Software

Owned by Former user (Deleted)
Last updated: Jul 08, 2022
20 min read


Several free and open source software and libraries are installed and accessible using the module command. A few licensed software from https://software.lehigh.edu are also available. Since, all Sol nodes have infiniband interconnect while Hawk nodes do not, the default MPI implementation is mvapich2 on Sol and mpich on Hawk. The default compiler for building applications is Intel 20.0.3 while the default compiler for GPU applications is 19.0.3. All software is compiled with both mvapich2 and mpich for AVX, AVX2 and AVX512 instruction set. All libraries are built with multiple compilers - gcc 8.3.1 and 9.3.0, and intel 19.0.3 and 20.0.3 

Module Environment

The Module package provides for the dynamic modification of a users's environment via module files. Module can be used:

  • to manage necessary changes to the environment, such as changing the default path or defining environment variables
  • to manage multiple versions of applications, tools and libraries
  • to manage software where name conflicts with other software would cause problems

Modules have been created for many of the software packages installed on Sol. They make your job easier by defining environment variables and adding directories to your path which are necessary when using a given package. 

Some useful module commands are:

Command

Description

module avail

lists all the available modules

module help foo

displays help on module foo, for some applications usage information is also displayed

module show foo

indicates what changes would be made to the environment by loading module foo without actually loading it

module load foo

loads module foo

module list

displays your currently loaded modules

module swap foo1 foo2

switches loaded module foo1 with module foo2

module unload foo

reverses all changes to the environment made by previously loading module foo

module spider fooQuery all modules in MODULEPATH and any module hierarchy
module use [-a] [path]Prepend or Append path to MODULEPATH
module unuse [path]Remove path from MODULEPATH

Since Feb 1 2021, LMOD is used to provide the module environment and not all modules are available. Only modules for applications and libraries built with the loaded compiler and mpi combination are visible. On the Sol head node, intel 20.0.3 and mvapich2 2.3.4 are loaded by default. To see GPU enabled packages, load the intel 19.0.3 module. To use applications and libraries built with the system default compiler, gcc 8.3.1, unload the intel compiler.

Installed Software

For software with multiple version installed, default modules are listed in bold face.

Please feel free to build your own software stack. If you need to fine tune or rebuild (for e.g. different compiler/mpi combination) some of the installed packages, please feel free to use the installation scripts (not all are available) from https://gogs.cc.lehigh.edu/alp514/solsoftware (Lehigh IP or VPN required). SPACK is used to built the HPC software stack and the installation scripts are not updated for the current compiler and module names, nor have they been tested for the current versions of software.

Available Software on Sol (replace mvapich2 with mpich for Hawk) 
[2021-08-06 07:08.25] ~
[alp514.sol](1001): module av

------------------------------------------------------------- /share/Apps/share/Modules/lmod/linux-centos8-x86_64/mvapich2/2.3.4/intel/20.0.3 --------------------------------------------------------------
   crystal17/1.0.2    dl_poly/4.09    lammps/20200303-anj6    namd/2.14    nwchem/7.0.2    openmolcas/19.11    opensees/3.3.0 (D)    vasp/5.4.4.pl2-neb    vasp/5.4.4.pl2    vasp/5.4.4    vasp/6.1.2 (D)

---------------------------------------------------- /share/Apps/lusoft/share/spack/lmod/avx2/linux-centos8-x86_64/mvapich2/2.3.4-wguydha/intel/20.0.3 -----------------------------------------------------
   adios2/2.6.0         globalarrays/5.7             hdf5/1.10.7     (D)    lammps/20201029 (D)    netcdf-cxx/4.2       (D)    petsc/3.14.1         quantum-espresso/6.5        shengbte/1.1.1-8a63749
   almabte/1.3.2        gromacs/2020.4-plumed        hypre/2.20.0           mumps/5.3.3            netcdf-fortran/4.5.3 (D)    plumed/2.6.2         quantum-espresso/6.6 (D)    superlu-dist/6.3.1
   boost/1.74.0  (D)    gromacs/2020.4        (D)    lammps/20200303        netcdf-c/4.7.4  (D)    parmetis/4.0.3              py-espresso/4.0.2    relion/3.1.1

---------------------------------------------------------------- /share/Apps/lusoft/share/spack/lmod/avx2/linux-centos8-x86_64/intel/20.0.3 ----------------------------------------------------------------
   arpack-ng/3.7.0 (D)    gsl/2.5              (D)    metis/5.1.0    (D)      netcdf-c/4.7.4          openblas/0.3.10 (D)    py-pyparsing/2.4.2 (D)    suite-sparse/5.7.2 (D)
   boost/1.74.0           hdf5/1.10.7                 mpich/3.3.2    (D)      netcdf-cxx/4.2          openmpi/4.0.5   (D)    qhull/2020.1       (D)    superlu-mt/3.1     (D)
   fftw/3.3.8      (D)    intel-mkl/2020.3.279 (D)    mvapich2/2.3.4 (L,D)    netcdf-fortran/4.5.3    opensees/3.3.0         qrupdate/1.1.2     (D)    superlu/5.2.1      (D)

-------------------------------------------------------------------- /share/Apps/lusoft/share/spack/lmod/avx2/linux-centos8-x86_64/Core --------------------------------------------------------------------
   angsd/0.933          canu/1.8                             gatk/4.1.0.0                   libarchive/3.4.3        ngstools/2019-06-24          picard/2.20.8             snpeff/5.0
   arpack-ng/3.7.0      cuda/10.2.89                         gcc/9.3.0                      magma/2.5.4             nlopt/2.6.2                  pilon/1.22                stacks/2.55
   bamtools/2.5.1       cuda/11.0.2                          gmap-gsnap/2020-06-01          masurca/3.4.2           nvhpc/20.9                   py-pyparsing/2.4.2        star/2.7.0e
   bartender/1.1        cuda/11.1.0                   (D)    gnuplot/5.2.8                  metis/5.1.0             octave/5.2.0                 pythia8/8303              subread/2.0.0
   bayescan/2.1         cudnn/8.0.4.30-11.0-linux-x64        gsl/2.5                        miniasm/2018-3-30       openbabel/3.0.0              python/3.8.6       (L)    suite-sparse/5.7.2
   bayestraits/3.0.2    eigen/3.3.8                          hal/2.1                        minimap2/2.14           openblas/0.3.10              qhull/2020.1              superlu-mt/3.1
   bgc/1.03             exonerate/2.4.0                      hdf5/1.10.7                    mpich/3.3.2             openjdk/1.8.0_222-b10        qrupdate/1.1.2            superlu/5.2.1
   blast-plus/2.9.0     express/1.5.2                        hisat2/2.2.0                   mvapich2/2.3.4          openjdk/11.0.2        (D)    r/4.0.3                   swig/4.0.2         (D)
   blat/35              fastjet/3.3.3                        intel-mkl/2020.3.279           nccl/2.7.8-1            openmpi/4.0.5                rmcprofile/6.7.9          tabix/2013-12-16
   boost/1.74.0         fastqc/0.11.7                        intel/19.0.3                   netcdf-c/4.7.4          paml/4.9j                    root/6.20.08              trimmomatic/0.39
   bowtie/1.3.0         fastx-toolkit/0.0.14                 intel/20.0.3          (L,D)    netcdf-cxx/4.2          pear/0.9.11                  rsem/1.3.1                trinity/2.12.0
   bowtie2/2.4.1        fftw/3.3.8                           jellyfish/2.2.7                netcdf-fortran/4.5.3    perl/5.32.0                  salmon/0.14.1             vcftools/0.1.15
   bwa/0.7.17           freebayes/1.1.0                      kallisto/0.46.2                ngmlr/0.2.7             phast/1.4                    samtools/1.10             vesta/3.4.6

------------------------------------------------------------------ /share/Apps/lusoft/share/spack/lmod/default/linux-centos8-x86_64/Core -------------------------------------------------------------------
   anaconda3/2019.10        axel/2.16.1     graphviz/2.44.1    libxp/1.0.3    ncdu/1.13            pwgui/6.1              scons/3.1.2     tcl/8.6.10        valgrind/3.15.0
   anaconda3/2020.07 (D)    cmake/3.18.4    julia/1.5.2        motif/2.3.8    parallel/20200822    qcachegrind/20.08.0    screen/4.8.0    tk/8.6.10         vmd/1.9.3
   aria2/1.35.0             ddd/3.3.12      krb5/1.18.2        nano/5.6.1     povray/3.7.0.10      rclone/1.53.3          swig/4.0.2      tmux/3.1b  (L)

--------------------------------------------------------------------------- /share/Apps/share/Modules/lmod/applications/licensed ---------------------------------------------------------------------------
   abaqus/2019        cactus/1.2.3        comsol/5.4          guppy/3.1.5-gpu     guppy/4.0.14  (D)    mathematica/12.0    simmodeler/8.0    xds/feb2021 (D)
   ansys/20.2         cactus/1.3.0 (D)    gaussian/g09 (D)    guppy/3.1.5         gurobi/8.1.1         matlab/R2020a       stata/15          xds/jan2020
   ansys/21.1  (D)    ccp4/7.0            gaussian/g16        guppy/4.0.14-gpu    knitro/10.3.0        phenix/1.16         sysweld/2020.5

---------------------------------------------------------------------------------- /share/Apps/share/Modules/lmod/default ----------------------------------------------------------------------------------
   cent7    gpu    hawk    hawkgpu    sol (L)    solgpu    soltools (L)

--------------------------------------------------------------- /share/Apps/share/Modules/lmod/linux-centos8-x86_64/py_venv/pythonapps/avx2 ----------------------------------------------------------------
   all                        htseq/0.11.2-m5yqkbo        matplotlib/3.3.3-dttvy5f  (D)    pandas/1.1.4-sdbbcxk       pytorch/1.7.0-cuda               seaborn/0.9.0-7xrppb4
   biopython/1.73-aoor5vo     jupyter/1.0.0-7ew3qb6       mdanalysis/1.0.0-tfngrft         phonopy/1.10.0-iuaj2xc     scikit-build/0.10.0-vww4qdm      six/1.15.0-obed3ik
   cclib/1.5.post1-wv3arnb    jupyterlab/2.2.7-ln6bc44    moltemplate/2.5.8-iclz2ic        pip/20.2-ig2u7ky           scikit-image/0.17.2-qhu4bnf      tensorflow/2.4.1-cuda
   cython/0.29.21-trlkbz5     keras/2.2.4-cuda-rihsv3p    multiqc/1.7-xi6ehki              porechop/0.2.4-tgrse4w     scikit-learn/0.23.2-nnpi22y      theano/1.0.4-cuda-srh7rqj
   dask/2.16.0-hcixvbx        lxml/4.5.2-2d2z266          numba/0.50.1-orbwfra             pyparsing/2.4.2-yktitpw    scikit-optimize/0.5.2-xngjbiq    virtualenv/16.7.6-yh3ujrd
   horovod/0.21.3-cuda        matplotlib/2.2.5-fimnl7l    numpy/1.19.4-hyxetpw             pyspark/3.0.1-f3qh2hw      scipy/1.5.4-fbs3ffk              virtualenvwrapper/4.8.2-vozt6md

  Where:
   L:  Module is loaded
   D:  Default Module

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


Available GPU enabled software on Hawk (replace mpich with mvapich2 for Sol) 
[2021-08-06 07:11.02] ~
[alp514.sol](1003): module av

--------------------------------------------------------------- /share/Apps/share/Modules/lmod/linux-centos8-x86_64/mpich/3.3.2/intel/19.0.3 ---------------------------------------------------------------
   namd/2.14

------------------------------------------------------ /share/Apps/lusoft/share/spack/lmod/avx2/linux-centos8-x86_64/mpich/3.3.2-hj3gqoq/intel/19.0.3 ------------------------------------------------------
   boost/1.74.0          (D)    gromacs/2020.4 (D)    hypre/2.20.0       lammps/20201029 (D)    netcdf-c/4.7.4 (D)    netcdf-fortran/4.5.3 (D)    petsc/3.14.1    py-espresso/4.0.2    superlu-dist/6.3.1
   gromacs/2020.4-plumed        hdf5/1.10.7    (D)    lammps/20200303    mumps/5.3.3            netcdf-cxx/4.2 (D)    parmetis/4.0.3              plumed/2.6.2    relion/3.1.1

---------------------------------------------------------------- /share/Apps/lusoft/share/spack/lmod/avx2/linux-centos8-x86_64/intel/19.0.3 ----------------------------------------------------------------
   arpack-ng/3.7.0 (D)    gsl/2.5              (D)    metis/5.1.0    (D)      netcdf-c/4.7.4          openblas/0.3.10 (D)    qrupdate/1.1.2     (D)    superlu/5.2.1 (D)
   boost/1.74.0           hdf5/1.10.7                 mpich/3.3.2    (L,D)    netcdf-cxx/4.2          openmpi/4.0.5   (D)    suite-sparse/5.7.2 (D)
   fftw/3.3.8      (D)    intel-mkl/2020.3.279 (D)    mvapich2/2.3.4 (D)      netcdf-fortran/4.5.3    qhull/2020.1    (D)    superlu-mt/3.1     (D)

-------------------------------------------------------------------- /share/Apps/lusoft/share/spack/lmod/avx2/linux-centos8-x86_64/Core --------------------------------------------------------------------
   angsd/0.933          canu/1.8                             gatk/4.1.0.0                 libarchive/3.4.3        ngstools/2019-06-24          picard/2.20.8             snpeff/5.0
   arpack-ng/3.7.0      cuda/10.2.89                  (L)    gcc/9.3.0                    magma/2.5.4             nlopt/2.6.2                  pilon/1.22                stacks/2.55
   bamtools/2.5.1       cuda/11.0.2                          gmap-gsnap/2020-06-01        masurca/3.4.2           nvhpc/20.9                   py-pyparsing/2.4.2        star/2.7.0e
   bartender/1.1        cuda/11.1.0                   (D)    gnuplot/5.2.8                metis/5.1.0             octave/5.2.0                 pythia8/8303              subread/2.0.0
   bayescan/2.1         cudnn/8.0.4.30-11.0-linux-x64        gsl/2.5                      miniasm/2018-3-30       openbabel/3.0.0              python/3.8.6       (L)    suite-sparse/5.7.2
   bayestraits/3.0.2    eigen/3.3.8                          hal/2.1                      minimap2/2.14           openblas/0.3.10              qhull/2020.1              superlu-mt/3.1
   bgc/1.03             exonerate/2.4.0                      hdf5/1.10.7                  mpich/3.3.2             openjdk/1.8.0_222-b10        qrupdate/1.1.2            superlu/5.2.1
   blast-plus/2.9.0     express/1.5.2                        hisat2/2.2.0                 mvapich2/2.3.4          openjdk/11.0.2        (D)    r/4.0.3                   swig/4.0.2         (D)
   blat/35              fastjet/3.3.3                        intel-mkl/2020.3.279         nccl/2.7.8-1            openmpi/4.0.5                rmcprofile/6.7.9          tabix/2013-12-16
   boost/1.74.0         fastqc/0.11.7                        intel/19.0.3          (L)    netcdf-c/4.7.4          paml/4.9j                    root/6.20.08              trimmomatic/0.39
   bowtie/1.3.0         fastx-toolkit/0.0.14                 intel/20.0.3          (D)    netcdf-cxx/4.2          pear/0.9.11                  rsem/1.3.1                trinity/2.12.0
   bowtie2/2.4.1        fftw/3.3.8                           jellyfish/2.2.7              netcdf-fortran/4.5.3    perl/5.32.0                  salmon/0.14.1             vcftools/0.1.15
   bwa/0.7.17           freebayes/1.1.0                      kallisto/0.46.2              ngmlr/0.2.7             phast/1.4                    samtools/1.10             vesta/3.4.6

------------------------------------------------------------------ /share/Apps/lusoft/share/spack/lmod/default/linux-centos8-x86_64/Core -------------------------------------------------------------------
   anaconda3/2019.10        axel/2.16.1     graphviz/2.44.1    libxp/1.0.3    ncdu/1.13            pwgui/6.1              scons/3.1.2     tcl/8.6.10        valgrind/3.15.0
   anaconda3/2020.07 (D)    cmake/3.18.4    julia/1.5.2        motif/2.3.8    parallel/20200822    qcachegrind/20.08.0    screen/4.8.0    tk/8.6.10         vmd/1.9.3
   aria2/1.35.0             ddd/3.3.12      krb5/1.18.2        nano/5.6.1     povray/3.7.0.10      rclone/1.53.3          swig/4.0.2      tmux/3.1b  (L)

--------------------------------------------------------------------------- /share/Apps/share/Modules/lmod/applications/licensed ---------------------------------------------------------------------------
   abaqus/2019        cactus/1.2.3        comsol/5.4          guppy/3.1.5-gpu     guppy/4.0.14  (D)    mathematica/12.0    simmodeler/8.0    xds/feb2021 (D)
   ansys/20.2         cactus/1.3.0 (D)    gaussian/g09 (D)    guppy/3.1.5         gurobi/8.1.1         matlab/R2020a       stata/15          xds/jan2020
   ansys/21.1  (D)    ccp4/7.0            gaussian/g16        guppy/4.0.14-gpu    knitro/10.3.0        phenix/1.16         sysweld/2020.5

---------------------------------------------------------------------------------- /share/Apps/share/Modules/lmod/default ----------------------------------------------------------------------------------
   cent7    gpu    hawk    hawkgpu (L)    sol    solgpu    soltools (L)

--------------------------------------------------------------- /share/Apps/share/Modules/lmod/linux-centos8-x86_64/py_venv/pythonapps/avx2 ----------------------------------------------------------------
   all                        htseq/0.11.2-m5yqkbo        matplotlib/3.3.3-dttvy5f  (D)    pandas/1.1.4-sdbbcxk       pytorch/1.7.0-cuda               seaborn/0.9.0-7xrppb4
   biopython/1.73-aoor5vo     jupyter/1.0.0-7ew3qb6       mdanalysis/1.0.0-tfngrft         phonopy/1.10.0-iuaj2xc     scikit-build/0.10.0-vww4qdm      six/1.15.0-obed3ik
   cclib/1.5.post1-wv3arnb    jupyterlab/2.2.7-ln6bc44    moltemplate/2.5.8-iclz2ic        pip/20.2-ig2u7ky           scikit-image/0.17.2-qhu4bnf      tensorflow/2.4.1-cuda
   cython/0.29.21-trlkbz5     keras/2.2.4-cuda-rihsv3p    multiqc/1.7-xi6ehki              porechop/0.2.4-tgrse4w     scikit-learn/0.23.2-nnpi22y      theano/1.0.4-cuda-srh7rqj
   dask/2.16.0-hcixvbx        lxml/4.5.2-2d2z266          numba/0.50.1-orbwfra             pyparsing/2.4.2-yktitpw    scikit-optimize/0.5.2-xngjbiq    virtualenv/16.7.6-yh3ujrd
   horovod/0.21.3-cuda        matplotlib/2.2.5-fimnl7l    numpy/1.19.4-hyxetpw             pyspark/3.0.1-f3qh2hw      scipy/1.5.4-fbs3ffk              virtualenvwrapper/4.8.2-vozt6md

  Where:
   L:  Module is loaded
   D:  Default Module

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


Most applications are optimized for AVX, AVX2 and AVX512 instruction set. The AVX2 compiled applications are loaded on the Sol head node and will not work on AVX based cpus i.e. debug partition. To use optimized applications, your should add the command source /etc/profile.d/zlmod.sh to your submit script before loading any modules. This script ensures that the MODULEPATH variable corresponds to the highest instruction set supported by the CPU rather than the default AVX2 compiled applications.

Software

Version

Type

Subject

module

GPU Support 
Abaqus2019ApplicationCFD

abaqus/2019


ADIOS22.6.0Dev ToolsLibraryadios2/2.6.0
almaBTE1.3.2ApplicationMaterialsalmabte/1.3.2
Anaconda32019.10 (Python 3.7.4)ApplicationVariousanaconda3/2019.10

Anaconda3

2020.07 (Python 3.8.6)

Application

Various

anaconda3/2020.07


ANGSD0.933ApplicationBioinformaticsangsd/0.933

Ansys

20.2

Application

CFD

ansys/20.2


aria2

1.35.0Dev ToolsUtilityaria2/1.35.0
ARPACK3.7.0Dev ToolsLibraryarpack-ng/3.7.0
AutoDock4.2.6ApplicationBiochemistryautodock/4.2.6
Avogadro

Visualization

ChemistryOpen OnDemand App
Axel 2.16.1Dev ToolsUtilityaxel/2.16.1

BamTools

2.5.1

Application

Bioinformatics

bamtools/2.5.1


Bartender

1.1

Application

Bioinformatics

bartender/1.1


BayeScan

2.1

Application

Bioinformatics

bayescan/2.1


BayesTraits3.0.2ApplicationBioinformaticsbayestraits/3.0.2
BerkeleyGW3.0.1ApplicationMaterialsberkeleygw/3.0.1

bgc

1.03

Application

Bioinformatics

bgc/1.03


BLAST2.9.0ApplicationBioinformaticsblast-plus/2.9.0
BLAT35ApplicationBioinformaticsblat/35
Blender

Visualization


Open Ondemand App
BOOST1.64.0Dev ToolsLibraryboost/1.74.0
Bowtie1.3.0ApplicationBioinformaticsbowtie/1.3.0

Bowtie2

2.4.1

Application

Bioinformatics

bowtie2/2.4.1


BWA

0.7.17

Application

Bioinformatics

bwa/0.7.15


Cactus1.3.0ApplicationBioinformaticscactus/1.3.0
Canu1.8ApplicationBioinformaticscanu/1.8
CCP47.0ApplicationChemistryccp4/7.0

CMake

3.18.4

Dev Tools

Utilities

cmake/3.18.4


COMSOL5.4ApplicationCFDcomsol/5.4
COMSOL6.0ApplicationCFDcomsol/6.0
CRYSTAL171.0.2ApplicationChemistrycrystal17/1.0.2

CUDA

10.2.89

Dev Tools

Programming

cuda/10.2.89


CUDA11.0.2

Dev Tools

Programmingcuda/11.0.2
CUDA11.1.0

Dev Tools

Programmingcuda/11.1.0
CUDNN8.0.4.30Dev ToolsLibrarycudnn/8.0.4.30-11.0-linux-x64
DDD3.3.12

Dev Tools

Utilitiesddd/3.3.12
DL_POLY_44.09ApplicationMaterialsdl_poly/4.09
DL_POLY_44.10ApplicationMaterialsdl_poly/4.10
DMTCP2.6.0Dev ToolsUtilitiesdmtcp/2.6.0

Eigen

3.3.8

Dev ToolsLibrary

eigen/3.3.8


ESPResSo4.0.2ApplicationMaterialspy-espresso/4.0.2
Exonerate2.4.0ApplicationBioinformaticsexonerate/2.4.0
eXpress1.5.2ApplicationBioinformaticsexpress/1.5.2
FastJet3.3.3ApplicationHigh Energy Physicsfastjet/3.3.3
Fastqc0.11.7ApplicationBioinformaticsfastqc/0.11.7

FASTX-Toolkit

0.0.14

Application

Bioinformatics

fastx-toolkit/0.0.14


FFTW3.3.8Dev ToolsLibraryfftw/3.3.8

FreeBayes

1.1.0

Application

Bioinformatics

freebayes/1.1.0


Gabedit

Visualization

ChemistryOpen Ondemand App

GAMESS

30 June 2021 R1

Application

Chemistry

gamess/30Jun2021


GAMS


Application

Math



GATK4.1.0.0ApplicationBioinformaticsgatk/4.1.0.0

Gaussian

09 Rev D01

Application

Chemistry

gaussian/g09


Gaussian16 Rev C01 (AVX2 enabled)ApplicationChemistrygaussian/g16

GaussView


Visualization

Chemistry

GCC 

8.3.1

Dev Tools

Programming

system default, no module needed


GCC

9.3.0

Dev Tools

Programming

gcc/9.3.0


Global Arrays5.7Dev ToolsLibraryglobalarrays/5.7
GMAP (with GSNAP) 2020-06-01ApplicationBioinformaticsgmap-gsnap/2020-06-01

GNU Parallel

20200822

Dev Tools

Utilities

parallel/20200822


GNUPlot5.2.8VisualizationUtilitiesgnuplot/5.2.8
Graphviz2.4.4.1VisualizationUtilitiesgraphviz/2.44.1

GROMACS

2020.4

Application

Biochemistry

gromacs/2020.4

(load intel/19.0.3 module)

GROMACS2020.4 + PlumedApplicationBiochemistrygromacs/2020.4-plumed(load intel/19.0.3 module)

GROMACS

2021.4

Application

Biochemistry

gromacs/2021.4

gromacs/2021.4-cuda-11.6.0
GROMACS2021.4 + PlumedApplicationBiochemistrygromacs/2021.4-plumedgromacs/2021.4-plumed-cuda-11.6.0
GSL2.5Dev ToolsLibrarygsl/2.5
Guppy3.1.5ApplicationBioinformaticsguppy/3.1.5guppy/3.1.5-gpu
Guppy4.0.14ApplicationBioinformaticsguppy/4.0.14guppy/4.0.14-gpu
Gurobi8.1.1ApplicationMathgurobi/8.1.1
Hadoop3.2.1ApplicationData Sciencehadoop/3.2.1
Hal2.1ApplicationBioinformaticshal/2.1
HDF51.10.7Dev ToolsLibraryhdf5/1.10.7
HISAT22.2.0ApplicationBioinformaticshisat2/2.2.0
Hive3.1.2ApplicationData Sciencehive/3.1.2
HYPRE2.20.0Dev ToolsLibraryhypre/2.20.0

Intel (default for gpu applications)

19.0.3

Dev Tools

Programming

intel/19.0.3


Intel

20.0.3

Dev Tools

Programming

intel/20.0.3


Intel

2021.3.0

Dev Tools

Programming

intel/2021.3.0


Intel MKL

2021.3.0

Dev Tools

Programming

intel-mkl/2021.3.0


Intel TBB

2021.3.0

Dev Tools

Programming

intel-tbb/2021.3.0


JELLYFISH2.2.7ApplicationBioinformaticsjellyfish/2.2.7
Julia1.5.2

Application

Programmingjulia/1.5.2
KaHIP2.00Dev ToolsLibrarykahip/2.00
kallisto0.46.2ApplicationBioinformaticskallisto/0.46.2

Knitro

10.3.0

Application

Math

knitro/10.3.0


LAMMPS

3Mar20

Application

Materials

lammps/20200303

(load intel/19.0.3 module)

LAMMPS

29Oct20

Application

Materials

lammps/20201029

(load intel/19.0.3 module)

LAMMPS

3Mar21

Application

Materials

lammps/20210310

lammps/20210310-cuda-11.6.0

Libarchive3.4.3Dev ToolsLibrarylibarchive/3.4.3

Magma (MATH package)

2.26

Application

Math

magma_math/2.26


Magma (GPU Library)2.5.4Dev ToolsLibrarymagma/2.5.4

Maple


Application

Math



MaSuRCA3.4.2ApplicationBioinformaticsmasurca/3.4.2

Mathematica

12.0

Application

Math

mathematica/12.0


MATLAB

R2020a

Application

Math

matlab/R2020a


MATLAB

R2021b

Application

Math

matlab/R2021b


METIS5.1.0Dev ToolsLibrarymetis/5.1.0
Miniasm2018-3-30ApplicationBioinformaticsminiasm/2018-3-30
Minimap22.14ApplicationBioinformaticsminimap2/2.14
Moose
Dev ToolsCFDmoose/devenv
MPICH3.3.2Dev ToolsLibrarympich/3.3.2
MUMPS5.3.3Dev ToolsProgrammingmumps/5.3.3
MVAPICH22.3.4Dev ToolsProgrammingmvapich2/2.3.4

NAMD

2.14

Application

Biochemistry

namd/2.14

(load intel/19.0.3 module)

NCCL

2.7.8-1

Dev Tools

Programming

nccl/2.7.8-1


Ncdu1.13Dev ToolsUtilityncdu/1.13
NETCDF-C4.7.4Dev ToolsLibrarynetcdf-c/4.7.4
NETCDF-CXX4.2Dev ToolsLibrarynetcdf-cxx/4.2
NETCDF-Fortran4.5.3Dev ToolsLibrarynetcdf-fortran/4.5.3
NGMLR0.2.7ApplicationBioinformaticsngmlr/0.2.7
NGS Tools2019-06-24ApplicationBioinformaticsngstools/2019-06-24
NLOpt2.6.2Dev ToolsLibrarynlopt/2.6.2
NVIDIA HPC SDK (formerly PGI compiler)20.9Dev ToolsProgrammingnvhpc/20.9

Built-in CUDA 11.0 and OpenACC Support 

NWChem

7.0.2

Application

Chemistry

nwchem/7.0.2


Octave5.2.0ApplicationMathoctave/5.2.0

OpenBabel

3.0.0

Dev ToolsLibrary

openbabel/3.0.0


OpenBLAS0.3.10Dev ToolsLibraryopenblas/0.3.10
OpenBLAS0.3.12Dev ToolsLibraryopenblas/0.3.12

OpenFOAM

v2006

Application

CFD

openfoam/2006


OpenFOAM

9

Application

CFD

openfoam-org/9


OpenJDK

1.8.0_222-b10

Dev Tools

Programming

openjdk/1.8.0_222-b10


OpenJDK11.0.2Dev ToolsProgrammingopenjdk/11.0.2
OpenMolcas19.11ApplicationChemistryopenmolcas/19.11
OpenMolcas22.02ApplicationChemistryopenmolcas/22.02
OpenMPI4.0.5Dev ToolsProgrammingopenmpi/4.0.5

OpenSees

3.3.0

Application

CFD

opensees/3.3.0


PAML4.9jApplicationBioinformaticspaml/4.9j
Paraview5.8.1VisualizationCFDparaview/5.8.1
ParMETIS4.0.3Dev ToolsLibraryparmetis/4.0.3
PEAR0.9.11ApplicationBioinformaticspear/0.9.11
Perl5.32.0ApplicationProgrammingperl/5.32.0
PETSc3.14.1Dev ToolsLibrarypetsc/3.14.1
PHAST1.4ApplicationBioinformaticsphast/1.4
PHENIX1.16ApplicationChemistryphenix/1.16
Picard2.20.8ApplicationBioinformaticspicard/2.20.8
Pilon1.22ApplicationBioinformaticspilon/1.22

Plumed

2.6.2

Application

Biochemistry

plumed/2.6.2


Plumed

2.7.3

Application

Biochemistry

plumed/2.7.3


Porechop0.2.4ApplicationBioinformatics

POV-RAY3.7.0.10VisualizationUtilitiespovray/3.7.0.10

PWGui

6.1

Visualization

Chemistry

pwgui/6.1


PyMol

1.8.6.0

Visualization

Chemistry

pyparsing2.4.2ApplicationUtilitiespy-pyparsing/2.4.2
PYTHIA88303ApplicationHigh Energy Physicspythia8/8303

Python

3.8.6

Application

Programming

python/3.8.6


QCacheGrind20.08.0Dev ToolsProgrammingqcachegrind/20.08.0
Qhull2020.1Dev ToolsLibraryqhull/2020.1
QRUpdate1.1.2Dev ToolsLibraryqrupdate/1.1.2

Quantum Espresso

6.5

Application

Chemistry

quantum-espresso/6.5


Quantum Espresso

6.6

Application

Chemistryquantum-espresso/6.6

Quantum Espresso + WEST

6.1.0 + 4.3.0

Application

Chemistryqe-west/6.1.0-4.3.0
R4.0.3ApplicationProgrammingr/4.0.3
Rclone1.53.3Dev ToolsUtilitiesrclone/1.53.3

RELION

3.1.1

Application

Bioinformatics

relion/3.1.1

(load intel/19.0.3 module)

RELION

3.1.3

Application

Bioinformatics

relion/3.1.3

relion/3.1.3-cuda-11.5.1
RMCProfile6.7.9ApplicationMaterialsrmcprofile/6.7.9
ROOT6.20.08ApplicationHigh Energy Physicsroot/6.20.08
RSEM1.3.1ApplicationBioinformaticsrsem/1.3.1
Salmon0.14.1ApplicationBioinformaticssalmon/0.14.1
SAM Tools1.10ApplicationBioinformaticssamtools/1.10
SAS9.4ApplicationAnalyticssas/9.4

Scons

3.1.2

Dev Tools

Utilities

scons/3.1.2


Scotch6.0.10Dev ToolsLibraryscotch/6.0.10
Screen4.8.0Dev ToolsUtilitiesscreen/4.8.0
ShengBTE1.1.1-8a63749ApplicationMaterialsshengbte/1.1.1-8a63749
SimModeler8.0ApplicationCFDsimmodeler/8.0
Singularity
Dev ToolsUtilitiesdefault, no module needed
SnpEff5.0ApplicationBioinformaticssnpeff/5.0
Spackreleases/v0.16 branchDev ToolsUtilitiesinstall your own, use /share/Apps/lusoft as upstream 
Spark3.2.0ApplicationData Sciencespark/3.2.0
Stacks2.55ApplicationBioinformaticsstacks/2.55
STAR2.7.0eApplicationBioinformaticsstar/2.7.0e
Stata15ApplicationAnalyticsstata/15
Stata17ApplicationAnalyticsstata/17 (serial only)
Subread2.0.0ApplicationBioinformaticssubread/2.0.0
SuiteSparse5.7.2Dev ToolsLibrarysuite-sparse/5.7.2
SuperLU5.2.1Dev ToolsLibrarysuperlu/5.2.1
SuperLU-MT3.1Dev ToolsLibrarysuperlu-mt/3.1
SuperLU-DIST6.3.1Dev ToolsLibrarysuperlu-dist/6.3.1
SWIG4.0.2ApplicationProgrammingswig/4.0.2
SYSWeld2020.5ApplicationCFDsysweld/2020.5

tabix

2013-12-16

Application

Bioinformatics

tabix/2013-12-16


TCL8.6.10Dev ToolsLibrarytcl/8.6.10
Tinker9ApplicationChemistrytinker/9
TK8.6.10Dev ToolsLibrarytk/8.6.10
Tmux3.1bDev ToolsUtilitiestmux/3.1b

trimmomatic

0.39

Application

Bioinformatics

trimmomatic/0.39


Trinity2.12.0ApplicationBioinformaticstrinity/2.12.0
Valgrind3.15.0Dev ToolsProgrammingvalgrind/3.15.0
VASP5.4.4ApplicationChemistryvasp/5.4.4
VASP5.4.4-pl2ApplicationChemistryvasp/5.4.4-pl2, vasp/5.4.4.pl2-neb
VASP6.1.2ApplicationChemistryvasp/6.1.2

VCFtools

0.1.15

Application

Bioinformatics

vcftools/0.1.15 


VESTA

3.4.6

Visualization

Chemistry

vesta/3.4.6


VMD

1.9.3

Visualization

Biochemistry

vmd/1.9.3


XCrysDen

1.5.60

Visualization

Chemistry



XDSFeb2021 (license expires Mar 2022)VisualizationChemistryxds/feb2021


All libraries are compiled with multiple compilers. Since in LMOD, you can only load one compiler module at a time, you should only see libraries built for the compiler that is loaded and the system default gcc 8.3.1 compiler. The loaded compiler (default is intel/20.0.3) takes precedence over the system compiler. To use the libraries compiled with the system default, unload compiler modules (intel, gcc or nvhpc). Use the module show command to find the path to the lib and include directories to add the LDFLAGS and CPPFLAGS when compiling applications.

MPI enabled libraries are built with both mpich and mvapich2. Since you can only load one mpi library at a time, you should one see one set of libraries built with mpich/mvapich2 with the compiler loaded. For libraries such as fftw, hdf5, etc that have serial as well as mpi versions, the mpi compiled libraries will take precedence. Unload the mpi library to use the serial library.


Library

Module Name

Version

GCC 8.3.1

GCC 9.3.0

Intel 19.0.3

Intel 20.0.3

OneAPI 2021.3.0NVIDIA 20.9

ARPACK

arpack-ng

3.7.0

YYYYY

BOOST

boost

1.74.0

YYYYY

FFTW

fftw

3.3.8

Y+MPIY+MPIY+MPIY+MPIY+MPI
GSLgsl2.5YYYYY

HDF5

hdf5

1.10.7

Y +MPIY+MPIY+MPIY+MPIY+MPI
HYPREhypre2.20.0Y +MPIY+MPIY+MPIY+MPIY+MPI

METIS

metis

5.1.0

YYYYY
MPICHmpich3.3.2YYYYYY

MUMPS

mumps

5.3.3

Y+MPIY+MPIY+MPIY+MPI

MVAPICH2

mvapich2

2.3.4

YYYYYY

NETCDF C

netcdf-c

4.7.4

Y+MPIY+MPIY+MPIY+MPIY+MPI

NETCDF CXX

netcdf-cxx4.2Y+MPIY+MPIY+MPIY+MPIY+MPI
NETCDF Fortrannetcdf-fortran4.5.3Y+MPIY+MPIY+MPIY+MPIY+MPI

OpenBLAS

openblas

0.3.10

YYYYY
OpenMPIopempi4.0.5YYYYYY

ParMETIS

parmetis

4.0.3

YYYYY

PETSc

petsc

3.14.1

Y+MPIY+MPIY+MPIY+MPIY+MPI

Qhull

qhull

2020.1

YYYYY

QRUpdate

qrupdate

1.1.2

YYYYY

SuiteSparse

suite-sparse

5.7.2

YYYYY

SuperLU

superlu

5.2.1

YYYYY

SuperLU_DIST

superlu-dist

6.3.1

YYYYY

SuperLU_MT

superlu-mt

3.1

YYYYY