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| - | FIXME **Cette page n'est pas encore traduite entièrement. Merci de terminer la traduction**\\ // | ||
| - | |||
| - | ====== 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/ | ||
| - | |||
| - | </ | ||
| - | |||
| - | </ | ||