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1. Start interactive job using command

   Code Block
   language bash title Interactive job
   srun -p plgrid-services --nodes=1 --ntasks=1 --time=0-1 --pty bash

   
   

2. Load cryoSPARC environment using modules

   Code Block
   language bash title Load cryoSPARC environment
   module add plgrid/apps/cryosparc/3.2

   
   

3. Copy cluster config cluster_info.json  and script template cluster_script.sh from $CRYOSPARC_ADDITIONAL_FILES_DIR directory  to your working directory

   Code Block
   language bash title Copy files
   cp $CRYOSPARC_ADDITIONAL_FILES_DIR/cluster_info.json . cp $CRYOSPARC_ADDITIONAL_FILES_DIR/cluster_script.sh .

   
   

4. Modify files accordingly
   1. in config cluster_info.json change name of lane/cluster to avoid overwriting default prometheus* lanes
   2. in cluster_script.sh change --time, --partition or other parts of script template accordingly

5. Start  cryoSPARC master

   Code Block
   language bash title run cryoSPARC master
   cryosparcm restart

   
   

6. run command cryosparcm cluster connect <name-of-cluster-form-cluster_info.json> to add lane/cluster

   Code Block
   language bash title add line
   cryosparcm cluster connect <name-of-cluster-form-cluster_info.json>

   
   

7. Repeat above points to create another lane if necessary

8. Stop cryoSPARC master

   Code Block
   language bash title run cryoSPARC master
   cryosparcm stop

   
   

9. End interactive job

   Code Block
   language bash title end interactive job
   exit

   
   

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