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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

   
   

   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

   
   

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

   
   

Known problems and issues

List of known problems and issues

After restart there is database: ERROR (spawn error)

Sometimes when cryoSPARC master is shut down it can not restart due to database error. It leads to

CryoSPARC is not already running.
If you would like to restart, use cryosparcm restart
Starting cryoSPARC System master process..
CryoSPARC is not already running.
database: ERROR (spawn error)

In such case you should check logs for errors

main log in  ~/.cryosparc/log/run/command_core.log


less ~/.cryosparc/log/run/command_core.log 

supervisor log in  ~/.cryosparc/log/run/supervisord.log

less ~/.cryosparc/log/run/supervisord.log 

database log in ~/.cryosparc/log/run/database.log

less ~/.cryosparc/log/run/database.log 

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AssertionError: {'code': 500, 'data': None, 'message': "OtherError: node is not in primary or recovering state, full error:
{'ok': 0.0, 'errmsg': 'node is not in primary or recovering state', 'code': 13436, 'codeName': 'NotMasterOrSecondary'}

then:

you have to move current cryoSPARC database

mv ~/.cryosparc/cryosparc_database ~/.cryosparc/cryosparc_database-$(date+"%Y-%m-%d")

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rerun  configuration of cryoSPARC to rebuild database

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