Software

Operating system

The operating system of Hummel-2 is Debian GNU/Linux.

Software provisioning

All nodes are running diskless.
The operating system images contain a minimal set of software.
Most software is installed in the /sw directory and made available via Environment Modules.

Modules are organised in three groups:

/sw/BASE: base software (environments for compiling source code)
/sw/TOOL: software tools (like text editors, version control)
/sw/APP: application software (e.g. for quantum chemistry)

Environments for compiling source code

Environments for compiling source code are called

env/environment.

An environment contains:

a compiler
optionally an MPI library

For example:

env/gcc-13.2.0
env/gcc-13.2.0_openmpi-4.1.6

The combination compiler/MPI is fixed, i.e. here is no modularity (in contrast to what the name Modules suggests). Only a single env Module can be loaded at a time. Therefore env Modules are switched (not loaded):

module switch env env/newEnvironment

(The first env is a shortcut for the env currently chosen.)

An env can offer additional Modules, in particular sub-program libraries or CUDA. These modules can only be loaded in that env. They are located in:

/sw/LIB/environment

Modules loaded from /sw/LIB will automatically be unloaded when switching envs.

pkgsrc Modules

pkgsrc is a software package manager which can install very many packages from source. On Hummel-2 it replaces software packages provided by the Linux distribution. (This keeps operation system images small and ensures that software versions do not change.) The pkgsrc Modules are called:

env/yyyyQq-compiler-MPI

For example

env/2023Q4-gcc-openmpi

provides pkgsrc release 2023Q4.

Switching to pkgsrc is the natural starting point for working on Hummel-2. The idea is that pkgsrc provides all tools and software dependences as well as some applications (in particular R) that are normally provided by the Linux distribution.

Software tools

For frequently needed software tools Modules exist in /sw/TOOL. If a tool is missing in the env you want to work with, please try this recipe:

switch to a pkgsrc Module
locate the tool with type or which
define an alias in your $HOME/.bashrc

Example:

$ module switch env env/2023Q4-gcc-openmpi
module: unloaded env/system-gcc
module: loaded env/2023Q4-gcc-openmpi
Module for pkgsrc-devel 2023Q4 loaded.
$ which vim
/sw/env/gcc-13.2.0_openmpi-4.1.6/pkgsrc/2023Q4/bin/vim
$ alias vim=/sw/env/gcc-13.2.0_openmpi-4.1.6/pkgsrc/2023Q4/bin/vim

Python

A listing of Python versions available can be obtained with:

module avail pythonversion

User-installed software

Binary software packages that can be automatically installed from the internet should be stored in the $USW directory.