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

1. Log into Prometheus login node

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

   
   

2. Move to Relion project directory

   Code Block
   language bash title Change directories
   cd $SCRATCH/<relion-project>

   
   

   Info
   title Usage of filesystems
   Relion project during computations should be stored in $SCRATCH filesystem on Prometheus. More info - https://kdm.cyfronet.pl/portal/Prometheus:Basics#Disk_storage. For longer storage user should use $PLG_GROUPS_STORAGE/<team_name> filesystem.

   
   

3. Submit job

   Code Block
   language bash title Job submision
   sbatch script.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>

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   2. Example GPU SLURM script

      Code Block
      language bash title Relion GPU 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-gpu # Number of GPUs per node #SBATCH --gres=gpu:2 # 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> --gpu $CUDA_VISIBLE_DEIVCES

      
      

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