3. Building and Running the UFS Weather Model

3.1. 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.

3.2. 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:

1. 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 README of the NCEPLIBS repository (be sure to look at the tag in that repository that matches the tag on the most recent WM release).

2. 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 README of 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.

3.3. 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.

3.4. Building the Weather Model

3.4.1. 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.

Table 3.1 CMake environment variables required to configure the build for the Weather Model

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>

3.4.2. 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.

3.4.2.1. 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"

3.4.2.2. 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"

3.4.2.3. NG-GODAS Configuration

For the ufs-weather-model NG-GODAS configuration (atm/ocean/ice/data assimilation):

export CMAKE_FLAGS="-DAPP=NG-GODAS"

3.4.2.4. 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"

3.4.3. 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.

3.5. 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.

3.5.1. 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.

3.5.1.1. 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.

3.5.1.2. The rt.sh File

This section contains additional information on command line options and troubleshooting for the rt.sh file.

3.5.1.2.1. 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.

3.5.1.2.2. 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.

3.5.1.3. 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.

Table 3.2 Regression Test Subdirectories

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

3.5.1.4. 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.

3.5.2. 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.

Table 3.3 Operational Requirements

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.