Verbosity = 0
::
# OCN #
OCN_model: mom6
OCN_petlist_bounds: 312 431
OCN_attributes::
Verbosity = 0
DumpFields = false
ProfileMemory = false
OverwriteSlice = true
mesh_ocn = mesh.mx025.nc
::
# ICE #
ICE_model: cice6
ICE_petlist_bounds: 432 479
ICE_attributes::
Verbosity = 0
DumpFields = false
ProfileMemory = false
OverwriteSlice = true
mesh_ice = mesh.mx025.nc
stop_n = 6
stop_option = nhours
stop_ymd = -999
::
# WAV #
WAV_model: ww3
WAV_petlist_bounds: 480 559
WAV_attributes::
Verbosity = 0
OverwriteSlice = false
::
# CMEPS warm run sequence
runSeq::
@1800
MED med_phases_prep_ocn_avg
MED -> OCN :remapMethod=redist
OCN -> WAV
WAV -> OCN :srcMaskValues=1
OCN
@300
MED med_phases_prep_atm
MED med_phases_prep_ice
MED -> ATM :remapMethod=redist
MED -> ICE :remapMethod=redist
WAV -> ATM :srcMaskValues=1
ATM -> WAV
ICE -> WAV
ATM phase1
ATM -> CHM
CHM
CHM -> ATM
ATM phase2
ICE
WAV
ATM -> MED :remapMethod=redist
MED med_phases_post_atm
ICE -> MED :remapMethod=redist
MED med_phases_post_ice
MED med_phases_prep_ocn_accum
@
OCN -> MED :remapMethod=redist
MED med_phases_post_ocn
MED med_phases_restart_write
@
::
# CMEPS variables
DRIVER_attributes::
::
MED_attributes::
ATM_model = fv3
ICE_model = cice6
OCN_model = mom6
history_n = 1
history_option = nhours
history_ymd = -999
coupling_mode = nems_frac
history_tile_atm = 384
::
ALLCOMP_attributes::
ScalarFieldCount = 2
ScalarFieldIdxGridNX = 1
ScalarFieldIdxGridNY = 2
ScalarFieldName = cpl_scalars
start_type = startup
restart_dir = RESTART/
case_name = ufs.cpld
restart_n = 6
restart_option = nhours
restart_ymd = -999
dbug_flag = 0
use_coldstart = false
use_mommesh = true
eps_imesh = 1.0e-1
stop_n = 6
stop_option = nhours
stop_ymd = -999
::
For the fully coupled S2S application that receives atmosphere-ocean fluxes from mediator, a sample nems.configure is shown below :
# EARTH #
EARTH_component_list: MED ATM CHM OCN ICE WAV
EARTH_attributes::
Verbosity = 0
::
# MED #
MED_model: cmeps
MED_petlist_bounds: 0 143
::
# ATM #
ATM_model: fv3
ATM_petlist_bounds: 0 149
ATM_attributes::
Verbosity = 0
DumpFields = false
ProfileMemory = false
OverwriteSlice = true
::
# OCN #
OCN_model: mom6
OCN_petlist_bounds: 150 269
OCN_attributes::
Verbosity = 0
DumpFields = false
ProfileMemory = false
OverwriteSlice = true
mesh_ocn = mesh.mx025.nc
::
# ICE #
ICE_model: cice6
ICE_petlist_bounds: 270 317
ICE_attributes::
Verbosity = 0
DumpFields = false
ProfileMemory = false
OverwriteSlice = true
mesh_ice = mesh.mx025.nc
stop_n = 840
stop_option = nhours
stop_ymd = -999
::
# CMEPS warm run sequence
runSeq::
@720
MED med_phases_prep_ocn_avg
MED -> OCN :remapMethod=redist
OCN
@720
MED med_phases_aofluxes_run
MED med_phases_prep_atm
MED med_phases_prep_ice
MED -> ATM :remapMethod=redist
MED -> ICE :remapMethod=redist
ATM
ICE
ATM -> MED :remapMethod=redist
MED med_phases_post_atm
ICE -> MED :remapMethod=redist
MED med_phases_post_ice
MED med_phases_prep_ocn_accum
@
OCN -> MED :remapMethod=redist
MED med_phases_post_ocn
MED med_phases_restart_write
MED med_phases_history_write
@
::
# CMEPS variables
DRIVER_attributes::
::
MED_attributes::
ATM_model = fv3
ICE_model = cice6
OCN_model = mom6
history_n = 3
history_option = nhours
history_ymd = -999
coupling_mode = nems_frac_aoflux
history_tile_atm = 96
aoflux_grid = 'xgrid'
aoflux_code = 'ccpp'
aoflux_ccpp_suite = 'FV3_sfc_ocean'
ccpp_restart_interval = -1
ccpp_ini_mosaic_file = 'INPUT/C96_mosaic.nc'
ccpp_input_dir = 'INPUT/'
ccpp_ini_file_prefix = 'INPUT/sfc_data.tile'
ccpp_nstf_name = 2,1,0,0,0
ccpp_ini_read = true
::
ALLCOMP_attributes::
ScalarFieldCount = 2
ScalarFieldIdxGridNX = 1
ScalarFieldIdxGridNY = 2
ScalarFieldName = cpl_scalars
start_type = startup
restart_dir = RESTART/
case_name = ufs.cpld
restart_n = 12
restart_option = nhours
restart_ymd = -999
dbug_flag = 0
use_coldstart = false
use_mommesh = true
eps_imesh = 1.0e-1
stop_n = 840
stop_option = nhours
stop_ymd = -999
::
Note
The aoflux_grid option is used to select the grid/mesh to perform atmosphere-ocean flux calculation. The possible options are xgrid (exchange grid), agrid (atmosphere model grid) and ogrid (ocean model grid).
Note
The aoflux_code option is used to define the algorithm that will be used to calculate atmosphere-ocean fluxes. The possible options are cesm and ccpp. If ccpp is selected then the suite file provided in the aoflux_ccpp_suite option is used to calculate atmosphere-ocean fluxes through the use of CCPP host model.
For the ATMAQ application, a sample nems.configure is shown below :
EARTH_component_list: ATM AQM
EARTH_attributes::
Verbosity = 0
::
# ATM #
ATM_model: fv3
ATM_petlist_bounds: 0 271
ATM_attributes::
Verbosity = 0
::
# AQM #
AQM_model: aqm
AQM_petlist_bounds: 0 271
AQM_attributes::
Verbosity = 0
::
# Run Sequence #
runSeq::
@180
ATM phase1
ATM -> AQM
AQM
AQM -> ATM
ATM phase2
@
::
The Suite Definition File (SDF) File¶
There are two SDFs currently supported for the UFS Medium Range Weather App configuration:
suite_FV3_GFS_v15p2.xml
suite_FV3_GFS_v16beta.xml
There are four SDFs currently supported for the UFS Short Range Weather App configuration:
suite_FV3_GFS_v16.xml
suite_FV3_RRFS_v1beta.xml
suite_FV3_HRRR.xml
suite_FV3_WoFS_v0.xml
Detailed descriptions of the supported suites can be found with the CCPP v6.0.0 Scientific Documentation.
datm.streams¶
A data stream is a time series of input forcing files. A data stream configuration file (datm.streams) describes the information about those input forcing files.
Parameter |
Meaning |
|---|---|
taxmode01 |
time axis mode |
mapalgo01 |
type of spatial mapping (default=bilinear) |
tInterpAlgo01 |
time interpolation algorithm option |
readMode01 |
number of forcing files to read in (current option is single) |
dtimit01 |
ratio of max/min stream delta times (default=1.0. For monthly data, the ratio is 31/28.) |
stream_offset01 |
shift of the time axis of a data stream in seconds (Positive offset advances the time axis forward.) |
yearFirst01 |
the first year of the stream data |
yearLast01 |
the last year of the stream data |
yearAlign01 |
the simulation year corresponding to yearFirst01 |
stream_vectors01 |
the paired vector field names |
stream_mesh_file01 |
stream mesh file name |
stream_lev_dimname01 |
name of vertical dimension in data stream |
stream_data_files01 |
input forcing file names |
stream_data_variables01 |
a paired list with the name of the variable used in the file on the left and the name of the Fortran variable on the right |
A sample of the data stream file is shown below:
stream_info: cfsr.01
taxmode01: cycle
mapalgo01: bilinear
tInterpAlgo01: linear
readMode01: single
dtlimit01: 1.0
stream_offset01: 0
yearFirst01: 2011
yearLast01: 2011
yearAlign01: 2011
stream_vectors01: "u:v"
stream_mesh_file01: DATM_INPUT/cfsr_mesh.nc
stream_lev_dimname01: null
stream_data_files01: DATM_INPUT/cfsr.201110.nc
stream_data_variables01: "slmsksfc Sa_mask" "DSWRF Faxa_swdn" "DLWRF Faxa_lwdn" "vbdsf_ave Faxa_swvdr" "vddsf_ave Faxa_swvdf" "nbdsf_ave Faxa_swndr" "nddsf_ave Faxa_swndf" "u10m Sa_u10m" "v10m Sa_v10m" "hgt_hyblev1 Sa_z" "psurf Sa_pslv" "tmp_hyblev1 Sa_tbot" "spfh_hyblev1 Sa_shum" "ugrd_hyblev1 Sa_u" "vgrd_hyblev1 Sa_v" "q2m Sa_q2m" "t2m Sa_t2m" "pres_hyblev1 Sa_pbot" "precp Faxa_rain" "fprecp Faxa_snow"
datm_in¶
Parameter |
Meaning |
|---|---|
datamode |
data mode (such as CFSR, GEFS, etc.) |
factorfn_data |
file containing correction factor for input data |
factorfn_mesh |
file containing correction factor for input mesh |
flds_co2 |
if true, prescribed co2 data is sent to the mediator |
flds_presaero |
if true, prescribed aerosol data is sent to the mediator |
flds_wiso |
if true, water isotopes data is sent to the mediator |
iradsw |
the frequency to update the shortwave radiation in number of steps (or hours if negative) |
model_maskfile |
data stream mask file name |
model_meshfile |
data stream mesh file name |
nx_global |
number of grid points in zonal direction |
ny_global |
number of grid points in meridional direction |
restfilm |
model restart file namelist |
A sample of the data stream namelist file is shown below:
&datm_nml
datamode = "CFSR"
factorfn_data = "null"
factorfn_mesh = "null"
flds_co2 = .false.
flds_presaero = .false.
flds_wiso = .false.
iradsw = 1
model_maskfile = "DATM_INPUT/cfsr_mesh.nc"
model_meshfile = "DATM_INPUT/cfsr_mesh.nc"
nx_global = 1760
ny_global = 880
restfilm = "null"
/
blkdat.input¶
The HYCOM model reads parameters from a custom formatted configuraiton file, blkdat.input. The HYCOM User’s Guide provides an in depth description of the configuration settings.
Namelist file input.nml¶
The atmosphere model reads many parameters from a Fortran namelist file, named input.nml. This file contains several Fortran namelist records, some of which are always required, others of which are only used when selected physics options are chosen:
The CCPP Scientific Documentation provides an in-depth description of the namelist settings. Information describing the various physics-related namelist records can be viewed here.
The Stochastic Physics Documentation describes the stochastic physics namelist records.
The FV3 Dynamical Core Technical Documentation describes some of the other namelist records (dynamics, grid, etc).
The namelist section
&interpolator_nmlis not used in this release, and any modifications to it will have no effect on the model results.
fms_io_nml¶
The namelist section &fms_io_nml of input.nml contains variables that control
reading and writing of restart data in netCDF format. There is a global switch to turn on/off
the netCDF restart options in all of the modules that read or write these files. The two namelist
variables that control the netCDF restart options are fms_netcdf_override and fms_netcdf_restart.
The default values of both flags are .true., so by default, the behavior of the entire model is
to use netCDF IO mode. To turn off netCDF restart, simply set fms_netcdf_restart to .false..
The namelist variables used in &fms_io_nml are described in Table 4.30.
Variable Name |
Description |
Data Type |
Default Value |
|---|---|---|---|
fms_netcdf_override |
If true, |
logical |
.true. |
fms_netcdf_restart |
If true, all modules using restart files will operate under netCDF mode. If false, all modules using restart files will operate under binary mode. This flag is effective only when |
logical |
.true. |
threading_read |
Can be ‘single’ or ‘multi’ |
character(len=32) |
‘multi’ |
format |
Format of restart data. Only netCDF format is supported in fms_io. |
character(len=32) |
‘netcdf’ |
read_all_pe |
Reading can be done either by all PEs (default) or by only the root PE. |
logical |
.true. |
iospec_ieee32 |
If set, call mpp_open single 32-bit ieee file for reading. |
character(len=64) |
‘-N ieee_32’ |
max_files_w |
Maximum number of write files |
integer |
40 |
max_files_r |
Maximum number of read files |
integer |
40 |
time_stamp_restart |
If true, |
logical |
.true. |
print_chksum |
If true, print out chksum of fields that are read and written through save_restart/restore_state. |
logical |
.false. |
show_open_namelist_file_warning |
Flag to warn that open_namelist_file should not be called when INTERNAL_FILE_NML is defined. |
logical |
.false. |
debug_mask_list |
Set |
logical |
.false. |
checksum_required |
If true, compare checksums stored in the attribute of a field against the checksum after reading in the data. |
logical |
.true. |
This release of the UFS Weather Model sets the following variables in the &fms_io_nml namelist:
&fms_io_nml
checksum_required = .false.
max_files_r = 100
max_files_w = 100
/
namsfc¶
The namelist section &namsfc contains the filenames of the static datasets (i.e., fix files).
Table 4.2 contains a brief description of the climatological information in these files.
The variables used in &namsfc to set the filenames are described in Table 4.31.
Variable Name |
File contains |
Data Type |
Default Value |
|---|---|---|---|
fnglac |
Climatological glacier data |
character*500 |
‘global_glacier.2x2.grb’ |
fnmxic |
Climatological maximum ice extent |
character*500 |
‘global_maxice.2x2.grb’ |
fntsfc |
Climatological surface temperature |
character*500 |
‘global_sstclim.2x2.grb’ |
fnsnoc |
Climatological snow depth |
character*500 |
‘global_snoclim.1.875.grb’ |
fnzorc |
Climatological surface roughness |
character*500 |
‘global_zorclim.1x1.grb’ |
fnalbc |
Climatological snowfree albedo |
character*500 |
‘global_albedo4.1x1.grb’ |
fnalbc2 |
Four albedo fields for seasonal mean climatology |
character*500 |
‘global_albedo4.1x1.grb’ |
fnaisc |
Climatological sea ice |
character*500 |
‘global_iceclim.2x2.grb’ |
fntg3c |
Climatological deep soil temperature |
character*500 |
‘global_tg3clim.2.6x1.5.grb’ |
fnvegc |
Climatological vegetation cover |
character*500 |
‘global_vegfrac.1x1.grb’ |
fnvetc |
Climatological vegetation type |
character*500 |
‘global_vegtype.1x1.grb’ |
fnsotc |
Climatological soil type |
character*500 |
‘global_soiltype.1x1.grb’ |
fnsmcc |
Climatological soil moisture |
character*500 |
‘global_soilmcpc.1x1.grb’ |
fnmskh |
High resolution land mask field |
character*500 |
‘global_slmask.t126.grb’ |
fnvmnc |
Climatological minimum vegetation cover |
character*500 |
‘global_shdmin.0.144x0.144.grb’ |
fnvmxc |
Climatological maximum vegetation cover |
character*500 |
‘global_shdmax.0.144x0.144.grb’ |
fnslpc |
Climatological slope type |
character*500 |
‘global_slope.1x1.grb’ |
fnabsc |
Climatological maximum snow albedo |
character*500 |
‘global_snoalb.1x1.grb’ |
A sample subset of this namelist is shown below:
&namsfc
FNGLAC = 'global_glacier.2x2.grb'
FNMXIC = 'global_maxice.2x2.grb'
FNTSFC = 'RTGSST.1982.2012.monthly.clim.grb'
FNSNOC = 'global_snoclim.1.875.grb'
FNZORC = 'igbp'
FNALBC = 'global_snowfree_albedo.bosu.t126.384.190.rg.grb'
FNALBC2 = 'global_albedo4.1x1.grb'
FNAISC = 'CFSR.SEAICE.1982.2012.monthly.clim.grb'
FNTG3C = 'global_tg3clim.2.6x1.5.grb'
FNVEGC = 'global_vegfrac.0.144.decpercent.grb'
FNVETC = 'global_vegtype.igbp.t126.384.190.rg.grb'
FNSOTC = 'global_soiltype.statsgo.t126.384.190.rg.grb'
FNSMCC = 'global_soilmgldas.t126.384.190.grb'
FNMSKH = 'seaice_newland.grb'
FNVMNC = 'global_shdmin.0.144x0.144.grb'
FNVMXC = 'global_shdmax.0.144x0.144.grb'
FNSLPC = 'global_slope.1x1.grb'
FNABSC = 'global_mxsnoalb.uariz.t126.384.190.rg.grb'
/
Additional variables for the &namsfc namelist can be found in the FV3/ccpp/physics/physics/sfcsub.F
file.
atmos_model_nml¶
The namelist section &atmos_model_nml contains information used by the atmosphere model.
The variables used in &atmos_model_nml are described in Table 4.32.
Variable Name |
Description |
Data Type |
Default Value |
|---|---|---|---|
blocksize |
Number of columns in each |
integer |
1 |
chksum_debug |
If true, compute checksums for all variables passed into the GFS physics, before and after each physics timestep. This is very useful for reproducibility checking. |
logical |
.false. |
dycore_only |
If true, only the dynamical core (and not the GFS physics) is executed when running the model, essentially running the model as a solo dynamical core. |
logical |
.false. |
debug |
If true, turn on additional diagnostics for the atmospheric model. |
logical |
.false. |
sync |
If true, initialize timing identifiers. |
logical |
.false. |
ccpp_suite |
Name of the CCPP physics suite |
character(len=256) |
FV3_GFS_v15p2, set in |
avg_max_length |
Forecast interval (in seconds) determining when the maximum values of diagnostic fields in FV3 dynamics are computed. |
real |
A sample of this namelist is shown below:
&atmos_model_nml
blocksize = 32
chksum_debug = .false.
dycore_only = .false.
ccpp_suite = 'FV3_GFS_v16beta'
/
The namelist section relating to the FMS diagnostic manager &diag_manager_nml is described in Section 4.4.1.
gfs_physics_nml¶
The namelist section &gfs_physics_nml contains physics-related information used by the atmosphere model and
some of the variables are only relevant for specific parameterizations and/or configurations.
The small set of variables used in &gfs_physics_nml are described in Table 4.33.
Variable Name |
Description |
Data Type |
Default Value |
|---|---|---|---|
cplflx |
Flag to activate atmosphere-ocean coupling. If true, turn on receiving exchange fields from other components such as ocean. |
logical |
.false. |
use_med_flux |
Flag to receive atmosphere-ocean fluxes from mediator. If true, atmosphere-ocean fluxes will be received into the CCPP physics and used there, instead of calculating them. |
logical |
.false. |
A sample subset of this namelist is shown below:
&gfs_physics_nml
use_med_flux = .true.
cplflx = .true.
/
Additional variables for the &gfs_physics_nml namelist can be found in the FV3/ccpp/data/GFS_typedefs.F90
file.
Output files¶
FV3Atm¶
The output files generated when running fv3.exe are defined in the diag_table file. For the default global configuration, the following files are output (six files of each kind, corresponding to the six tiles of the model grid):
atmos_4xdaily.tile[1-6].nc
atmos_static.tile[1-6].nc
sfcfHHH.nc
atmfHHH.nc
grid_spec.tile[1-6].nc
Note that the sfcf* and atmf* files are not output on the 6 tiles, but instead as a single global gaussian grid file. The specifications of the output files (format, projection, etc) may be overridden in the model_configure input file, see Section 4.2.3.
The regional configuration will generate similar output files, but the tile[1-6] is not included in the filename.
Two files (model_configure and diag_table) control the output that is generated by the UFS Weather Model. The output files that contain the model variables are written to a file as shown in the figure below. The format of these output files is selected in model_configure as NetCDF. The information in these files may be remapped, augmented with derived variables, and converted to GRIB2 by the Unified Post Processor (UPP). Model variables are listed in the diag_table in two groupings, fv3_history and fv3_history2d, as described in Section 4.2.1. The names of the files that contain these model variables are specified in the model_configure file. When quilting is set to .true. for the write component, the variables listed in the groups fv3_history and fv3_history2d are converted into the two output files named in the model_configure file, e.g. atmfHHH. and sfcfHHH.. The bases of the file names (atm and sfc) are specified in the model_configure file, and HHH refers to the forecast hour.
Relationship between diag_table, model_configure and generated output files¶
Standard output files are logfHHH (one per forecast hour), and out and err as specified by the job submission. ESMF may also produce log
files (controlled by variable print_esmf in the model_configure file), called PETnnn.ESMF_LogFile (one per MPI task).
Additional output files include: nemsusage.xml, a timing log file; time_stamp.out, contains the model init time; RESTART/*nc, files needed for restart runs.
MOM6¶
MOM6 output is controlled via the FMS diag_manager using the diag_table. When MOM6 is present, the diag_table shown above includes additional requested MOM6 fields.
A brief example of the diag_table is shown below. "..." denotes where lines have been removed.
######################
"ocn%4yr%2mo%2dy%2hr", 6, "hours", 1, "hours", "time", 6, "hours", "1901 1 1 0 0 0"
"SST%4yr%2mo%2dy", 1, "days", 1, "days", "time", 1, "days", "1901 1 1 0 0 0"
##############################################
# static fields
"ocean_model", "geolon", "geolon", "ocn%4yr%2mo%2dy%2hr", "all", .false., "none", 2
"ocean_model", "geolat", "geolat", "ocn%4yr%2mo%2dy%2hr", "all", .false., "none", 2
...
# ocean output TSUV and others
"ocean_model", "SSH", "SSH", "ocn%4yr%2mo%2dy%2hr","all",.true.,"none",2
"ocean_model", "SST", "SST", "ocn%4yr%2mo%2dy%2hr","all",.true.,"none",2
"ocean_model", "SSS", "SSS", "ocn%4yr%2mo%2dy%2hr","all",.true.,"none",2
...
# save daily SST
"ocean_model", "geolon", "geolon", "SST%4yr%2mo%2dy", "all", .false., "none", 2
"ocean_model", "geolat", "geolat", "SST%4yr%2mo%2dy", "all", .false., "none", 2
"ocean_model", "SST", "sst", "SST%4yr%2mo%2dy", "all", .true., "none", 2
# Z-Space Fields Provided for CMIP6 (CMOR Names):
#===============================================
"ocean_model_z","uo","uo" ,"ocn%4yr%2mo%2dy%2hr","all",.true.,"none",2
"ocean_model_z","vo","vo" ,"ocn%4yr%2mo%2dy%2hr","all",.true.,"none",2
"ocean_model_z","so","so" ,"ocn%4yr%2mo%2dy%2hr","all",.true.,"none",2
"ocean_model_z","temp","temp" ,"ocn%4yr%2mo%2dy%2hr","all",.true.,"none",2
# forcing
"ocean_model", "taux", "taux", "ocn%4yr%2mo%2dy%2hr","all",.true.,"none",2
"ocean_model", "tauy", "tauy", "ocn%4yr%2mo%2dy%2hr","all",.true.,"none",2
...
HYCOM¶
HYCOM output configuration is set in the blkdat.input file. A few common configuration options are described in Table 4.34
Parameter |
Description |
|---|---|
dsurfq |
Number of days between model diagnostics at the surface |
diagfq |
Number of days between model diagnostics |
meanfq |
Number of days between model time averaged diagnostics |
rstrfq |
Number of days between model restart output |
itest |
i grid point where detailed diagnostics are desired |
jtest |
j grid point where detailed diagnostics are desired |
HYCOM outpus multiple datasets. These datasets contain both dot-a (.a), dot-b (.b), and dot-txt (.txt) files. Dot-a files contain data written as 32-bit IEEE real values (idm*jdm). Dot-b files contain plain text metadata for each field in the dot-a file. Dot-txt files contain plain text data for a single cell for profiling purposes. Post-processing utilties are available in the HYCOM-tools repository.
Filename |
Description |
|---|---|
archs.YYYY_DDD_HH.(a,b,txt) |
HYCOM surface archive data |
archv.YYYY_DDD_HH.(a,b,txt) |
HYCOM archive data |
restart_out.(a,b) |
HYCOM restart files |
CICE6¶
CICE6 output is controlled via the namelist ice_in. The relevant configuration settings are
...
histfreq = 'm','d','h','x','x'
histfreq_n = 0 , 0 , 6 , 1 , 1
hist_avg = .true.
...
In this example, histfreq_n and hist_avg specify that output will be 6-hour means. No monthly (m),
daily (d), yearly (x) or per-timestep (x) output will be produced.The hist_avg can
also be set .false. to produce, for example, instaneous fields every 6 hours.
The output of any field is set in the appropriate ice_in namelist. For example,
...
&icefields_nml
f_aice = 'mdhxx'
f_hi = 'mdhxx'
f_hs = 'mdhxx'
...
where the ice concentration (aice), ice thickness (hi) and snow thickness (hs) are set to be output on the monthly, daily, hourly, yearly or timestep intervals set by the histfreq_n setting. Since histfreq_n is 0 for both monthly and daily frequencies and neither yearly nor per-timestep output is requested, only 6-hour mean history files will be produced.
Further details of the configuration of CICE model output can be found in the CICE documentation 3.1.4
WW3¶
The run directory includes WW3 binary outputs for the gridded outputs (YYYYMMDD.HHMMSS.out_grd.<grd>), point outputs (YYYYMMDD.HHMMSS.out_pnt.points) and restart files (YYYYMMDD.HHMMSS.restart.<grd>).
CMEPS¶
The CMEPS mediator writes general information about the run-time configuration to the file mediator.log in the model run directory. Optionally, the CMEPS mediator can be configured to write history files for the purposes of examining the field exchanges at various points in the model run sequence.
Additional Information about the FMS Diagnostic Manager¶
The FMS (Flexible Modeling System) diagnostic manager (FMS/diag_manager) manages the output for the ATM and, if present, the MOM6 component in the UFS Weather Model. It is configured using the diag_table file. Data can be written at any number of sampling and/or averaging intervals
specified at run-time. More information about the FMS diagnostic manager can be found at:
https://data1.gfdl.noaa.gov/summer-school/Lectures/July16/03_Seth1_DiagManager.pdf
Diagnostic Manager Namelist¶
The diag_manager_nml namelist contains values to control the behavior of the diagnostic manager. Some
of the more common namelist options are described in Table 4.36. See
FMS/diag_manager/diag_manager.F90 for the complete list or view the FMS documentation
here for additional information.
Namelist variable |
Type |
Description |
Default value |
|---|---|---|---|
max_files |
INTEGER |
Maximum number of files allowed in diag_table |
31 |
max_output_fields |
INTEGER |
Maximum number of output fields allowed in diag_table |
300 |
max_input_fields |
INTEGER |
Maximum number of registered fields allowed |
300 |
prepend_date |
LOGICAL |
Prepend the file start date to the output file. .TRUE. is only supported if the diag_manager_init routine is called with the optional time_init parameter. |
.TRUE. |
do_diag_field_log |
LOGICAL |
Write out all registered fields to a log file |
.FALSE. |
use_cmor |
LOGICAL |
Override the missing_value to the CMOR value of -1.0e20 |
.FALSE. |
issue_oor_warnings |
LOGICAL |
Issue a warning if a value passed to diag_manager is outside the given range |
.TRUE. |
oor_warnings_fatal |
LOGICAL |
Treat out-of-range errors as FATAL |
.FALSE. |
debug_diag_manager |
LOGICAL |
Check if the diag table is set up correctly |
.FALSE. |
This release of the UFS Weather Model uses the following namelist:
&diag_manager_nml
prepend_date = .false.
/
Additional Information about the Write Component¶
The UFS Weather Model is built using the Earth System Modeling Framework (ESMF). As part of this framework, the output history files written by the model use an ESMF component, referred to as the write component. This model component is configured with settings in the model_configure file, as described in Section 4.2.3. By using the ESMF capabilities, the write component can generate output files in several different formats and several different map projections. For example, a Gaussian global grid in NEMSIO format, or a native grid in NetCDF format. The write component also runs on independent MPI tasks, and so the computational tasks can continue while the write component completes its work asynchronously. The configuration of write component tasks, balanced with compute tasks, is part of the tuning for each specific application of the model (HPC, write frequency, i/o speed, model domain, etc). For the global grid, if the write component is not selected (quilting=.false.), the FV3 code will write tiled output in the native projection in NetCDF format. The regional grid requires the use of the write component.
Configuration Parameters¶
Build Configuration Parameters¶
Configuration Options¶
-DAPP:Sets the WM configuration to build. Valid values:
ATM,ATMW,ATMAERO,ATMAQ,S2S,S2SA,S2SW,S2SWA,NG-GODAS,HAFS,HAFSW,HAFS-ALL
Physics Options¶
-DCCPP_SUITES:Sets the physics suites that will be made available when the WM is built.
Physics suites supported in regression testing:
FV3_GFS_cpld_rasmgshocnsstnoahmp_ugwpFV3_GFS_v15p2FV3_GFS_v15_thompson_mynnFV3_GFS_v15_thompson_mynn_lam3kmFV3_GFS_v16FV3_GFS_v16_csawmgFV3_GFS_v16_fv3wamFV3_GFS_v16_noahmpFV3_GFS_v16_rasFV3_GFS_v16_ugwpv1FV3_GFS_v17_p8FV3_GFS_v17_p8_rrtmgpFV3_GFS_v17_coupled_p8FV3_GFS_v17_coupled_p8_sfcocnFV3_HAFS_v0_gfdlmp_tedmfFV3_HAFS_v0_gfdlmp_tedmf_nonsstFV3_HAFS_v0_thompson_tedmf_gfdlsfFV3_HRRRFV3_HRRR_smokeFV3_RAPFV3_RAP_RRTMGPFV3_RAP_sfcdiffFV3_RRFS_v1betaFV3_RRFS_v1nsslOther valid values:
FV3_CPT_v0FV3_GFS_2017FV3_GFS_2017_csawmgFV3_GFS_2017_csawmgshocFV3_GFS_2017_gfdlmpFV3_GFS_2017_gfdlmp_noahmpFV3_GFS_2017_gfdlmp_regionalFV3_GFS_2017_gfdlmp_regional_c768FV3_GFS_2017_h2ophysFV3_GFS_2017_myjFV3_GFS_2017_ntiedtkeFV3_GFS_2017_ozphys_2015FV3_GFS_2017_sasFV3_GFS_2017_satmedmfFV3_GFS_2017_satmedmfqFV3_GFS_2017_shinhongFV3_GFS_2017_stretchedFV3_GFS_2017_ysuFV3_GFS_cpld_rasmgshocFV3_GFS_cpld_rasmgshocnsstFV3_GFS_cpld_rasmgshocnsst_flakeFV3_GFS_cpld_rasmgshocnsst_ugwpFV3_GFS_cpldnst_rasmgshocFV3_GFS_rasmgshocFV3_GFS_v15FV3_GFS_v15_gfFV3_GFS_v15_gf_thompsonFV3_GFS_v15_mynnFV3_GFS_v15_rasFV3_GFS_v15_rasmgshocFV3_GFS_v15_thompsonFV3_GFS_v15p2_no_nsstFV3_GFS_v15plusFV3_GFS_v15plusrasFV3_GFS_v16_coupledFV3_GFS_v16_coupled_noahmpFV3_GFS_v16_coupled_nsstNoahmpFV3_GFS_v16_coupled_nsstNoahmpUGWPv1FV3_GFS_v16_coupled_p8FV3_GFS_v16_coupled_p8_sfcocnFV3_GFS_v16_couplednsstFV3_GFS_v16_flakeFV3_GFS_v16_no_nsstFV3_GFS_v16_nsstNoahmpUGWPv1FV3_GFS_v16_p8FV3_GFS_v16_thompsonFV3_GFSv17alp_cpldnsstrasnoahmpFV3_GFSv17alp_cpldnsstrasugwpnoahmpFV3_GFSv17alp_cpldnsstsasugwpnoahmpFV3_GFSv17alpha_cpldnsstrasFV3_GFSv17alpha_cpldnsstras_flakeFV3_GFSv17alpha_cpldnsstras_ugwpFV3_GFSv17alpha_cpldnsstrasnoshalFV3_GFSv17alpha_cpldnsstsasFV3_GFSv17alpha_cpldnsstsas_ugwpFV3_GFSv17alpha_rasFV3_GFSv17alpha_ras_flakeFV3_GFSv17alpha_ras_ugwpFV3_GFSv17alpha_sasFV3_RAP_cires_ugwpFV3_RAP_flakeFV3_RAP_noahFV3_RAP_noah_sfcdiff_cires_ugwpFV3_RAP_noah_sfcdiff_ugwpv1FV3_RAP_noah_sfcdiff_unified_ugwpFV3_RAP_unified_ugwpFV3_RRFS_v1alpha
Other Build Options¶
-DCMEPS_AOFLUX: (Default: OFF)Enables atmosphere-ocean flux calculation in mediator. Valid values:
ON|OFF-DDEBUG: (Default: OFF)Enables DEBUG mode. Valid values:
ON|OFF-D32BIT: (Default: OFF)Enables 32-bit, single precision arithmetic in dycore and fast physics. Valid values:
ON|OFF-DCCPP_32BIT: (Default: OFF)Enables 32-bit, single precision arithmetic in slow physics. Valid values:
ON|OFF-DMOVING_NEST: (Default: OFF)Enables moving nest code. Valid values:
ON|OFF-DMULTI_GASES: (Default: OFF)Enable
MULTI_GASES. Valid values:ON|OFF
Automated Testing¶
The UFS Weather Model repository on GitHub employs two types of automated testing:
CI/CD (Continuous Integration/Continuous Development) testing on the cloud
AutoRT on NOAA R&D platforms
Both are application level tests and utilize the regression testing framework discussed in Section 3.5.1.
CI/CD¶
The UFS Weather Model (WM) uses GitHub Actions (GHA), a GitHub-hosted continuous integration service, to perform CI/CD testing. Build jobs are done on GHA-provided virtual machines. Test jobs are performed on the Amazon Web Services (AWS) cloud platform using a number of EC2 instances. Builds and tests are carried out in a Docker container. The container includes a pre-installed version of the HPC-Stack, which includes all prerequisite libraries. Input data needed to run the tests are stored as a separate Docker container.
When a developer makes a pull request (PR) to the UFS WM repository, a code manager may add the run-ci label, which triggers the CI/CD workflow. The CI/CD workflow then executes the following steps:
A check is performed to make sure the UFS Weather Model and its first level subcomponents are up to date with the top of the
developbranch.If the check is successful, build jobs are started on GHA-provided virtual machines by downloading the hpc-stack Docker container stored in Docker Hub.
Once all build jobs are successful, the created executable files are stored as artifacts in GHA.
A number of AWS EC2 instances are started.
Test jobs are started on AWS after downloading the hpc-stack Docker container, the executable file from the build job, and the input-data Docker container.
When all tests are complete, EC2 instances are stopped. Test results are reported on GitHub.
The GHA-related yaml scripts are located in the .github/workflows/ directory.
build_test.yml is the main workflow file, and aux.yml is an auxiliary
file responsible for (1) checking that the PR branch is up-to-date and
(2) starting/stopping the EC2 instances.
Other CI-related scrips are located in the tests/ci/ directory. ci.sh is the main script that
invokes Docker build and run. Dockerfile is used to build the UFS Weather Model.
Other shell and python scripts help with various tasks. For example:
repo_check.shchecks that the PR branch is up-to-date.
check_status.pychecks the status of EC2 instances.
setup.pyandci.testconfigure the test cases to execute in the CI/CD workflow.
Auto RT¶
The Automated Regression Testing (AutoRT) system is a python program that automates the process of regression testing on NOAA HPC platforms. It contains the files in Table 6.1 below:
File Name |
Description |
|---|---|
start_rt_auto.sh |
Verifies HPC name, sets the python paths |
rt_auto.py |
Python interface between the HPC and the github API |
jobs/bl.py |
Functions for the baseline job |
jobs/rt.py |
Functions for the regression test job |
AutoRT Workflow¶
On supported HPC systems, a cron job runs the start_rt_auto.sh bash script every 15 minutes.
This script checks the HPC name and sets certain python paths. Then, it runs rt_auto.py,
which uses the Github API (through pyGitHub) to check the labels on pull requests to
ufs-weather-model. If a PR label matches the HPC name
(e.g., hera-intel-RT or cheyenne-gnu-BL), the label provides the HPC
with the compiler and job information to run a test or task on the machine.
If no PR label matches HPC name, the script exits.
For example, a PR labeled gaea-intel-BL will be recognized by the HPC machine ‘Gaea’.
It will set the RT_COMPILER variable to ‘intel’ and run the baseline creation script (bl.py).
This script creats a job class that contains all information from the machine that the job will need to run.
That information is sent into the jobs/rt[bl].py script.
rt.py sets directories for storage, gets repo information, runs the regression test, and
completes any required post processing.
def run(job_obj):
logger = logging.getLogger('RT/RUN')
workdir = set_directories(job_obj)
branch, pr_repo_loc, repo_dir_str = clone_pr_repo(job_obj, workdir)
run_regression_test(job_obj, pr_repo_loc)
post_process(job_obj, pr_repo_loc, repo_dir_str, branch)
bl.py: (similar to rt.py) Adds functionality to create baselines before running regression testing.
def run(job_obj):
logger = logging.getLogger('BL/RUN')
workdir, rtbldir, blstore = set_directories(job_obj)
pr_repo_loc, repo_dir_str = clone_pr_repo(job_obj, workdir)
bldate = get_bl_date(job_obj, pr_repo_loc)
bldir = f'{blstore}/develop-{bldate}/{job_obj.compiler.upper()}'
bldirbool = check_for_bl_dir(bldir, job_obj)
run_regression_test(job_obj, pr_repo_loc)
post_process(job_obj, pr_repo_loc, repo_dir_str, rtbldir, bldir)
FAQ¶
How do I build and run a single test of the UFS Weather Model?¶
An efficient way to build and run the UFS Weather Model is to use the regression test
(rt.sh). This script is widely used by model developers on Tier 1 and 2 platforms
and is described in the UFS WM GitHub wiki. The advantages to this approach are:
It does not require a workflow, pre- or post-processing steps.
The batch submission script is generated.
Any required input data is already available for machines used by the regression test.
Once the
rt.shtest completes, you will have a working copy in your run directory where you can make modifications to the namelist and other files, and then re-run the executable.
The steps are:
Clone the source code and all the submodules as described in Section 3.3, then go into the
testsdirectory:cd ufs-weather-model (or the top level where you checked out the code) cd testsFind a configure (
*.conf) file that contains the machine and compiler you are using. For this example, the Intel compiler on Cheyenne is used. To create a custom configure file, two lines are needed: aCOMPILEline and aRUNline. TheCOMPILEline should contain the name of the machine and compilercheyenne.inteland the desiredSUITESfor the build. Choose aRUNline under thisCOMPILEcommand that uses the desiredSUITE. For example:COMPILE | 32BIT=Y CCPP=Y STATIC=Y SUITES=FV3_GFS_v15p2,FV3_GFS_v16beta,FV3_GFS_v15p2_no_nsst,FV3_GFS_v16beta_no_nsst | standard | cheyenne.intel | fv3 RUN | fv3_ccpp_gfs_v16beta | standard | | fv3 |Put these two lines into a file called
my_test.conf. The parameters used in this run can be found in thefv3_ccpp_gfs_v16betafile in theufs-weather-model/tests/testsdirectory.Note
These two lines are long and may not appear in entirety in your browser. Scroll to the right to see the entire line.
Modify the
rt.shscript to put the output in a run directory where you have write permission:if [[ $MACHINE_ID = cheyenne.* ]]; then stanza: ... dprefix=/glade/scratchThis works for Cheyenne, since
$USER/FV3_RTwill be appended. Also check thatRTPWDpoints to a diretory that exists:if [[ $MACHINE_ID = cheyenne.* ]]; then RTPWD=${RTPWD:-$DISKNM/ufs-public-release-20200224/${COMPILER^^}}Run the
rt.shscript from thetestsdirectory:./rt.sh -k -l my_test.conf >& my_test.out &Check
my_test.outfor build and run status, plus other standard output. Check/glade/scratch/$USER/FV3_RT/rt_PIDfor the model run, wherePIDis a process ID. The build will take about 10-15 minutes and the run will be fast, depending on how long it waits in the queue. A message"REGRESSION TEST WAS SUCCESSFUL"will be written to this file, along with other entertainment:'Elapsed time: 00h:14m:12s. Have a nice day!'.When the build and run are complete, modify the namelist or
model_configurefiles and re-run by submitting thejob_cardfile:qsub job_card
How do I change the length of the model run?¶
In your run directory, there is a file named model_configure. Change the
variable nhours_fcst to the desired number of hours.
How do I select the file format for the model output (netCDF or NEMSIO)?¶
In your run directory, there is a file named model_configure. Change the
variable output_file to 'netcdf' or 'nemsio'. The variable output_file
is only valid when the write component is activated by setting quilting to .true.
in the model_configure file.
How do I set the output history interval?¶
The interval at which output (history) files are written is controlled in two
places, and depends on whether you are using the write component to generate your output files.
Table 7.1 describes the relevant variables. If the write_component is used, then the variables listed as model_configure are required. It is however, also required that the settings in input.nml match those same settings in model_configure. If these settings are inconsistent, then unpredictable output files and intervals may occur!
Namelist variable |
Location |
Default Value |
Description |
|---|---|---|---|
fdiag |
input.nml |
0 |
Array with dimension |
fhmax |
input.nml |
384 |
The maximal forecast time for output. |
fhmaxhf |
input.nml |
120 |
The maximal forecast hour for high frequency output. |
fhout |
input.nml |
3 |
Output frequency during forecast time from 0 to |
fhouthf |
input.nml |
1 |
The high frequency output frequency during the forecast time from 0 to |
nfhmax_hf |
model_configure |
0 |
forecast length of high history file |
nfhout_hf |
model_configure |
1 |
high history file output frequency |
nfhout |
model_configure |
3 |
history file output frequency |
How do I set the total number of tasks for my job?¶
The total number of MPI tasks used by the UFS Weather Model is a combination of compute and quilt tasks, and can be calculated using the following relationship:
total tasks =
compute tasks + quilt taskscompute tasks =
x layout * y layout * number of tilesquilt tasks =
write_groups * write_tasks_per_groupifquilting==.true.
The layout and tiles settings are in input.nml, and the quilt task settings are in model_configure
Acronyms¶
Acronyms |
Explanation |
|---|---|
AOML |
NOAA’s Atlantic Oceanographic and Meteorological Laboratory |
API |
Application Programming Interface |
b4b |
Bit-for-bit |
CCPP |
Common Community Physics Package |
dycore |
Dynamical core |
EDMF |
Eddy-Diffusivity Mass Flux |
EMC |
Environmental Modeling Center |
ESMF |
The Earth System Modeling Framework |
ESRL |
NOAA Earth System Research Laboratories |
FMS |
Flexible Modeling System |
FV3 |
Finite-Volume Cubed Sphere |
GFDL |
NOAA Geophysical Fluid Dynamics Laboratory |
GFS |
Global Forecast System |
GSD |
Global Systems Division |
HTML |
Hypertext Markup Language |
LSM |
Land Surface Model |
MPI |
Message Passing Interface |
NCAR |
National Center for Atmospheric Research |
NCEP |
National Centers for Environmental Predicction |
NEMS |
NOAA Environmental Modeling System |
NOAA |
National Oceanic and Atmospheric Administration |
NSSL |
National Severe Storms Laboratory |
PBL |
Planetary Boundary Layer |
PR |
Pull request |
RRTMG |
Rapid Radiative Transfer Model for Global Circulation Models |
SAS |
Simplified Arakawa-Schubert |
SDF |
Suite Definition File |
sfc |
Surface |
SHUM |
Perturbed boundary layer specific humidity |
SKEB |
Stochastic Kinetic Energy Backscatter |
SPPT |
Stochastically Perturbed Physics Tendencies |
TKE |
Turbulent Kinetic Energy |
UFS |
Unified Forecast System |
WM |
Weather Model |
Glossary¶
- advect¶
To transport substances in the atmostphere by advection.
- advection¶
According to the American Meteorological Society (AMS) definition, advection is “The process of transport of an atmospheric property solely by the mass motion (velocity field) of the atmosphere.” In common parlance, advection is movement of atmospheric substances that are carried around by the wind.
- ATM¶
The Weather Model configuration that runs only the standalone atmospheric model.
- AQM¶
The Air Quality Model (AQM) is a UFS Application that dynamically couples the Community Multiscale Air Quality (CMAQ) model with the UFS Weather Model through the NUOPC Layer to simulate temporal and spatial variations of atmospheric compositions (e.g., ozone and aerosol compositions). The CMAQ, treated as a column chemistry model, updates concentrations of chemical species (e.g., ozone and aerosol compositions) at each integration time step. The transport terms (e.g., advection and diffusion) of all chemical species are handled by the UFS Weather Model as tracers.
- CCPP¶
The Common Community Physics Package is a forecast-model agnostic, vetted collection of code containing atmospheric physical parameterizations and suites of parameterizations for use in Numerical Weather Prediction (NWP) along with a framework that connects the physics to the host forecast model.
- CCPP-Framework¶
The infrastructure that connects physics schemes with a host model; also refers to a software repository of the same name
- CCPP-Physics¶
The pool of CCPP-compliant physics schemes; also refers to a software repository of the same name
- CDEPS¶
The Community Data Models for Earth Predictive Systems repository (CDEPS) contains a set of NUOPC-compliant data components and ESMF-based “stream” code that selectively removes feedback in coupled model systems. In essence, CDEPS handles the static Data Atmosphere (DATM) integration with dynamic coupled model components (e.g., MOM6). The CDEPS data models perform the basic function of reading external data files, modifying those data, and then sending the data back to the CMEPS mediator. The fields sent to the mediator are the same as those that would be sent by an active component. This takes advantage of the fact that the mediator and other CMEPS-compliant model components have no fundamental knowledge of whether another component is fully active or just a data component. More information about DATM is available in the CDEPS Documentation.
- CESM¶
The Community Earth System Model (CESM) is a fully-coupled global climate model developed at the National Center for Atmospheric Research (NCAR) in collaboration with colleagues in the research community.
- chgres_cube¶
The preprocessing software used to create initial and boundary condition files to “coldstart” the forecast model. It is part of UFS_UTILS.
- CICE¶
- CICE6¶
- Sea Ice Model¶
CICE is a computationally efficient model for simulating the growth, melting, and movement of polar sea ice. It was designed as one component of a coupled atmosphere-ocean-land-ice global climate model. CICE has several interacting components, including a model of ice dynamics, a transport model that describes advection of different state variables; and a vertical physics package called “Icepack”.
- CMAQ¶
The Community Multiscale Air Quality Model (CMAQ, pronounced “cee-mak”) is a numerical air quality model that predicts the concentration of airborne gases and particles and the deposition of these pollutants back to Earth’s surface. The purpose of CMAQ is to provide fast, technically sound estimates of ozone, particulates, toxics, and acid deposition. CMAQ is an active open-source development project of the U.S. Environmental Protection Agency (EPA). Code is publicly availably at https://github.com/USEPA/CMAQ.
- CMEPS¶
The Community Mediator for Earth Prediction Systems (CMEPS) is a NUOPC-compliant mediator used for coupling Earth system model components. It is currently being used in NCAR’s Community Earth System Model (CESM) and NOAA’s subseasonal-to-seasonal (S2S) coupled system. More information is available in the CMEPS Documentation.
- cron¶
- cron job¶
- crontab¶
- cron table¶
Cron is a job scheduler accessed through the command-line on UNIX-like operating systems. It is useful for automating tasks such as regression testing. Cron periodically checks a cron table (aka crontab) to see if any tasks are are ready to execute. If so, it runs them.
- DATM¶
DATM is the Data Atmosphere component of CDEPS. It uses static atmospheric forcing files (derived from observations or previous atmospheric model runs) instead of output from an active atmospheric model. This reduces the complexity and computational cost associated with coupling to an active atmospheric model. The Data Atmosphere component is particularly useful when employing computationally intensive Data Assimilation (DA) techniques to update ocean and/or sea ice fields in a coupled model. In general, use of DATM in place of ATM can be appropriate when users are running a coupled model and only want certain components of the model to be active. More information about DATM is available in the CDEPS Documentation.
- dycore¶
- dynamical core¶
Global atmospheric model based on fluid dynamics principles, including Euler’s equations of motion.
- EMC¶
The Environmental Modeling Center is one of NCEP’s nine centers and leads the National Weather Service’s modeling efforts.
- ESMF¶
Earth System Modeling Framework. The ESMF defines itself as “a suite of software tools for developing high-performance, multi-component Earth science modeling applications.” It is a community-developed software infrastructure for building and coupling models.
- FMS¶
The Flexible Modeling System (FMS) is a software framework for supporting the efficient development, construction, execution, and scientific interpretation of atmospheric, oceanic, and climate system models.
- FV3¶
- FV3 dycore¶
- FV3 dynamical core¶
The Finite-Volume Cubed-Sphere dynamical core (dycore). Developed at NOAA’s Geophysical Fluid Dynamics Laboratory (GFDL), it is a scalable and flexible dycore capable of both hydrostatic and non-hydrostatic atmospheric simulations. It is the dycore used in the UFS Weather Model.
- GOCART¶
NASA’s Goddard Chemistry Aerosol Radiation and Transport (GOCART) model simulates the distribution of major tropospheric aerosol types, including sulfate, dust, organic carbon (OC), black carbon (BC), and sea salt aerosols. The UFS Weather Model integrates a prognostic aerosol component using GOCART. The code is publicly available on GitHub at https://github.com/GEOS-ESM/GOCART.
- HPC-Stack¶
The HPC-Stack is a repository that provides a unified, shell script-based build system for building the software stack required for numerical weather prediction (NWP) tools such as the Unified Forecast System (UFS) and the Joint Effort for Data assimilation Integration (JEDI) framework.
- HAFS¶
The Hurricane Analysis and Forecast System (HAFS) is a UFS application for hurricane forecasting. It is an FV3-based multi-scale model and data assimilation (DA) system capable of providing analyses and forecasts of the inner core structure of tropical cyclones (TC) — including hurricanes and typhoons — out to 7 days. This is key to improving size and intensity predictions. HAFS also provides analyses and forecasts of the large-scale environment that is known to influence a TC’s motion. HAFS development targets an operational analysis and forecast system for hurricane forecasters with reliable, robust and skillful guidance on TC track and intensity (including rapid intensification), storm size, genesis, storm surge, rainfall, and tornadoes associated with TCs. Currently, HAFS is under active development with collaborative efforts among NCEP/EMC, AOML/HRD, GFDL, ESRL/GSD, ESRL/NESII, OFCM/AOC, and NCAR/DTC.
- HYCOM¶
The HYbrid Coordinate Ocean Model (HYCOM) was developed to address known shortcomings in the vertical coordinate scheme of the Miami Isopycnic-Coordinate Ocean Model (MICOM). HYCOM is a primitive equation, general circulation model with vertical coordinates that remain isopycnic in the open, stratified ocean. However, the isopycnal vertical coordinates smoothly transition to z-coordinates in the weakly stratified upper-ocean mixed layer, to terrain-following sigma coordinates in shallow water regions, and back to z-level coordinates in very shallow water. The latter transition prevents layers from becoming too thin where the water is very shallow. See the HYCOM User’s Guide for more information on using the model. The HYCOM model code is publicly available on GitHub.
- Mediator¶
A mediator, sometimes called a coupler, is a software component that includes code for representing component interactions. Typical operations include merging data fields, ensuring consistent treatment of coastlines, computing fluxes, and temporal averaging.
- MOM¶
- MOM6¶
- Modular Ocean Model¶
MOM6 is the latest generation of the Modular Ocean Model. It is numerical model code for simulating the ocean general circulation. MOM6 was originally developed by the Geophysical Fluid Dynamics Laboratory. Currently, MOM6 code and an extensive suite of test cases are available under an open-development software framework. Although there are many public forks of MOM6, the NOAA EMC fork is used in the UFS Weather Model.
- MRW¶
- MRW App¶
The Medium-Range Weather Application is a UFS Application that targets predictions of atmospheric behavior out to about two weeks. It packages a prognostic atmospheric model (the UFS Weather Model), pre- and post-processing tools, and a community workflow.
- NCAR¶
- NCEP¶
National Centers for Environmental Prediction (NCEP) is a branch of the National Weather Service and consists of nine centers, including the Environmental Modeling Center. More information can be found at https://www.ncep.noaa.gov.
- NCEPLIBS¶
The software libraries created and maintained by NCEP that are required for running chgres_cube, the UFS Weather Model, and the UPP. They are included in the HPC-Stack and in spack-stack.
- NCEPLIBS-external¶
A collection of third-party libraries required to build NCEPLIBS, chgres_cube, the UFS Weather Model, and the UPP. They are included in the HPC-Stack and in spack-stack.
- NEMS¶
The NOAA Environmental Modeling System is a common modeling framework whose purpose is to streamline components of operational modeling suites at NCEP.
- NG-GODAS¶
Next Generation-Global Ocean Data Assimilation System. NG-GODAS is a UFS Weather Model configuration that couples ocean (MOM6), sea ice (CICE6), and Data Assimilation (DA) capabilities with the DATM component of CDEPS.
- NUOPC¶
- National Unified Operational Prediction Capability¶
The National Unified Operational Prediction Capability is a consortium of Navy, NOAA, and Air Force modelers and their research partners. It aims to advance the weather modeling systems used by meteorologists, mission planners, and decision makers. NUOPC partners are working toward a common model architecture — a standard way of building models — in order to make it easier to collaboratively build modeling systems.
- NUOPC Layer¶
The NUOPC Layer “defines conventions and a set of generic components for building coupled models using the Earth System Modeling Framework (ESMF).” NUOPC applications are built on four generic components: driver, model, mediator, and connector. For more information, visit the NUOPC website.
- NWP¶
- Numerical Weather Prediction¶
Numerical Weather Prediction (NWP) takes current observations of weather and processes them with computer models to forecast the future state of the weather.
- NWS¶
The National Weather Service (NWS) is an agency of the United States government that is tasked with providing weather forecasts, warnings of hazardous weather, and other weather-related products to organizations and the public for the purposes of protection, safety, and general information. It is a part of the National Oceanic and Atmospheric Administration (NOAA) branch of the Department of Commerce.
- Parameterizations¶
Simplified functions that approximate the effects of small-scale processes (e.g., microphysics, gravity wave drag) that cannot be explicitly resolved by a model grid’s representation of the earth. Common categories of parameterizations include radiation, surface layer, planetary boundary layer and vertical mixing, deep and shallow cumulus, and microphysics. Parameterizations can be grouped together into physics suites (such as the CCPP physics suites), which are sets of parameterizations known to work well together.
- Post-processor¶
Software that enhances the value of the raw forecasts produced by the modeling application to make them more useful. At NCEP, the UPP (Unified Post Processor) software is used to convert data from spectral to gridded format, de-stagger grids, interpolate data vertically (e.g., to isobaric levels) and horizontally (to various predefined grids), and to compute derived variables. Some types of post-processors, such as statistical post-processors, use historical information of previous runs and observations to de-bias and calibrate its output.
- SRW¶
- SRW App¶
- Short-Range Weather Application¶
The Short-Range Weather Application is a UFS Application that targets predictions of atmospheric behavior on a limited spatial domain and on time scales from minutes out to about two days. It packages a prognostic atmospheric model (the UFS Weather Model), pre- and post-processing tools, and a community workflow.
- spack-stack¶
The spack-stack is a collaborative effort between the NOAA Environmental Modeling Center (EMC), the UCAR Joint Center for Satellite Data Assimilation (JCSDA), and the Earth Prediction Innovation Center (EPIC). spack-stack is a repository that provides a Spack-based method for building the software stack required for numerical weather prediction (NWP) tools such as the Unified Forecast System (UFS) and the Joint Effort for Data assimilation Integration (JEDI) framework. spack-stack uses the Spack package manager along with custom Spack configuration files and Python scripts to simplify installation of the libraries required to run various applications. The spack-stack can be installed on a range of platforms and comes pre-configured for many systems. Users can install the necessary packages for a particular application and later add the missing packages for another application without having to rebuild the entire stack.
- Suite Definition File (SDF)¶
An external file containing information about the construction of a physics suite. It describes the schemes that are called, in which order they are called, whether they are subcycled, and whether they are assembled into groups to be called together
- Suite¶
A collection of primary physics schemes and interstitial schemes that are known to work well together
- tracer¶
According to the American Meteorological Society (AMS) definition, a tracer is “Any substance in the atmosphere that can be used to track the history [i.e., movement] of an air mass.” Tracers are carried around by the motion of the atmosphere (i.e., by advection). These substances are usually gases (e.g., water vapor, CO2), but they can also be non-gaseous (e.g., rain drops in microphysics parameterizations). In weather models, temperature (or potential temperature), absolute humidity, and radioactivity are also usually treated as tracers. According to AMS, “The main requirement for a tracer is that its lifetime be substantially longer than the transport process under study.”
- UFS¶
- Unified Forecast System¶
The Unified Forecast System (UFS) is a community-based, coupled, comprehensive Earth system modeling system. The UFS numerical applications span regional to global domains and sub-hourly to seasonal time scales. The UFS is designed to support the Weather Enterprise and to be the source system for NOAA’s operational numerical weather prediction (NWP) applications. For more information, visit https://ufscommunity.org/.
- UFS_UTILS¶
The UFS Utilities repository (UFS_UTILS) contains a collection of pre-processing programs for use with the UFS Weather Model and UFS applications. These programs set up the model grid and create coldstart initial conditions. The code is publicly available on the UFS_UTILS Github repository.
- UPP¶
- Unified Post Processor¶
The Unified Post Processor is the post-processor software developed at NCEP. It is used operationally to convert the raw output from a variety of NCEP’s NWP models, including the FV3 dycore, to a more useful form.
- WW3¶
- WWIII¶
- WaveWatch III¶
WAVEWATCH III (WW3) is a community wave modeling framework that includes the latest scientific advancements in the field of wind-wave modeling and dynamics. The core of the framework consists of the WAVEWATCH III third-generation wave model (WAVE-height, WATer depth and Current Hindcasting), developed at NOAA/NCEP. WAVEWATCH III differs from its predecessors in many important points such as governing equations, model structure, numerical methods and physical parameterizations. The model code is publicly available on GitHub at https://github.com/NOAA-EMC/WW3.
- Weather Enterprise¶
Individuals and organizations from public, private, and academic sectors that contribute to the research, development, and production of weather forecast products; primary consumers of these weather forecast products.
- WM¶
- Weather Model¶
A prognostic model that can be used for short- and medium-range research and operational forecasts. It can be an atmosphere-only model or be an atmospheric model coupled with one or more additional components, such as a wave or ocean model. The UFS Weather Model repository is publicly available on GitHub.