Software

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 foo	Query 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
Abaqus	2019	Application	CFD	abaqus/2019
ADIOS2	2.6.0	Dev Tools	Library	adios2/2.6.0
almaBTE	1.3.2	Application	Materials	almabte/1.3.2
Anaconda3	2019.10 (Python 3.7.4)	Application	Various	anaconda3/2019.10
Anaconda3	2020.07 (Python 3.8.6)	Application	Various	anaconda3/2020.07
ANGSD	0.933	Application	Bioinformatics	angsd/0.933
Ansys	20.2	Application	CFD	ansys/20.2
aria2	1.35.0	Dev Tools	Utility	aria2/1.35.0
ARPACK	3.7.0	Dev Tools	Library	arpack-ng/3.7.0
AutoDock	4.2.6	Application	Biochemistry	autodock/4.2.6
Avogadro		Visualization	Chemistry	Open OnDemand App
Axel	2.16.1	Dev Tools	Utility	axel/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
BayesTraits	3.0.2	Application	Bioinformatics	bayestraits/3.0.2
BerkeleyGW	3.0.1	Application	Materials	berkeleygw/3.0.1
bgc	1.03	Application	Bioinformatics	bgc/1.03
BLAST	2.9.0	Application	Bioinformatics	blast-plus/2.9.0
BLAT	35	Application	Bioinformatics	blat/35
Blender		Visualization		Open Ondemand App
BOOST	1.64.0	Dev Tools	Library	boost/1.74.0
Bowtie	1.3.0	Application	Bioinformatics	bowtie/1.3.0
Bowtie2	2.4.1	Application	Bioinformatics	bowtie2/2.4.1
BWA	0.7.17	Application	Bioinformatics	bwa/0.7.15
Cactus	1.3.0	Application	Bioinformatics	cactus/1.3.0
Canu	1.8	Application	Bioinformatics	canu/1.8
CCP4	7.0	Application	Chemistry	ccp4/7.0
CMake	3.18.4	Dev Tools	Utilities	cmake/3.18.4
COMSOL	5.4	Application	CFD	comsol/5.4
COMSOL	6.0	Application	CFD	comsol/6.0
CRYSTAL17	1.0.2	Application	Chemistry	crystal17/1.0.2
CUDA	10.2.89	Dev Tools	Programming	cuda/10.2.89
CUDA	11.0.2	Dev Tools	Programming	cuda/11.0.2
CUDA	11.1.0	Dev Tools	Programming	cuda/11.1.0
CUDNN	8.0.4.30	Dev Tools	Library	cudnn/8.0.4.30-11.0-linux-x64
DDD	3.3.12	Dev Tools	Utilities	ddd/3.3.12
DL_POLY_4	4.09	Application	Materials	dl_poly/4.09
DL_POLY_4	4.10	Application	Materials	dl_poly/4.10
DMTCP	2.6.0	Dev Tools	Utilities	dmtcp/2.6.0
Eigen	3.3.8	Dev Tools	Library	eigen/3.3.8
ESPResSo	4.0.2	Application	Materials	py-espresso/4.0.2
Exonerate	2.4.0	Application	Bioinformatics	exonerate/2.4.0
eXpress	1.5.2	Application	Bioinformatics	express/1.5.2
FastJet	3.3.3	Application	High Energy Physics	fastjet/3.3.3
Fastqc	0.11.7	Application	Bioinformatics	fastqc/0.11.7
FASTX-Toolkit	0.0.14	Application	Bioinformatics	fastx-toolkit/0.0.14
FFTW	3.3.8	Dev Tools	Library	fftw/3.3.8
FreeBayes	1.1.0	Application	Bioinformatics	freebayes/1.1.0
Gabedit		Visualization	Chemistry	Open Ondemand App
GAMESS	30 June 2021 R1	Application	Chemistry	gamess/30Jun2021
GAMS		Application	Math
GATK	4.1.0.0	Application	Bioinformatics	gatk/4.1.0.0
Gaussian	09 Rev D01	Application	Chemistry	gaussian/g09
Gaussian	16 Rev C01 (AVX2 enabled)	Application	Chemistry	gaussian/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 Arrays	5.7	Dev Tools	Library	globalarrays/5.7
GMAP (with GSNAP)	2020-06-01	Application	Bioinformatics	gmap-gsnap/2020-06-01
GNU Parallel	20200822	Dev Tools	Utilities	parallel/20200822
GNUPlot	5.2.8	Visualization	Utilities	gnuplot/5.2.8
Graphviz	2.4.4.1	Visualization	Utilities	graphviz/2.44.1
GROMACS	2020.4	Application	Biochemistry	gromacs/2020.4	(load intel/19.0.3 module)
GROMACS	2020.4 + Plumed	Application	Biochemistry	gromacs/2020.4-plumed	(load intel/19.0.3 module)
GROMACS	2021.4	Application	Biochemistry	gromacs/2021.4	gromacs/2021.4-cuda-11.6.0
GROMACS	2021.4 + Plumed	Application	Biochemistry	gromacs/2021.4-plumed	gromacs/2021.4-plumed-cuda-11.6.0
GSL	2.5	Dev Tools	Library	gsl/2.5
Guppy	3.1.5	Application	Bioinformatics	guppy/3.1.5	guppy/3.1.5-gpu
Guppy	4.0.14	Application	Bioinformatics	guppy/4.0.14	guppy/4.0.14-gpu
Gurobi	8.1.1	Application	Math	gurobi/8.1.1
Hadoop	3.2.1	Application	Data Science	hadoop/3.2.1
Hal	2.1	Application	Bioinformatics	hal/2.1
HDF5	1.10.7	Dev Tools	Library	hdf5/1.10.7
HISAT2	2.2.0	Application	Bioinformatics	hisat2/2.2.0
Hive	3.1.2	Application	Data Science	hive/3.1.2
HYPRE	2.20.0	Dev Tools	Library	hypre/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
JELLYFISH	2.2.7	Application	Bioinformatics	jellyfish/2.2.7
Julia	1.5.2	Application	Programming	julia/1.5.2
KaHIP	2.00	Dev Tools	Library	kahip/2.00
kallisto	0.46.2	Application	Bioinformatics	kallisto/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
Libarchive	3.4.3	Dev Tools	Library	libarchive/3.4.3
Magma (MATH package)	2.26	Application	Math	magma_math/2.26
Magma (GPU Library)	2.5.4	Dev Tools	Library	magma/2.5.4
Maple		Application	Math
MaSuRCA	3.4.2	Application	Bioinformatics	masurca/3.4.2
Mathematica	12.0	Application	Math	mathematica/12.0
MATLAB	R2020a	Application	Math	matlab/R2020a
MATLAB	R2021b	Application	Math	matlab/R2021b
METIS	5.1.0	Dev Tools	Library	metis/5.1.0
Miniasm	2018-3-30	Application	Bioinformatics	miniasm/2018-3-30
Minimap2	2.14	Application	Bioinformatics	minimap2/2.14
Moose		Dev Tools	CFD	moose/devenv
MPICH	3.3.2	Dev Tools	Library	mpich/3.3.2
MUMPS	5.3.3	Dev Tools	Programming	mumps/5.3.3
MVAPICH2	2.3.4	Dev Tools	Programming	mvapich2/2.3.4
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
Ncdu	1.13	Dev Tools	Utility	ncdu/1.13
NETCDF-C	4.7.4	Dev Tools	Library	netcdf-c/4.7.4
NETCDF-CXX	4.2	Dev Tools	Library	netcdf-cxx/4.2
NETCDF-Fortran	4.5.3	Dev Tools	Library	netcdf-fortran/4.5.3
NGMLR	0.2.7	Application	Bioinformatics	ngmlr/0.2.7
NGS Tools	2019-06-24	Application	Bioinformatics	ngstools/2019-06-24
NLOpt	2.6.2	Dev Tools	Library	nlopt/2.6.2
NVIDIA HPC SDK (formerly PGI compiler)	20.9	Dev Tools	Programming	nvhpc/20.9	Built-in CUDA 11.0 and OpenACC Support
NWChem	7.0.2	Application	Chemistry	nwchem/7.0.2
Octave	5.2.0	Application	Math	octave/5.2.0
OpenBabel	3.0.0	Dev Tools	Library	openbabel/3.0.0
OpenBLAS	0.3.10	Dev Tools	Library	openblas/0.3.10
OpenBLAS	0.3.12	Dev Tools	Library	openblas/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
OpenJDK	11.0.2	Dev Tools	Programming	openjdk/11.0.2
OpenMolcas	19.11	Application	Chemistry	openmolcas/19.11
OpenMolcas	22.02	Application	Chemistry	openmolcas/22.02
OpenMPI	4.0.5	Dev Tools	Programming	openmpi/4.0.5
OpenSees	3.3.0	Application	CFD	opensees/3.3.0
PAML	4.9j	Application	Bioinformatics	paml/4.9j
Paraview	5.8.1	Visualization	CFD	paraview/5.8.1
ParMETIS	4.0.3	Dev Tools	Library	parmetis/4.0.3
PEAR	0.9.11	Application	Bioinformatics	pear/0.9.11
Perl	5.32.0	Application	Programming	perl/5.32.0
PETSc	3.14.1	Dev Tools	Library	petsc/3.14.1
PHAST	1.4	Application	Bioinformatics	phast/1.4
PHENIX	1.16	Application	Chemistry	phenix/1.16
Picard	2.20.8	Application	Bioinformatics	picard/2.20.8
Pilon	1.22	Application	Bioinformatics	pilon/1.22
Plumed	2.6.2	Application	Biochemistry	plumed/2.6.2
Plumed	2.7.3	Application	Biochemistry	plumed/2.7.3
Porechop	0.2.4	Application	Bioinformatics
POV-RAY	3.7.0.10	Visualization	Utilities	povray/3.7.0.10
PWGui	6.1	Visualization	Chemistry	pwgui/6.1
PyMol	1.8.6.0	Visualization	Chemistry
pyparsing	2.4.2	Application	Utilities	py-pyparsing/2.4.2
PYTHIA8	8303	Application	High Energy Physics	pythia8/8303
Python	3.8.6	Application	Programming	python/3.8.6
QCacheGrind	20.08.0	Dev Tools	Programming	qcachegrind/20.08.0
Qhull	2020.1	Dev Tools	Library	qhull/2020.1
QRUpdate	1.1.2	Dev Tools	Library	qrupdate/1.1.2
Quantum Espresso	6.5	Application	Chemistry	quantum-espresso/6.5
Quantum Espresso	6.6	Application	Chemistry	quantum-espresso/6.6
Quantum Espresso + WEST	6.1.0 + 4.3.0	Application	Chemistry	qe-west/6.1.0-4.3.0
R	4.0.3	Application	Programming	r/4.0.3
Rclone	1.53.3	Dev Tools	Utilities	rclone/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
RMCProfile	6.7.9	Application	Materials	rmcprofile/6.7.9
ROOT	6.20.08	Application	High Energy Physics	root/6.20.08
RSEM	1.3.1	Application	Bioinformatics	rsem/1.3.1
Salmon	0.14.1	Application	Bioinformatics	salmon/0.14.1
SAM Tools	1.10	Application	Bioinformatics	samtools/1.10
SAS	9.4	Application	Analytics	sas/9.4
Scons	3.1.2	Dev Tools	Utilities	scons/3.1.2
Scotch	6.0.10	Dev Tools	Library	scotch/6.0.10
Screen	4.8.0	Dev Tools	Utilities	screen/4.8.0
ShengBTE	1.1.1-8a63749	Application	Materials	shengbte/1.1.1-8a63749
SimModeler	8.0	Application	CFD	simmodeler/8.0
Singularity		Dev Tools	Utilities	default, no module needed
SnpEff	5.0	Application	Bioinformatics	snpeff/5.0
Spack	releases/v0.16 branch	Dev Tools	Utilities	install your own, use /share/Apps/lusoft as upstream
Spark	3.2.0	Application	Data Science	spark/3.2.0
Stacks	2.55	Application	Bioinformatics	stacks/2.55
STAR	2.7.0e	Application	Bioinformatics	star/2.7.0e
Stata	15	Application	Analytics	stata/15
Stata	17	Application	Analytics	stata/17 (serial only)
Subread	2.0.0	Application	Bioinformatics	subread/2.0.0
SuiteSparse	5.7.2	Dev Tools	Library	suite-sparse/5.7.2
SuperLU	5.2.1	Dev Tools	Library	superlu/5.2.1
SuperLU-MT	3.1	Dev Tools	Library	superlu-mt/3.1
SuperLU-DIST	6.3.1	Dev Tools	Library	superlu-dist/6.3.1
SWIG	4.0.2	Application	Programming	swig/4.0.2
SYSWeld	2020.5	Application	CFD	sysweld/2020.5
tabix	2013-12-16	Application	Bioinformatics	tabix/2013-12-16
TCL	8.6.10	Dev Tools	Library	tcl/8.6.10
Tinker	9	Application	Chemistry	tinker/9
TK	8.6.10	Dev Tools	Library	tk/8.6.10
Tmux	3.1b	Dev Tools	Utilities	tmux/3.1b
trimmomatic	0.39	Application	Bioinformatics	trimmomatic/0.39
Trinity	2.12.0	Application	Bioinformatics	trinity/2.12.0
Valgrind	3.15.0	Dev Tools	Programming	valgrind/3.15.0
/wiki/spaces/hpc/pages/45253153	5.4.4	Application	Chemistry	vasp/5.4.4
/wiki/spaces/hpc/pages/45253153	5.4.4-pl2	Application	Chemistry	vasp/5.4.4-pl2, vasp/5.4.4.pl2-neb
/wiki/spaces/hpc/pages/45253153	6.1.2	Application	Chemistry	vasp/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
XDS	Feb2021 (license expires Mar 2022)	Visualization	Chemistry	xds/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 2021.3.0	NVIDIA 20.9
ARPACK	arpack-ng	3.7.0	Y	Y	Y	Y	Y
BOOST	boost	1.74.0	Y	Y	Y	Y	Y
FFTW	fftw	3.3.8	Y+MPI	Y+MPI	Y+MPI	Y+MPI	Y+MPI
GSL	gsl	2.5	Y	Y	Y	Y	Y
HDF5	hdf5	1.10.7	Y +MPI	Y+MPI	Y+MPI	Y+MPI	Y+MPI
HYPRE	hypre	2.20.0	Y +MPI	Y+MPI	Y+MPI	Y+MPI	Y+MPI
METIS	metis	5.1.0	Y	Y	Y	Y	Y
MPICH	mpich	3.3.2	Y	Y	Y	Y	Y	Y
MUMPS	mumps	5.3.3	Y+MPI	Y+MPI	Y+MPI	Y+MPI
MVAPICH2	mvapich2	2.3.4	Y	Y	Y	Y	Y	Y
NETCDF C	netcdf-c	4.7.4	Y+MPI	Y+MPI	Y+MPI	Y+MPI	Y+MPI
NETCDF CXX	netcdf-cxx	4.2	Y+MPI	Y+MPI	Y+MPI	Y+MPI	Y+MPI
NETCDF Fortran	netcdf-fortran	4.5.3	Y+MPI	Y+MPI	Y+MPI	Y+MPI	Y+MPI
OpenBLAS	openblas	0.3.10	Y	Y	Y	Y	Y
OpenMPI	opempi	4.0.5	Y	Y	Y	Y	Y	Y
ParMETIS	parmetis	4.0.3	Y	Y	Y	Y	Y
PETSc	petsc	3.14.1	Y+MPI	Y+MPI	Y+MPI	Y+MPI	Y+MPI
Qhull	qhull	2020.1	Y	Y	Y	Y	Y
QRUpdate	qrupdate	1.1.2	Y	Y	Y	Y	Y
SuiteSparse	suite-sparse	5.7.2	Y	Y	Y	Y	Y
SuperLU	superlu	5.2.1	Y	Y	Y	Y	Y
SuperLU_DIST	superlu-dist	6.3.1	Y	Y	Y	Y	Y
SuperLU_MT	superlu-mt	3.1	Y	Y	Y	Y	Y

Research Computing Systems

Software

Module Environment

Installed Software

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