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Configurations/TATL025BIO.md
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* [Examples of output fields](#tatl025bio-description-examples-of-output-fields) * [Examples of output fields](#tatl025bio-description-examples-of-output-fields)
* [Download Instructions](#tatl025bio-download-instructions) * [Download Instructions](#tatl025bio-download-instructions)
* [Prerequisites](#tatl025bio-download-instructions-prerequisites) * [Prerequisites](#tatl025bio-download-instructions-prerequisites)
* [NEMO_CFGS directory](#tatl025bio-download-instructions-nemo_cfgs-directory) * [NEMO_CONFIGS directory](#tatl025bio-download-instructions-nemo_configs-directory)
* [Tools repos](#tatl025bio-download-instructions-tools-repos) * [NEMO_TOOLS repos](#tatl025bio-download-instructions-nemo-tools-repos)
<a name="tatl025bio-description"></a> <a name="tatl025bio-description"></a>
...@@ -32,7 +32,7 @@ The reference version of this configuration uses the basic PISCES modules refere ...@@ -32,7 +32,7 @@ The reference version of this configuration uses the basic PISCES modules refere
#### Experience study #### Experience study
| Configurations | Name | Model | Res. | Lat<br>Lon</br> | ix<br>iy</br><br>iz</br> | Type | Tests on | Cluster | Cpus<br>/model</br> | Time elapse<br>/yr</br> | | Configurations | Name | Model | Res. | Lat<br>Lon</br> | ix<br>iy</br><br>iz</br> | Type | Duration Tests | Cluster | Cpus<br>/model</br> | Time elapse<br>/yr</br> |
|:-:|:-:|:-:|:-:|:-:|:-:|:-:|:-:|:-:|:-:|:-:| |:-:|:-:|:-:|:-:|:-:|:-:|:-:|:-:|:-:|:-:|:-:|
| TATL025BIO (P4Z) | Tropical Atlantic | NEMO4.0.1 (rev.11837)<br>PISCESv2 (P4Z)</br><br>XIOS2.5 (rev.1646)</br> | 0.25° | [-34,05;34,46N]<br>[-99;20E]</br> | 477<br>293</br><br>75</br> | Forced | 1993 <br>to 1997</br> | Irene (TGCC-cea) | 138<br>6</br> | 4h00 | TATL025BIO (P4Z) | Tropical Atlantic | NEMO4.0.1 (rev.11837)<br>PISCESv2 (P4Z)</br><br>XIOS2.5 (rev.1646)</br> | 0.25° | [-34,05;34,46N]<br>[-99;20E]</br> | 477<br>293</br><br>75</br> | Forced | 1993 <br>to 1997</br> | Irene (TGCC-cea) | 138<br>6</br> | 4h00
| TATL025BIO (P5Z) | ✓ | NEMO4.0.1 (rev.11837)<br>PISCESv2 (P5Z)</br><br>XIOS2.5 (rev.1646)</br> | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | 5h30 | TATL025BIO (P5Z) | ✓ | NEMO4.0.1 (rev.11837)<br>PISCESv2 (P5Z)</br><br>XIOS2.5 (rev.1646)</br> | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | 5h30
...@@ -82,7 +82,7 @@ flow relaxation scheme (rimwidth = 4 / Because of instability at the gulf stream ...@@ -82,7 +82,7 @@ flow relaxation scheme (rimwidth = 4 / Because of instability at the gulf stream
| Boundary Condition | Mercator GLORYS2V4 | T,S, UV2d, UV_3d daily interanual | 4 layers relaxation scheme | Boundary Condition | Mercator GLORYS2V4 | T,S, UV2d, UV_3d daily interanual | 4 layers relaxation scheme
| Atmo | Reanalysis Drakkar Forcing Set (DFS5.2) (mix ERA5 ERAinterim and correction) | UV10(3h) / (TQ)2(3h) / rad(sw/lw) (24h) / precip/snow/spl (24h) interanual | - | | Atmo | Reanalysis Drakkar Forcing Set (DFS5.2) (mix ERA5 ERAinterim and correction) | UV10(3h) / (TQ)2(3h) / rad(sw/lw) (24h) / precip/snow/spl (24h) interanual | - |
| Runoff | ISBA-CTRIP land surface model | Runoff daily interanual | - | | Runoff | ISBA-CTRIP land surface model | Runoff daily interanual | - |
| Flux solaire | RGB + Seawiffs | CHL clim monthly | - | | Solar flux | RGB + Seawiffs | CHL clim monthly | - |
<a name="tatl025bio-description-bio"></a> <a name="tatl025bio-description-bio"></a>
...@@ -115,75 +115,68 @@ flow relaxation scheme (rimwidth = 4 / Because of instability at the gulf stream ...@@ -115,75 +115,68 @@ flow relaxation scheme (rimwidth = 4 / Because of instability at the gulf stream
======================== ========================
#### Prerequisites #### Prerequisites
- Define your path (as user want), hereafter, we assume your current directory:
```console ```console
WRKDIR=$(pwd) WRKDIR=$(pwd)
``` ```
The git clone command needs your username you use for log into gitlab - The git clone command needs your username you are using to log into gitlab
<a name="tatl025bio-download-instructions-nemo_cfgs-directory"></a> <a name="tatl025bio-download-instructions-nemo_configs-directory"></a>
======================== ========================
#### NEMO_CFGS directory #### Creation of your NEMO_CONFIGS directory
###### NEMOREF repos ###### NEMOREF repos
- Download official nemo repository:
``` ```
cd $WRKDIR
mkdir -p NEMOREF mkdir -p NEMOREF
cd ${WRKDIR}/NEMOREF cd ${WRKDIR}/NEMOREF
#svn co -r11837 https://forge.ipsl.jussieu.fr/nemo/svn/NEMO/releases/release-4.0.1 dev_r11837_config_legos git clone https://username@git.outils-is.ird.fr/legos_atnum/repos/nemoref.git dev_r11837_config_legos
git clone https://username@git.outils-is.ird.fr/legos_atnum/repos2/nemoref.git dev_r11837_config_legos
cd $WRKDIR/NEMOREF/dev_r11837_config_legos cd $WRKDIR/NEMOREF/dev_r11837_config_legos
git checkout dev_r11837_config_nemo_legos git checkout dev_r11837_config_nemo_legos
``` ```
###### NEMOSRC repos (legos) ###### NEMOSRC repository (legos)
-> lister les tags depots distants - Listing of tags or configurations on remote repos:
```console ```console
git ls-remote --tag https://username@git.outils-is.ird.fr/legos_atnum/repos2/nemo_cfgs.git git ls-remote --tag https://username@git.outils-is.ird.fr/legos_atnum/repos/nemo_configs.git
``` ```
- Download legos repos:
```console ```console
cd $WRKDIR/ cd $WRKDIR/
git clone https://username@git.outils-is.ird.fr/legos_atnum/repos2/nemo_cfgs.git NEMO_CFGS git clone https://username@git.outils-is.ird.fr/legos_atnum/repos/nemo_configs.git NEMO_CFGS
``` ```
-> lister tags dispo: - Listing of tags available locally:
```console ```console
cd $WRKDIR/NEMO_CFGS/ cd $WRKDIR/NEMO_CFGS/
git tag git tag
``` ```
> **Note:** > **Note:**
TAG = TATL025BIO_P4Z et TATL025BIO_P5Z du dépôt associée à la révision 11837 du dépot officiel NEMO TAG = TATL025BIO_P4Z et TATL025BIO_P5Z associated with official nemo repository (revision 11837)
-> creation of branches, as user want - Switch for Configurations as user want:
```console ```console
git checkout -b TATLBIOp4z TATL025BIO_P4Z git checkout -b TATLBIOp4z TATL025BIO_P4Z
#git checkout -b TATLBIOp5z TATL025BIO_P5Z #git checkout -b TATLBIOp5z TATL025BIO_P5Z
git branch
``` ```
<a name="tatl025bio-download-instructions-nemo-tools-repos"></a>
Then create new nemo directories...:
```
mkdir -p ${WRKDIR}/NEMO_CFGS/setup/TATL025BIO/
mv -f ${WRKDIR}/NEMO_CFGS/setup/* ${WRKDIR}/NEMO_CFGS/setup/TATL025BIO/. 2> /dev/null
rsync -av ${WRKDIR}/NEMO_CFGS/models/NEMO/* ${WRKDIR}/NEMOREF/dev_r11837_config_legos/.
rm -rf ${WRKDIR}/NEMO_CFGS/models/NEMO/*
mv ${WRKDIR}/NEMOREF/dev_r11837_config_legos/ ${WRKDIR}/NEMO_CFGS/models/NEMO/.
```
<a name="tatl025bio-download-instructions-tools-repos"></a>
======================== ========================
#### Tools repos #### NEMO TOOLS repos
```console ```console
cd $WRKDIR/ cd $WRKDIR/
git clone https://username@git.outils-is.ird.fr/legos_atnum/repos2/tools.git TOOLS git clone https://username@git.outils-is.ird.fr/legos_atnum/repos/nemo_tools.git NEMO_TOOLS
cd $WRKDIR/TOOLS cd $WRKDIR/NEMO_TOOLS
git checkout dev_r11837_config_nemo_legos git checkout dev_r11837_config_nemo_legos
``` ```
...@@ -191,25 +184,22 @@ git checkout dev_r11837_config_nemo_legos ...@@ -191,25 +184,22 @@ git checkout dev_r11837_config_nemo_legos
#### Preparation Environment #### Preparation Environment
```console ```console
set -a cd $WRKDIR/NEMO_TOOLS/preprocessing/setup_environment/
[ "$WRKDIR" == "" ] && WRKDIR=$(pwd) chmod 750 setup_directories.sh
. ${WRKDIR}/NEMO_CFGS/setup/TATL025BIO/conf/includefile.ini ./setup_directories.sh TATL025BIO 11837
set +a
chmod 750 -Rf ${WRKDIR}/NEMO_CFGS/setup/TATL025BIO/script/*ksh
chmod 750 -Rf ${WRKDIR}/TOOLS/preprocessing/*
``` ```
then go to [setup models](https://git.outils-is.ird.fr/legos_atnum/repos2/nemo_cfgs/wikis/setup_nemo#setup-models)
#### Module Cluster Irene #### Loaded Modules for Cluster Irene
```console ```console
module purge # (Better to do it) module purge # (Better to do it)
module load mpi/openmpi/2.0.4.14 netcdf-fortran/4.4.4 hdf5/1.8.20 python/2.7.14 nco/4.6.0 module load mpi/openmpi/2.0.4.14 netcdf-fortran/4.4.4 hdf5/1.8.20 python/2.7.14 nco/4.6.0
``` ```
then go to [setup models](https://git.outils-is.ird.fr/legos_atnum/repos/nemo_configs/wikis/setup_nemo#setup-models) ...
## Articles,references ## Articles,references
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