Update 'README.md'

README.md

@@ -7,55 +7,44 @@ The goal of this project is to adapt this model for our needs in TECLIM: install
 
 **YOU MUST HAVE YOUR `~/.ssh/id_rsa.pub` FILE BEFORE STARTING TO WORK WITH GIT ON ZENOBE**.
 
-```
-mv $HOME/.ssh/config $HOME/.ssh/config_old
-cat config | sed -e 's/pbarriat/'$USER'/g' > $HOME/.ssh/config
-
-[ ! -f ~/.ssh/id_rsa.pub ] && ssh-keygen -t rsa
-ssh-copy-id -i ~/.ssh/id_rsa.pub gwceci.cism.ucl.ac.be
-```
-
 ## Install
 
 First, clone the `pbarriat/ecearth_patch` repository:
 ```bash
-mkdir ~/modeles
-cd ~/modeles
-mkdir ecearth
-git clone ssh://regit/pbarriat/ecearth_patch.git
+mkdir -p ~/modeles/ecearth
+cd ~/modeles/ecearth
+git clone ssh://git@www.climate.be:3022/pbarriat/ecearth_patch.git
 ```
 
 Now, update your shell startup script (`~/.bashrc`) to add ecearth globals variables to your environment. 
 
-For instance **on Zenobe**, you need to add:
+### Zenobe
+
 ```bash
 configure_ecearth()
 {
-  if [ `hostname` != "frontal1" ]; then
-    echo "First, we move to frontal1..."
-    touch ~/.configure_ecearth
-    ssh frontal1
-  fi
   export EC_DEP=/projects/acad/ecearth/opt
   if [ -f $EC_DEP/modules.load ]; then
     source $EC_DEP/modules.load
   fi
-  [[ -f ~/.configure_ecearth ]] && rm ~/.configure_ecearth
 }
-if [ `hostname` = "frontal1" ]; then
-  [[ -f ~/.configure_ecearth ]] && configure_ecearth
-fi
-if [ `hostname` = "frontal3" ]; then
-  PATH="/projects/acad/ecearth/opt/apps/lua/lua/bin:$PATH"
-  . /projects/acad/ecearth/opt/lmod/lmod/init/profile
-  ulimit -u 8192
-  export OMP_NUM_THREADS=2
-fi
 ```
 
+### Lemaitre3
+
+```bash
+configure_ecearth()
+{
+  module purge
+  module load 2016a netCDF-Fortran/4.4.4-intel-2016a grib_api/1.16.0-intel-2016a openjpeg/1.5.2-intel-2016a
+}
+```
+
+### Source code
+
 Then, checkout the EC-Earth SVN repository. Four alternatives:
 ```bash
-cd ecearth
+cd ~/modeles/ecearth
 
 svn co https://svn.ec-earth.org/ecearth3/tags/3.2.2 ecearth_3.2.2
 
@@ -66,24 +55,25 @@ svn co https://svn.ec-earth.org/ecearth3/branches/projects/primavera ecearth_pri
 svn co https://svn.ec-earth.org/ecearth3/trunk ecearth_trunk
 ```
 
-Final step, go to the `pbarriat/ecearth_patch` repository and run the `install.sh` script:
+Final step, go to the `ecearth_patch` repository and run the `install.sh` script:
 ```
-cd ecearth_patch
+cd ~/modeles/ecearth/ecearth_patch
 ./install.sh
 ```
 
 ## Compile
 
-### Lemaitre3
+**YOU MUST COMPILE ON frontal1 for ZENOBE (ssh frontal1 from zenobe)**
 
-* Go to `ecearth sources` and create all the Makefile's with lemaitre3 configuration:
+* Go to `ecearth sources` and create all the Makefile's with corresponding configuration:
 
 ```bash
-cd ecearth_3.2.2/sources
-./util/ec-conf/ec-conf -p lemaitre3-intelmpi config-build.xml
+TAG=3.2.2
+CONF=lemaitre3
 
-module purge
-module load 2016a netCDF-Fortran/4.4.4-intel-2016a grib_api/1.16.0-intel-2016a openjpeg/1.5.2-intel-2016a
+configure_ecearth
+cd ~/modeles/ecearth/ecearth_$TAG/sources
+./util/ec-conf/ec-conf -p $CONF-intelmpi config-build.xml
 ```
 
 * Compile **oasis3**:
@@ -148,75 +138,13 @@ sed -i 's/ORCA025/ORCA1/g' src/namelist_mpp
 cd ../..
 ```
 
-### Zenobe
-
-First, **sign out of Zenobe** and sign in again. Then, type `configure_ecearth`.
-
-Compile the model:
-
-1. Go to `~/modeles/ecearth_$tag/sources` and:
-```
-./util/ec-conf/ec-conf -p zenobe-intelmpi config-build.xml
-```
-2. Go to `./oasis3-mct/util/make_dir` and:
-```
-make BUILD_ARCH=ecconf -f TopMakefileOasis3
-```
-3. Go to `./ifs-36r4` and:
-```
-./makeifs -j 4
-```
-4. Go to `./xios-2` and:
-```
-./make_xios --prod --arch ecconf --use_oasis oasis3_mct --netcdf_lib netcdf4_par -j 4
-```
-5. Go to `./nemo-3.6/CONFIG` and:
-```
-./makenemo -n ORCA1L75_LIM3 -m ecconf -j4
-```
-6. Go to `./runoff-mapper/src` and:
-```
-make
-```
-
-Primavera context:
-
-7. Go to `./amip-forcing/src` and:
-```
-make
-```
-8. Go to `./util/ELPiN` and:
-
-```bash
-cd util/ELPiN
-mkdir bathymetries
-ln -s /scratch/ucl/elic/pbarriat/DATA/EC-EARTH/nemo/initial/ORCA1L75/bathy_meter.nc bathymetries/nemo_bathy_meter_ORCA1.nc
-ln -s /scratch/ucl/elic/pbarriat/DATA/EC-EARTH/nemo/initial/ORCA1L75/bathy_meter.nc bathymetries/nemo_bathy_meter_ORCA1.nc
-sed -i 's/ORCA025/ORCA1/g' src/namelist_mpp
-./Configure
-cd ../
-
 ## Run
 
-### Lemaitre3
-
 ```bash
-cd ../runtime/classic
-../../sources/util/ec-conf/ec-conf -p lemaitre3 config-run.xml
+cd ~/modeles/ecearth/ecearth_$TAG/runtime/classic
+../../sources/util/ec-conf/ec-conf -p $CONF config-run.xml
 vi ece-ifs+nemo.sh
-sbatch ece-ifs+nemo.sh
-```
-
-### Zenobe
-
-For a quick classical run test:
-- Go to `~/modeles/ecearth_$tag/runtime/classic` and:
-```
-../../sources/util/ec-conf/ec-conf -p zenobe config-run.xml
-```
-- Submit the script `ece-ifs+nemo.sh` to the PBS batch system:
-```
-qsub ece-ifs+nemo.sh
+sbatch (or qsub) ece-ifs+nemo.sh
 ```
 
 ## Benchmarks
@@ -235,12 +163,13 @@ qsub ece-ifs+nemo.sh
 | ---- | ---- | --- | ------ | -------------- | ------ |
 | 1    |  64  |  78 |    1   |      **5h**    |   144  |
 | 22   |  72  | 288 |    1   |    **3h15**    |   384  |
+| 1    |  86  | 320 |    1   |    **2h47**    |   408  |
 | 22   | 144  | 432 |    1   |                |   600  |
 
 ## Contributors
 
-- ELIC members [@pbarriat](http://www.climate.be:3000/pbarriat)
+- ELIC members [@pbarriat](https://gogs.elic.ucl.ac.be/pbarriat)
 
 ## License
 
-This project is under the Creative Commons CC0 1.0 Universal License. See the [LICENSE](http://www.climate.be:3000/TECLIM/LOVECLIM/src/master/LICENSE) file for the full license text.
+This project is under the Creative Commons CC0 1.0 Universal License. See the [LICENSE](https://gogs.elic.ucl.ac.be/TECLIM/LOVECLIM/src/master/LICENSE) file for the full license text.