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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 17:58 (modification externe)