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

gmake (GNU Make)
Fortran and C compilers (Intel, PGI, GNU, Cray, and NAG have been tested)
NetCDF
MPI (this is actually optional but without it you can only run on 1 processor)

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. 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,

Intel 15.0.3.187
Intel 16.0.1.150
Intel 17.0.1.132
Intel 17.0.2.174
Intel 17.0.5.239
Intel 18.0.1.163
Intel 19.0.2
Intel 19.0.3.199
PGI 16.10.0
GNU 6.3.0
GNU 7.2.0
GNU 7.3.0
Cray 8.5.8
Cray 8.6.4
NAG 6.2

The Consortium has tested the following mpi versions,

MPICH 7.3.2
MPICH 7.5.3
MPICH 7.6.2
MPICH 7.6.3
MPICH 7.7.6
Intel MPI 18.0.1
MPT 2.14
MPT 2.17
MPT 2.18
MPT 2.19
OpenMPI 1.6.5

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 4.4.1.1.32
NetCDF 4.4.1.1
NetCDF 4.4.2
NetCDF 4.5.0
NetCDF 4.6.1.3

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 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 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
cd mycase

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

env.[machine] 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] 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 simply submits the cice.run script. You can also submit the cice.run script on the command line.

Some hints:

To change the block sizes required at build time, edit the cice.settings file.
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
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 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 directory 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.
--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[[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.
--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 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 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.

3.2.2.3. 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 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

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, boxdyn, 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.

3.2.3. 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.

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 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_ENVNAME	string	machine name
ICE_MACHINE_COMPILER	string	compiler
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 precedent 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. 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. 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.

3.2.5. 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.

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

3.2.6. 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.

3.2.7. 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 Compliance 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/