Changes between Version 4 and Version 5 of Projects/INSPECT/ShaCoNEMO-ORCA1-ARCHER
- Timestamp:
- 22/11/16 17:48:34 (4 years ago)
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Projects/INSPECT/ShaCoNEMO-ORCA1-ARCHER
v4 v5 25 25 * PISCES is the biogeochemical model 26 26 27 NEMO uses an external library to handle model output diagnostics cal kled XIOS, which is documented here:27 NEMO uses an external library to handle model output diagnostics called XIOS, which is documented here: 28 28 http://forge.ipsl.jussieu.fr/ioserver/wiki 29 29 … … 34 34 * XIOS-1.0 r703 35 35 * NEMO_3.6_stable r6969 36 * ShaCoNEMO r60 36 * ShaCoNEMO r60 37 37 * ORCA1 input data set v9 38 38 39 39 Note: Although XIOS-2.0 is now recommended, revision 932 which is suggested for ORCA1 gave a link-time error which was not investigated. 40 41 Note: This is based on the latest version of ShaCoNEMO as of October 2016, and the recommended version of NEMO for this. Both are under active development, so you may wish to use newer versions as they become available. 40 42 41 43 == Code extract == … … 75 77 /work/n02/n02/annette/nemo/xios-1.0_r703 76 78 }}} 77 To build your own XIOS, see the notes [#BuildingXIOS below]. 78 79 It is advisable to build NEMO with the same key modules as the library: 79 It is advisable to build NEMO with the same key modules as the library. The above version was built with: 80 80 * `cce/8.4.1` 81 81 * `cray-netcdf-hdf5parallel/4.3.3.1` 82 82 * `cray-mpich/7.2.6` 83 84 (To build your own XIOS, see the notes [#BuildingXIOS below].) 85 86 To build the NEMO code: 83 87 84 88 1. Navigate to the directory holding the build definition files: … … 111 115 qsub build_nemo.pbs 112 116 }}} 113 A new directory O1L3P117 This creates a new directory under `CONFIG/` called `O1L3P`. This differentiates between changes made to the original configuration. `O1L3P` will contain the executable plus namelists to be read in by the model. 114 118 115 119 == Model run == 116 120 117 1. 118 Copy in the XIOS-1 XML files (by default the configuration is set up for XIOS-2): 121 Once the build has completed successfully, set up the inputs required for the model to run. 122 123 1. Download the ORCA1 input data set, and untar. This needs to go on your work space on ARCHER (`/work/n02/n02/<username>/`): 119 124 {{{ 120 cd EXP00 121 m v ForXIOS1/* .122 cd ../ 125 wget http://prodn.idris.fr/thredds/catalog/ipsl_public/romr006/SHACONEMO/eORCA1/catalog.html?dataset=DatasetScanipsl_public/romr006/SHACONEMO/eORCA1/INPUTS_ORCA1_LIM3_PISCES_V9.tar 126 mkdir INPUTS_ORCA1_LIM3_PISCES_V9 127 tar -xvf INPUTS_ORCA1_LIM3_PISCES_V9.tar -C INPUTS_ORCA1_LIM3_PISCES_V9 123 128 }}} 129 130 2. Go to the run directory: 131 {{{ 132 cd NEMOGCM_3.6_r6969/CONFIG/O1L3P/EXP00 133 }}} 134 NEMO expects the input data in its working directory, so create symlinks: 135 {{{ 136 ln -s <path-to-data>/INPUTS_ORCA1_LIM3_PISCES_V9/* . 137 }}} 138 139 3. In the same directory, copy in the XIOS-1 XML files (by default the configuration is set up for XIOS-2): 140 {{{ 141 mv ../../ORCA1_LIM3_PISCES/EXP00/ForXIOS1/* . 142 }}} 143 144 4. Make namelist changes: 145 {{{ 146 147 }}} 148 149 5. Copy over to work filesystem 150 151 6. Submit run. 152 153 154 124 155 125 156 == Working practices ==