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1. Under the "Running" tab for a given calculation, set the option "Submit to queue?" to "Yes". 
2. You'll need to set "Queue name:" to the Slurm partition you wish to use:
   1. If you want to only run on CPUs, then set this to "cryo-cpu"
   2. If you want to run on the shared cryoEM GPUs, then set this to "cryo-gpu"
   3. If you want to run on a lab-reserved node, then set this to the appropriate partition (e.g. "blanchard_reserve")
3. Set "Queue submit command" to "sbatch"
4. Set the number of nodes/GPUs to the desired values

5. Relion requires a set of template Slurm submission scripts that enables it to submit jobs. You'll need to set "Standard submission script" to the path where the needed template script is. A set of template submission scripts, which are no longer maintained, can be found here: 

   Code Block
   /softlib/apps/EL7/slurm_relion_submit_templates # select the template script that is appropriate for your job

   
   

6. Give the "Current job" an alias if desired and click "Run!" # assumes everything else is set. Checking job status (and other Slurm functionality) is described here and here.

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To achieve this goal change the Slurm submission options and Relion command line arguments.  For example the above script, for a single node, can be submitted to 3 nodes with the following changes:

# report whether relion crashes
# remove particles from scratch
# if it crashes
if [ $? -eq 0 ]
  then
     echo -e "$SLURM_JOB_ID exited successfully"
  else
     user=$SLURM_JOB_USER
     MY_TMP_DIR=/scratchLocal/${user}_${SLURM_JOB_ID}
     echo -e "$SLURM_JOB_ID failed so cleaning up $MY_TMP_DIR"
     rm -rf $MY_TMP_DIR
fi#!/bin/bash
#SBATCH --job-name=n3_bench
#SBATCH -p cryo-gpu-v100
#SBATCH --mem=170g
#SBATCH --nodes=3
#SBATCH --ntasks=13
#SBATCH --ntasks-per-node=5
#SBATCH --cpus-per-task=4
#SBATCH --gres=gpu:4

mpirun -display-allocation -display-map -v -n 13 relion_refine_mpi --o Refine3D/quackmaster/run_multi_node/${user}_${SLURM_JOB_ID} --split_random_halves --i Select/job088/particles.star --ref 012218_CS_256.mrc --firstiter_cc --ini_high 30 --dont_combine_weights_via_disc --scratch_dir /scratchLocal --pad 2  --ctf --particle_diameter 175 --flatten_solvent --zero_mask --oversampling 1 --healpix_order 2 --auto_local_healpix_order 4 --offset_range 5 --offset_step 2 --sym C1 --low_resol_join_halves 40 --norm --scale --j 6 --gpu --pool 100 --auto_refine

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