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Environment modules (program selection)

Environment modules (program selection)

A key reason for using the cluster (or other Linux server) is the ability to build and install new programs. This can be done either by the user, or system support staff and made available for all users.
A standard tool to aid this effort is the environment module system, a flexible framework to add or remove programs from a users’ current environment variables (the $PATH , etc.). From the point of view of the user, this provides a (partial) menu of the available programs on the system. A good link for more information on environment modules is http://www.admin-magazine.com/HPC/Articles/Environment-Modules.
A good place to start with environment modules is with the module_avail command, which will show the list of programs.
 

                                    Based on CentOS Linux 7

                                                                    ID: #000002

 

Use the following commands to adjust your environment:

 

'module avail'            - show available modules

'module add <module>'     - adds a module to your environment for this session

'module initadd <module>' - configure module to be loaded at every login

 

-------------------------------------------------------------------------------

/usr/bin/xauth:  file /home/kevin.brandt/

[kevin.brandt@thunder ~]$ module avail

 

------------------------------------------------- /cm/local/modulefiles --------------------------------------------------

   cluster-tools/8.2    cm-upgrade/8.2    dot                   ipmitool/1.8.18    module-info    python2

   cm-scale/8.2         cmd               freeipmi/1.6.2        lua/5.3.5          null           shared  (L)

   cm-setup/8.2         cmsh              gcc/8.2.0      (L)    module-git         openldap

 

------------------------------------------------- /usr/share/modulefiles -------------------------------------------------

  DefaultModules (L)

 

---------------------------------------------- /cm/shared/modulefiles_local ----------------------------------------------

   ANT/1.10.7                               blast/2.10.0                                                  (D)

  CSC/592                                  boost/1.68.0-openmpi-3.1.3

   EE/492                                   boost/1.68.0

   FFX/1.0.0-beta                           boost/1.68.0.1                                                (D)

   MCR/R2017b                               busco/3.0.2

   MCR/R2018b                        (D)    busco/4.0.5-singularity

   MET/0.1                                  busco/4.0.5                                                   (D)

   NCL/6.5.0                                bwa/0.7.17

   PHENIX/1.17                              cellprofiler/3.1.8

   R/3.5.1-mkl-nox11                        cmake/3.13.1

   R/3.5.1-mkl                       (D)    cp2k/6.1

   R/3.5.1                                  cuda/9.2.88

   R/3.6.0                                  cudnn/7.4.1

   R/3.6.1-jupyter                          curl/7.62.0

lines 1-24...skipping...

 

------------------------------------------------- /cm/local/modulefiles --------------------------------------------------

   cluster-tools/8.2    cm-upgrade/8.2    dot                   ipmitool/1.8.18    module-info    python2

   cm-scale/8.2         cmd               freeipmi/1.6.2        lua/5.3.5          null           shared  (L)

   cm-setup/8.2         cmsh              gcc/8.2.0      (L)    module-git         openldap

 

------------------------------------------------- /usr/share/modulefiles -------------------------------------------------

   DefaultModules (L)

 

---------------------------------------------- /cm/shared/modulefiles_local ----------------------------------------------

   ANT/1.10.7                               blast/2.10.0                                                  (D)

   CSC/592                                  boost/1.68.0-openmpi-3.1.3

   EE/492                                   boost/1.68.0

   FFX/1.0.0-beta                           boost/1.68.0.1                                                (D)

   MCR/R2017b                               busco/3.0.2

   MCR/R2018b                        (D)    busco/4.0.5-singularity

   MET/0.1                                  busco/4.0.5                                                   (D)

   NCL/6.5.0                                bwa/0.7.17

   PHENIX/1.17                              cellprofiler/3.1.8

   R/3.5.1-mkl-nox11                        cmake/3.13.1

   R/3.5.1-mkl                       (D)    cp2k/6.1

   R/3.5.1                                  cuda/9.2.88

   R/3.6.0                                  cudnn/7.4.1

   R/3.6.1-jupyter                          curl/7.62.0

   R/3.6.1-mkl                              dbgwas/0.5.2

   R/3.6.1-tensorflow-cpu                   diamond/0.9.30

   R/3.6.1-tensorflow-gpu                   doge/0.1

   R/3.6.1                                  e-mapper/1.0.3

   ROOT/6.18.04                             ebic/0.4

   SPAdes/3.5.0                             envi/5.5.2

   SPAdes/3.13.0                     (D)    fastai/0.7.2-gpu

   WRF/3.9.1                                fastqc/0.11.8

   abyss/2.1.5                              fio/3.13

   amrex/18.12                              flash/1.2.11

   apache-ant/1.10.5                        gaussian/g09

   augustus/3.3.2                           gcc/4.7.4

   bamtools/2.5.1                           gcc/5.5.0

   bazel/0.18.1-gcc-5.5.0            (D)    gcc/6.5.0

   bazel/0.18.1                             gcc/7.3.0

   bazel/0.19.2                             gdal/3.0.2

   bbtools/38.79                            geant4/1.0

   bcftools/1.9                             geant4/10.04.p02

   beagle/3.1.2-cuda                        geant4/10.05.p01-Mar-20

   beagle/3.1.2                      (D)    geant4/10.05.p01                                              (D)

   beast/2.5.1                              geos/3.8.0

   bio/BRAKER/2.1.2                         globus/2.3.6

   bio/DESeq2/1.22.2                        gnuplot/4.6.7

   bio/FALCON/0.0.5                         gridlab-d/3.2

   bio/FALCON/0.0.6                  (D)    gsce/xyz

   bio/FLASH2/2.2.0                         gsl/2.5

   bio/FastUniq/1.1                         h5py/2.8.0                                                    (D)

   bio/GATK/4.0.3                           h5py/2.10.0

   bio/GATK/4.1.2.0                  (D)    hdf4/4.2.14

   bio/GeneMark-ET/4.38                     hdf5/1.10.4-cuda

   bio/GenomeThreader/1.7.1                 hdf5/1.10.4-for-netcdf

   bio/IGV/2.6.3                            hdf5/1.10.4-mpich-3.3

   bio/LR_Gapcloser/2019.05                 hdf5/1.10.4                                                   (D)

   bio/MUMmer/3.23                          hdf5/1.10.4-zlib-1.2.11

   bio/MUMmer/4.0.0.b2                      hdfview/2.9.0

   bio/MUMmer/4.4.0.b2               (D)    hmmer/3.2.1

   bio/NSEG/2019.01.31                      hpl/2.3-mpich-3.3

   bio/PBSuite/15.8.24                      hpl/2.3-openmpi-3.1.3                                         (D)

   bio/PURC/2019.5.18                       htseq/0.11.1

   bio/PacBioAssemblyToolSuite/0.0.5        htslib/1.9

   bio/Platanus/1.2.4                       intel/2019.5

   bio/Platanus_allee/2.0.2                 intel/2019.5.1                                                (D)

   bio/Platanus_allee/2.2.2          (D)    java/1.8.0_192

   bio/PyPHLAWD/2019.7.9                    kat/2.4.1

   bio/QUBIC/1.10.0                         lapack/3.8.0-mpich-3.3

   bio/RAxML/8.2.12                         lapack/3.8.0-openmpi-3.1.3                                    (D)

   bio/RECON/1.08                           libarchive/3.3.3

   bio/RepeatMasker/4.0.8                   libexpat/2.2.6

   bio/RepeatMasker/4.1.0            (D)    libgd/2.2.4

   bio/RepeatModeler/1.0.11                 libjpeg-turbo/2.0.4

   bio/RepeatScout/1.0.5                    libuv/1.24.0

   bio/SMRTLink/6.0.0                       libzmq/4.3.0

   bio/SMRTLink/7.0.1                (D)    lp_solve/5.5

   bio/SSPACE-GapFiller/1.10                matlab/R2018b

   bio/SSPACE-LongRead/1.1                  matlab/R2019b

   bio/SSPACE-STANDARD/3.0                  matlab/R2020a                                                 (D)

   bio/STAR/2.7.2b                          megahit/1.2.1

   bio/Spaln/2.3.1                          megan/6.0

   bio/SyMAP/4.2                            metawrap/1.1.3

   bio/TandemRepeatsFinder/4.0.4     (D)    mkl/2019.1.144

   bio/TandemRepeatsFinder/4.0.9            mothur/1.41.1

   bio/Trinity/2.8.4                        mothur/1.41.3

   bio/WGCNA/1.66                           mothur/1.42.3                                                 (D)

   bio/abricate/1.0.1                       mpi4py/2.0.0

   bio/albacore/2.0.2                       mpi4py/3.0.0-cuda

   bio/albacore/2.1.10                      mpi4py/3.0.0                                                  (D)

   bio/albacore/2.3.4                (D)    mpich/3.2.1

   bio/annovar/2.1.1                        mpich/3.3                                                     (D)

   bio/ballgown/3.8                         ncbi-blast/2.3.0

   bio/bedtools/2.28.0                      ncbi-blast/2.4.0

   bio/bionano-solve/3.5.1                  ncbi-blast/2.5.0

   bio/bionano-tools/access-1.5.1           ncbi-blast/2.6.0

   bio/blasr/1.3.1                          ncbi-blast/2.7.1

   bio/blasr/5.3.3                   (D)    ncbi-blast/2.8.1

  bio/blat/36                              ncbi-blast/2.9.0

   bio/bowtie/1.2.2                         ncbi-blast/2.10.0                                             (D)

   bio/bowtie2/2.3.4                        ncurses/6.1

   bio/canu/1.8                             netcdf/c/4.6.2-hdf5-1.10.4-mpich-3.3-pio                      (D)

   bio/canu/1.9                      (D)    netcdf/c/4.6.2-hdf5-1.10.4-mpich-3.3

   bio/circos/0.69.6                        netcdf/c/4.6.2-hdf5-1.10.4

   bio/clustalw/2.1                         netcdf/c/4.6.2-hdf5-1.10.4-zlib-1.2.11

   bio/crispr/2019.8.14                     netcdf/fortran/4.4.5-netcdf-c-4.6.2-hdf5-1.10.4-mpich-3.3-pio (D)

   bio/cufflinks/2.2.1                      netcdf/fortran/4.4.5-netcdf-c-4.6.2-hdf5-1.10.4-mpich-3.3

   bio/cummeRbund/2.24.0                    nextclip/1.3.1

   bio/cutadapt/2.0                         nlopt/2.6.1

   bio/edgeR/3.24.3                         node/13.8.0

   bio/eugene/4.2a                          ondemand/rstudio

   bio/exonerate/2.2.0                      openblas/0.2.20

   bio/fastx_toolkit/0.0.14                 openfoam-com/18.12

   bio/filtlong/0.2.0                       openfoam-org/2.2.0

   bio/fluidigm2purc/0.2.1                  openfoam/18.12

   bio/gapcloser/1.12                       openmpi/1.8.5

   bio/gatk/4.1.5                           openmpi/2.1.5-cuda-no-mpifortran

   bio/gm_et/4.38                           openmpi/2.1.5-cuda

   bio/gth/1.7.1                            openmpi/2.1.5

   bio/hisat2/2.1.0                         openmpi/3.1.3-cuda-no-mpifortran

   bio/jellyfish/2.3.0                      openmpi/3.1.3-cuda

   bio/kaiju/1.6.3                          openmpi/3.1.3

   bio/krakenuniq/0.5.8                     openmpi/3.1.4

   bio/libgtextutils/0.7                    openmpi/4.0.0-cuda-no-mpifortran

   bio/longranger/2.2.2                     openmpi/4.0.0-cuda

   bio/lumpy/0.2.13                         openmpi/4.0.0

   bio/macs2/2.1.2                          openmpi/4.0.2                                                 (D)

   bio/mafft/7.429                          parmetis/4.0.3

   bio/mageck/0.5.9.2                       pelelm/18.12

   bio/mageck/0.5.9.3                (D)    perl/5.10.1

   bio/minimap2/2.16                        perl/5.16.3

   bio/multiqc/1.7                          perl/5.18.4

   bio/nanostat/1.2.0                       perl/5.28.1                                                   (D)

   bio/ncbi-rmblastn/2.2.28                 petsc/3.10.3_debug

   bio/ngs/2.9.4                            petsc/3.10.3_opt                                              (D)

   bio/ont-guppy/3.4.5-cpu                  phyml/3.3

   bio/panX/2020.04                         phyml/3.3.1                                                   (D)

   bio/parallel-fastq-dump/0.6.3            phyx/0.999-python3

   bio/phlawd_db_maker/0.2                  postgresql/12.2

   bio/phyutility/2.7.1                     proj/6.2.1

   bio/picardtools/2.20.4                   prokka/1.13.3

   bio/pilon/1.23                           python/2.7

   bio/porechop/0.2.4                       python/3.6

   bio/prinseq/0.20.4                       python/3.7                                                    (D)

   bio/prokka/1.14.5                        python/3.7.0

   bio/purge_haplotigs/1.0.4                pytorch/1.0

   bio/qiime2/2018.11                       raxml/8.2.12

   bio/qiime2/2019.4                        readline/7.0

   bio/qiime2/2020.2                 (D)    root/6.18.04

   bio/quake/0.3.5                          rstudio/2020.04

   bio/salmon/0.13.1                        samstat/1.5.1

   bio/samblaster/0.1.21                    samtools/1.9

   bio/shovill/1.1.0                        singularity/3.1.1

   bio/sickle/1.33                          spack/0.12.0

   bio/sra-tools/2.9.1                      sparsehash/2.0.3

   bio/stringtie/1.3.5                      specl/1.0

   bio/subread/1.6.3                        starccm+/12.04

   bio/tophat/2.1.1                         starccm+/12.04.010

   bio/trf/4.0.4                     (D)    starccm+/15.02.007                                            (D)

   bio/trf/4.0.9                            tbb/2019.U3

   bio/trimmomatic/0.38                     tensorflow/1.11.0-gpu

   bio/trimmomatic/0.39              (D)    tensorflow/1.14.0                                             (D)

   bio/wtdbg2/2019.12.06                    texlive/2018.12.02

   blast/2.3.0                              usearch/11.0.667

   blast/2.4.0                              valgrind/3.15.0

   blast/2.5.0                              vcftools/0.1.16

   blast/2.6.0                              w2rap-contigger/0.1

   blast/2.7.1                              w2rap/2018.12

   blast/2.8.1                              xerces-c/3.2.2

   blast/2.9.0                              zlib/1.2.11

 

------------------------------------------------- /cm/shared/modulefiles -------------------------------------------------

   blacs/openmpi/gcc/64/1.1patch03      gdb/8.2                                   mpich/ge/gcc/64/3.3

   blas/gcc/64/3.8.0                    globalarrays/openmpi/gcc/64/5.7           mvapich2/gcc/64/2.3

   bonnie++/1.97.3                      gpfs/4.0                                  netcdf/gcc/64/4.6.1

   cm-pmix3/3.0.2                       hdf5/1.10.1                               netperf/2.7.0

   cuda92/blas/9.2.88                   hdf5_18/1.8.20                            openblas/dynamic/0.2.20        (D)

   cuda92/fft/9.2.88                    hpl/2.2                                   openmpi/gcc/64/1.10.7

   cuda92/nsight/9.2.88                 htop/2.2.0                                parallel/20190522

   cuda92/profiler/9.2.88               hwloc/1.11.11                             scalapack/openmpi/gcc/64/2.0.2

   cuda92/toolkit/9.2.88                intel-tbb-oss/ia32/2019_20190410oss       sge/2011.11p1

   default-environment                  intel-tbb-oss/intel64/2019_20190410oss    slurm/18.08.4                  (L)

   fftw2/openmpi/gcc/64/double/2.1.5    iozone/3_482                              sysbench/1.0.18

   fftw2/openmpi/gcc/64/float/2.1.5     lapack/gcc/64/3.8.0

   fftw3/openmpi/gcc/64/3.3.8           lmsensors/3.4.0

 

  Where:

   L:  Module is loaded

   D:  Default Module

 

Module defaults are chosen based on Find First Rules due to Name/Version/Version modules found in the module tree.

See https://lmod.readthedocs.io/en/latest/060_locating.html for details.

 

Use "module spider" to find all possible modules.

Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".