Ci-dessous, les différences entre deux révisions de la page.
Les deux révisions précédentesRévision précédenteProchaine révision | Révision précédente | ||
en:documentation:tools:modules [2020/07/16 07:48] – fleroux | en:documentation:tools:modules [2023/01/12 09:49] (Version actuelle) – supprimée ltaulell | ||
---|---|---|---|
Ligne 1: | Ligne 1: | ||
- | ====== Environment Modules ====== | ||
- | |||
- | |||
- | '' | ||
- | |||
- | Each program requires an environment (see the '' | ||
- | |||
- | <note tip> | ||
- | \\ | ||
- | '' | ||
- | |||
- | To work, you have to connect, from '' | ||
- | See how [[documentation: | ||
- | </ | ||
- | ===== Modèles ===== | ||
- | |||
- | Some **examples** of initialization for PSMN users are available in the following files : | ||
- | * ''/ | ||
- | * ''/ | ||
- | * ''/ | ||
- | * ''/ | ||
- | |||
- | You can copy them, or include them in your own initialization files. | ||
- | |||
- | <code bash> | ||
- | cp / | ||
- | cp / | ||
- | cp / | ||
- | |||
- | or | ||
- | |||
- | cp / | ||
- | </ | ||
- | |||
- | Reconnect to take into account the changes. | ||
- | ===== interactive use ===== | ||
- | |||
- | |||
- | ==== Load " | ||
- | |||
- | * for bash | ||
- | |||
- | <code bash> | ||
- | source / | ||
- | </ | ||
- | |||
- | Can be added in '' | ||
- | |||
- | * for csh/tcsh | ||
- | |||
- | <code bash> | ||
- | source / | ||
- | </ | ||
- | |||
- | Can be added in '' | ||
- | |||
- | * for zsh | ||
- | |||
- | <code bash> | ||
- | source / | ||
- | </ | ||
- | |||
- | PCan be added in '' | ||
- | ==== pour tous les shell ==== | ||
- | |||
- | * see the available modules (it may take a few minutes before being displayed, it's normal !) | ||
- | |||
- | <code bash> | ||
- | # list all modules | ||
- | module avail | ||
- | |||
- | # list the modules related to OpenMPI | ||
- | module avail openmpi | ||
- | </ | ||
- | |||
- | |||
- | * module loading : | ||
- | |||
- | <code bash> | ||
- | module load < | ||
- | |||
- | # for exemple load OpenMPI 2.1.1 (compilé avec GCC 6.4.0) | ||
- | module load GCC/ | ||
- | # then load GCC 6.4.0 | ||
- | module load GCC/6.4.0 | ||
- | </ | ||
- | |||
- | * Getting help from a module | ||
- | <code bash> | ||
- | module help < | ||
- | # ou | ||
- | module help < | ||
- | </ | ||
- | |||
- | |||
- | * Show loaded modules | ||
- | <code bash> | ||
- | module list | ||
- | </ | ||
- | |||
- | * Unloading a module | ||
- | <code bash> | ||
- | module unload < | ||
- | </ | ||
- | |||
- | |||
- | ===== In a script ===== | ||
- | |||
- | exemple for bash (script excerpt) : | ||
- | |||
- | <code bash> | ||
- | # init env (should be in ~/.profile) | ||
- | source / | ||
- | |||
- | # easybuild modules do not load dependencies | ||
- | module load GCC/ | ||
- | module load GCC/6.4.0 | ||
- | |||
- | # tests | ||
- | env > resultat.txt | ||
- | gcc -v >> resultat.txt | ||
- | which mpirun >> resultat.txt | ||
- | |||
- | </ | ||
- | |||
- | ===== References ===== | ||
- | |||
- | * https:// | ||
- | * http:// | ||
- | * http:// | ||
- | |||
- | |||
- | < | ||
- | --------------------------------------------------- | ||
- | ==== pour csh/tcsh ==== | ||
- | |||
- | * Load the environment of the PSMN (**shell csh/tcsh**) | ||
- | <code bash> | ||
- | source / | ||
- | module use / | ||
- | module load Base/psmn | ||
- | </ | ||
- | You can add in your '' | ||
- | |||
- | <code bash> | ||
- | source / | ||
- | module use / | ||
- | module load Base/psmn | ||
- | </ | ||
- | |||
- | ==== for bash ==== | ||
- | |||
- | * Load the environment of the PSMN (**shell bash**) | ||
- | <code bash> | ||
- | source / | ||
- | module use / | ||
- | module load Base/psmn | ||
- | </ | ||
- | |||
- | You can add in your '' | ||
- | |||
- | <code bash> | ||
- | source / | ||
- | module use / | ||
- | module load Base/psmn | ||
- | </ | ||
- | |||
- | ==== for all shells ==== | ||
- | |||
- | * List available modules | ||
- | <code bash> | ||
- | module avail | ||
- | </ | ||
- | |||
- | * Get the description of a module | ||
- | <code bash> | ||
- | module whatis < | ||
- | |||
- | module whatis openmpi/ | ||
- | openmpi/ | ||
- | </ | ||
- | |||
- | * Obtenir l'aide d'un module | ||
- | <code bash> | ||
- | module help < | ||
- | |||
- | module help Base/psmn | ||
- | |||
- | ----------- Module Specific Help for ' | ||
- | |||
- | loads the modules software & base application environment for PSMN | ||
- | |||
- | This adds specifics to several of the environment variables. | ||
- | automatically load Base/ | ||
- | |||
- | Compatible with Modules version 3.2.9 | ||
- | |||
- | </ | ||
- | |||
- | * Charger un module pour un logiciel | ||
- | <code bash> | ||
- | module load < | ||
- | </ | ||
- | |||
- | * Afficher les modules chargés | ||
- | <code bash> | ||
- | module list | ||
- | </ | ||
- | |||
- | * Décharger un module | ||
- | <code bash> | ||
- | module unload < | ||
- | </ | ||
- | |||
- | * Décharger l' | ||
- | <code bash> | ||
- | module unuse / | ||
- | </ | ||
- | |||
- | |||
- | :!: Certains modules chargent automatiquement leurs dépendances, | ||
- | |||
- | |||
- | ===== Usage dans les scripts (non-interactif) ===== | ||
- | |||
- | :!: Certains modules chargent automatiquement leurs dépendances, | ||
- | |||
- | ==== pour csh/tcsh ==== | ||
- | |||
- | * ajouter dans le début des scripts : | ||
- | <code bash> | ||
- | source / | ||
- | module use / | ||
- | module load Base/psmn | ||
- | </ | ||
- | |||
- | Ajoutez ensuite les modules dont vous avez besoin (voir '' | ||
- | |||
- | ==== pour bash ==== | ||
- | |||
- | |||
- | * ajouter dans le début des scripts : | ||
- | |||
- | <code bash> | ||
- | source / | ||
- | module use / | ||
- | module load Base/psmn | ||
- | </ | ||
- | |||
- | Ajoutez ensuite les modules dont vous avez besoin (voir '' | ||
- | |||
- | |||
- | :!: Certains modules chargent automatiquement leurs dépendances, | ||
- | |||
- | |||
- | ===== Modules disponibles (avril 2016) ===== | ||
- | |||
- | Cette liste **n' | ||
- | |||
- | |||
- | < | ||
- | ~$ module avail | ||
- | |||
- | ----------------------------------------------- / | ||
- | ADF/ | ||
- | ADF/ | ||
- | ADF/ | ||
- | ADF/ | ||
- | ADF/ | ||
- | ADF/ | ||
- | Abinit/ | ||
- | Abinit/ | ||
- | AllPathsLG/ | ||
- | Amber/ | ||
- | Amber/ | ||
- | Amber/ | ||
- | Amber/ | ||
- | Amber/ | ||
- | Amber/ | ||
- | Amber/ | ||
- | Amber/ | ||
- | Amber/ | ||
- | Amber/ | ||
- | Amber/ | ||
- | Amber/ | ||
- | Amber/ | ||
- | Amber/ | ||
- | Amber/ | ||
- | Amber/ | ||
- | Amber/ | ||
- | Amber/ | ||
- | Augustus/ | ||
- | Avogadro/ | ||
- | BCFtools/ | ||
- | BEDTools/ | ||
- | BLAT/ | ||
- | Base/ | ||
- | Base/ | ||
- | Base/ | ||
- | Base/ | ||
- | Base/ | ||
- | Base/ | ||
- | Bismark/ | ||
- | Blender/ | ||
- | Bowtie/ | ||
- | Bowtie/ | ||
- | Bowtie/ | ||
- | Bowtie/ | ||
- | Bwakit/ | ||
- | CAFS/ | ||
- | CP2K/ | ||
- | CP2K/ | ||
- | CP2K/ | ||
- | CP2K/ | ||
- | Cassandra/ | ||
- | Celera/ | ||
- | Celera/ | ||
- | ClonalFrameML/ | ||
- | Corset/ | ||
- | Crystal/ | ||
- | Cufflinks/ | ||
- | DMAP/ | ||
- | Dalton/ | ||
- | DiscoSNP/ | ||
- | FastQC/ | ||
- | FastTree/ | ||
- | FreeFem++/ | ||
- | GATK/ | ||
- | GDL/ | ||
- | GFOLD/ | ||
- | GMAP/ | ||
- | Gaussian/ | ||
- | Gaussian/ | ||
- | Gaussian/ | ||
- | Gaussian/ | ||
- | Gaussian/ | ||
- | Gaussian/ | ||
- | Gaussian/ | ||
- | Gaussian/ | ||
- | Gaussian/ | ||
- | Gaussian/ | ||
- | HDF5/ | ||
- | HDF5/ | ||
- | HDF5/ | ||
- | HDF5/ | ||
- | HDF5/ | ||
- | HISAT/ | ||
- | HISAT/ | ||
- | HMMER/ | ||
- | HTSeq/ | ||
- | HTSeq/ | ||
- | HTSeq/ | ||
- | HTSlib/ | ||
- | Java/ | ||
- | Java/ | ||
- | Java/ | ||
- | Jellyfish/ | ||
- | Jmol/ | ||
- | LSDalton/ | ||
- | Lammps/ | ||
- | Lammps/ | ||
- | Lammps/ | ||
- | Lammps/ | ||
- | Lammps/ | ||
- | MAFFT/ | ||
- | MAPS/ | ||
- | MEME/ | ||
- | MIRA/ | ||
- | Matlab/ | ||
- | |||
- | </ | ||
- | |||
- | </ | ||