en:documentation:tools:modules

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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.

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 one of the compilation servers.
See how connect to clusters.

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.

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

Reconnect to take into account the changes.

interactive use

Load "Environment Modules"

for bash

source /usr/share/lmod/lmod/init/bash

Can be added in ~/.profile.

for csh/tcsh

source /usr/share/lmod/lmod/init/tcsh

Can be added in ~/.cshrc.

for zsh

source /usr/share/lmod/lmod/init/zsh

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 !)

# list all modules
module avail
 
# list the modules related to OpenMPI
module avail openmpi

module loading :

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

Getting help from a module

module help <software>/<version>
# ou
module help <compilateur>/<version>/<software>/<version>

Show loaded modules

module list

Unloading a module

module unload <software>/<version>

In a script

exemple for bash (script excerpt) :

# 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

References

Cliquez pour afficher ⇲

Cliquez pour masquer ⇱

pour csh/tcsh

Load the environment of the PSMN (shell csh/tcsh)

source /usr/share/modules/init/tcsh
module use /applis/PSMN/Modules
module load Base/psmn

You can add in your ~/.cshrc, the following lines :

source /usr/share/modules/init/tcsh
module use /applis/PSMN/Modules
module load Base/psmn

for bash

Load the environment of the PSMN (shell bash)

source /usr/share/modules/init/bash
module use /applis/PSMN/Modules
module load Base/psmn

You can add in your ~/.profile, the following lines :

source /usr/share/modules/init/bash
module use /applis/PSMN/Modules
module load Base/psmn

for all shells

List available modules

module avail

Get the description of a module

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

Obtenir l'aide d'un module

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

Charger un module pour un logiciel

module load <software>/<version>

Afficher les modules chargés

module list

Décharger un module

module unload <software>/<version>

Décharger l'environnement du PSMN

module unuse /applis/PSMN/Modules

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 :

source /usr/share/modules/init/tcsh
module use /applis/PSMN/Modules
module load Base/psmn

Ajoutez ensuite les modules dont vous avez besoin (voir module avail).

pour bash

ajouter dans le début des scripts :

source /usr/share/modules/init/bash
module use /applis/PSMN/Modules
module load Base/psmn

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.

~$ 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

en/documentation/tools/modules.1594821440.txt.gz · Dernière modification : 2020/08/25 15:58 (modification externe)

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