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1. Apply  for apply for membership in plggcryospar team in Portal PLGrid and ask for registration in Cyfronet's internal cryoSPARC users database and dedicated port for access to cryoSPARC master  through Helpdesk PLGrid.

2. Log in to Prometheus login node

   Code Block
   language bash title Log into Prometheus login node
   ssh <login>@pro.cyfronet.pl

   
   

3. Load cryoSPARC module  using command

   Code Block
   language bash title Set cryoSPARC environment
   module add plgrid/apps/cryosparc/3.1

   
   

4. Run cryoSPARC configuration script. It will configure your cryoSPARC environment and create your user in cryoSPARC database and configure two lanes for external jobs - prometheus-gpu which is going to use plgrid-gpu partition for GPU jobs and prometheus-gpu-v100 for plgrid-gpu-v100 partition. Both lanes are going to use plgrid partition for CPU only jobs. As argument for script pass license id, your e-mail and password (they are going to be used to login to cryoSPARC webapp), your first and last name.

   Code Block
   language bash title Configure cryoSPARC
   cryosparc_configuration --license <XXXX> --email <your-email> --password <password> --firstname <Givenname> --lastname <Surname>

   
   

   Info
   title Access problems
   In case of "cryosparc_configuration: command not found" error run in terminal Code Block language bash newgrp plggcryospar to start new subshell with permissions of plggcryospar team.

   
   

   Info
   title Optional lanes/clusters
   You could create additional lanes/clusters for other maximal duration of SLURM job: copy cluster config cluster_info.json  and script template cluster_script.sh from directory  /net/software/local/cryosparc/3.1/cyfronet to your working directory modify files accordingly in config cluster_info.json change name of lane/cluster to avoid overwriting default prometheus lane in cluster_script.sh change --time, --partition or other parts of script template accordingly run command cryosparcm cluster connect <name-of-cluster-form-cluster_info.json> to add lane/cluster repeat above points to create another lane if nessesary

   
   

   Info
   title Access to GPU partitions
   To use GPUs on Promehteus cluster you have to apply for GPU resources at Portal PLGrid.  To check whether you have an access to partition on Prometheus login node run below command and check whether your accounts are on AllowAccounts list partition plgrid-gpu Code Block language bash scontrol show partition plgrid-gpu-v100| grep Accounts partition plgrid-gpu-v100 Code Block language bash scontrol show partition plgrid-gpu-v100| grep Accounts If you do not have access to one or both of both above partitions please contact Helpdesk PLGrid

   
   

5. Your cryoSPARC master setup already done. All succeeding crypoSPARC master instances  should be run in batch jobs.

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Above script is located at /net/software/local/cryosparc/3.1/cyfronet/cryosparc-master.slurm.  You could copy it your working folder

cp /net/software/local/cryosparc/3.1/cyfronet/cryosparc-master.slurm .

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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`

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