Essential components


The NEMO source code is written in Fortran 2008 and some of its prerequisite tools and libraries are already included in the download.
It contains the AGRIF mesh refinement library; the FCM build system ; the PPR polynomial reconstruction library and the IOIPSL library for parts of the output.

System prerequisites

The following should be provided natively by your system, if not, they need to be installed from the official repositories:

  • You need a Unix-like machine (e.g. Linux Distributions, MacOS)

  • subversion (svn) for version control of XIOS sources

  • git for version control of NEMO sources

  • Perl interpreter

  • Fortran compiler (ifort, gfortran, pgfortran, ftn, …),

  • Message Passing Interface (MPI) implementation (e.g. OpenMPI or MPICH).

  • Network Common Data Form (NetCDF) library with its underlying Hierarchical Data Form (HDF)


By default, NEMO requires MPI-3. However, it is possible to circumnavigate this by using the following work-arounds:
  • Activate the key_mpi2 preprocessor key at compile time. This will allow you to run the model using MPI-2, but keep in mind that you will lose some performance benefits.

  • Activate the key_mpi_off preprocessor key at compile time. This will allow you to run the model only on a single process (no MPI parallelization) and you will not be able to use XIOS.

Specifics for NetCDF and HDF

In order to take full advantage of the XIOS IO-server (one_file option; i.e. combines all of your output into one file), HDF (C library) and NetCDF (C and Fortran libraries) must be compiled with MPI support. To do this:

  • You need to compile these libraries with the same version of the MPI implementation that both NEMO and XIOS will be compiled and linked with (see below).

  • When compiling the HDF library, you need to use the --enable-parallel option when calling configure:

    $ ./configure --enable-parallel ...


For XIOS you need to use NetCDF-4. NetCDF-3 can still be used in NEMO if you do not wish to use XIOS.


The output created by XIOS are NetCDF-4 and not NetCDF4-classic, and are therefore incompatible with NetCDF-3 software. In order to handle any XIOS output, you need a software which is compatible with true NetCDF-4 files (e.g. ncview, Matlab, Python). If you would like to use other software (which is not compatible with NetCDF-4), then you can convert your XIOS output into NetCDF4-classic format by using the following command:
$ cdo -f nc4c copy infile outfile


$ ncks -7 infile outfile

Install XIOS library

With the sole exception of running NEMO without MPI (in which case output options are limited to the default minimum), diagnostic outputs from NEMO are handled by the third party XIOS library.

For more details, refer the to section on configuring XIOS outputs below.

Instructions on how to install XIOS can be found on its wiki.


Prior to NEMO version 4.2.0 it was recommended to use XIOS 2.5 release. However, versions 4.2.0 and beyond utilise some newer features of XIOS2 and users will need to upgrade to the trunk version of XIOS2. Note 4.2.1 does support the use of XIOS3 by activating “key_xios3” (in this case you cannot use the tiling capability).

XIOS2 trunk can be checked out with:

$ svn co

If you find problems at this stage, support can be found by subscribing to the XIOS mailing list and sending a mail message to it.

Download and install the NEMO code

Checkout the NEMO source

There are several ways to obtain the NEMO source code. Users who are not familiar with git and simply want a fixed code to compile and run, can download a tarball from the 4.2.1 release site

Users who are familiar with git and likely to use it to manage their own local branches and modifications, can clone the repository at the release tag:

git clone --branch 4.2.1 nemo_4.2.1

Experienced developers who may wish to experiment with other branches or code more recent than the release (perhaps with a view to returning developements to the system), can clone the main repository and then switch to the tagged release:

git clone
cd nemo
git switch --detach 4.2.1

Description of main NEMO directories


Compilation settings


Reference configurations


Dependencies included (AGRIF, FCM, PPR & IOIPSL)


Compilation scripts


NEMO codebase


Test cases


Utilities to {pre,post}process data


SETTE a code testing framework

Setup your architecture configuration file

All compiler options in NEMO are controlled using files in ./arch/arch-'my_arch'.fcm where my_arch is the name you use to refer to your computing environment.


You can use to automatically setup your arch file.
cd arch

If you want further help on how to use this functionality: ./ -h

The will create an arch file called arch-auto.fcm

Alternatively, you can copy, rename and edit a configuration file from an architecture similar to your own. You will need to set appropriate values for all of the variables in the file. In particular the variables: %NCDF_HOME; %HDF5_HOME and %XIOS_HOME should be set to the installation directories used for XIOS installation. For example:

%NCDF_HOME    /usr/local/path/to/netcdf
%HDF5_HOME    /usr/local/path/to/hdf5
%XIOS_HOME    /home/$( whoami )/path/to/xios-trunk
%OASIS_HOME   /home/$( whoami )/path/to/oasis

Preparing an experiment

Create and compile a new configuration

The main script to {re}compile and create an executable is called makenemo, it is located at the root of the working copy. It is used to identify the routines you need from the source code, to build the makefile and run it. As an example, compile a MY_GYRE configuration from GYRE, which can be found in the cfgs directory (more information on GYRE can be found in the NEMO Reference Manual). The following example uses the ‘auto’ arch file (if you used the automatic build):

./makenemo -h # This is for help
./makenemo –m 'auto' –r GYRE -n 'MY_GYRE'

Then at the end of the configuration compilation, the MY_GYRE directory will have the following structure.




BuiLD folder: target executable, libraries, preprocessed routines, …


Run folder: link to executable, namelists, *.xml and IOs


Files under version control only for official configurations


Your new routines or your modified copies of NEMO sources


Links to all fortran routines that you will compile.

After successful execution of makenemo command, the executable called nemo is available in the EXP00 directory

Viewing and changing list of active CPP keys

A CPP key is used to activate/disactivate certain parts of the code at the pre-compilation stage.

For a given configuration located in the cfgs directory (here called MY_CONFIG), the list of active CPP keys can be found in ./cfgs/'MYCONFIG'/cpp_MY_CONFIG.fcm

This text file can be edited by hand or with makenemo to change the list of active CPP keys. Once changed, one needs to recompile nemo in order for this change to be taken into account. Note that most NEMO configurations will need to specify the following CPP keys: key_xios for IOs. MPI parallelism is activated by default. Use key_mpi_off to compile without MPI.

./makenemo –m 'auto' -r 'MY_CONFIG' add_key 'key_mykey1 key_mykey2' del_key 'key_notwanted'

Configure XIOS outputs

XIOS allows for an efficient management of diagnostic outputs. This page gives a basic introduction to using XIOS with NEMO. Additional information are available at the XIOS wiki and in the NEMO reference manual.

Use of XIOS for NEMO IOs is activated using the pre-compiler key key_xios.

XIOS is controlled by means of XML input files that should be copied to your model run directory before running the model. Examples of these files can be found in the reference configurations’ subdirectories (./cfgs). The XIOS executable expects to find a file called iodef.xml in the model run directory. To improve readability, NEMO has the following ‘include’ statements in the iodef.xml file:

  • field_def_nemo-oce.xml (potential output variable definition for physics)

  • field_def_nemo-ice.xml (potential output variable definition for ice)

  • field_def_nemo-pisces.xml (potential output variable definition for biogeochemistry)

  • domain_def.xml and axis_def.xml (horizontal and vertical grid information)

All these files are available in the ./cfgs/SHARED directory.


Most users will not modify the above xml files unless they want to add new diagnostics to the NEMO code.
The user, instead, defines the selection of output files that is of interest to them in file_def_nemo-oce/ice/pisces.xml files.

XIOS can be used along with NEMO in two different modes:

Detached Mode

In detached mode the XIOS executable is executed on separate cores from the NEMO model. This is the recommended method for using XIOS for realistic model runs. To use this mode set using_server to true at the bottom of the iodef.xml file:

<variable id="using_server" type="boolean">true</variable>

Make sure there is a copy (or link to) your XIOS executable in the working directory and in your job submission script allocate processors to XIOS.

Attached Mode

In attached mode XIOS runs on each of the cores used by NEMO. This method is less efficient than the detached mode but can be more convenient for testing or with small configurations. To activate this mode simply set using_server to false in the iodef.xml file


For both of these options, you can activate the option for “one_file” or “multiple_file” mode. For the former, output is collected and collated to directly produce one single file for your domain. For the latter option, you will have as many output files as your number of NEMO processes (if in attached) or XIOS processes (if in detatched).

More makenemo options

makenemo has several other options that can control which source files are selected and the operation of the build process itself.

Output of makenemo -h
./makenemo -[aru] CONFIG -m ARCH [-[dehjntv] ...] [{list_key,clean,clean_config}]
                                                  [{add_key,del_key} ...]

   -m    Computing architecture (./arch), FCM file describing the compilation settings

   and one of the following option (use 'all' arg to list available items)

   -r    Reference configuration (./cfgs), proven with long-term support
   -a    Academic test case (./tests), ready-to-use configuration with no support over time
   -u    Scripted remote configuration (see ./tests/rmt_cfgs.txt)

   -d    New set of sub-components (subfolders from ./src directory)
   -e    Path for alter patch  location (default: 'MY_SRC' in configuration folder)
   -h    Print this help
   -j    Number of processes to compile (0: dry run with no build)
   -n    Name for new configuration
   -s    Path for alter source location (default: 'src' root directory)
   -t    Path for alter build  location (default: 'BLD' in configuration folder)
   -v    Level of verbosity ([0-3])

   ¤ Configuration creation
        Build          : ./makenemo         -[aru] ... [...]
        Copy           : ./makenemo -n ...  -[aru] ... [...]
   ¤ Configuration management
        List CPP keys  : ./makenemo -n ... list_key
        Add-Remove keys: ./makenemo -n ... add_key '...' del_key '...'
        Fresh start    : ./makenemo -n ... clean
        Removal        : ./makenemo -n ... clean_config

These options can be useful for maintaining several code versions with only minor differences but they should be used sparingly. Note however the -j option which should be used more routinely to speed up the build process. For example:

./makenemo –m 'my_arch' –r GYRE -n 'MY_GYRE' -j 8

will compile with up to 8 processes simultaneously.

Default behaviour

The first time you call makenemo, you need the -m option to specify the architecture configuration file (compiler and its options, routines and libraries to include), then for next compilation, it is assumed that you will be using the same compiler.

Tools used during the process

The various bash scripts used by makenemo (for instance, to create the WORK directory) are located in the mk subdirectory. In most cases, there should be no need for user intervention with these scripts. Occasionally, incomplete builds can leave the environment in a indeterminate state. If problems are experienced with subsequent attempts then try running:

./makenemo –m 'my_arch' –r 'MY_GYRE' clean

will prepare the directories for a fresh attempt and remove any intermediate files that may be causing issues.

The reference configurations that may be provided to the -r argument of makenemo are listed in the cfgs/ref_cfgs.txt file:


User added configurations will be listed in cfgs/work_cfgs.txt

Running the model

Once makenemo has run successfully, a symbolic link to the nemo executable is available in ./cfgs/MY_CONFIG/EXP00. For the reference configurations, the EXP00 folder also contains the initial input files (namelists, *.xml files for the IOs, …). If the configuration needs other input files, they have to be placed here.

mpirun -n $NPROCS ./nemo   # $NPROCS is the number of processes
                           # mpirun is your MPI wrapper