Working on UPPMAX

$HOME dir and project dir


  • Disk usage and number of files

  • $HOME has always 32 GB and 300,000 files

  • You typically have one project per project, their size dependent on type of project

  • Compute projects both have disk space (128 GB) and computing time attached to them

  • Check your quota with

$ uquota

Core hours

  • You get core hours only from compute project

  • When they are used you can still get “BONUS” jobs if the resources allow.

  • You can find your current projects (and other projects that you have run jobs in) with the program projinfo.

$ projinfo <username>


$ projinfo <project name>
  • For example, if your project is named NAISS 2017/1-334 you specify naiss2017-1-234

What kind of work will you perform?


:Rackham login Node;
if (Do CPU/memory intensive work) then (yes)
  :Use calculation node;
  if (Do interactive work) then (yes)
    :$ interactive -A <proj> <options>;
  else (no)
    :Make a batch script;
    :$ sbatch <script>;
else (no)
  :Stay on login node and laod your module(s):
  $module load <software/tool>;
  :Run tool: 
  $<toolname> [- options, input, output];

UPPMAX Cluster overview again!

graph TB

  Node1 -- interactive --> SubGraph2Flow
  Node1 -- sbatch --> SubGraph2Flow
  subgraph "Snowy"
  SubGraph2Flow(calculation nodes) 

        thinlinc -- usr-sensXXX + 2FA----> SubGraph1Flow
        Node1 -- usr-sensXXX + 2FA----> SubGraph1Flow
        subgraph "Bianca"
        SubGraph1Flow(Bianca login) -- usr+passwd --> private(private cluster)
        private -- interactive --> calcB(calculation nodes)
        private -- sbatch --> calcB

        subgraph "Rackham"
        Node1[Login] -- interactive --> Node2[calculation nodes]
        Node1 -- sbatch --> Node2


  • Use your disk spaces wisely

    • home folder just for general stuff and files needed by several projects

      • always read and write protected for others by default

    • otherside project folder which will more easily become public for other’s

      • by default available for all project members.

  • Use the computing resources wisely

    • low intensity work on login node

    • high intensity work on compute nodes (core hours are counted)

      • for development use the interactive sessions

      • otherwise make batch jobs!

Common problems

  • Conda environment clash with loaded python modules

  • Forgotten environment variables defined in your .bashrc may give unexeptected errors when you run other programs or new versions of a program

  • A full $HOME folder may cause unexpected errors

    • check with uquota