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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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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: