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Several free and open source software and libraries are installed on Sol 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, the default MPI implementation is mvapich2. The default compiler for building applications on Sol is Intel 16.0.3. mvapich2 compiled with GCC 6.1.0 and PGI 16.5 is available for building and developing applications. All software installed after Jan 2018 are optimized for AVX, AVX2 and AVX512 instruction set using the Intel 18.0.1 compiler and mvapich2 2.2.

In our testing, we have found that mvapich2 gives better performance than openmpi. Research Computing staff will not build and maintain applications with every combination of compiler and mvapich2 (or openmpi, mpich etc). However, commonly used libraries are built with different compilers to aid developers who require additional flexibility with the software environment.

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 display foo

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


module show foo

module load foo

loads module foo


module add 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 rm foo

Installed Software

For software with multiple version install, 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

Software

Version

Type

Subject

module

GPU Support

Abaqus

6.14

Application

CFD

abaqus/6.14


Abaqus

2016

Application

CFD

abaqus/2016


Abaqus2019ApplicationCFD

abaqus/2019


ANGSD0.921ApplicationBioinformaticsangsd/0.921

Ansys

17.1

Application

CFD

ansys/17.1


bamtools

2.4.1

Application

Bioinformatics

bamtools/2.4.1


bartender

1.1

Application

Bioinformatics

bartender/1.1


bayescan

2.1

Application

Bioinformatics

bayescan/2.1


BayesTraits3.0.1ApplicationBioinformaticsbayestraits/3.0.1

bgc

1.03

Application

Bioinformatics

bgc/1.03


BLAST2.9.0ApplicationBioinformaticsblast-plus/2.9.0
BLAT35ApplicationBioinformaticsblat/35
bowtie1.2.2_p1ApplicationBioinformaticsbowtie/1.2.2_p1

bowtie2

2.3.4.1

Application

Bioinformatics

bowtie2/2.3.4.1


bowtie22.3.5ApplicationBioinformaticsbowtie2/2.3.5
bte1.0ApplicationBioinformaticsbte/1.0

bwa

0.7.15

Application

Bioinformatics

bwa/0.7.15


cactus
ApplicationBioinformatics

canu1.5ApplicationBioinformaticscanu/1.5

comsol

5.2a

Application

CFD

comsol/5.2a


CPMD

4.1

Application

Chemistry

cpmd/4.1


express1.5.2ApplicationBioinformaticsexpress/1.5.2
fastjet3.3.2ApplicationHigh Energy Physicsfastjet/3.3.2
fastqc0.11.7ApplicationBioinformaticsfastqc/0.11.7

fastx-toolkit

0.0.14

Application

Bioinformatics

fastx-toolkit/0.0.14


freebayes

1.1.0

Application

Bioinformatics

freebayes/1.1.0


GAMESS

5Dec2014

Application

Chemistry

gamess/5Dec2014


GAMS

24.8.5

Application

Math

gams/24.8.5


GATK4.1.0.0ApplicationBioinformaticsgatk/4.1.0.0

Gaussian

09 Rev D01

Application

Chemistry

gaussian/g09


GROMACS

5.1.2

Application

Biochemistry

gromacs/5.1.2 

gromacs/5.1.2-gpu

GROMACS

2016.4

Application

Biochemistry

gromacs/2016.4

gromacs/2016.4-gpu

GROMACS2016.4 + PlumedApplicationBiochemistrygromacs/2016.4-plgromacs/2016.4-gpu-pl

GROMACS

2018.1

Application

Biochemistry

gromacs/2018.1

gromacs/2018.1-gpu

GROMACS2018.1 + PlumedApplicationBiochemistrygromacs/2018.1-plgromacs/2018.1-gpu-pl

GROMACS

2018.1 (AVX512 Optimized)

Application

Biochemistry

gromacs/2018.1-avx512

gromacs/2018.1-avx512-gpu

GROMACS2019.2ApplicationBiochemistrygromacs/2019.2
GROMACS2019.2 (AVX512 Optimized)ApplicationBiochemistrygromacs/2019.2-avx512
guppy3.1.5ApplicationBioinformaticsguppy/3.1.5guppy/3.1.5-gpu
gurobi8.1.1ApplicationMathgurobi/8.1.1
hal2.1ApplicationBioinformaticshal/2.1
jellyfish2.2.7ApplicationBioinformaticsjellyfish/2.2.7
kallisto0.43.1ApplicationBioinformaticskallisto/0.43.1

knitro

10.3.0

Application

Math

knitro/10.3.0


LAMMPS

14May16

Application

Materials

lammps/14may16

lammps/14may16-gpu

LAMMPS

17Nov16

Application

Materials

lammps/17nov16

lammps/17nov16-gpu

LAMMPS

31Mar17

Application

Materials

lammps/31mar17

lammps/31mar17-gpu

LAMMPS

11Aug17

Application

Materials

lammps/11aug17

lammps/11aug17-gpu

LAMMPS

16Mar18

Application

Materials

lammps/16mar18

lammps/16mar18-gpu

LAMMPS

12Dec18

Application

Materials

lammps/12dec18

lammps/12dec18-gpu2080

Quantum Espresso

5.4.0

Application

Chemistry

espresso/5.4.0


Magma

2.22-5

Application

Math

magma/2.22


Maple

2016

Application

Math

maple/2016


Mathematica

10.4

Application

Math

mathematica/10.4


Matlab

R2016a

Application

Math

matlab/R2016a


Matlab

R2016b

Application

Math

matlab/R2016b


Matlab

R2018a

Application

Math

matlab/R2018a


Matlab Compiler Runtime

9.0.1

Application

Math

matlab/mcrv901


Matlab Compiler Runtime

9.1

Application

Math

matlab/mcrv91


miniasm2018-3-30ApplicationBioinformaticsminiasm/2018-3-30
minimap22.2ApplicationBioinformaticsminimap2/2.2

NAMD

2.11

Application

Biochemistry

namd/2.11 

namd/2.11-gpu

NAMD

2.12

Application

Biochemistry

namd/2.12

namd/2.12-gpu

NAMD

2.13

Application

Biochemistry

namd/2.13

namd/2.13-gpu

NGS Tools19apr12ApplicationBioinformaticsngstools/19apr12

NWChem

6.5

Application

Chemistry

nwchem/6.5


NWChem

6.6

Application

Chemistry

nwchem/6.6


NWChem

6.8

Application

Chemistry

nwchem/6.8


GNU Octave

4.2.0

Application

Math

octave/4.2.0


openfoam

v1606+

Application

CFD

openfoam/v1606+


openModeller

1.5.0

Application


openmodeller/1.5.0


opensees

6303

Application

CFD

opensees/6303


opensees

6303-mp

Application

CFD

opensees/6303-mp


paml4.9hApplicationBioinformaticspaml/4.9h
pear0.9.11ApplicationBioinformaticspear/0.9.11
Perl5.24.1ApplicationProgrammingperl/5.24.1
Perl5.26.2ApplicationProgrammingperl/5.26.2-gcc-5.3.0
Perl5.26.2ApplicationProgrammingperl/5.26.2-gcc-6.1.0
Perl5.30.0ApplicationBioinformaticsperl/5.30.0-gcc-5.3.0
PHAST1.4ApplicationBioinformaticsphast/1.4
pilon1.22ApplicationBioinformaticspilon/1.22

Plumed

2.4.1

Application

Biochemistry

plumed/2.4.1 


Plumed

dev-1804

Application

Biochemistry

plumed/dev-1804


Plumed

2.4.3

Application

Biochemistry

plumed/2.4.3


porechop0.2.3ApplicationBioinformaticsporechop/0.2.3
pythia88235ApplicationHigh Energy Physicspythia8/8235

Python

2.7.10

Application

Programming

anaconda/python2


Python

3.5.1

Application

Programming

anaconda/python3


Python3.7.4ApplicationBioinformaticspython/3.7.4

Tensorflow

1.3.0

Application

Data Science

anaconda/tensorflow


ASE

3.9

Application

Chemistry

python/ase


RDKIT

Release_2017.03.3

Application

Chemistry

python/rdkit


R

3.3.3

Application

Programming

r-project/3.3.3


R

3.4.2

Application

Programming

r-project/3.4.2


R

3.4.3

Application

Programming

anaconda/python3


R

3.5.3

Application

Programming

r-project/3.5.3


R3.5.3ApplicationBioinformaticsr-bio/3.5.3

relion

3.0.6

Application

Bioinformatics

relion/3.0.6

relion/3.0.6-gpu
ROOT6.10.08ApplicationHigh Energy Physicsroot/6.10.08
rsem1.3.1ApplicationBioinformaticsrsem/1.3.1
salmon0.12.0ApplicationBioinformaticssalmon/0.12.0
samtools1.4ApplicationBioinformaticssamtools/1.4
samtools1.9ApplicationBioinformaticssamtools/1.9
SnpEff4.3tApplicationBioinformaticssnpEff/v4.3t
star2.7.0eApplicationBioinformaticsstar/2.7.0e
swig3.0.12ApplicationProgrammingswig/3.0.12

tabix

2013-12-16

Application

Bioinformatics

tabix/2013-12-16


trimmomatic

0.36

Application

Bioinformatics

trimmomatic/0.36


trinity2.6.6ApplicationBioinformatics

VASP

5.4.1

Application

Chemistry

vasp/5.4.1, vasp/5.4.1-neb


VASP5.4.4ApplicationChemistryvasp/5.4.4

vcftools

0.1.14

Application

Bioinformatics

vcftools/0.1.14


vcftools

0.1.15

Application

Bioinformatics

vcftools/0.1.15 


avogadro

1.1.1

Visualization

Chemistry

avogadro/1.1.1


GaussView


Visualization

Chemistry

gaussian/gview


GNUplot

5.0.3

Visualization

Utilities

gnuplot/5.0.3


GNUplot5.2.0VisualizationUtilitiesgnuplot/5.2.0
GNUplot5.2.5VisualizationUtilitiesgnuplot/5.2.5

PWGui

5.4.0

Visualization

Chemistry

pwgui/5.4.0


PyMol

1.8.6.0

Visualization

Chemistry

pymol/1.8.6.0


VESTA

3.4.0

Visualization

Chemistry

vesta/3.4.0


VMD

1.9.2

Visualization

Biochemistry

vmd/1.9.2


XCrysDen

1.5.60

Visualization

Chemistry

xcrysden/1.5.60


ActiveTCL

8.5

Library

Utilities

activetcl/8.5


Eigen

3.2.9

Library

Utilities

eigen/3.2.9


OpenBabel

2.4.1

Library

Utilities

openbabel/2.4.1


TCL8.6.8LibraryUtilitiestcl/8.6.8
TK8.6.8LibraryUtilitiestk/8.6.8

TCL+TK

8.5

Library

Utilities

tcltk/8.5


TCL+TK

8.6

Library

Utilities

tcltk/8.6


Cmake

3.5.2

Dev Tools

Utilities

cmake/3.5.2


CUDA

7.0

Dev Tools

Programming

cuda/7.0


CUDA

8.0

Dev Tools

Programming

cuda/8.0


CUDA

9.2

Dev Tools

Programming

cuda/9.2


CUDA

10.0

Dev Tools

Programming

cuda/10.0


GCC

5.3.0

Dev Tools

Programming

gcc/5.3.0


GCC

6.1.0

Dev Tools

Programming

gcc/6.1.0


GCC

7.1.0

Dev Tools

Programming

gcc/7.1.0


GCC8.1.0

Dev Tools

Programming

gcc/8.1.0


GNU Parallel

20170322

Dev Tools

Utilities

parallel/20170322


Intel

16.0.3

Dev Tools

Programming

intel/16.0.3


Intel

17.0.0

Dev Tools

Programming

intel/17.0.0


Intel

17.0.3

Dev Tools

Programming

intel/17.0.3


Intel

18.0.1

Dev Tools

Programming

intel/18.0.1


Java

1.8.0_202-b08

Dev Tools

Programming

jdk/1.8.0_202-b08


Java11.0.2Dev ToolsProgrammingjdk/11.0.2

PGI

16.5

Dev Tools

Programming

pgi/16.5

Built-in OpenACC Support

PGI

16.10

Dev Tools

Programming

pgi/16.10

Built-in OpenACC Support

PGI

17.4

Dev Tools

Programming

pgi/17.4

Built-in OpenACC Support

PGI

17.7

Dev Tools

Programming

pgi/17.7

Built-in OpenACC Support

PGI

18.3

Dev Tools

Programming

pgi/18.3

Built-in OpenACC Support

PGI

19.1

Dev Tools

Programming

pgi/19.1

Built-in OpenACC Support

Scons

2.5.0

Dev Tools

Utilities

scons/2.5.0


screen4.6.2Dev ToolsUtilitiesscreen/4.6.2

Spack

0.10.0

Dev Tools

Utilities

spack/0.10.0


tmux2.8Dev ToolsUtilitiestmux/2.8

Most libraries are compiled with multiple compilers. The nomenclature for module names is libraryname/version/compiler-compilerversion. If the library requires a MPI compiler, then -mvapich2-2.1 is appended to the above labeling scheme. If the library is GPU enabled, then cuda-x.0 is appended to its name where x (default 8) is the CUDA Toolkit version.

Library

Version

GCC 6.1.0

Intel 16.0.3

Intel 17.0.3

Intel 18.0.1

PGI 16.10

ARPACK

3.3.0

Y

Y




BOOST

1.61.0

Y

Y




FFTW

3.3.4

Y

Y




FFTW

3.3.7




Y


GSL

2.1

Y

Y




GSL2.5


Y

HDF5

1.10.0

Y

Y



Y

HDF5

1.10.1




Y


HDF51.10.4


Y

LAPACK

3.6.0

Y

Y




METIS

5.1.0

Y

Y




MUMPS

5.0.2


With MPI




MVAPICH2

2.1

Y + CUDA7,8

Y + CUDA7,8



Y

MVAPICH2

2.2



Y + CUDA

Y + CUDA9


NETCDF

4.4.0

Y

Y



Y

PARMETIS

4.0.3

Y

Y




PETSc

3.7.3


With MPI




Qhull

2015.2

Y





QRUpdate

1.1.2

Y





Scalapack

2.0.2

With MPI

With MPI




SuiteSparse

4.5.3

Y

Y




SuperLU

5.2.1


Y




SuperLU_DIST

5.1.0


With MPI




SuperLU_MT

3.0


Y




Libraries and packages built with intel 18.0.1 have support for Intel's AVX512 Vector Extension available on Intel Xeon Phis and Scalable Xeon Processors. Please use PGI 18.3 or PGI 2018 to compile code on the Scalable Xeon Processors.


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