3.2. Running CICE¶

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

3.2.1. Software Requirements¶

To run stand-alone, CICE requires

bash and csh
gmake (GNU Make)
Fortran and C compilers (Intel, PGI, GNU, Cray, NVHPC, AOCC, and NAG have been tested)
NetCDF (optional, but required to test standard configurations that have netCDF grid, input, and forcing files)
MPI (optional, but required for running on more than 1 processor)
PIO (optional, but required for running with PIO I/O interfaces)

Below are lists of software versions that the Consortium has tested at some point. There is no guarantee that all compiler versions work with all CICE model versions. At any given point, the Consortium is regularly testing on several different compilers, but not necessarily on all possible versions or combinations. CICE supports both PIO1 and PIO2. To use PIO1, the USE_PIO1 macro should also be set. A CICE goal is to be relatively portable across different hardware, compilers, and other software. As a result, the coding implementation tends to be on the conservative side at times. If there are problems porting to a particular system, please let the Consortium know.

The Consortium has tested the following compilers at some point,

AOCC 3.0.0
Intel ifort 15.0.3.187
Intel ifort 16.0.1.150
Intel ifort 17.0.1.132
Intel ifort 17.0.2.174
Intel ifort 17.0.5.239
Intel ifort 18.0.1.163
Intel ifort 18.0.5
Intel ifort 19.0.2
Intel ifort 19.0.3.199
Intel ifort 19.1.0.166
Intel ifort 19.1.1.217
Intel ifort 19.1.2.254
Intel ifort 2021.4.0
Intel ifort 2021.6.0
Intel ifort 2021.8.0
Intel ifort 2021.9.0
Intel ifort 2022.2.1
PGI 16.10.0
PGI 19.9-0
PGI 20.1-0
PGI 20.4-0
GNU 6.3.0
GNU 7.2.0
GNU 7.3.0
GNU 7.7.0
GNU 8.3.0
GNU 9.3.0
GNU 10.1.0
GNU 11.2.0
GNU 12.1.0
GNU 12.2.0
Cray CCE 8.5.8
Cray CCE 8.6.4
Cray CCE 13.0.2
Cray CCE 14.0.3
Cray CCE 15.0.1
NAG 6.2
NVC 23.5-0

The Consortium has tested the following MPI implementations and versions,

MPICH 7.3.2
MPICH 7.5.3
MPICH 7.6.2
MPICH 7.6.3
MPICH 7.7.0
MPICH 7.7.6
MPICH 7.7.7
MPICH 7.7.19
MPICH 7.7.20
MPICH 8.1.14
MPICH 8.1.21
MPICH 8.1.25
Intel MPI 18.0.1
Intel MPI 18.0.4
Intel MPI 2019 Update 6
Intel MPI 2019 Update 8
MPT 2.14
MPT 2.17
MPT 2.18
MPT 2.19
MPT 2.20
MPT 2.21
MPT 2.22
MPT 2.25
mvapich2-2.3.3
OpenMPI 1.6.5
OpenMPI 4.0.2

The NetCDF implementation is relatively general and should work with any version of NetCDF 3 or 4. The Consortium has tested

NetCDF 4.3.0
NetCDF 4.3.2
NetCDF 4.4.0
NetCDF 4.4.1.1.3
NetCDF 4.4.1.1.6
NetCDF 4.4.1.1
NetCDF 4.4.2
NetCDF 4.5.0
NetCDF 4.5.2
NetCDF 4.6.1.3
NetCDF 4.6.3
NetCDF 4.6.3.2
NetCDF 4.7.2
NetCDF 4.7.4
NetCDF 4.8.1
NetCDF 4.8.1.1
NetCDF 4.8.1.3
NetCDF 4.9.0.1
NetCDF 4.9.0.3
NetCDF 4.9.2

CICE has been tested with

PIO 1.10.1
PIO 2.5.4
PIO 2.5.9
PIO 2.6.0
PIO 2.6.1
PnetCDF 1.12.2
PnetCDF 1.12.3
PnetCDF 2.6.2

Please email the Consortium if this list can be extended.

3.2.2. Scripts¶

The CICE 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.

3.2.2.1. Overview¶

Most of the scripts that configure, build and run CICE are contained in the directory configuration/scripts/, except for cice.setup, which is in the main directory. cice.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.

cice.setup -h will provide the latest information about how to use the tool. cice.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 CICE section.

Again, cice.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 cice.setup:

cice.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 environment
cice.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
cice.build is a script that calls the Makefile and compiles the model
ice_in is the namelist input file
setup_run_dirs.csh is a script that will create the run directories. This will be called automatically from the cice.run script if the user does not invoke it.
cice.run is a batch run script
cice.submit is a simple script that submits the cice.run script

Once the case is created, all scripts and namelist are fully resolved. 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 cice.build in the list are edited, cice.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 cice.build script should be run interactively and then the case should be submitted by executing the cice.submit script interactively. The cice.submit script submits the cice.run script or cice.test script. These scripts can also be run interactively or submitted manually without the cice.submit script.

Some hints:

To change namelist, manually edit the ice_in file
To change batch settings, manually edit the top of the cice.run or cice.test (if running a test) file
When the run scripts are submitted, the current ice_in, cice.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. cice.settings can be sourced to establish the case values in the login shell.
Some useful aliases can be found in the Use of Shell Aliases section
To turn on the debug compiler flags, set ICE_BLDDEBUG in cice.setttings to true. It is also possible to use the debug option (-s debug) when creating the case with cice.setup to set this option automatically.
To change compiler options, manually edit the Macros file. To add user defined preprocessor macros, modify ICE_CPPDEFS in cice.settings using the syntax -DCICE_MACRO.
To clean the build before each compile, set ICE_CLEANBUILD in cice.settings to true (this is the default value), or use the buildclean option (-s buildclean) when creating the case with cice.setup. To not clean before the build, set ICE_CLEANBUILD in cice.settings to false, or use the buildincremental option (-s buildincremental) when creating the case with cice.setup. It is recommended that the ICE_CLEANBUILD be set to true if there are any questions about whether the build is proceeding properly.

To build and run:

./cice.build
./cice.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 cice.settings via the ICE_RUNDIR variable. To modify the case setup, changes should be made in the case directory, NOT the run directory.

3.2.2.2. cice.setup Command Line Options¶

cice.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 CICE section.

--help, -h: prints cice.setup help information to the terminal and exits.
--version: prints the CICE version to the terminal and exits.
--setvers VERSION: internally updates the CICE version in your sandbox. Those changes can then be commited (or not) to the repository. –version will show the updated value. The argument VERSION is typically a string like “5.1.2” but could be any alphanumeric string.
--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 and is paired with --env to define the compilation environment.

--env, -e ENVIRONMENT1,ENVIRONMENT2,ENVIRONMENT3 specifies 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 MxN[[xBXxBY[xMB]: 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. BX, BY, and MB can also be set via this option where BX is the x-direction blocksize, BY is the y-direction blocksize, and MB is the max-blocks setting. If BX, BY, and MB are not set, they will be computed automatically based on the grid size and the task/thread count. More specifically, this option has three modes, –pes MxN, –pes MxNxBXxBY, and –pes MxNxBXxBYxMB. (default is 4x1)
--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 CICE driver, gx1, gx3, and tx1 are supported. (default = gx3)
--set, -s SET1,SET2,SET3: specifies the optional settings for the case. 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 cice.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 cases and tests (not suites), settings defined in ~/.cice_set (if it exists) will be included in the –set options. This behaviour can be overridden with the –ignore-user-set` command line option.
--ignore-user-set: ignores settings defined in ~/.cice.set (if it exists) for cases and tests. ~/.cice_set is always ignored for test suites.

For CICE, when setting up cases, the --case and --mach must be specified. It’s also recommended that --env be set explicitly as well. --pes and --grid can be very useful. --acct and --queue are 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.

3.2.2.3. 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 cice.setup --help.

The default CICE namelist and CICE settings are specified in the files configuration/scripts/ice_in and configuration/scripts/cice.settings respectively. When picking settings (options), the set_env.setting and set_nml.setting will be used to change the defaults. This is done as part of the cice.setup and the modifications are resolved in the cice.settings and ice_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.

Settings defined in ~/.cice_set (if it exists) will be included in the --set options. This behaviour can be overridden with the –ignore-user-set` command line option. The format of the ~/.cice_set file is a identical to the --set option, a single comma-delimited line of options. Settings on the command line will take precedence over settings defined in ~/.cice_set.

Some of the options are

debug which turns on the compiler debug flags

buildclean which turns on the option to clean the build before each compile

buildincremental which turns off the option to clean the build before each compile

short, medium, long which change the batch time limit

gx3, gx1, tx1 are associate with grid specific settings

diag1 which turns on diagnostics each timestep

run10day, run1year, etc which specifies a run length

dslenderX1, droundrobin, dspacecurve, etc specify decomposition options

bgcISPOL and bgcNICE specify bgc options

boxadv, boxnodyn, and boxrestore are simple box configurations

alt* which turns on various combinations of dynamics and physics options for testing

and there are others. These may change as needed. Use cice.setup --help to see the latest. To add a new option, just add the appropriate file in configuration/scripts/options. For more information, see Test Options

3.2.2.4. Examples¶

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

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

To add some optional settings, one might do:

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

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

3.2.2.5. More about cice.build¶

cice.build is copied into the case directory and should be run interactively from the case directory to build the model. CICE is built with make and there is a generic Makefile and a machine specific Macros file in the case directory. cice.build is a wrapper for a call to make that includes several other features.

CICE is built as follows. First, the makdep binary is created by compiling a small C program. The makdep binary is then run and dependency files are created. The dependency files are included into the Makefile automatically. As a result, make dependencies do not need to be explicitly defined by the user. In the next step, make compiles the CICE code and generates the cice binary.

The standard and recommended way to run is with no arguments

cice.build

However, cice.build does support a couple other use modes.

cice.build [-h|--help]

provides a summary of the usage.

cice.build [make arguments] [target]

turns off most of the features of the cice.build script and turns it into a wrapper for the make call. The arguments and/or target are passed to make and invoked more or less like make [make arguments] [target]. This will be the case if either or both the arguments or target are passed to cice.build. Some examples of that are

cice.build --version

which will pass –version to make.

cice.build targets

is a valid target of the CICE Makefile and simply echos all the valid targets of the Makefile.

cice.build cice

or

cice.build all

are largely equivalent to running cice.build without an argument, although as noted earlier, many of the extra features of the cice.build script are turned off when calling cice.build with a target or an argument. Any of the full builds will compile makdep, generate the source code dependencies, and compile the source code.

cice.build [clean|realclean]
cice.build [db_files|db_flags]
cice.build [makdep|depends]

are other valid options for cleaning the build, writing out information about the Makefile setup, and building just the makdep tool or the dependency file. It is also possible to target a particular CICE object file.

Finally, there is one important parameter in cice.settings. The ICE_CLEANBUILD variable defines whether the model is cleaned before a build is carried out. By default, this variable is true which means each invokation of cice.build will automatically clean the prior build. If incremental builds are desired to save time during development, the ICE_CLEANBUILD setting in cice.settings should be modified.

3.2.2.6. C Preprocessor (CPP) Macros¶

There are a number of C Preprocessing Macros supported in the CICE model. These allow certain coding features like NetCDF, MPI, or specific Fortran features to be excluded or included during the compile.

The CPPs are defined by the CPPDEFS variable in the Makefile. They are defined by passing the -D[CPP] to the C and Fortran compilers (ie. -DUSE_NETCDF) and this is what needs to be set in the CPPDEFS variable. The value of ICE_CPPDEFS in cice.settings is copied into the Makefile CPPDEFS variable as are settings hardwired into the Macros.[machine]_[environment] file.

In general, -DFORTRANUNDERSCORE should always be set to support the Fortran/C interfaces in ice_shr_reprosum.c. In addition, if NetCDF is used, -DUSE_NETCDF should also be defined. A list of available CPPs can be found in Table of C Preprocessor (CPP) Macros.

3.2.3. Porting¶

There are four basic issues that need to be addressed when porting, and these are addressed in four separate files in the script system,

setup of the environment such as compilers, environment variables, and other support software (in env.[machine]_[environment])
setup of the Macros file to support the model build (in Macros.[machine]_[environment])
setup of the batch submission scripts (in cice.batch.csh)
setup of the model launch command (in cice.launch.csh)

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/cice.batch.csh and configuration/scripts/cice.launch.csh files need to be modified. In general, the machine is specified in cice.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 cice.batch.csh script to add a section for your machine with batch settings
Edit the cice.batch.csh script to add a section for your machine with 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/cice.batch.csh and configuratin/scripts/cice.launch.csh files, retest, and then add and commit the updated machine files to the repository.

3.2.3.1. 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.

*Machine Settings*¶
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_MAXPES	integer	machine maximum total processors per job (optional)
ICE_MACHINE_MAXTHREADS	integer	machine maximum threads per mpi task (optional)
ICE_MACHINE_MAXRUNLENGTH	integer	batch wall time limit in hours (optional)
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)

3.2.3.2. 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

3.2.3.3. 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 cice.setup to define the account number. The order of precedence is cice.setup command line option, .cice_proj setting, and then value in the env.[machine] file.

3.2.3.4. Machine Queue Settings¶

Supported machines will have a default queue specified by the variable ICE_MACHINE_QUEUE in the env.[machine] file. This can also be manually changed in the cice.run or cice.test scripts or even better, use the --queue option in cice.setup.

3.2.4. Porting to Laptops or Personal Computers¶

To get the required software necessary to build and run CICE, and use the plotting and quality control scripts included in the repository, 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 cice conda environment by following the procedures in this section, CICE should run on your machine without having to go through the formal Porting process outlined above.

3.2.4.1. 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 ~/miniconda.sh
curl -L https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -o ~/miniconda.sh
# Install Miniconda
bash ~/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

3.2.4.2. 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 CICE.

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

3.2.4.3. 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 CICE. 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

3.2.4.4. Creating CICE directories and the conda environment¶

The conda configuration expects some directories and files to be present at $HOME/cice-dirs:

cd $HOME
mkdir -p cice-dirs/runs cice-dirs/baseline cice-dirs/input
# Download the required forcing from https://github.com/CICE-Consortium/CICE/wiki/CICE-Input-Data
# and untar it at $HOME/cice-dirs/input

This step needs to be done only once.

If you prefer that some or all of the CICE directories be located somewhere else, you can create a symlink from your home to another location:

# Create the CICE directories at your preferred location
cd ${somewhere}
mkdir -p cice-dirs/runs cice-dirs/baseline cice-dirs/input
# Download the required forcing from https://github.com/CICE-Consortium/CICE/wiki/CICE-Input-Data
# and untar it at cice-dirs/input

# Create a symlink to cice-dirs in your $HOME
cd $HOME
ln -s ${somewhere}/cice-dirs cice-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 “cice” conda environment from the environment.yml file in the CICE source code repository. You will need to clone CICE to run the following command:

conda env create -f configuration/scripts/machines/environment.yml

This step needs to be done only once and will maintain a static conda environment. To update the conda environment later, use

conda env create -f configuration/scripts/machines/environment.yml --force

This will update the conda environment to the latest software versions.

3.2.4.5. Using the conda configuration¶

Follow the general instructions in Overview, using the conda machine name and macos or linux as compiler names.

On macOS:

./cice.setup -m conda -e macos -c ~/cice-dirs/cases/case1
cd ~/cice-dirs/cases/case1
./cice.build
./cice.run

On GNU/Linux:

./cice.setup -m conda -e linux -c ~/cice-dirs/cases/case1
cd ~/cice-dirs/cases/case1
./cice.build
./cice.run

A few notes about the conda configuration:

This configuration always runs the model interactively, such that ./cice.run and ./cice.submit are the same.
You should not update the packages in the cice conda environment, nor install additional packages.
Depending on the numbers of CPUs in your machine, you might not be able to run with the default MPI configuration (-p 4x1). You likely will get an OpenMPI error such as:

There are not enough slots available in the system to satisfy the 4 slots that were requested by the application: ./cice

You can run CICE in serial mode by specifically requesting only one process:
```
./cice.setup -m conda -e linux -p 1x1 ...
```
If you do want to run with more MPI processes than the number of available CPUs in your machine, you can add the --oversubscribe flag to the mpirun call in cice.run:
```
# For a specific case:
# Open cice.run and replace the line
mpirun -np <num> ./cice >&! $ICE_RUNLOG_FILE
# with
mpirun -np <num> --oversubscribe ./cice >&! $ICE_RUNLOG_FILE

# For all future cases:
# Open configuration/scripts/cice.launch.csh and replace the line
mpirun -np ${ntasks} ./cice >&! \$ICE_RUNLOG_FILE
# with
mpirun -np ${ntasks} --oversubscribe ./cice >&! \$ICE_RUNLOG_FILE
```
It is not recommeded to run other test suites than quick_suite or travis_suite on a personal computer.
The conda environment is automatically activated when compiling or running the model using the ./cice.build and ./cice.run scripts in the case directory. These scripts source the file env.conda_{linux.macos}, which calls conda activate cice.
To use the “cice” conda environment with the Python plotting (see Timeseries Plotting) and quality control (QC) scripts (see Code Validation Testing Procedure), you must manually activate the environment:
```
cd ~/cice-dirs/cases/case1
conda activate cice
python timeseries.py ~/cice-dirs/cases/case1/logs
conda deactivate  # to deactivate the environment
```

The environment also contains the Sphinx package necessesary to build the HTML documentation :

cd doc
conda activate cice
make html
# Open build/html/index.html in your browser
conda deactivate  # to deactivate the environment

3.2.5. 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.

CICE input datasets are stored on an anonymous ftp server. More information about how to download the input data can be found at https://github.com/CICE-Consortium/CICE/wiki/CICE-Input-Data. Test forcing datasets are available for various grids at the ftp site. 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.

3.2.6. Run Directories¶

The cice.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 cice.settings file. It’s important to note that when the run scripts are submitted, the current ice_in, cice.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.

3.2.8. Use of Shell Aliases¶

This section provides a list of some potentially useful shell aliases that leverage the CICE scripts. These are not defined by CICE and are not required for using CICE. They are provided as an example of what can be done by users. The current ice_in, cice.settings, and env.[machine] files are copied from the case directory into the run directory when the model is run. Users can create aliases leveraging the variables in these files. Aliases like the following can be established in shell startup files or otherwise at users discretion:

#!/bin/tcsh
# From a case or run directory, source the necessary environment files to run CICE
alias cice_env 'source env.*; source cice.settings'
# Go from case directory to run directory and back (see https://stackoverflow.com/a/34874698/)
alias cdrun  'set rundir=`\grep "setenv ICE_RUNDIR" cice.settings | awk "{print "\$"NF}"` && cd $rundir'
alias cdcase 'set casedir=`\grep "setenv ICE_CASEDIR" cice.settings | awk "{print "\$"NF}"` && cd $casedir'

#!/bin/bash
# From case/test directory, go to run directory
alias cdrun='cd $(cice_var ICE_RUNDIR)'
# From run directory, go to case/test directory
alias cdcase='cd $(cice_var ICE_CASEDIR)'
# monitor current cice run (from ICE_RUNDIR directory)
alias cice_tail='tail -f $(ls -1t cice.runlog.* |head -1)'
# open log from last CICE run (from ICE_CASEDIR directory)
alias cice_lastrun='$EDITOR $(ls -1t logs/cice.runlog.* |head -1)'
# open log from last CICE build (from ICE_CASEDIR directory)
alias cice_lastbuild='$EDITOR $(ls -1t logs/cice.bldlog.* |head -1)'
# show CICE run directory when run in the case directory
alias cice_rundir='cice_var ICE_RUNDIR'
# open a tcsh shell and source env.* and cice.settings (useful for launching CICE in a debugger)
alias cice_shell='tcsh -c "cice_env; tcsh"'

## Functions
# Print the value of a CICE variable ($1) from cice.settings
cice_var() {
\grep "setenv $1" cice.settings | awk "{print "\$"3}"
}

3.2.9. Timeseries Plotting¶

The CICE scripts include two scripts that will generate timeseries figures from a diagnostic output file, a Python version (timeseries.py) and a csh version (timeseries.csh). Both scripts create the same set of plots, but the Python script has more capabilities, and it’s likely that the csh script will be removed in the future.

To use the timeseries.py script, the following requirements must be met:

Python v2.7 or later
numpy Python package
matplotlib Python package
datetime Python package

See Code Validation Testing Procedure for additional information about how to setup the Python environment, but we recommend using pip as follows:

pip install --user numpy
pip install --user matplotlib
pip install --user datetime

When creating a case or test via cice.setup, the timeseries.csh and timeseries.py scripts are automatically copied to the case directory. Alternatively, the plotting scripts can be found in ./configuration/scripts, and can be run from any directory.

The Python script can be passed a directory, a specific log file, or no directory at all:

If a directory is passed, the script will look either in that directory or in directory/logs for a filename like cice.run*. As such, users can point the script to either a case directory or the logs directory directly. The script will use the file with the most recent creation time.

If a specific file is passed the script parses that file, assuming that the file matches the same form of cice.run* files.

If nothing is passed, the script will look for log files or a logs directory in the directory from where the script was run.

For example:

Run the timeseries script on the desired case.

$ python timeseries.py /p/work1/turner/CICE_RUNS/conrad_intel_smoke_col_1x1_diag1_run1year.t00/

or

$ python timeseries.py /p/work1/turner/CICE_RUNS/conrad_intel_smoke_col_1x1_diag1_run1year.t00/logs

The output figures are placed in the directory where the timeseries.py script is run.

The plotting script will plot the following variables by default, but you can also select specific plots to create via the optional command line arguments.

total ice area ($km^2$)

total ice extent ($km^2$)

total ice volume ($m^3$)

total snow volume ($m^3$)

RMS ice speed ($m/s$)

For example, to plot only total ice volume and total snow volume

$ python timeseries.py /p/work1/turner/CICE_RUNS/conrad_intel_smoke_col_1x1_diag1_run1year.t00/ --volume --snw_vol

To generate plots for all of the cases within a suite with a testid, create and run a script such as

#!/bin/csh
foreach dir (`ls -1  | grep testid`)
  echo $dir
  python timeseries.py $dir
end

Plots are only made for a single output file at a time. The ability to plot output from a series of cice.run* files is not currently possible, but may be added in the future. However, using the --bdir option will plot two datasets (from log files) on the same figure.

For the latest help information for the script, run

$ python timeseries.py -h

The timeseries.csh script works basically the same way as the Python version, however it does not include all of the capabilities present in the Python version.

To use the C-Shell version of the script,

$ ./timeseries.csh /p/work1/turner/CICE_RUNS/conrad_intel_smoke_col_1x1_diag1_run1year.t00/