= Install the modelling framework (NEMO and XIOS)

Last edition: '''[[Wikinfo(changed_ts)]]''' by '''[[Wikinfo(changed_by)]]'''

[[PageOutline(2-3)]]




== 1. Extract the NEMO code

Using your `my_login` /pw registered on this web site:
{{{#!sh
svn --username "mylogin" co http://forge.ipsl.jussieu.fr/nemo/svn/branches/2015/nemo_v3_6_STABLE/NEMOGCM
}}}

== 2. Extract and install XIOS

Diagnostic outputs from NEMO are handled by the third party XIOS library. Instructions on how to obtain and install the softward see [[ModelInterfacing/InputsOutputs]].

When you compile NEMO you will need to specify the following cpp keys:
   * key_iomput
   * key_mpp_mpi (if you want to use "detached mode")
   * key_xios2 if you wish to use XIOS2 in nemo_v3_6_STABLE. XIOS2 is the only version available in the trunk.


== 3. Setup your ARCH file

All compiler options in NEMO are controlled using files in NEMOGCM/ARCH/arch-my_arch_name.fcm where ''my_arch_name'' is the name of your architecture. It is recommended to modify an ARCH file from an architecture similar to your own architecture. You will need to set appropriate values for all of the variables in the file. the variables %NCDF_HOME, %HDF5_HOME and %XIOS_HOME should be set to the installation directories used above.

== 4. Compile and create NEMO executable

The main script to compile and create executable is called `makenemo` and located in the `CONFIG` directory. To identify the source code you need, to build the makefile and run it.[[BR]]
As an example, compile `GYRE`, with ifort on linux to create a `MY_GYRE` configuration:
{{{#!sh
cd NEMOGCM/CONFIG; ./makenemo –m my_arch_name –r GYRE -n MY_GYRE
}}}

=== More options

* `–n` [CONFIG]: for configuration name, existant or new config to install
* `–m` [COMPILER]: compiler choice (use files names in `NEMOGCM/ARCH`, see examples below)
* `–h`: help
* `–r` [REFCONFIG]: reference configuration as first guess when installing a new one
* `–j`[num]: number of processes to compile (`-j 0`:no compilation)
* `–d` [DIR]: NEMO subdirectory (not needed)
* `–t` [DIR]: temporary directory to store libraries
* `-clean` [CONFIG_NAME] : remove the Makefile and all the files created afterwards

At the first use, you need the `-m` option to specify compiler, its options and libraries, then for next compilation, it is assumed you will be using the same compiler.[[BR]]
If `–n` option is not specified, `ORCA2_LIM` is the default configuration used. `-d` option has been implemented for use in non-interactive shell. The `WORK` directory is created under each configuration directory.

=== Tools used during the process

* `functions.sh` : bash functions used by `makenemo`, for instance to create the `WORK` directory
* `cfg.txt` : text list of configurations and source directories
* `bld.cfg` : FCM rules to compile

=== Description of directories

* `ARCH` : compilation option files, with format `arch_compiler.fcm`, the compiler name has to be provided with `–m` option
* `CONFIG` : all configurations and a `cpp.fcm` file containing the list of CPP keys to each configuration
* `EXTERNAL` : package to implement an embbeded model (AGRIF)
* `NEMO` : source codes
* `SETTE` : package to make tests to ensure the reproducibility and restartability of the code after user changes
* `TOOLS` : useful softwares to different utilities. For example a tool under MPP_PREP computes the number of water processors for all possible decompositions (up to a maximum number of processors). 

=== Examples

Compiling `GYRE`, with ifort on linux to create a `MY_GYRE` configuration
{{{#!sh
makenemo –m ifort_linux –r GYRE -n MY_GYRE
}}}

Recompile it[[BR]]
{{{#!sh
makenemo
}}}

Now, create and compile `ORCA_LIM3`
{{{#!sh
makenemo –n ORCA_LIM3 (and answer)
}}}

Now ORCA_LIM3_v2 based on the previous one
{{{#!sh
makenemo –n ORCA_LIM3_v2 -r ORCA_LIM3
}}}

Now, create and compile ORCA2_LIM_2_2, add (`add_key`) and delete (`del_key`) keys, based on `ORCA2_LIM` (just un example)
{{{#!sh
makenemo –n ORCA2_LIM_2_2 -r ORCA2_LIM del_key "key_iomput" (and answer)
}}}

To remove a bad configuration
{{{#!sh
makenemo –n ORCA2_LIM_2_2 clean_config (and answer)
}}}


== 4. Viewing and changing list of active cpp keys

For a given configuration (here called "MY_CONFIG", the list of active cpp keys can be found in 
{{{
NEMOGCM/CONFIG/"MYCONFIG"/cpp_"MY_CONFIG".fcm
}}}

This text file can be edited to change the list of active cpp keys. Once changed, one needs to recompile NEMO using the makenemo command in order for this change to be taken in account.