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| - | FIXME **Cette page n'est pas encore traduite entièrement. Merci de terminer la traduction**\\ //(supprimez ce paragraphe une fois la traduction terminée)// | ||
| - | |||
| - | ====== Environment Modules ====== | ||
| - | |||
| - | |||
| - | ''Environment Modules'' is used to **configure the execution environment** of a program (shell, job, interactive and non-interactive), it is now managed by lmod and EasyBuild. | ||
| - | |||
| - | Each program requires an environment (see the ''env'' command in a shell) properly configured to work optimally. | ||
| - | |||
| - | <note tip>**Reminder** :\\ | ||
| - | \\ | ||
| - | ''allo-psmn'' is a connection server; it allows you to access and transfer your files, and **that's all**. | ||
| - | |||
| - | To work, you have to connect, from ''allo-psmn'', to **[[documentation:clusters:services#serveurs_de_compilation_frontales|one of the compilation servers]]**.\\ | ||
| - | See how [[documentation:tutorials:ssh:accueil|connect to clusters]]. | ||
| - | </note> | ||
| - | ===== Modèles ===== | ||
| - | |||
| - | Some **examples** of initialization for PSMN users are available in the following files : | ||
| - | * ''/applis/PSMN/debian9/skels/modeles/Profile'' | ||
| - | * ''/applis/PSMN/debian9/skels/modeles/Bashrc'' | ||
| - | * ''/applis/PSMN/debian9/skels/modeles/Bash_aliases'' | ||
| - | * ''/applis/PSMN/debian9/skels/modeles/Cshrc'' | ||
| - | |||
| - | You can copy them, or include them in your own initialization files. | ||
| - | |||
| - | <code bash> | ||
| - | cp /applis/PSMN/debian9/skels/modeles/Profile ~/.profile | ||
| - | cp /applis/PSMN/debian9/skels/modeles/Bashrc ~/.bashrc | ||
| - | cp /applis/PSMN/debian9/skels/modeles/Bash_aliases ~/.bash_aliases | ||
| - | |||
| - | or | ||
| - | |||
| - | cp /applis/PSMN/debian9/skels/modeles/Cshrc ~/.cshrc | ||
| - | </code> | ||
| - | |||
| - | Reconnect to take into account the changes. | ||
| - | ===== interactive use ===== | ||
| - | |||
| - | |||
| - | ==== Load "Environment Modules" ==== | ||
| - | |||
| - | * for bash | ||
| - | |||
| - | <code bash> | ||
| - | source /usr/share/lmod/lmod/init/bash | ||
| - | </code> | ||
| - | |||
| - | Can be added in ''~/.profile''. | ||
| - | |||
| - | * for csh/tcsh | ||
| - | |||
| - | <code bash> | ||
| - | source /usr/share/lmod/lmod/init/tcsh | ||
| - | </code> | ||
| - | |||
| - | Can be added in ''~/.cshrc''. | ||
| - | |||
| - | * for zsh | ||
| - | |||
| - | <code bash> | ||
| - | source /usr/share/lmod/lmod/init/zsh | ||
| - | </code> | ||
| - | |||
| - | PCan be added in ''~/.zshenv'' (ou ''~/.zshrc''). | ||
| - | ==== 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 | ||
| - | </code> | ||
| - | |||
| - | |||
| - | * module loading : | ||
| - | |||
| - | <code bash> | ||
| - | module load <compilateur>/<version>/<software>/<version> | ||
| - | |||
| - | # for exemple load OpenMPI 2.1.1 (compilé avec GCC 6.4.0) | ||
| - | module load GCC/6.4.0/OpenMPI/2.1.1 | ||
| - | # then load GCC 6.4.0 | ||
| - | module load GCC/6.4.0 | ||
| - | </code> | ||
| - | |||
| - | * Getting help from a module | ||
| - | <code bash> | ||
| - | module help <software>/<version> | ||
| - | # ou | ||
| - | module help <compilateur>/<version>/<software>/<version> | ||
| - | </code> | ||
| - | |||
| - | |||
| - | * Show loaded modules | ||
| - | <code bash> | ||
| - | module list | ||
| - | </code> | ||
| - | |||
| - | * Unloading a module | ||
| - | <code bash> | ||
| - | module unload <software>/<version> | ||
| - | </code> | ||
| - | |||
| - | |||
| - | ===== In a script ===== | ||
| - | |||
| - | exemple for bash (script excerpt) : | ||
| - | |||
| - | <code bash> | ||
| - | # init env (should be in ~/.profile) | ||
| - | source /usr/share/lmod/lmod/init/bash | ||
| - | |||
| - | # easybuild modules do not load dependencies | ||
| - | module load GCC/6.4.0/OpenMPI/2.1.1 | ||
| - | module load GCC/6.4.0 | ||
| - | |||
| - | # tests | ||
| - | env > resultat.txt | ||
| - | gcc -v >> resultat.txt | ||
| - | which mpirun >> resultat.txt | ||
| - | |||
| - | </code> | ||
| - | |||
| - | ===== References ===== | ||
| - | |||
| - | * https://www.tacc.utexas.edu/research-development/tacc-projects/lmod | ||
| - | * http://modules.sourceforge.net/index.html | ||
| - | * http://modules.sourceforge.net/man/modulefile.html | ||
| - | |||
| - | |||
| - | <hidden> | ||
| - | --------------------------------------------------- | ||
| - | ==== pour csh/tcsh ==== | ||
| - | |||
| - | * Load the environment of the PSMN (**shell csh/tcsh**) | ||
| - | <code bash> | ||
| - | source /usr/share/modules/init/tcsh | ||
| - | module use /applis/PSMN/Modules | ||
| - | module load Base/psmn | ||
| - | </code> | ||
| - | You can add in your ''~/.cshrc'', the following lines : | ||
| - | |||
| - | <code bash> | ||
| - | source /usr/share/modules/init/tcsh | ||
| - | module use /applis/PSMN/Modules | ||
| - | module load Base/psmn | ||
| - | </code> | ||
| - | |||
| - | ==== for bash ==== | ||
| - | |||
| - | * Load the environment of the PSMN (**shell bash**) | ||
| - | <code bash> | ||
| - | source /usr/share/modules/init/bash | ||
| - | module use /applis/PSMN/Modules | ||
| - | module load Base/psmn | ||
| - | </code> | ||
| - | |||
| - | You can add in your ''~/.profile'', the following lines : | ||
| - | |||
| - | <code bash> | ||
| - | source /usr/share/modules/init/bash | ||
| - | module use /applis/PSMN/Modules | ||
| - | module load Base/psmn | ||
| - | </code> | ||
| - | |||
| - | ==== for all shells ==== | ||
| - | |||
| - | * List available modules | ||
| - | <code bash> | ||
| - | module avail | ||
| - | </code> | ||
| - | |||
| - | * Get the description of a module | ||
| - | <code bash> | ||
| - | module whatis <software>/<version> | ||
| - | |||
| - | module whatis openmpi/1.6.4-gnu-4.7.2 | ||
| - | openmpi/1.6.4-gnu-4.7.2: loads openmpi 1.6.4 (gnu-4.7.2/Debian7) environment | ||
| - | </code> | ||
| - | |||
| - | * Obtenir l'aide d'un module | ||
| - | <code bash> | ||
| - | module help <software>/<version> | ||
| - | |||
| - | module help Base/psmn | ||
| - | |||
| - | ----------- Module Specific Help for 'Base/psmn' ------------------ | ||
| - | |||
| - | loads the modules software & base application environment for PSMN | ||
| - | |||
| - | This adds specifics to several of the environment variables. | ||
| - | automatically load Base/debian7 and Base/sge modulefiles | ||
| - | |||
| - | Compatible with Modules version 3.2.9 | ||
| - | |||
| - | </code> | ||
| - | |||
| - | * Charger un module pour un logiciel | ||
| - | <code bash> | ||
| - | module load <software>/<version> | ||
| - | </code> | ||
| - | |||
| - | * Afficher les modules chargés | ||
| - | <code bash> | ||
| - | module list | ||
| - | </code> | ||
| - | |||
| - | * Décharger un module | ||
| - | <code bash> | ||
| - | module unload <software>/<version> | ||
| - | </code> | ||
| - | |||
| - | * Décharger l'environnement du PSMN | ||
| - | <code bash> | ||
| - | module unuse /applis/PSMN/Modules | ||
| - | </code> | ||
| - | |||
| - | |||
| - | :!: Certains modules chargent automatiquement leurs dépendances, ce qui peut engendrer des conflits. | ||
| - | |||
| - | |||
| - | ===== Usage dans les scripts (non-interactif) ===== | ||
| - | |||
| - | :!: Certains modules chargent automatiquement leurs dépendances, ce qui peut engendrer des conflits. | ||
| - | |||
| - | ==== pour csh/tcsh ==== | ||
| - | |||
| - | * ajouter dans le début des scripts : | ||
| - | <code bash> | ||
| - | source /usr/share/modules/init/tcsh | ||
| - | module use /applis/PSMN/Modules | ||
| - | module load Base/psmn | ||
| - | </code> | ||
| - | |||
| - | Ajoutez ensuite les modules dont vous avez besoin (voir ''module avail''). | ||
| - | |||
| - | ==== pour bash ==== | ||
| - | |||
| - | |||
| - | * ajouter dans le début des scripts : | ||
| - | |||
| - | <code bash> | ||
| - | source /usr/share/modules/init/bash | ||
| - | module use /applis/PSMN/Modules | ||
| - | module load Base/psmn | ||
| - | </code> | ||
| - | |||
| - | Ajoutez ensuite les modules dont vous avez besoin (voir ''module avail''). | ||
| - | |||
| - | |||
| - | :!: Certains modules chargent automatiquement leurs dépendances, ce qui peut engendrer des conflits. | ||
| - | |||
| - | |||
| - | ===== Modules disponibles (avril 2016) ===== | ||
| - | |||
| - | Cette liste **n'est pas à jour**, utilisez la commande ''module avail'' pour avoir la liste en cours. | ||
| - | |||
| - | |||
| - | <code> | ||
| - | ~$ module avail | ||
| - | |||
| - | ----------------------------------------------- /applis/PSMN/Modules ----------- | ||
| - | ADF/2010.02 Molden/5.0.6 | ||
| - | ADF/2012.01 Molden/5.4 | ||
| - | ADF/2013.01 Molpro/2010.1-intel-14.0.1 | ||
| - | ADF/2013.01.platformmpi Molpro/2010.1-intel-14.0.1-openmp | ||
| - | ADF/2014.02 MrBayes/3.2.1-intel-mpi | ||
| - | ADF/2014.10 MrBayes/3.2.1-intel-seq | ||
| - | Abinit/7.2.1-gnu-4.7.2-x86_64 NAMD/2.11-ibverbs | ||
| - | Abinit/7.6.4 NAMD/2.11-ibverbs-smp | ||
| - | AllPathsLG/r42874-gnu-4.7.1 NAMD/2.11-ibverbs-smp-CUDA | ||
| - | Amber/12-20150109-intel-14.0.1-openmp NAMD/2.11-multicore | ||
| - | Amber/12-20150109-intel-14.0.1-openmpi-1.8.4 NAMD/2.11-multicore-CUDA | ||
| - | Amber/12-20150109-intel-14.0.1-seq NAMD/2.9-ibverbs | ||
| - | Amber/12-20150109-intel-14.0.1-seq-K20-DPDP NAMD/2.9-ibverbs-smp | ||
| - | Amber/12-20150109-intel-14.0.1-seq-K20-SPFP NAMD/2.9-ibverbs-smp-CUDA | ||
| - | Amber/12-20150109-intel-14.0.1-seq-M2090-DPDP NAMD/2.9-multicore | ||
| - | Amber/12-20150109-intel-14.0.1-seq-M2090-SPFP NAMD/2.9-multicore-CUDA | ||
| - | Amber/12-intel-14.0.1-openmp NucleoMiner/1.0 | ||
| - | Amber/12-intel-14.0.1-openmpi-1.6.4 Oases/0.2.8 | ||
| - | Amber/12-intel-14.0.1-openmpi-1.6.4-K20-DPDP OpenAlea/2016 | ||
| - | Amber/12-intel-14.0.1-openmpi-1.6.4-K20-SPFP OpenAlea/svn-r4239 | ||
| - | Amber/12-intel-14.0.1-openmpi-1.6.4-M2070-DPDP PBSuite/15.2.20 | ||
| - | Amber/12-intel-14.0.1-openmpi-1.6.4-M2070-SPFP ParaView/3.12.0 | ||
| - | Amber/12-intel-14.0.1-seq ParaView/4.0.1 | ||
| - | Amber/12-intel-14.0.1-seq-K20-DPDP ParaView/4.4.0 | ||
| - | Amber/12-intel-14.0.1-seq-K20-SPFP PhyML/20120412 | ||
| - | Amber/12-intel-14.0.1-seq-M2070-DPDP PhyML/20140223 | ||
| - | Amber/12-intel-14.0.1-seq-M2070-SPFP PhyML/3.0 | ||
| - | Augustus/3.1 PhyloMerge/0.2 | ||
| - | Avogadro/1.1.1 Phylobayes/3.3b | ||
| - | BCFtools/1.1 Phylobayes/3.3e | ||
| - | BEDTools/2.24.0 Povray/3.7 | ||
| - | BLAT/35 Prank/140603 | ||
| - | Base/FR.UTF-8 Primer3/2.3.4 | ||
| - | Base/debian7 Qbox/1.62.3 | ||
| - | Base/psmn Quast/3.2 | ||
| - | Base/sge R/2.15.1 | ||
| - | Base/test R/3.0.2 | ||
| - | Base/test.tcl R/3.2.0 | ||
| - | Bismark/0.15.0 R/3.2.4 | ||
| - | Blender/2.76b RSEM/1.2.19 | ||
| - | Bowtie/0.12.7 RSeQC/2.3.1 | ||
| - | Bowtie/1.1.1 RSeQC/2.3.3 | ||
| - | Bowtie/2.0.2 SAMtools/0.1.19 | ||
| - | Bowtie/2.2.4 SAMtools/1.1 | ||
| - | Bwakit/0.7.12 SPAdes/3.6.2 | ||
| - | CAFS/1.0 SRAToolkit/2.3.3-2 | ||
| - | CP2K/2.2.426 SRAToolkit/2.3.4-2 | ||
| - | CP2K/2.5.1 STAR/2.4.1d | ||
| - | CP2K/2.5.1-complete Sage/7.0 | ||
| - | CP2K/2.5.1-minimal Spinevolution/3.4.4 | ||
| - | Cassandra/2.5.4 Spinevolution/3.4.5 | ||
| - | Celera/WGS-7.0 StringTie/1.0.1 | ||
| - | Celera/WGS-8.3rc2 StringTie/1.2.0 | ||
| - | ClonalFrameML/1.25 TopHat/2.0.13 | ||
| - | Corset/1.03 Trimmomatic/0.36 | ||
| - | Crystal/2.0.1 Trinity/2.0.6 | ||
| - | Cufflinks/2.2.1 Trinity/2.1.1 | ||
| - | DMAP/20151019 Trinity/r2012-06-08 | ||
| - | Dalton/2016.0 Trinity/r20140413 | ||
| - | DiscoSNP/2.2.4 Trinity/r20140717 | ||
| - | FastQC/0.11.2 Trinotate/2.0.2 | ||
| - | FastTree/2.1.7 UCSC/287 | ||
| - | FreeFem++/3.42-seq VASP/4.6.36-gnu-4.7.2 | ||
| - | GATK/3.4-46 VASP/5.3.2-intel-11.1-debian7 | ||
| - | GDL/1.0 VASP/5.3.3-gnu-4.7.2 | ||
| - | GFOLD/1.1.4 VASP/5.3.3-intel-14.0.1-debian7 | ||
| - | GMAP/2014-10-22 VASP/5.3.5-intel-14.0.1-debian7 | ||
| - | Gaussian/g03-lasim VESTA/3.1.7 | ||
| - | Gaussian/g09-chimie VMD/1.9.2 | ||
| - | Gaussian/g09-geol Velvet/1.2.10 | ||
| - | Gaussian/g09c01-chimie ViennaRNA/2.1.9 | ||
| - | Gaussian/g09c01-geol aTRAM/1.01 | ||
| - | Gaussian/g09c01-icbms breseq/0.26.1 | ||
| - | Gaussian/g09d01-chimie fftw/3.3.3-intel-14.0.1-openmp | ||
| - | Gaussian/g09d01-geol fftw/3.3.3-intel-14.0.1-openmpi-1.6.4 | ||
| - | Gaussian/g09d01-icbms fftw/3.3.3-intel-14.0.1-openmpi-1.8.4 | ||
| - | Gaussian/g09d01-lasim fftw/3.3.3-intel-14.0.1-seq | ||
| - | HDF5/1.8.15-p1-mpi fftw/3.3.4-intel-14.0.1-openmp-dp | ||
| - | HDF5/1.8.15-p1-seq fftw/3.3.4-intel-14.0.1-openmp-sp | ||
| - | HDF5/1.8.16-mpich2 fftw/3.3.4-intel-14.0.1-openmpi-1.6.4-dp | ||
| - | HDF5/1.8.16-openmpi fftw/3.3.4-intel-14.0.1-openmpi-1.6.4-sp | ||
| - | HDF5/1.8.16-seq fftw/3.3.4-intel-14.0.1-openmpi-1.8.4-dp | ||
| - | HISAT/0.1.5b fftw/3.3.4-intel-14.0.1-openmpi-1.8.4-sp | ||
| - | HISAT/2.0.0b fftw/3.3.4-intel-14.0.1-seq-dp | ||
| - | HMMER/3.1b1 fftw/3.3.4-intel-14.0.1-seq-sp | ||
| - | HTSeq/0.5.3p3 gromacs/5.0.5 | ||
| - | HTSeq/0.5.3p9 intel/11.1.069 | ||
| - | HTSeq/0.6.1 intel/12.0.084 | ||
| - | HTSlib/1.1 intel/14.0.1 | ||
| - | Java/1.6d7 intel/15.0.2 | ||
| - | Java/1.7d7 modules.psmn | ||
| - | Java/1.8.0u77 openmpi/1.4.1-intel-11.1.069 | ||
| - | Jellyfish/2.2.5 openmpi/1.4.5-gnu-4.7.2 | ||
| - | Jmol/14.4.0 openmpi/1.5.4-gnu-4.7.2 | ||
| - | LSDalton/2016.0 openmpi/1.5.4-intel-12.0.084 | ||
| - | Lammps/11Nov13-mpi-1.6.4-intel-14.0.1 openmpi/1.6.4-gnu-4.7.2 | ||
| - | Lammps/15May15-mpi-1.8.4-intel-14.0.1 openmpi/1.6.4-intel-12.0.084 | ||
| - | Lammps/28Jun14-mpi-1.6.4-intel-14.0.1 openmpi/1.6.4-intel-14.0.1 | ||
| - | Lammps/28Jun14-mpi-1.8.4-intel-14.0.1 openmpi/1.8.4-intel-14.0.1 | ||
| - | Lammps/7Dec15-mpi-1.8.4-intel-14.0.1 picard/1.140 | ||
| - | MAFFT/7.187 prinseq/lite-0.20.4 | ||
| - | MAPS/3.4.2 python/2.7 | ||
| - | MEME/4.10.2 python/3.2 | ||
| - | MIRA/4.0.2 tablemaker/2.1.1 | ||
| - | Matlab/R2011b | ||
| - | |||
| - | </code> | ||
| - | |||
| - | </hidden> | ||