Using cyclone

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Revision as of 14:12, 29 September 2018 by Csp001 (talk | contribs)

Connection and first steps

Use ssh to connect

ssh -Y <username>

or just simply:

ssh -Y

if you're connecting from a computer where you are logged in under the same name. When you are connecting for the first time, you will be asked to verify a signature. Reply "yes" to this question.

Home directories shares home directories with the new hexagon cluster. These home directories are separate from your standard UiB home directory. The contents of your home directories will not be synced, so you will manually need to transfer your scripts to the new system.

How to access software

In contrast to the old skd-cyclone, most scientific software is only available through software modules. Modules need to be loaded manually before the respective software can be used. We use software modules, because they provide are a clean and handy way to offer conflicting software or software versions: Instead of updating software and potentially breaking user scripts and programs new software is then made available in parallel to those that require it.

Start-up scripts

It might be handy to automatically load modules for software that you use frequently every time you login to cyclone. To accomplish that for bash, there are two relevant files, $HOME/.bashrc and $HOME/.bash_profile . .bash_profile should contain things that need to be defined at login time only, like PATH and other environment variables, startup programs, etc. You just need things once, not in every shell you open. In most cases, you also need the things from .bashrc in your login shell. That's why .bash_profile sources .bashrc as well, but .bashrc doesn't usually source .bash_profile. In contrast, .bashrc should typically contain things you want to set in every shell you open, like aliases, functions, etc. These are per shell session items that are not inherited from environment (source and detailed explanation).

An example .bash_profile for inspiration

module load cdo/1.6.9
module load ncarg/6.3.0-login

alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"

if [ -f ~/.bashrc ]; then
   . ~/.bashrc

An example .bash_profile for inspiration

alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"

Available software

Data analysis and plotting

Text editors

Compilers and libraries

Accessing the data from your own machines