Software on JADE

The software initially installed on the machine is listed in the following table:

Application	Version	Note
GNU compiler suite	4.8.5	part of O/S
Intel compiler suite	2021.3
OpenMPI	2.1.6
OpenMPI	4.0.5	Inlcudes multi-thread support
Gromacs	2016.3	Supplied by Nvidia
NAMD	2.14

This software has been built from source and installed as modules. To list the source built applications do:

$ module avail
----------------------------------------------- /jmain02/apps/Modules/modulefiles/packages ------------------------------------------------------------------------------
autodock-gpu/1.5.2   gnuplot/5.2.8                 gromacs/2021.1       namd/2.14            opencv/4.2.0   pytorch/1.9.0     tmux/3.2a (D)
emacs/27.1           gromacs/2020.3                gromacs/2021.2 (D)   namd/3.0-alpha7 (D)  openmm/7.5.0   sox/14.4.2        vim/8.2
ffmpeg/4.2.2         gromacs/2020.4-plumed-2.6.2   mdtraj/1.9.5         nano/5.3             plumed/2.6.2   tensorflow/2.3.1

The following are the available applications, libraries and development tools on the JADE cluster:

• Machine Learning
  • Caffe
  • Tensorflow
  • Torch
• Molecular Dynamics
  • Gromacs
  • NAMD
• Python
  • Using standard Python
  • Using conda Python
• Git
  • Cloning/pushing to/pulling from online Git repositories
• Dataset Repositories
  • Dataset List