Software Administration

• Editing these documents
  • Using the Singularity image
  • Editing the documentation manually
• Installing Packages in User Locations
  • Overview: GNU Build System
  • Additional Documentation
• Linear Algebra
  • Compiling Reference BLAS and LAPACK
  • Installing Numpy and Scipy using OpenBLAS
  • Multithreading with OpenBLAS
  • ScaLapack 2.2.0 on Spruce with GCC 10.3.0
  • ELPA 2021.11 on Spruce with GCC 10.3
  • ELPA 2021.11 on Thorny with Intel 2022
• Boost 1.79
  • Downloading the code
  • Bootstrap for GCC 9.3
  • Compile and install boost
• Message Passing Interface
  • MPI Standards
  • Useful Books
  • Libraries
• HDF5 and NetCDF
  • HDF5
  • NetCDF
• Fast Fourier Transforms
• Force Field Molecular Dynamics
  • Plumed
  • AMBER 22
  • Gromacs
  • LAMMPS
• CHARM++ and NAMD
  • Compiling Charm++
  • Compiling NAMD2
  • Quick test NAMD2 for Alanin
  • Script summarizing compilation of NAMD
  • Benchmarking NAMD2
  • Conclusions
• Density Functional Theory
  • ABINIT
  • CASTEP
  • VASP
  • Octopus
  • Quantum Espresso
  • ELK
  • Siesta
• Big Data
  • What is Hadoop
  • Using Hadoop on the cluster
  • R Interface with Hadoop - Rhipe
  • Further Information
• Python 3.9.7
  • Modules
  • Download
  • Configure
  • Numpy and Scipy
• Matlab N-D multithreaded matrix operations (MMX)
  • Download the code
  • Edit the building script
  • Build a custom MKL library
  • Compile MMX
  • Teting the 3 compilations of MMX
  • Conclusions
• Building Julia
• Tinker9
  • Clone the repository
  • Create a build folder
  • Modules for compilation
  • Configuring tinker9
  • Running the tests
• Updating NVIDIA Driver and CUDA Toolkit
  • Draining the nodes
  • Updating the NVIDIA Driver and CUDA Toolkit
  • Verify NVIDIA Driver and CUDA Toolkit versions