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euler-user-setup.md

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seting up a user profile on Euler

submission rights

  • D-BSSE admins need to add user to group owning the shares (e.g.: BSSE-Beerenwinkel-Euler)
  • check cluster shares with my_share_info (or listing member of a share, e.g.: bugroup es_beere)

files in home directory

  • ~/.bashrc add umask 0007

  • ~/.screenrc for a more comfortable screen terminal multiplexing experience.

  • ~/.netrc MUST NOT be LDAP passwords of regular users

  • ~/.ssh/config controls various parameters of SSH connection.

    • ControlMaster MUST NOT be enabled (otherwise part of the parallelism gains are lost)
    • Hosts:
      • bs-bewi08.ethz.ch: specify the @d domain-suffix for D-BSSE
  • ~/.ssh/authorized_keys

    • operators
    • forced commands
      • batman.sh subcommands for remote bs-bewi08 calls, both directly and from belfry dispatcher (2 different user keys)
  • ~/rsyncd.secrets MUST NOT be LDAP password, MUST be in sync with rsyncd.pass.euler

  • ~/rsyncd.conf

    • symlink to the conf file
    • ~/log : used to store logs
    • ~/log/rotate: symlink to log rotate script
    • ~/log/rotate.conf: symlink to log rotate conf

conda environments

Notes:

  • most of the environments will be auto-magically handled by snakemake using mamba
  • the conda installation is system-wide in /cluster/project/pangolin and already done by the quick_install.sh installer
  • custom environment from conda-qa.yaml already installed there