1 | ******************* |
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2 | Build the framework |
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3 | ******************* |
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4 | |
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5 | .. contents:: |
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6 | :local: |
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7 | |
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8 | Prerequisites |
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9 | ============= |
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10 | |
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11 | | The NEMO source code is written in *Fortran 95* and |
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12 | some of its prerequisite tools and libraries are already included in the download. |
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13 | | It contains the AGRIF_ preprocessing program ``conv``; the FCM_ build system and |
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14 | the IOIPSL_ library for parts of the output. |
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15 | |
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16 | System dependencies |
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17 | ------------------- |
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18 | |
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19 | In the first place the other requirements should be provided natively by your system or |
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20 | can be installed from the official repositories of your Unix-like distribution: |
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21 | |
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22 | - *Perl* interpreter |
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23 | - *Fortran* compiler (``ifort``, ``gfortran``, ``pgfortran``, ...), |
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24 | - *Message Passing Interface (MPI)* implementation (e.g. |OpenMPI|_ or |MPICH|_). |
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25 | - |NetCDF|_ library with its underlying |HDF|_ |
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26 | |
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27 | **NEMO, by default, takes advantage of some MPI features introduced into the MPI-3 standard.** |
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28 | |
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29 | .. hint:: |
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30 | |
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31 | The MPI implementation is not strictly essential |
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32 | since it is possible to compile and run NEMO on a single processor. |
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33 | However most realistic configurations will require the parallel capabilities of NEMO and |
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34 | these use the MPI standard. |
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35 | |
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36 | .. note:: |
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37 | |
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38 | On older systems, that do not support MPI-3 features, |
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39 | the ``key_mpi2`` preprocessor key should be used at compile time. |
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40 | This will limit MPI features to those defined within the MPI-2 standard |
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41 | (but will lose some performance benefits). |
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42 | |
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43 | .. |OpenMPI| replace:: *OpenMPI* |
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44 | .. _OpenMPI: https://www.open-mpi.org |
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45 | .. |MPICH| replace:: *MPICH* |
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46 | .. _MPICH: https://www.mpich.org |
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47 | .. |NetCDF| replace:: *Network Common Data Form (NetCDF)* |
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48 | .. _NetCDF: https://www.unidata.ucar.edu |
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49 | .. |HDF| replace:: *Hierarchical Data Form (HDF)* |
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50 | .. _HDF: https://www.hdfgroup.org |
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51 | |
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52 | Specifics for NetCDF and HDF |
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53 | ---------------------------- |
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54 | |
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55 | NetCDF and HDF versions from official repositories may have not been compiled with MPI support. |
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56 | However access to all the options available with the XIOS IO-server will require |
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57 | the parallelism of these libraries. |
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58 | |
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59 | | **To satisfy these requirements, it is common to have to compile from source |
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60 | in this order HDF (C library) then NetCDF (C and Fortran libraries)** |
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61 | | It is also necessary to compile these libraries with the same version of the MPI implementation that |
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62 | both NEMO and XIOS (see below) have been compiled and linked with. |
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63 | |
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64 | .. hint:: |
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65 | |
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66 | | It is difficult to define the options for the compilation as |
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67 | they differ from one architecture to another according to |
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68 | the hardware used and the software installed. |
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69 | | The following is provided without any warranty |
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70 | |
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71 | .. code-block:: console |
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72 | |
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73 | $ ./configure [--{enable-fortran,disable-shared,enable-parallel}] ... |
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74 | |
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75 | It is recommended to build the tests ``--enable-parallel-tests`` and run them with ``make check`` |
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76 | |
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77 | Particular versions of these libraries may have their own restrictions. |
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78 | State the following requirements for netCDF-4 support: |
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79 | |
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80 | .. caution:: |
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81 | |
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82 | | When building NetCDF-C library versions older than 4.4.1, use only HDF5 1.8.x versions. |
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83 | | Combining older NetCDF-C versions with newer HDF5 1.10 versions will create superblock 3 files |
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84 | that are not readable by lots of older software. |
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85 | |
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86 | Extract and install XIOS |
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87 | ======================== |
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88 | |
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89 | With the sole exception of running NEMO in mono-processor mode |
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90 | (in which case output options are limited to those supported by the ``IOIPSL`` library), |
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91 | diagnostic outputs from NEMO are handled by the third party ``XIOS`` library. |
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92 | It can be used in two different modes: |
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93 | |
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94 | :*attached*: Every NEMO process also acts as a XIOS server |
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95 | :*detached*: Every NEMO process runs as a XIOS client. |
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96 | Output is collected and collated by external, stand-alone XIOS server processors. |
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97 | |
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98 | Instructions on how to install XIOS can be found on its :xios:`wiki<>`. |
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99 | |
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100 | .. hint:: |
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101 | |
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102 | It is recommended to use XIOS 2.5 release. |
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103 | This version should be more stable (in terms of future code changes) than the XIOS trunk. |
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104 | It is also the one used by the NEMO system team when testing all developments and new releases. |
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105 | |
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106 | This particular version has its own branch and can be checked out with: |
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107 | |
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108 | .. code:: console |
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109 | |
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110 | $ svn co https://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5 |
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111 | |
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112 | Download and install the NEMO code |
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113 | ================================== |
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114 | |
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115 | Checkout the NEMO sources |
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116 | ------------------------- |
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117 | |
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118 | .. code:: console |
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119 | |
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120 | $ svn co https://forge.ipsl.jussieu.fr/nemo/svn/NEMO/trunk |
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121 | |
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122 | Description of 1\ :sup:`st` level tree structure |
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123 | ------------------------------------------------ |
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124 | |
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125 | +-----------+----------------------------------------+ |
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126 | | ``arch`` | Compilation settings | |
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127 | +-----------+----------------------------------------+ |
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128 | | ``cfgs`` | :doc:`Reference configurations <cfgs>` | |
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129 | +-----------+----------------------------------------+ |
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130 | | ``doc`` | :doc:`Documentation <doc>` | |
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131 | +-----------+----------------------------------------+ |
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132 | | ``ext`` | Dependencies included | |
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133 | | | (``AGRIF``, ``FCM`` & ``IOIPSL``) | |
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134 | +-----------+----------------------------------------+ |
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135 | | ``mk`` | Compilation scripts | |
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136 | +-----------+----------------------------------------+ |
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137 | | ``src`` | :doc:`Modelling routines <src>` | |
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138 | +-----------+----------------------------------------+ |
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139 | | ``tests`` | :doc:`Test cases <tests>` | |
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140 | | | (unsupported) | |
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141 | +-----------+----------------------------------------+ |
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142 | | ``tools`` | :doc:`Utilities <tools>` | |
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143 | | | to {pre,post}process data | |
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144 | +-----------+----------------------------------------+ |
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145 | |
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146 | Setup your architecture configuration file |
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147 | ------------------------------------------ |
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148 | |
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149 | All compiler options in NEMO are controlled using files in :file:`./arch/arch-'my_arch'.fcm` where |
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150 | ``my_arch`` is the name of the computing architecture |
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151 | (generally following the pattern ``HPCC-compiler`` or ``OS-compiler``). |
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152 | It is recommended to copy and rename an configuration file from an architecture similar to your owns. |
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153 | You will need to set appropriate values for all of the variables in the file. |
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154 | In particular the FCM variables: |
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155 | ``%NCDF_HOME``; ``%HDF5_HOME`` and ``%XIOS_HOME`` should be set to |
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156 | the installation directories used for XIOS installation |
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157 | |
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158 | .. code-block:: sh |
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159 | |
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160 | %NCDF_HOME /usr/local/path/to/netcdf |
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161 | %HDF5_HOME /usr/local/path/to/hdf5 |
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162 | %XIOS_HOME /home/$( whoami )/path/to/xios-2.5 |
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163 | %OASIS_HOME /home/$( whoami )/path/to/oasis |
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164 | |
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165 | Create and compile a new configuration |
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166 | ====================================== |
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167 | |
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168 | The main script to {re}compile and create executable is called ``makenemo`` located at |
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169 | the root of the working copy. |
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170 | It is used to identify the routines you need from the source code, to build the makefile and run it. |
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171 | As an example, compile a :file:`MY_GYRE` configuration from GYRE with 'my_arch': |
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172 | |
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173 | .. code-block:: sh |
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174 | |
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175 | ./makenemo –m 'my_arch' –r GYRE -n 'MY_GYRE' |
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176 | |
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177 | Then at the end of the configuration compilation, |
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178 | :file:`MY_GYRE` directory will have the following structure. |
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179 | |
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180 | +------------+----------------------------------------------------------------------------+ |
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181 | | Directory | Purpose | |
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182 | +============+============================================================================+ |
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183 | | ``BLD`` | BuiLD folder: target executable, headers, libs, preprocessed routines, ... | |
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184 | +------------+----------------------------------------------------------------------------+ |
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185 | | ``EXP00`` | Run folder: link to executable, namelists, ``*.xml`` and IOs | |
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186 | +------------+----------------------------------------------------------------------------+ |
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187 | | ``EXPREF`` | Files under version control only for :doc:`official configurations <cfgs>` | |
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188 | +------------+----------------------------------------------------------------------------+ |
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189 | | ``MY_SRC`` | New routines or modified copies of NEMO sources | |
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190 | +------------+----------------------------------------------------------------------------+ |
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191 | | ``WORK`` | Links to all raw routines from :file:`./src` considered | |
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192 | +------------+----------------------------------------------------------------------------+ |
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193 | |
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194 | After successful execution of ``makenemo`` command, |
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195 | the executable called `nemo` is available in the :file:`EXP00` directory |
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196 | |
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197 | More ``makenemo`` options |
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198 | ------------------------- |
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199 | |
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200 | ``makenemo`` has several other options that can control which source files are selected and |
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201 | the operation of the build process itself. |
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202 | |
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203 | .. literalinclude:: ../../../makenemo |
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204 | :language: text |
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205 | :lines: 119-143 |
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206 | :caption: Output of ``makenemo -h`` |
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207 | |
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208 | These options can be useful for maintaining several code versions with only minor differences but |
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209 | they should be used sparingly. |
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210 | Note however the ``-j`` option which should be used more routinely to speed up the build process. |
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211 | For example: |
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212 | |
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213 | .. code-block:: sh |
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214 | |
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215 | ./makenemo –m 'my_arch' –r GYRE -n 'MY_GYRE' -j 8 |
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216 | |
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217 | will compile up to 8 processes simultaneously. |
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218 | |
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219 | Default behaviour |
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220 | ----------------- |
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221 | |
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222 | At the first use, |
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223 | you need the ``-m`` option to specify the architecture configuration file |
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224 | (compiler and its options, routines and libraries to include), |
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225 | then for next compilation, it is assumed you will be using the same compiler. |
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226 | If the ``-n`` option is not specified the last compiled configuration will be used. |
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227 | |
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228 | Tools used during the process |
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229 | ----------------------------- |
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230 | |
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231 | * ``functions.sh`` : bash functions used by ``makenemo``, for instance to create the WORK directory |
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232 | * ``cfg.txt`` : text list of configurations and source directories |
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233 | * ``bld.cfg`` : FCM rules to compile |
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234 | |
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235 | Examples |
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236 | -------- |
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237 | |
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238 | .. literalinclude:: ../../../makenemo |
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239 | :language: text |
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240 | :lines: 146-153 |
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241 | |
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242 | Running the model |
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243 | ================= |
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244 | |
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245 | Once ``makenemo`` has run successfully, |
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246 | the ``nemo`` executable is available in ``./cfgs/MY_CONFIG/EXP00``. |
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247 | For the reference configurations, the ``EXP00`` folder also contains the initial input files |
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248 | (namelists, ``*.xml`` files for the IOs, ...). |
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249 | If the configuration needs other input files, they have to be placed here. |
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250 | |
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251 | .. code-block:: sh |
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252 | |
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253 | cd 'MY_CONFIG'/EXP00 |
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254 | mpirun -n $NPROCS ./nemo # $NPROCS is the number of processes |
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255 | # mpirun is your MPI wrapper |
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256 | |
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257 | Viewing and changing list of active CPP keys |
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258 | ============================================ |
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259 | |
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260 | For a given configuration (here called ``MY_CONFIG``), |
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261 | the list of active CPP keys can be found in :file:`./cfgs/'MYCONFIG'/cpp_MY_CONFIG.fcm` |
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262 | |
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263 | This text file can be edited by hand or with ``makenemo`` to change the list of active CPP keys. |
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264 | Once changed, one needs to recompile ``nemo`` in order for this change to be taken in account. |
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265 | Note that most NEMO configurations will need to specify the following CPP keys: |
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266 | ``key_iomput`` for IOs and ``key_mpp_mpi`` for parallelism. |
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