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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
Load cryoSPARC environment using modules
Code Block language bash title Load cryoSPARC environment module add plgrid/apps/cryosparc/3.2
Copy cluster config
cluster_info.json
and script templatecluster_script.sh
from$CRYOSPARC_ADDITIONAL_FILES_DIR
directory to your working directoryCode Block language bash title Copy files cp $CRYOSPARC_ADDITIONAL_FILES_DIR/cluster_info.json . cp $CRYOSPARC_ADDITIONAL_FILES_DIR/cluster_script.sh .
- Modify files accordingly
- in config
cluster_info.json
change name of lane/cluster to avoid overwriting default prometheus* lanes - in
cluster_script.sh
change--time
,--partition
or other parts of script template accordingly
- in config
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
run command
cryosparcm cluster connect <name-of-cluster-form-cluster_info.json>
to add lane/clusterCode Block language bash title add line cryosparcm cluster connect <name-of-cluster-form-cluster_info.json>
- Repeat above points to create another lane if necessary
Stop cryoSPARC master
Code Block language bash title run cryoSPARC master cryosparcm stop
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
Code Block | ||
---|---|---|
| ||
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 your database log in
Code Block title database log less ~/.cryosparc/log/run/database.log