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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. 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

   Warning
   title cryoSPARC master job
   There should be only one job which run cryoSPARC master per user. Therefore you should stop job with cryoSPARC master before this step.

   
   

   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

   
   

Upgrading do newer version

cryoSPARC is updated frequently with updates and patches (see https://cryosparc.com/updates). For each new version new module in plgrid/apps/cryosparc is created, which is made default after testing (among other test also with standard benchmark). To upgrade to new version one has to

1. End all running cryoSPARC jobs.
2. Update cryosparc-master.slurm script (or check that it uses default cryoSPARC module).
3. Manually update all lanes created (both those created during configuration and added later). Script described in Known problems and issues section could used to automate this process.
4. Restart cryoSPARC master server.

Known problems and issues

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