Changes between Version 4 and Version 5 of Projects/INSPECT/ShaCoNEMO-ORCA1-ARCHER

Timestamp:

22/11/16 17:48:34 (3 years ago)

Author:

annette

Comment:

—

Projects/INSPECT/ShaCoNEMO-ORCA1-ARCHER

@@ -25 +25 @@
 * PISCES is the biogeochemical model 
 
-NEMO uses an external library to handle model output diagnostics calkled XIOS, which is documented here: 
+NEMO uses an external library to handle model output diagnostics called XIOS, which is documented here: 
 http://forge.ipsl.jussieu.fr/ioserver/wiki
 
@@ -34 +34 @@
 * XIOS-1.0 r703
 * NEMO_3.6_stable r6969
-* ShaCoNEMO r60
+* ShaCoNEMO r60  
 * ORCA1 input data set v9
 
 Note: Although XIOS-2.0 is now recommended, revision 932 which is suggested for ORCA1 gave a link-time error which was not investigated. 
+
+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. 
 
 == Code extract == 
@@ -75 +77 @@
 /work/n02/n02/annette/nemo/xios-1.0_r703
 }}}
-To build your own XIOS, see the notes [#BuildingXIOS below]. 
-
-It is advisable to build NEMO with the same key modules as the library: 
+It is advisable to build NEMO with the same key modules as the library. The above version was built with: 
 * `cce/8.4.1`
 * `cray-netcdf-hdf5parallel/4.3.3.1`
 * `cray-mpich/7.2.6`
+
+(To build your own XIOS, see the notes [#BuildingXIOS below].) 
+
+To build the NEMO code: 
 
 1. Navigate to the directory holding the build definition files: 
@@ -111 +115 @@
 qsub build_nemo.pbs
 }}}  
-A new directory O1L3P 
+ 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. 
 
 == Model run == 
 
-1.   
- Copy in the XIOS-1 XML files (by default the configuration is set up for XIOS-2): 
+Once the build has completed successfully, set up the inputs required for the model to run.
+
+1. Download the ORCA1 input data set, and untar. This needs to go on your work space on ARCHER (`/work/n02/n02/<username>/`): 
 {{{
-cd EXP00
-mv ForXIOS1/* . 
-cd ../
+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
+mkdir INPUTS_ORCA1_LIM3_PISCES_V9
+tar -xvf INPUTS_ORCA1_LIM3_PISCES_V9.tar -C INPUTS_ORCA1_LIM3_PISCES_V9
 }}}
+
+2. Go to the run directory: 
+{{{
+cd NEMOGCM_3.6_r6969/CONFIG/O1L3P/EXP00
+}}}
+ NEMO expects the input data in its working directory, so create symlinks: 
+{{{
+ln -s <path-to-data>/INPUTS_ORCA1_LIM3_PISCES_V9/* . 
+}}}
+
+3. In the same directory, copy in the XIOS-1 XML files (by default the configuration is set up for XIOS-2): 
+{{{
+mv ../../ORCA1_LIM3_PISCES/EXP00/ForXIOS1/* . 
+}}}
+
+4. Make namelist changes: 
+{{{
+
+}}}
+
+5. Copy over to work filesystem 
+
+6. Submit run. 
+
+
+
 
 == Working practices ==