source: NEMO/trunk/INSTALL.rst @ 10557

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1*********************
2Install the framework
3*********************
4
5.. contents::
6   :local:
7     
8Prerequisites
9=============
10
11- The NEMO source code is written in Fortran 95 and some of its prerequisite
12  tools and libraries are already included in the (``./ext``) subdirectory. These
13  include: the AGRIF preprocessing program "conv"; the FCM build system and the
14  IOIPSL library for parts of the output.
15|
16- Other requirements that your system needs to provide include: a Perl 5 interpreter; a modern
17  Fortran compiler (ifort, gfortran, pgfortran, ...) and (in most cases) a MPI library
18  (e.g. OpenMPI or MPICH). The latter is not strictly essential since it is possible
19  to compile and run NEMO on a single processor. However most realistic configurations
20  will require the parallel capabilities of NEMO and these use the Message Passing
21  Interface (MPI) library. NEMO v4.0, by default, uses some MPI features introduced
22  into the MPI-3 standard. On older systems, that do not support these features,
23  the key_mpi2 preprocessor key should be used at compile time. This will limit MPI
24  features to those defined within the MPI-2 standard (but will lose some performance
25  benefits).
26|
27The following prerequisites may already be installed or be available from the
28official repositories of your Linux distribution. However access to all the
29options available with the XIOS IO-server will require the parallel form of the
30netcdf4 library and its underlying HDF5 library. It is also necessary to compile
31these libraries with the same version of the MPI library that both NEMO and XIOS
32(see below) are compiled and linked with. To satisfy these requirements, it is common
33to have to compile the following from source.
34
35- `HDF5`_   (C library) (use: --enable-fortran --enable-parallel with configure)
36- `NetCDF4`_ (C and Fortran libraries)
37
38Note that particular versions of these libraries may have their own
39restrictions. For example, the latest versions of the netCDF libraries:
40netcdf-c-4.6.2 and netcdf-fortran-4.4.4, state the following requirements for netCDF-4 support:
41
42* HDF5 1.8.9 or later.
43* HDF5 1.10.1 or later.
44* zlib 1.2.5 or later (for netCDF-4 compression)
45* curl 7.18.0 or later (for DAP remote access client support)
46
47|
48`Important Note: When building netCDF-C library versions older than 4.4.1,
49use only HDF5 1.8.x versions. Combining older netCDF-C versions with newer
50HDF5 1.10 versions will create superblock 3 files that are not readable by
51lots of older software.`
52
53Extract and install XIOS
54========================
55
56With the sole exception of running NEMO in mono-processor mode (in which case
57output options are limited to those supported by the IOIPSL library), diagnostic
58outputs from NEMO are handled by the third party XIOS library. This can be used
59in two different modes:
60
61* attached - Every NEMO process also acts as a XIOS server
62* dettached - Every NEMO process runs as a XIOS client. Output is collected and collated by external,
63  stand-alone XIOS server processors.
64
65In either case, it is important to note that XIOS needs to be compiled before
66NEMO, since the libraries are needed to successfully create the NEMO executable.
67
68Instructions on how to obtain and install the software can be found on the `XIOS Wiki`_ .
69
70It is recommended to use XIOS version 2.5 with NEMOv4.0. This version should be more stable (in terms of
71future code changes) than the XIOS trunk. It is also the version used by the NEMO system team when
72testing all developments and new releases. This particular version has its own branch and can be
73checked out and downloaded with:
74
75.. code:: console
76
77        $ svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5
78
79Download the NEMO source code
80=============================
81
82.. code:: console
83
84   $ svn co http://forge.ipsl.jussieu.fr/nemo/svn/NEMO/releases/release-4.0
85
86Description of directory tree
87-----------------------------
88
89+-----------+------------------------------------------------------------+
90| Folder    | Purpose                                                    |
91+===========+============================================================+
92| ``arch``  | Settings (per architecture-compiler pair)                  |
93+-----------+------------------------------------------------------------+
94| ``cfgs``  | :doc:`Reference configurations <configurations>`           |
95+-----------+------------------------------------------------------------+
96| ``doc``   | - ``latex``: reference manuals for |OPA|, |SI3| & |TOP|    |
97|           | - ``namelists``: k start guide                             |
98|           | - ``rst``:   quick start guide                             |
99+-----------+------------------------------------------------------------+
100| ``ext``   | Dependencies included (AGRIF, FCM & IOIPSL)                |
101+-----------+------------------------------------------------------------+
102| ``mk``    | Building  routines                                         |
103+-----------+------------------------------------------------------------+
104| ``src``   | Modelling routines                                         |
105|           |                                                            |
106|           | - ``ICE``: |SI3| for sea ice                               |
107|           | - ``NST``: AGRIF for embedded zooms                        |
108|           | - ``OCE``: |OPA| for ocean dynamics                        |
109|           | - ``TOP``: |TOP| for tracers                               |
110+-----------+------------------------------------------------------------+
111| ``tests`` | :doc:`Test cases <test_cases>` (unsupported)               |
112+-----------+------------------------------------------------------------+
113| ``tools`` | :doc:`Utilities <tools>` to [pre|post]process data         |
114+-----------+------------------------------------------------------------+
115
116Setup your architecture configuration file
117==========================================
118
119All compiler options in NEMO are controlled using files in
120NEMOGCM/ARCH/arch-'my_arch'.fcm where 'my_arch' is the name of the computing
121architecture.  It is recommended to copy and rename an configuration file from
122an architecture similar to your owns. You will need to set appropriate values
123for all of the variables in the file. In particular the FCM variables:
124``%NCDF_HOME``; ``%HDF5_HOME`` and ``%XIOS_HOME`` should be set to the
125installation directories used for XIOS installation.
126
127.. code-block:: sh
128
129        %NCDF_HOME           /opt/local
130        %HDF5_HOME           /opt/local
131        %XIOS_HOME           /Users/$( whoami )/xios-2.5
132        %OASIS_HOME          /not/defined
133
134Compile and create NEMO executable
135==================================
136
137The main script to compile and create executable is called makenemo and located in the CONFIG directory, it is used to identify the routines you need from the source code, to build the makefile and run it.
138As an example, compile GYRE with 'my_arch' to create a 'MY_GYRE' configuration:
139
140.. code-block:: sh
141
142   ./makenemo –m 'my_arch' –r GYRE -n 'MY_GYRE'
143
144The image below shows the structure and some content of "MY_CONFIG" directory from the launching of the configuration creation (directories and fundamental files created by makenemo).
145
146+------------+----------------------------------------------------+
147| Folder     | Purpose                                            |
148+============+====================================================+
149| ``BLD``    |                                                    |
150+------------+----------------------------------------------------+
151| ``EXP00``  |                                                    |
152+------------+----------------------------------------------------+
153| ``EXPREF`` |                                                    |
154+------------+----------------------------------------------------+
155| ``MY_SRC`` |                                                    |
156+------------+----------------------------------------------------+
157| ``WORK``   |                                                    |
158+------------+----------------------------------------------------+
159
160Folder with the symbolic links to all unpreprocessed routines considered in the configuration
161Compilation folder (executables, headers files, libraries, preprocessed routines, flags, …)
162Computation folder for running the model (namelists, xml, executables and inputs-outputs)
163Folder intended to contain your customised routines (modified from initial ones or new entire routines)
164
165When you compile NEMO you will need to specify the following CPP keys:
166
167*   key_iomput
168*   key_mpp_mpi
169
170After successful execution of makenemo command, the executable called opa is created in the EXP00 directory (in the example above, the executable is created in CONFIG/MY_GYRE/EXP00).
171More options
172
173..
174   .. literalinclude::
175
176Default behaviour
177-----------------
178
179    At the first use, 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 you will be using the same compiler.
180    If –n option is not specified, ORCA2_LIM is the default configuration used.
181
182Tools used during the process
183-----------------------------
184
185    functions.sh : bash functions used by makenemo, for instance to create the WORK directory
186    cfg.txt : text list of configurations and source directories
187    bld.cfg : FCM rules to compile
188
189Examples
190--------
191
192        echo "Example to install a new configuration MY_CONFIG";
193        echo "with OPA_SRC and LIM_SRC_2 ";
194        echo "makenemo -n MY_CONFIG -d \"OPA_SRC LIM_SRC_2\"";
195        echo "";
196        echo "Available configurations :"; cat ${CONFIG_DIR}/cfg.txt;
197        echo "";
198        echo "Available unsupported (external) configurations :"; cat ${CONFIG_DIR}/uspcfg.txt;
199        echo "";
200        echo "Example to remove bad configuration ";
201        echo "./makenemo -n MY_CONFIG clean_config";
202        echo "";
203        echo "Example to clean ";
204        echo "./makenemo clean";
205        echo "";
206        echo "Example to list the available keys of a CONFIG ";
207        echo "./makenemo list_key";
208        echo "";
209        echo "Example to add and remove keys";
210        echo "./makenemo add_key \"key_iomput key_mpp_mpi\" del_key \"key_agrif\" ";
211        echo "";
212        echo "Example to add and remove keys for a new configuration, and do not compile";
213        echo "./makenemo -n MY_CONFIG -j0 add_key \"key_iomput key_mpp_mpi\" del_key \"key_agrif\" ";
214
215Running the model
216=================
217
218Once makenemo has run successfully, the opa executable is available in ``CONFIG/MY_CONFIG/EXP00``
219For the reference configurations, the EXP00 folder also contains the initial input files (namelists, \*xml files for the IOs…). If the configuration also needs NetCDF input files, this should be downloaded here from the corresponding tar file, see Users/Reference Configurations
220
221   cd 'MY_CONFIG'/EXP00
222   mpirun -n $NPROCS ./opa    # $NPROCS is the number of processes ; mpirun is your MPI wrapper
223
224Viewing and changing list of active CPP keys
225============================================
226
227For a given configuration (here called MY_CONFIG), the list of active CPP keys can be found in::
228
229   NEMOGCM/CONFIG/'MYCONFIG'/cpp_'MY_CONFIG'.fcm
230
231This text file can be edited to change the list of active CPP keys. Once changed, one needs to recompile opa executable using makenemo command in order for this change to be taken in account.
232
233.. _HDF5:   http://www.hdfgroup.org/downloads/hdf5
234.. _NetCDF4: http://www.unidata.ucar.edu/downloads/netcdf
235.. _XIOS Wiki:    http://forge.ipsl.jussieu.fr/ioserver/wiki/documentation
236.. _XIOSSRC: http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5
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