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SciPyhttp://www.scipy.orgSciPy is a Python-based ecosystem of open-source software for mathematics, science, and engineering
NumPyhttp://www.numpy.orgBase N-dimensional array package
pyspreadhttps://pyspread.gitlab.io/pyspread is a non-traditional spreadsheet application that is based on and written in the programming language Python


Code Block
module load py3.6-numpy
module load pyspread
pyspread


IO Libraries

Adioshttp://www.olcf.ornl.gov/center-projects/adios

The Adaptable IO System (ADIOS).

HDF5/PHDF5http://www.hdfgroup.org/HDF5

A general purpose library and file format for storing scientific data.

NetCDFhttp://www.unidata.ucar.edu/software/netcdfFortran, C, and C++ libraries for the Unidata network Common Data
PnetCDFhttp://cucis.ece.northwestern.edu/projects/PnetCDF

A Parallel NetCDF library

ScionLibhttp://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html

Scalable I/O Library for Parallel Access to Task-Local Files.

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Boosthttp://www.boost.org

Free peer-reviewed portable C++ source libraries.

FFTWhttp://www.fftw.org

Fast Fourier Transform library.

Hyprehttp://www.llnl.gov/casc/hypre

Scalable algorithms for solving linear systems of equations.

MFEMhttp://mfem.org

Lightweight, general, scalable C++ library for finite element methods.

MUMPShttp://mumps.enseeiht.fr

A MUltifrontal Massively Parallel Sparse direct Solver.

PETSChttp://www.mcs.anl.gov/petsc

Portable Extensible Toolkit for Scientific Computation.

PT-SCOTCHhttp://www.labri.fr/perso/pelegrin/scotch

Graph, mesh and hypergraph partitioning library using MPI.

SLEPC http://slepc.upv.esA library for solving large scale sparse eigenvalue problems.
SuperLUhttp://crd.lbl.gov/~xiaoye/SuperLUA general purpose library for the direct solution of linear equations.
Trilinos https://trilinos.org/An object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. 

Capacitance Extraction/Field Solving

FasterCaphttps://www.fastfieldsolvers.com/fastercap.htmA powerful three- and two-dimensional capactiance extraction program


Code Block
languagebash
/usr/local/fastercap/FasterCap_6.0.7/FasterCap [-b]


Density Functional Approaches

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Archimedes/Rappture
https://www.gnu.org/software/archimedes
 https://nanohub.org/infrastructure/rappture
Archimedes belongs to the well-known family of TCAD software, i.e. tools utilized to assist the development of technologically relevant products. In particular, this package assists engineers in designing and simulating submicron and mesoscopic semiconductor devices.
Rappture is the GUI for Archimedes.


Code Block
languagebash
module load rappture


DevSim
https://devsim.org/

DEVSIM is semiconductor device simulation software which uses the finite volume method. It solves partial differential equations on a mesh. The Python interface allows users to specify their own equations.


Code Block
languagebash
bash
module load devsim
source /usr/local/intel/mkl/bin/mklvars.sh intel64


ElmerGNU7/OpenMPIhttps://www.csc.fi/web/elmer/elmer

Elmer is an open source multiphysical simulation software mainly developed by CSC - IT Center for Science (CSC). Elmer development was started 1995 in collaboration with Finnish Universities, research institutes and industry. After it's open source publication in 2005, the use and development of Elmer has become international.

Elmer includes physical models of fluid dynamics, structural mechanics, electromagnetics, heat transfer and acoustics, for example. These are described by partial differential equations which Elmer solves by the Finite Element Method (FEM).


Code Block
languagebash
module load elmer


HOOME-blueSingularity

http://glotzerlab.engin.umich.edu/hoomd-blue/index.html

https://glotzerlab-software.readthedocs.io/en/latest/software.html

https://glotzerlab-software.readthedocs.io/en/latest/

HOOMD-blue is a  general-purpose  particle simulation toolkit. It scales from a single CPU to thousands.


Code Block
languagebash
module load singularity
# Use this package for non-mpi jobs
singularity exec /usr/local/glotzerlab/glotzerlab-software-master-latest.simg [command-in-glotzerlab-package]
# Use this package for MPI jobs
singularity exec /usr/local/glotzerlab/glotzerlab-software-mpi-flux.simg [command-in-glotzerlab-package]


OpenFOAM v6 and v8
https://openfoam.comA Computational Fluid Dynamics (CFD) package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics.


Code Block
languagebash
bash
source /usr/local/openFOAM/OpenFOAM-6/etc/bashrc # for version 6
source /usr/local/openFOAM/OpenFOAM-8/etc/bashrc # for version 8
mkdir -p $FOAM_FUNRUN
run



Linear Algebra Operations

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BLAShttp://netlib.org/blas/The BLAS (Basic Linear Algebra Subprograms) are routines that provide standard building blocks for performing basic vector and matrix operations.
(OpenBLAS is also available... see above)


Code Block
languagebash
module load blas



Tomographic Data Processing and Image Reconstruction

TomoPy

https://tomopy.readthedocs.io/

https://tomopycli.readthedocs.io/

Tomographic reconstruction creates three-dimensional views of an object by combining two-dimensional images taken from multiple directions, for example, this is how a CAT (computer-aided tomography) scanner generates 3D views of the heart or brain.

Included is the tomopy-cli commandline interface.


Code Block
languagebash
bash
module load miniconda
conda activate tomopy
source /usr/local/miniconda3/envs/tomopy/bin/complete_tomopy.sh



Cluster HowTos: