3.2. Running Icepack¶

Quick-start instructions are provided in the Quick Start section.

3.2.1. Scripts¶

The icepack scripts are written to allow quick setup of cases and tests. Once a case is generated, users can manually modify the namelist and other files to custom configure the case. Several settings are available via scripts as well.

3.2.1.1. Overview¶

Most of the scripts that configure, build and run Icepack are contained in the directory configuration/scripts/, except for icepack.setup, which is in the main directory. icepack.setup is the main script that generates a case.

Users may need to port the scripts to their local machine. Specific instructions for porting are provided in Porting.

icepack.setup -h will provide the latest information about how to use the tool. icepack.setup --help will provide an extended version of the help. There are three usage modes,

--case or -c creates individual stand alone cases.
--test creates individual tests. Tests are just cases that have some extra automation in order to carry out particular tests such as exact restart.
--suite creates a test suite. Test suites are predefined sets of tests and --suite provides the ability to quick setup, build, and run a full suite of tests.

All modes will require use of --mach or -m to specify the machine and case and test modes can use --set or -s to define specific options. --test and --suite will require --testid to be set and both of the test modes can use --bdir, --bgen, --bcmp, and --diff to generate (save) results and compare results with prior results as well as --tdir to specify the location of the test directory. Testing will be described in greater detail in the Testing Icepack section.

Again, icepack.setup --help will show the latest usage information including the available --set options, the current ported machines, and the test choices.

To create a case, run icepack.setup:

icepack.setup -c mycase -m machine
cd mycase

Once a case/test is created, several files are placed in the case directory

env.[machine] defines the environment
icepack.settings defines many variables associated with building and running the model
makdep.c is a tool that will automatically generate the make dependencies
Macros.[machine] defines the Makefile macros
Makefile is the makefile used to build the model
icepack.build is a script that builds and compiles the model
icepack_in is the namelist input file
icepack.run is a batch run script
icepack.submit is a simple script that submits the icepack.run script

All scripts and namelist are fully resolved in the case. Users can edit any of the files in the case directory manually to change the model configuration, build options, or batch settings. The file dependency is indicated in the above list. For instance, if any of the files before icepack.build in the list are edited, icepack.build should be rerun.

The casescripts/ directory holds scripts used to create the case and can largely be ignored. Once a case is created, the icepack.build script should be run interactively and then the case should be submitted by executing the icepack.submit script interactively. The icepack.submit script simply submits the icepack.run script. You can also submit the icepack.run script on the command line.

Some hints:

To change namelist, manually edit the icepack_in file
To change batch settings, manually edit the top of the icepack.run or icepack.test (if running a test) file
To turn on the debug compiler flags, set ICE_BLDDEBUG in icepack.setttings to true
To change compiler options, manually edit the Macros file
To clean the build before each compile, set ICE_CLEANBUILD in icepack.settings to true. To not clean before the build, set ICE_CLEANBUILD in icepack.settings to false

To build and run:

./icepack.build
./icepack.submit

The build and run log files will be copied into the logs directory in the case directory. Other model output will be in the run directory. The run directory is set in icepack.settings via the ICE_RUNDIR variable. To modify the case setup, changes should be made in the case directory, NOT the run directory.

3.2.1.2. Command Line Options¶

icepack.setup -h provides a summary of the command line options. There are three different modes, --case, --test, and --suite. This section provides details about the relevant options for setting up cases with examples. Testing will be described in greater detail in the Testing Icepack section.

--help, -h: prints icepack.setup help information to the terminal and exits.
--version: prints the Icepack version to the terminal and exits.
--setvers: Updates the stored value of the Icepack version in the sandbox and exits See Model Version Control for more information
--case, -c CASE: specifies the case name. This can be either a relative path of an absolute path. This cannot be used with –test or –suite. Either --case, --test, or --suite is required.
--mach, -m MACHINE: specifies the machine name. This should be consistent with the name defined in the Macros and env files in configurations/scripts/machines. This is required in all modes.
--env, -e ENVIRONMENT1,ENVIRONMENT2,ENVIRONMENT3: specifies the environment or compiler associated with the machine. This should be consistent with the name defined in the Macros and env files in configurations/scripts/machines. Each machine can have multiple supported environments including support for different compilers or other system setups. When used with --suite or --test, the ENVIRONMENT can be a set of comma deliminated values with no spaces and the tests will then be run for all of those environments. With --case, only one ENVIRONMENT should be specified. (default is intel)
--pes, -p MxN: specifies the number of tasks and threads the case should be run on. This only works with --case. The format is tasks x threads or “M”x”N” where M is tasks and N is threads and both are integers. The current icepack driver is purely serial so setting multiple tasks or multiple threads will have no impact. (default is 1x1)
--acct ACCOUNT: specifies a batch account number. This is optional. See Machine Account Settings for more information.
--queue QUEUE: specifies a batch queue name. This is optional. See Machine Queue Settings for more information.
--grid, -g GRID: specifies the grid. This is a string and for the current icepack driver, only col is supported. (default = col)
--set, -s SET1,SET2,SET3: specifies the optional settings for the case. This is only used with --case or --test. The settings for --suite are defined in the suite file. Multiple settings can be specified by providing a comma deliminated set of values without spaces between settings. The available settings are in configurations/scripts/options and icepack.setup --help will also list them. These settings files can change either the namelist values or overall case settings (such as the debug flag).

For Icepack, when setting up cases, the --case and --mach must be specified. It’s also recommended that --env be set explicitly as well. At the present time, --pes and --grid cannot vary from 1x1 and col respectively which are the defaults. --acct is not normally used. A more convenient method is to use the ~/cice_proj file, see Machine Account Settings. The --set option can be extremely handy. The --set options are documented in Preset Options.

3.2.1.3. Preset Options¶

There are several preset options. These are hardwired in configurations/scripts/options and are specfied for a case or test by the --set command line option. You can see the full list of settings by doing icepack.setup --help.

The default icepack namelist and icepack settings are specified in the files configuration/scripts/icepack_in and configuration/scripts/icepack.settings respectively. When picking a preset setting (option), the set_env.setting and set_nml.setting will be used to change the defaults. This is done as part of the icepack.setup and the modifications are resolved in the icepack.settings and icepack_in file placed in the case directory. If multiple options are chosen and then conflict, then the last option chosen takes precedent. Not all options are compatible with each other.

Some of the options are

debug which turns on the compiler debug flags

short, medium, long which change the batch time limit

diag1 which turns on diagnostics each timestep

leap which turns on the leap year

pondcesm, pondlvl, pondtopo which turn on the various pond schemes

run10day, run1year, etc which specifies a run length

swccsm3 which turns on the ccsm3 shortwave and albedo computation

thermo1 which on turns on the Bitz-Lipscomb thermodynamics model (default is mushy-layer)

bgc* which turns of various bgc configurations

and there are others. To add a new option, just add the appropriate file in configuration/scripts/options. Some of the options settings like smoke and restart are specifically geared toward setting up tests. For more information, see Preset Case Options

3.2.1.4. Examples¶

The simplest case is just to setup a default configurations specifying the case name, machine, and environment:

icepack.setup --case mycase1 --mach spirit --env intel

To add some optional settings, one might do:

icepack.setup --case mycase2 --mach spirit --env intel --set debug,diag1,run1year,pondtopo

Once the cases are created, users are free to modify the icepack.settings and icepack_in namelist to further modify their setup.

3.2.1.5. Model Version Control¶

Managing the internal representation of the model version is handled through the icepack.setup script. The --version option displays the version value on the terminal. The --setvers option updates the version defined in the sandbox. It is highly recommended that any changes to the version name be done through this interface to make sure it’s done correctly and comprehensively. The version name should just include the string associated with the major, minor, and similar. For instance,:

icepack.setup --version

returns

./icepack.setup: This is ICEPACK_v1.0.0.d0003

and:

icepack.setup --setvers v1.0.0.d0004

would update the version. Always check the string by doing icepack.setup --version after invoking icepack.setup --setvers.

The version is not updated in the repository unless the code changes associated with the new version are pushed to the repository.

3.2.1.6. Other Scripts Tools¶

There are other scripts that come with icepack. These include

setup_run_dirs.csh. This scripts is added to the case directory. Invoking it creates all the run directories manually. This script is automatically called as part of the run script, but sometimes it’s useful to create these directories before submitting in order to stage custom input files or other data.

3.2.2. Porting¶

To port, an env.[machine]_[environment] and Macros.[machine]_[environment] file have to be added to the configuration/scripts/machines/ directory and the configuration/scripts/icepack.batch.csh file needs to be modified. In general, the machine is specified in icepack.setup with --mach and the environment (compiler) is specified with --env.

cd to configuration/scripts/machines/
Copy an existing env and a Macros file to new names for your new machine
Edit your env and Macros files
cd .. to configuration/scripts/
Edit the icepack.batch.csh script to add a section for your machine with batch settings and job launch settings
Download and untar a forcing dataset to the location defined by ICE_MACHINE_INPUTDATA in the env file

In fact, this process almost certainly will require some iteration. The easiest way to carry this out is to create an initial set of changes as described above, then create a case and manually modify the env.[machine] file and Macros.[machine] file until the case can build and run. Then copy the files from the case directory back to configuration/scripts/machines/ and update the configuration/scripts/icepack.batch.csh file, retest, and then add and commit the updated machine files to the repository.

3.2.2.1. Cross-compiling¶

It can happen that the model must be built on a platform and run on another, for example when the run environment is only available in a batch queue. The program makdep (see Overview), however, is both compiled and run as part of the build process.

In order to support this, the Makefile uses a variable CFLAGS_HOST that can hold compiler flags specfic to the build machine for the compilation of makdep. If this feature is needed, add the variable CFLAGS_HOST to the Macros.[machine]_[environment] file. For example :

CFLAGS_HOST = -xHost

3.2.2.2. Machine Account Settings¶

The machine account default is specified by the variable ICE_MACHINE_ACCT in the env.[machine] file. The easiest way to change a user’s default is to create a file in your home directory called .cice_proj and add your preferred account name to the first line. There is also an option (--acct) in icepack.setup to define the account number. The order of precedent is icepack.setup command line option, .cice_proj setting, and then value in the env.[machine] file.

3.2.2.3. Machine Queue Settings¶

The machine queue default is specified by the variable ICE_MACHINE_QUEUE in the env.[machine] file. The easiest way to change a user’s default is to create a file in your home directory called .cice_queue and add your preferred account name to the first line. There is also an option (--queue) in icepack.setup to define the queue name on a case basis. The order of precedent is icepack.setup command line option, .cice_queue setting, and then value in the env.[machine] file.

3.2.3. Forcing data¶

The input data space is defined on a per machine basis by the ICE_MACHINE_INPUTDATA variable in the env.[machine] file. That file space is often shared among multiple users, and it can be desirable to consider using a common file space with group read and write permissions such that a set of users can update the inputdata area as new datasets are available.

The code is currently configured to run in standalone mode on a 4-cell grid using atmospheric data, available as detailed on the wiki. These data files are designed only for testing the code, not for use in production runs or as observational data. Please do not publish results based on these data sets. Module configuration/driver/icedrv_forcing.F90 can be modified to change the forcing data.

Icepack requires near surface atmospheric data at a single point which are set in forcing_nml with the atm_data_type in the namelist (see Table of Icepack Settings). The required fields to force icepack include: downwelling long wave and shortwave radiative fluxes, latent and sensible heat fluxes, precipitation rate, and near surface potential temperature and specific humidity. The filenames atm_data_file, ocn_data_file, ice_data_file, and bgc_data_file must also be provided for options other than the default and climatological forcing cases. Current filenames can be found in the options scripts in configuration/scripts/options and in the forcing data directories.

Climate Forecast System (CFS)

Hourly atmospheric forcing from the National Centers for Environmental Prediction’s (NCEP) Climate Forecast System, version 2 (CFSv2) [45] were utilized to generate a one-year time series for Icepack testing. These data were used to create the annual cycle at a point in the Beaufort Sea (70N, 220W) for the period of January 1 00:00UTC - December 31 23:00UTC, 2015. Additional locations can be provided for both hemispheres for the period of 1999-2015 for future testing. This dataset can be used to run for several years to reach equilibrium of the annual cycle.

Atmospheric forcing fields consist of 2-m air temperature (K), specific humidity (kg/kg), 10-m wind velocity in the x and y directions (m/s), downward solar radiation (\(W/m^2\)), downward longwave radiation (\(W/m^2\)), and precipitation (\(kg/m^2/s\)). Icepack’s boundary layer calculation is used to derive sensible and latent heat fluxes. In the namelist, set atm_data_type = CFS to use CFS atmospheric forcing.
Field campaign derived
1. Norwegian Young Sea Ice cruise (N-ICE)
Atmospheric, oceanic, and biogeochemical forcing are available from the 2015 Norwegian Young Sea Ice Cruise (N-ICE) [9]. These data are available daily, except for incoming atmospheric radiative forcing, which are available 6-hourly. The data correspond to the Arctic Ocean north of Svalbard along the N-ICE drift track (83N, 16E to 80N, 5E) from April 24, 2015 to June 6, 2015.

Atmospheric forcing fields from [9] consist of 2-m air temperature (K), 2-m specific humidity (kg/kg), 10-m wind velocity in the x and y directions (m/s), downward solar radiation (\(W/m^2\)), and precipitation (\(kg/m^2/s\)). Icepack’s boundary layer calculation is used to derive sensible and latent heat fluxes. In the namelist, set atm_data_type = NICE to use N-ICE atmospheric forcing.

Oceanic forcing fields are available from a Parallel Ocean Program (POP) 1-degree (gx1v3) simulation [8]. These fields consist of sea surface temperature (K), sea surface salinity (ppt), boundary layer depth (m), ocean velocity in the x and y direction (m/s), and deep ocean heat flux (\(W/m^2\)). In the namelist, set ocn_data_type = NICE to use N-ICE oceanic forcing.

Biogeochemical forcing fields are available from the World Ocean Atlas [17]. The biogeochemical fields provided are nitrate concentration (\(mmol/m^3\)) and silicate concentration (\(mmol/m^3\)). In the namelist, set bgc_data_type = NICE to use N-ICE biogeochemical forcing.
1. Ice Station Polarstern (ISPOL)
Atmospheric, oceanic, and biogeochemical forcing are available from the 2004 Ice Station Polarstern (ISPOL) [25]. These data can be used with both [6] and mushy layer thermodynamics. These data are available daily, except for incoming atmospheric radiative forcing, which are available 6-hourly. The data correspond to the Weddell Sea (67.9S, 54W) from June 16, 2004 to December 31, 2004.

Atmospheric forcing fields from [25] consist of 2-m air temperature (K), 2-m specific humidity (kg/kg), 10-m wind velocity in the x and y directions (m/s), downward solar radiation (\(W/m^2\)), and precipitation (\(kg/m^2/s\)). Icepack’s boundary layer calculation is used to derive sensible and latent heat fluxes. In the namelist, set atm_data_type = ISPOL to use ISPOL atmospheric forcing.

Oceanic forcing fields are available from [25] derived from a POP 1-degree (gx1v3 simulation) [8]. These consist of sea surface temperature (K), sea surface salinity (ppt), boundary layer depth (m), ocean velocity in the x and y direction (m/s), and deep ocean heat flux (\(W/m^2\)). In the namelist, set ocn_data_type = ISPOL to use ISPOL oceanic forcing.

Biogeochemical forcing fields are available from the World Ocean Atlas [17]. The biogeochemical fields provided are nitrate concentration (\(mmol/m^3\)) and silicate concentration (\(mmol/m^3\)). In the namelist, set bgc_data_type = ISPOL to use ISPOL biogeochemical forcing.
1. Surface HEat Budget of the Arctic (SHEBA)
The ice opening and closing rates (1/s) are derived from the SHEBA data and have been used previously in Cecilia Bitz’s column model. For additional information see the following websites:
- https://atmos.washington.edu/~bitz/column_model/
- https://atmos.washington.edu/~bitz/column_model/notes_forcing_data
At present, only the opening and closing rates (1/s) are used from the forcing data. In the namelist, set ocn_data_type = SHEBA to use this forcing in Icepack.
Climatological - Maykut and Untersteiner 1971 [39]

The climatological forcing consists of a monthly climatology of downward radiative fluxes, air temperature, relative humidity and wind speed compiled from Arctic ice station observations shown in Table 1 from [30]. Icepack’s boundary layer calculation is used to derive sensible and latent heat fluxes. The snowfall follows the idealized specification used by [47] . To adjust the ice thickness a fixed heating of 6 \(W/m^2\) is applied to the bottom of the ice. This may be thought of as containing about 2 \(W/m^2\) of ocean heating and an adjustment of about 4 \(W/m^2\) for biases in the forcings or the model. In the namelist, set atm_data_type = clim to use climatological atmospheric forcing.

3.2.4. Run Directories¶

The icepack.setup script creates a case directory. However, the model is actually built and run under the ICE_OBJDIR and ICE_RUNDIR directories as defined in the icepack.settings file.

Build and run logs will be copied from the run directory into the case logs/ directory when complete.

3.2.5. Local modifications¶

Scripts and other case settings can be changed manually in the case directory and used. Source code can be modified in the main sandbox. When changes are made, the code should be rebuilt before being resubmitted. It is always recommended that users modify the scripts and input settings in the case directory, NOT the run directory. In general, files in the run directory are overwritten by versions in the case directory when the model is built, submitted, and run.