Relion Prometheus usage guide

Relion could be used at Prometheus supercomputer in three ways:

• inside graphical interactive job using pro-viz service (Main documentation - polish -  Obliczenia w trybie graficznym: pro-viz)
• in SLURM batch job though SLURM script submitted from command line
• in SLURM batch job submitted from Relion GUI started via pro-viz service in dedicated partition

Interactive Relion job with Relion GUI

In order to start interactive Relion job with access to Relion GUI

1. Log into Prometheus login node

   Log into Prometheus login node

   ssh <login>@pro.cyfronet.pl

2. Load pro-viz module 

   Load pro-viz module

   module load tools/pro-viz

3. Start pro-viz job

   1. Submit pro-viz job to qeuue

      1. CPU-only job

         Submission of CPU pro-viz job

         pro-viz start -N <number-of-nodes> -P <cores-per-node> -p <partition/queue> -t <maximal-time> -m <memory>

      2. GPU job

         Submission of GPU pro-viz job

         pro-viz start -N <number-of-nodes> -P <cores-per-node> -g <number-of-gpus-per-node> -p <partition/queue> -t <maximal-time> -m <memory>

   2. Check status of submitted job
      Status of pro-viz job(s)

      pro-viz list

   3. Get password to pro-viz session (when job is already running)\

      Pro-viz job password

      pro-viz password <JobID>

      exemple output

      Pro-viz password example output

      Web Access link:
        https://viz.pro.cyfronet.pl/go?c=<hash>&token=<token> 
      link is valid until: Sun Nov 14 02:04:02 CET 2021
      
      session password (for external client): <password>
      full commandline (for external client): vncviewer -SecurityTypes=VNC,UnixLogin,None -via <username>@pro.cyfronet.pl -password=<password> <worker-node>:<display>

   4. Connect to graphical pro-viz session
      1. you could use weblink obtained in previous point
      2. you could use VNC client (i.e. TurboVNC). Configuration of client described in Obliczenia w trybie graficznym: pro-viz (in polish)
4. Setup Relion environment

   1. When connected to GUI open Terminal and load Relion module 

      Load Relion module

      module load plgrid/tools/relion

   2. Start Relion GUI in background

      Start relion

      relion &

5. Use Relion GUI for computation.