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1. Log into Prometheus login node

   Code Block
   language bash title Log into Prometheus login node
   ssh <login>@pro.cyfronet.pl

   
   

2. Load pro-viz module 

   Code Block
   language bash title 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

         Code Block
         language bash title 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

         Code Block
         language bash title 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

      
      

      Code Block
      language bash title Status of pro-viz job(s)
      pro-viz list

      
      

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

      Code Block
      language bash title Pro-viz job password
      pro-viz password <JobID>

      exemple output

      Code Block
      language bash title 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 

      Code Block
      language bash title Load Relion module
      module load plgrid/tools/relion

      
      

   2. Start Relion GUI in background

      Code Block
      language bash title Start relion
      relion &

      
      

5. Use Relion GUI for computation. 

Relion in SLURM batch jobs

Most of Relion jobs could be run as batch jobs using SLURM

1. Example CPU-only SLURM script

   Code Block
   language bash title Relion CPU-only SLURM script
   #!/bin/bash # Number of allocated nodes #SBATCH --nodes=1 # Number of MPI processes per node #SBATCH --ntasks-per-node=4 # Number of threads per MPI process #SBATCH --cpus-per-task=6 # Partition #SBATCH --partition=plgrid # Requested maximal walltime #SBATCH --time=0-1 # Requested memory per node #SBATCH --mem=110GB # Computational grant #SBATCH --account=<name-of-grant> export RELION_SCRATCH_DIR=$SCRATCHDIR module load plgrid/tools/relion/3.1.2 mpirun <relion-command>

   
   

2. Example GPU SLURM script