README.md

Example Codes, Use Cases & Documentation

Table of Contents below is not complete but only includes links to popular libaries. Other examples are contained in this repo that are in the directory tree, use search to look through the full repository.

Building Software

• Binaries
• CMake
• GNU Toolchain
• Spack

Singularity Containers

• Biocontainers
• MPI Applications
• OpenMPI Applications
• Working with Images

Programming Languages and Environments

• BASH
• C
• C++
• Fortran
• IDL
• Julia
• Mathematica
• MATLAB
• Perl
• Python
• R
• STATA

Numerical and I/O Libraries

• Armadillo
• BLAS
• FFTW
• GSL
• HDF5
• LAPACK
• MKL
• NETCDF
• OpenBLAS

Machine Learning Frameworks

• TensorFlow
• PyTorch
• MXNet

Parallel Computing

• Embarrassingly Parallel
• HDF5
• MATLAB
• MPI
• MPI-IO
• Mathematica
• NetCDF
• OpenMP
• PnetCDF
• Python
• R
• STATA
• ScaLAPACK

Applications

• AlphaFold
• CryoSPARC
• Dynamite
• Knitro
• LANDIS
• Schrodinger
• TotalView
• Weather Research and Forecasting (WRF) Model

Preformance

• TAU

Example Recipes

• Image processing with MATLAB
• Job Arrays
• MATLAB MEX files from C++ source code
• Movie processing and reading data from CSV files
• Parallel Job Arrays
• Pytorch Example