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Table of Contents

Configuration of cryoSPARC environment

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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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