Description des outils et procédures utiles à la formation LMDZ

Premier draft : Frédéric Hourdin, décembre 2019

Installation testée sur une installation Ubuntu 18.04

Before anything, to avoid run commands with "sudo"

sudo bash

1. Installations automatiques par apt

To start with

apt update
apt upgrade

Base :

apt install -y csh ksh keychain ncftp vim vim-gnome xournal nfs-common  # base

apt install -y lftp
apt install -y synaptic gdebi                            # install paquets
apt install -y xfig grads imagemagick gv grace           # graphique
apt install -y texlive-base texlive-latex-extra texlive-lang-french latexdiff  texlive-publishers  #LaTeX
apt isntall -y latexmk texlive-science
apt install -y latex2html
apt install -y texlive-extra-utils texlive-font-utils # pdfjam

apt install -y inkscape gimp                             # dessin
apt install -y unoconv # conversion associee a libreoffice
apt install -y qpdfview # un visualiseur remplissant mieux les pdf
apt install -y traceroute # aide systeme

# Pour compilation dont LMDZ [[BR]]
apt install -y cdo nco netcdf-bin libnetcdf-dev ncview   # netcdf
apt install -y gfortran g++ libblas-dev subversion git   # fortran et svn
apt install -y openmpi-common libopenmpi-dev openmpi-bin # openmpi
apt install -y gifsicle
apt install -y ekiga                                        # conf renater

sudo snap install pdftk # Autre package de concatenation de pdf
apt install -y dos2unix

2. Workspace

solution assez desagreable pour revenir vers un environnement de travaill multi-bureau utilisable ...

Other suggestions to be tested : use cinnamon, the window manager of the mint

See :

https://linuxconfig.org/how-to-install-gnome-shell-extensions-on-ubuntu-18-04-bionic-beaver-linux

sudo apt install gnome-tweak-tool
sudo apt install gnome-shell-extensions
apt install chrome-gnome-shell

Installer les "workspace grid" depuis un navigateur en suivant les informations sur

https://addons.mozilla.org/en-US/firefox/addon/gnome-shell-integration/

go to

 https://extensions.gnome.org

search for Gnome extensions you wish to install. For us : "Workspace Grid" Flip the ON switch to install the extension

3. Disable automatic rotation of the w orkspace

Problème Ubuntu sur les portables enseignement : l'orientation du bureau change quand on tourne l'ordinateur.

https://askubuntu.com/questions/1035209/how-to-turn-off-screen-rotation-in-ubuntu-18-04-lts 

Try this command to stop and disable

sudo systemctl stop iio-sensor-proxy.service
sudo systemctl disable iio-sensor-proxy.service

To completely remove :

sudo apt-get remove iio-sensor-proxy

Pour inverser le défilement verticale du pavé tactile (pour sortir du mode "portable")

Preferences > Périphériques > Pavé tactile => Désactiver défilement naturel

4. python

Not as root nor su

wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
chmod +x ./Miniconda3-latest-Linux-x86_64.sh
./Miniconda3-latest-Linux-x86_64.sh

On a new window to reinitiate the environment

conda install netcdf4 h5py jinja2 pip sqlalchemy basemap matplotlib numpy scipy
conda create --name python2 python=2.7
conda create --name python3 python=3.7

Jupyter notebooks

sudo apt install -y python3-notebook jupyter jupyter-core python-ipykernel  

Environnement : ajouter à la fin de .bashrc, pour éviter d'avoir python toujours actif

conda deactivate 

python se réactive alors avec

conda activate

ou

conda activate python2

5. ferret install from ferret

#​https://github.com/NOAA-PMEL/PyFerret/blob/master/README.md

conda create -n FERRET -c conda-forge pyferret ferret_datasets --yes

Pour passer en mode pyferret :

conda activate FERRET

6. acroread

Installation acrobat reader fournie par
​https://linuxconfig.org/how-to-install-adobe-acrobat-reader-on-ubuntu-18-04-bionic-beaver-linux

sudo  apt install -y libxml2:i386 gdebi-core
wget ftp://ftp.adobe.com/pub/adobe/reader/unix/9.x/9.5.5/enu/AdbeRdr9.5.5-1_i386linux_enu.deb
sudo gdebi AdbeRdr9.5.5-1_i386linux_enu.deb

7. rstudio, for tuning tools

sudo apt install r-base
wget https://download1.rstudio.org/desktop/bionic/amd64/rstudio-1.2.5001-amd64.deb
sudo gdebi rstudio-1.2.5001-amd64.deb

sudo apt install -y r-cran-rgl libx11-dev libglu1-mesa-dev libfreetype6-dev

install.packages(c("ncdf4","rstan","tensor","Hmisc","lhs","fields","rgl","shape","mco","far","DiceKriging","GenSA","mvtnorm","loo"))