Page History

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1. Submit job

   Code Block
   language bash title job submision
   sbatch cryosparc-master.slurm

   
   

   Warning
   title cryoSPARC master job
   There should be only one job which run cryoSPARC master in plgrid-servicies partition per user.

   
   

2. Check whether job was started

   Code Block
   language bash title jobs status
   squeue -j <JobID>

   
   

3. Common states of jobs

   • PD - PENDING - Job is awaiting resource allocation.
   • R - RUNNING - Job currently has an allocation and is running.
   • CF - CONFIGURING  - Job has been allocated resources, but are waiting for them to become ready for use (e.g. booting). On Prometheus CF state could last for up to 8 minutes in case when nodes that have been in power save mode.
   • CG - COMPLETING  - Job is in the process of completing. Some processes on some nodes may still be active.

4. Make a tunnel

   In your directory cat job log file:

   Code Block
   language bash title Listing of job's log
   cat cryosparc-master-log-<JobID>.txt

   where `XXXXXXX` is your sbatch job id which is displayed after you run it f.e. `cat cryosparc-master-log-49145683.txt`

   It will show you something like this:

   Code Block
   language bash title Example of job log
   Copy/Paste this in your local terminal to ssh tunnel with remote ----------------------------------------------------------------- ssh -o ServerAliveInterval=300 -N -L 40100:172.20.68.193:40100 plgusername@pro.cyfronet.pl ----------------------------------------------------------------- Then open a browser on your local machine to the following address ------------------------------------------------------------------ localhost:48511 ------------------------------------------------------------------

   
   

5. Exec in another shell at your local computer given command to make a tunnel:

   Code Block
   language bash title Tunneling
   ssh -o ServerAliveInterval=300 -N -L 40100:172.20.68.193:40100 plgusername@pro.cyfronet.pl

   
   

6. Log into cryoSPARK web application - open in browser: `localhost:40100`

Work in progres

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Adding optional lanes

You could create additional lanes

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for other maximal duration of SLURM job:

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

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1. Load cryoSPARC environment

   module add plgrid/apps/cryosparc/3.2

   
   

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

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

   
   

2. Modify files accordingly
   1. in config cluster_info.json change name of lane/cluster to avoid overwriting default prometheus

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1. 1. * lanes
   2. in cluster_script.sh change --time, --partition or other parts of script template accordingly

2. Start  cryoSPARC master

   Code Block
   language bash title run cryoSPARC master
   cryosparcm restart

   
   

3. 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>

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1. 
   

2. Repeat above points to create another lane if

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1. necessary

2. Stop cryoSPARC master

   Code Block
   language bash title run cryoSPARC master
   cryosparcm stop

   
   

3. End interactive job

   Code Block
   language bash title end interactive job
   exit