System Software

Cluster management software: OpenHPC 1.3 based on the CentOS 7.7 64-bit operating system
Cluster file system for Scratch: BeeGFS 7.1.4
Resource management and job scheduling system: Simple Linux Utility for Resource Management (SLURM) 18.08.8

Application Software


HPC3 uses Lmod to manage installations for most application software. With the modules system, user can set up the shell environment to give access to applications, and make running and compiling software easier. It also allows us multiple versions of the same software co-exist and be used and abstract things from the version and high dependencies of the OS.

When log into the cluster, a default, bare bone environment with minimal software available would be shown. The module system is used to manage the user environment and to activate software packages on demand. In order to use software installed on HPC3, the corresponding software module must first be loaded.  When loading a module, the system will set or modify the corresponding user environment variables to enable access to the software package provided by that module. For example, the $PATH environment variable might be updated so that appropriate executables for that package can be used.

Module Usage

The most common module commands are listed in the following table for reference.

Module command Description
module list List loaded modules in current environment
module avail List available software
module spider R Search for particular software, e.g, R
module whatis R Display information about a particular module, e.g, R
module load R Load a particular module, e.g, R
module load anaconda3/2021.05 Load a particular module with specific version, e.g, anaconda3 of version 2021.05
module unload R Unload a particular module, e.g, R
module swap gnu8 intel Swap modules, e.g, replace default GNU8 compiler with intel compiler
module purge Remove all modules

Table 1. common module commands


Module List

The following software are available as loadable module:

Module name Version Description
EasyBuild 3.9.4 Build and installation framework
anaconda3 2020.02 Package manager for Python/R
anaconda3 2021.05 Default version, Package manager for Python/R
autotools   Default loaded, Developer utilities
charliecloud 0.11 Lightweight user-defined software stacks for high-performance computing
cmake 3.15.4 Open-source, cross-platform family of tools designed to build, test and package software
cuda 10.2 CUDA toolkit for NVIDIA GPU, only useable in GPU nodes
cuda 11.2 Default version, CUDA toolkit for NVIDIA GPU, only useable in GPU nodes
gnu 5.4.0 GNU compilers
gnu8 8.3.0 Default loaded, GNU compilers
gnuplot 5.2 Portable command-line driven graphing utility
gromacs 2021.4 Molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids
hwloc 2.1.0 Package provides a portable abstraction of the hierarchical topology of modern architectures
intel Intel Parallel Studio XE 2019
llvm5 5.0.1 Compiler infrastructure LLVM
mathematica 12.2.0 Symbolic mathematical computation program
matlab R2019b MATLAB
matlab R2020a MATLAB
matlab R2020b Default version, MATLAB
nvhpc 21.9 NVIDIA HPC Software Development Kit
ohpc   Default loaded, OpenHPC module to load autotools, prun, gnu8 and openmpi3
openmpi3 3.1.4 Default loaded, An open source Message Passing Interface implementation
papi 5.7.0 Performance Application Programming Interface
pmix 2.2.2 Process Management Interface
prun 1.3 Default loaded, job launch utility for multiple MPI families
R 3.6.1 A programming language for statistical computing
singularity 3.4.1 Container platform
subversion 1.13.0 Open source version control system
valgrind 3.15.0 An instrumentation framework for building dynamic analysis tools

Table 2. available modules in HPC3

Software Installation

In general, if users find the listed software above can't meet their needs, they can install software in their own home directory or in the group share directory. Please note that users are responsible for the licenses and copyright of the software they install in the cluster. Users should also adhere to ITSC’s Acceptable Use Policy.