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 quickly setup, build, and run a full suite of tests.
All modes will require use of --mach
or -m
to specify the machine. Use of --env
is also recommended to specify the compilation environment. --case
and --test
modes can use --set
or -s
which will turn on various model options. --test
and --suite
will require --testid
to be set and can use --bdir
, --bgen
, --bcmp
, and --diff
to generate (save) results for regression testing (comparison with prior results). --tdir
will 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 -e intel
cd mycase
Once a case/test is created, several files are placed in the case directory
env.[machine]_[env] defines the machine 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]_[env] 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 submits the icepack.run or icepack.test script.
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
When the run scripts are submitted, the current icepack_in, icepack.settings, and env.[machine] files are copied from the case directory into the run directory. Users should generally not edit files in the run directory as these are overwritten when following the standard workflow. icepack.settings can be sourced to establish the case values in the login shell. An alias like the following can be established to quickly switch between case and run directories:
alias cdrun 'cd `\grep "setenv ICE_RUNDIR" icepack.settings | awk "{print "\$"NF}"`' alias cdcase 'cd `\grep "setenv ICE_CASEDIR" icepack.settings | awk "{print "\$"NF}"`'
To turn on the debug compiler flags, set
ICE_BLDDEBUG
in icepack.setttings to trueTo change compiler options, manually edit the Macros file. To add user defined preprocessor macros, modify
ICE_CPPDEFS
in icepack.settings using the syntax-DCICE_MACRO
.To clean the build before each compile, set
ICE_CLEANBUILD
in icepack.settings to true. To not clean before the build, setICE_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 subdirectory 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.
--docintfc
Runs a script that updates the public interfaces in the documentation. This script parses the source code directly. See Public Interfaces for more information.
--case
,-c
CASEspecifies 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
MACHINEspecifies 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 and is paired with
--env
to define the compilation environment.--env
,-e
ENVIRONMENT1,ENVIRONMENT2,ENVIRONMENT3specifies the compilation environment 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, different compiler versions, different mpi libraries, or other system settigs. 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
MxNspecifies 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
ACCOUNTspecifies a batch account number. This is optional. See Machine Account Settings for more information.
--queue
QUEUEspecifies a batch queue name. This is optional. See Machine Queue Settings for more information.
--grid
,-g
GRIDspecifies the grid. This is a string and for the current icepack driver, only col is supported. (default = col)
--set
,-s
SET1,SET2,SET3specifies 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 andicepack.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 that conflict, then the last
option chosen takes precedence. 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
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. C Preprocessor (CPP) Macros¶
There are a few C Preprocessor Macros supported in the Icepack model. These support certain coding features to be excluded or included during the compile. They exist in part to support the CICE model and other applications that use Icepack.
For standalone Icepack, The CPPs are defined by the CPPDEFS variable in the Icepack
Makefile. They are defined
by passing the -D[CPP] to the C and Fortran compilers (ie. -DNO_I8) and this
is what needs to be set in the CPPDEFS
variable. The value of ICE_CPPDEFS
in
icepack.settings is copied into the Makefile CPPDEFS
variable as are settings
hardwired into the Macros.[machine]_[environment] file.
A list of available CPPs can be found in Table of C Preprocessor (CPP) Macros.
3.2.1.6. 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.
3.2.1.7. 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 addition configuration/scripts/icepack.launch.csh may need to
be modified if simply running the binary directly will not work.
In general, the machine is specified in icepack.setup
with --mach
and the environment (compiler) is specified with --env
. mach and env
in combination define the compiler, compiler version, supporting libaries,
and batch information. Multiple compilation environments can be created for
a single machine by choosing unique env names.
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, update as needed
cd .. to configuration/scripts/
Edit the icepack.batch.csh script to add a section for your machine with batch settings and job launch settings
Edit the icepack.launch.csh script to add a section for your machine if executing the binary directly is not supported
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. Machine variables¶
There are several machine specific variables defined in the env.$[machine]. These variables are used to generate working cases for a given machine, compiler, and batch system. Some variables are optional.
variable |
format |
description |
---|---|---|
ICE_MACHINE_MACHNAME |
string |
machine name |
ICE_MACHINE_MACHINFO |
string |
machine information |
ICE_MACHINE_ENVNAME |
string |
env/compiler name |
ICE_MACHINE_ENVINFO |
string |
env/compiler information |
ICE_MACHINE_MAKE |
string |
make command |
ICE_MACHINE_WKDIR |
string |
root work directory |
ICE_MACHINE_INPUTDATA |
string |
root input data directory |
ICE_MACHINE_BASELINE |
string |
root regression baseline directory |
ICE_MACHINE_SUBMIT |
string |
batch job submission command |
ICE_MACHINE_TPNODE |
integer |
machine maximum MPI tasks per node |
ICE_MACHINE_ACCT |
string |
batch default account |
ICE_MACHINE_QUEUE |
string |
batch default queue |
ICE_MACHINE_BLDTHRDS |
integer |
number of threads used during build |
ICE_MACHINE_QSTAT |
string |
batch job status command (optional) |
ICE_MACHINE_QUIETMODE |
true/false |
flag to reduce build output (optional) |
3.2.2.2. 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
3.2.2.3. 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 precedence is icepack.setup command line option,
.cice_proj setting, and then value in the env.[machine] file.
3.2.2.4. 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 precedence is icepack.setup command line option,
.cice_queue setting, and then value in the env.[machine] file.
3.2.3. Porting to Laptop or Personal Computers¶
To get the required software necessary to build and run Icepack, a conda environment file is available at :
configuration/scripts/machines/environment.yml
.
This configuration is supported by the Consortium on a best-effort basis on macOS and GNU/Linux. It is untested under Windows, but might work using the Windows Subsystem for Linux.
Once you have installed Miniconda and created the icepack
conda environment by following the procedures in this section, Icepack should run on your machine without having to go through the formal Porting process outlined above.
3.2.3.1. Installing Miniconda¶
We recommend the use of the Miniconda distribution to create a self-contained conda environment from the environment.yml
file.
This process has to be done only once.
If you do not have Miniconda or Anaconda installed, you can install Miniconda by following the official instructions, or with these steps:
On macOS:
# Download the Miniconda installer to ~/Downloads/miniconda.sh
curl -L https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -o ~/Downloads/miniconda.sh
# Install Miniconda
bash ~/Downloads/miniconda.sh
# Follow the prompts
# Close and reopen your shell
On GNU/Linux:
# Download the Miniconda installer to ~/miniconda.sh
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh
# Install Miniconda
bash ~/miniconda.sh
# Follow the prompts
# Close and reopen your shell
Note: on some Linux distributions (including Ubuntu and its derivatives), the csh shell that comes with the system is not compatible with conda. You will need to install the tcsh shell (which is backwards compatible with csh), and configure your system to use tcsh as csh:
# Install tcsh
sudo apt-get install tcsh
# Configure your system to use tcsh as csh
sudo update-alternatives --set csh /bin/tcsh
3.2.3.2. Initializing your shell for use with conda¶
We recommend initializing your default shell to use conda. This process has to be done only once.
The Miniconda installer should ask you if you want to do that as part of the installation procedure. If you did not answer “yes”, you can use one of the following procedures depending on your default shell. Bash should be your default shell if you are on macOS (10.14 and older) or GNU/Linux.
Note: answering “yes” during the Miniconda installation procedure will only initialize the Bash shell for use with conda.
If your Mac has macOS 10.15 or higher, your default shell is Zsh.
These instructions make sure that the conda
command is available when you start your shell by modifying your shell’s startup file.
Also, they make sure not to activate the “base” conda environment when you start your shell.
This conda environment is created during the Miniconda installation but is not used for Icepack.
For Bash:
# Install miniconda as indicated above, then initialize your shell to use conda:
source $HOME/miniconda3/bin/activate
conda init bash
# Don't activate the "base" conda environment on shell startup
conda config --set auto_activate_base false
# Close and reopen your shell
For Zsh (Z shell):
# Initialize Zsh to use conda
source $HOME/miniconda3/bin/activate
conda init zsh
# Don't activate the "base" conda environment on shell startup
conda config --set auto_activate_base false
# Close and reopen your shell
For tcsh:
# Install miniconda as indicated above, then initialize your shell to use conda:
source $HOME/miniconda3/etc/profile.d/conda.csh
conda init tcsh
# Don't activate the "base" conda environment on shell startup
conda config --set auto_activate_base false
# Close and reopen your shell
For fish:
# Install miniconda as indicated above, then initialize your shell to use conda:
source $HOME/miniconda3/etc/fish/conf.d/conda.fish
conda init fish
# Don't activate the "base" conda environment on shell startup
conda config --set auto_activate_base false
# Close and reopen your shell
For xonsh:
# Install miniconda as indicated above, then initialize your shell to use conda:
source-bash $HOME/miniconda3/bin/activate
conda init xonsh
# Don't activate the "base" conda environment on shell startup
conda config --set auto_activate_base false
# Close and reopen your shell
3.2.3.3. Initializing your shell for conda manually¶
If you prefer not to modify your shell startup files, you will need to run the appropriate source
command below (depending on your default shell) before using any conda command, and before compiling and running Icepack.
These instructions make sure the conda
command is available for the duration of your shell session.
For Bash and Zsh:
# Initialize your shell session to use conda:
source $HOME/miniconda3/bin/activate
For tcsh:
# Initialize your shell session to use conda:
source $HOME/miniconda3/etc/profile.d/conda.csh
For fish:
# Initialize your shell session to use conda:
source $HOME/miniconda3/etc/fish/conf.d/conda.fish
For xonsh:
# Initialize your shell session to use conda:
source-bash $HOME/miniconda3/bin/activate
3.2.3.4. Creating Icepack directories and the conda environment¶
The conda configuration expects some directories and files to be present at $HOME/icepack-dirs
:
cd $HOME
mkdir -p icepack-dirs/runs icepack-dirs/baseline icepack-dirs/input
# Download the required forcing from https://github.com/CICE-Consortium/Icepack/wiki/Icepack-Input-Data
# and untar it at $HOME/icepack-dirs/input
This step needs to be done only once.
If you prefer that some or all of the Icepack directories be located somewhere else, you can create a symlink from your home to another location:
# Create the Icepack directories at your preferred location
cd ${somewhere}
mkdir -p icepack-dirs/runs icepack-dirs/baseline icepack-dirs/input
# Download the required forcing from https://github.com/CICE-Consortium/Icepack/wiki/Icepack-Input-Data
# and untar it at icepack-dirs/input
# Create a symlink to icepack-dirs in your $HOME
cd $HOME
ln -s ${somewhere}/icepack-dirs icepack-dirs
Note: if you wish, you can also create a complete machine port for your computer by leveraging the conda configuration as a starting point. See Porting.
Next, create the “icepack” conda environment from the environment.yml
file in the Icepack source code repository. You will need to clone Icepack to run the following command:
conda env create -f configuration/scripts/machines/environment.yml
This step needs to be done only once. If you ever need to update the conda environment because the required packages change or packages are out of date, do
conda env update -f configuration/scripts/machines/environment.yml
3.2.3.5. Using the conda configuration¶
Follow the general instructions in Overview, using the conda
machine name and macos
or linux
as compiler names.
On macOS:
./icepack.setup -m conda -e macos -c ~/icepack-dirs/cases/case1
cd ~/icepack-dirs/cases/case1
./icepack.build
./icepack.run
On GNU/Linux:
./icepack.setup -m conda -e linux -c ~/icepack-dirs/cases/case1
cd ~/icepack-dirs/cases/case1
./icepack.build
./icepack.run
A few notes about the conda configuration:
This configuration always runs the model interactively, such that
./icepack.run
and./icepack.submit
are the same.You should not update the packages in the
icepack
conda environment, nor install additional packages.It is not recommeded to run other test suites than
quick_suite
ortravis_suite
on a personal computer.The conda environment is automatically activated when compiling or running the model using the
./icepack.build
and./icepack.run
scripts in the case directory. These scripts source the fileenv.conda_{linux.macos}
, which callsconda activate icepack
.The environment also contains the Sphinx package necessesary to build the HTML documentation. For this use case you must manually activate the environment:
cd doc conda activate icepack make html # Open build/html/index.html in your browser conda deactivate # to deactivate the environment
3.2.4. 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) [59] 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
Norwegian Young Sea Ice cruise (N-ICE)
Atmospheric, oceanic, and biogeochemical forcing are available from the 2015 Norwegian Young Sea Ice Cruise (N-ICE) [11]. 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 [11] 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 [9]. 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 [19]. 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.Ice Station Polarstern (ISPOL)
Atmospheric, oceanic, and biogeochemical forcing are available from the 2004 Ice Station Polarstern (ISPOL) [28]. 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 [28] 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 [28] derived from a POP 1-degree (gx1v3 simulation) [9]. 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 [19]. 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.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:
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 [45]
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 [36]. Icepack’s boundary layer calculation is used to derive sensible and latent heat fluxes. The snowfall follows the idealized specification used by [61] . 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.
3.2.5. Horizontal ice advection¶
When Icepack is run in standalone mode with a dynamical forcing (e.g., ocn_data_type = SHEBA
),
closing implies the lateral flux of ice or open water area into the grid cell. The default assumption
(in the namelist, lateral_flux_type = 'uniform_ice'
) is that the active grid cell is surrounded by grid cells
with identical ice properties to the active grid cell, i.e. the ice is uniform across all of those cells, and
when the dynamical forcing is net convergence, this uniform ice is fluxed into the grid cell. Alternatively, one may
assume that the active grid cell is surrounded by open water (in the namelist lateral_flux_type = 'open_water'
), in which case closing (i.e., ice convergence) will produce open water in
the grid cell. In either case, when the forcing is net divergence, ice area and volume are removed from the grid
cell to accommodate the formation of open water implied by the net divergence.
3.2.6. 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. It’s important to note that when the
run script is submitted, the current icepack_in, icepack.settings, and env.[machine]
files are copied from the case directory into the run directory. Users should
generally not edit files in the run directory as these are overwritten when following
the standard workflow.
Build and run logs will be copied from the run directory into the case logs/ directory when complete.
3.2.7. 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.