Environment and Modules¶
Shells on Clusters¶
The table shows which shells are available on the IT4Innovations clusters.
Note that bash is the only supported shell.
| Cluster Name | bash | tcsh | zsh | ksh | dash |
|---|---|---|---|---|---|
| Karolina | yes | yes | yes | yes | yes |
| Barbora | yes | yes | yes | yes | no |
| DGX-2 | yes | no | no | no | no |
Info
Bash is the default shell. Should you need a different shell, contact support[at]it4i.cz.
Environment Customization¶
After logging in, you may want to configure the environment. Write your preferred path definitions, aliases, functions, and module loads in the .bashrc file
# ./bashrc
# users compilation path
export MODULEPATH=${MODULEPATH}:/home/$USER/.local/easybuild/modules/all
# User specific aliases and functions
alias sq='squeue --me'
# load default intel compilator !!! is not recommended !!!
ml intel
# Display information to standard output - only in interactive ssh session
if [ -n "$SSH_TTY" ]
then
ml # Display loaded modules
fi
Note
Do not run commands outputting to standard output (echo, module list, etc.) in .bashrc for non-interactive SSH sessions. It breaks the fundamental functionality (SCP) of your account. Take care for SSH session interactivity for such commands as stated in the previous example.
Application Modules¶
In order to configure your shell for running a particular application on clusters, we use a module package interface.
Application modules on clusters are built using EasyBuild. The modules are divided into the following groups:
base: Default module class
bio: Bioinformatics, biology and biomedical
cae: Computer Aided Engineering (incl. CFD)
chem: Chemistry, Computational Chemistry and Quantum Chemistry
compiler: Compilers
data: Data management & processing tools
debugger: Debuggers
devel: Development tools
geo: Earth Sciences
ide: Integrated Development Environments (e.g. editors)
lang: Languages and programming aids
lib: General purpose libraries
math: High-level mathematical software
mpi: MPI stacks
numlib: Numerical Libraries
perf: Performance tools
phys: Physics and physical systems simulations
system: System utilities (e.g. highly depending on system OS and hardware)
toolchain: EasyBuild toolchains
tools: General purpose tools
vis: Visualization, plotting, documentation and typesetting
OS: singularity image
python: python packages
Note
The modules set up the application paths, library paths and environment variables for running a particular application.
The modules may be loaded, unloaded, and switched according to momentary needs. For details, see lmod.