Using Environmental Modules
Overview
Teaching: 45 min
Exercises: 15 minQuestions
How to load modules to access software that I want to use for my research?
Objectives
Learn about modules, how to search, load and unload modules
Environmental Modules
The modules software package allows you to dynamically modify your user environment by using “modulefiles.”
Each modulefile contains the information needed to configure the shell for an application. After the modules software package is initialized, the environment can be modified on a per-module basis using the module command, which interprets modulefiles. Typically, modulefiles instruct the module command to alter or set shell environment variables such as PATH, MANPATH, and others. The modulefiles can be shared by many users on a system, and users can have their own collection to supplement or replace the shared modulefiles.
As a user, you can add and remove modulefiles from the current environment. The environment changes contained in a modulefile can also be summarized through the module show command. You are welcome to change modules in your .bashrc or .cshrc, but be aware that some modules print information (to standard error) when loaded, this should be directed to a file or /dev/null when loaded in an initialization script.
More information on modules can be found by typing module help on the NICS systems. Ignore the module init* commands – these modify a .modulerc file which is incompatible with the way NICS modules are set up. If you run into any issues, remove any .modulerc and log in again.
Basic arguments
The following table lists the most common module command options
| Command | Description |
|---|---|
| module list | Lists modules currently loaded in a user’s environment. |
| module avail | Lists all available modules on a system. |
| module show | Shows environment changes that will be made by loading a given module. |
| module load | Loads a module. |
| module unload | Unloads a module. |
| module help | Shows help for a module. |
| module swap | Swaps a currently loaded module for an unloaded module. |
Creating a private repository
On day 3 we will show and example of how to create a private module. With private modules you or your research group can have control on the software of interest for the group.
The basic procedure is to locate modules on a folder accessible by relevant users
and add the variable MODULEPATH to your .bashrc
MODULEPATH controls the path that the module command searches when looking for
modulefiles.
Typically, it is set to a default value by the bootstrap procedure.
MODULEPATH can be set using ’module use’ or by the module initialization
script to search group or personal modulefile directories before or after
the master modulefile directory.
Modules on Spruce
---------------------------------------------- /usr/share/Modules/modulefiles ----------------------------------------------
dot modules null use.own
----------------------------------------------- /usr/share/Modules/software ------------------------------------------------
atomistic/abinit/8.0.8_ompi2.0.1_intel15 genomics/blast/2.3.0 genomics/plink
atomistic/abinit/8.2.3_intel17 genomics/bowtie genomics/qiime
atomistic/lammps/2016.11.17 genomics/bowtie2 genomics/repeatexplorer
atomistic/octopus/6.0_gcc63 genomics/breakdancer genomics/repeatmasker
atomistic/vasp/5.3.3_ompi2.0.1_intel15 genomics/bwa/0.7.10 genomics/rsem
chemistry/amber/12 genomics/bwa/0.7.12 genomics/samtools/0.1.19
chemistry/amber/14 genomics/celera genomics/samtools/1.2
chemistry/amber/16 genomics/clumpp genomics/sga
chemistry/autodock_vina genomics/cufflinks genomics/shapeit
chemistry/gamess genomics/delly genomics/sickle
chemistry/gaussian/g03 genomics/distruct genomics/soapdenovo
chemistry/gaussian/g09 genomics/dwgsim genomics/sratoolkit
chemistry/gromacs/4.6.5 genomics/eigensoft genomics/structure
chemistry/gromacs/5.0.5 genomics/emboss genomics/svseq
chemistry/gromacs/5.0.5-gpu genomics/errcorr_tools genomics/tabix
chemistry/gromacs/5.1.2 genomics/express genomics/tablet
chemistry/gromacs/5.1.2-gpu genomics/falcon genomics/tophat2
chemistry/namd/ibverbs/2.10 genomics/fasta36 genomics/trf
chemistry/namd/ibverbs/2.11 genomics/fastqc genomics/trinity/2.0.6
chemistry/namd/ibverbs/2.9 genomics/fastx_toolkit genomics/trinity/2.2.0
chemistry/namd/mpi genomics/gatk/2.8 genomics/vcftools/0.1.11
chemistry/orca genomics/gatk/3.5 genomics/vcftools/0.1.14
chemistry/schrodinger genomics/genometools gnu/coreutils
data/cdf/3.5.0.2 genomics/hmmer gnu/parallel
data/hdf5/1.8.12 genomics/htslib mae/cmg/2014.10
data/sqlite/3.9.2 genomics/igv mae/cmg/2015.10
engineering/damask/2.0.1 genomics/lastz mae/elk/2.2.10
genomics/abyss/1.3.6 genomics/ltrfinder mae/elk/2.3.16
genomics/abyss/1.9.0 genomics/mrsfast statistics/matlab/2013b
genomics/allpaths genomics/muscle statistics/matlab/2014a
genomics/bamtools genomics/pbdagcon statistics/rstudio/0.97.551
genomics/beagle genomics/phase visualization/paraview
genomics/bedtools genomics/phrap visualization/visit/2.10
genomics/bioperl genomics/picard-tools visualization/visit/2.10.2
genomics/blasr genomics/pindel/0.2.5b1 visualization/vtk/7.0.0
genomics/blast/2.2.28 genomics/pindel/0.2.5b8
---------------------------------------------- /usr/share/Modules/development ----------------------------------------------
compilers/binutils/2.26 compilers/swig/3.0.7 libraries/netcdf/4.4.1.1_gcc63
compilers/cuda/7.5 environment/gcc-mpi libraries/netcdf/fortran-4.4.4_gcc63
compilers/cython/0.23.4 environment/gcc-serial libraries/openfoam/3.0+
compilers/gcc/4.8.2 environment/intel libraries/petsc/3.7.3
compilers/gcc/4.9.0 git/2.8.3 libraries/Qt/4.7.3
compilers/gcc/5.3.0 libraries/bioconductor/3.2 libraries/Qt/5.5.1
compilers/gcc/6.3.0 libraries/boost/1.47.0 libraries/R/Rhipe
compilers/idl/8.5.1 libraries/boost/1.55.0 libraries/sqlite/3.9.2
compilers/intel/13.0.1 libraries/boost/1.57.0 linalg/armadillo/7.600.2
compilers/intel/14.0 libraries/bupc/2.2 linalg/armadillo/7.800.1
compilers/intel/15.0.1 libraries/DFS/myhadoop linalg/openblas/0.2.19
compilers/intel/17.0.1 libraries/fftw/2.1.5 mpi/intel/4.1.0.024
compilers/java/jre1.8.0 libraries/fftw/3.3.4 mpi/intel/4.1.1.036
compilers/julia/0.3.11 libraries/fftw/3.3.4-mpi mpi/intel/5.0.3.048
compilers/julia/0.5.1 libraries/fftw/3.3.6_gcc63 mpi/mpich2/1.2.1
compilers/python/2.7.10 libraries/gsl/2.1 mpi/mvapich2/1.9
compilers/python/2.7.13 libraries/gtest/1.7.0 mpi/mvapich2/2.0.1
compilers/python/2.7.3 libraries/hdf5/1.8.12 mpi/mvapich2/2.2.0
compilers/python/3.5.1 libraries/hdf5/1.8.13_intel mpi/openmpi/1.6.5
compilers/python/3.6.0 libraries/hdf5/1.8.17_intel mpi/openmpi/1.6.5-intel
compilers/python/virtualenv libraries/hdf5/1.8.18_gcc63 mpi/openmpi/1.8.4
compilers/R/3.1.0 libraries/jemalloc/3.6.0 mpi/openmpi/2.0.1
compilers/R/3.2.1 libraries/libgd/2.2.4 mpi/openmpi/2.0.1_intel15
compilers/R/3.2.2 libraries/log4cpp/1.1.2 mpi/openmpi/2.0.2_gcc63
compilers/R/3.3.2 libraries/mkl/11.2.1 xalt/0.6.0
compilers/ruby/2.2.3 libraries/mkl/4.1.1.036
Key Points
You can preload modules for each login by adding the load line on your .bashrc