Configuration of cryoSPARC environment
License
Each user should have their license obtained from https://cryosparc.com/download and apply for membership in plggcryospar
team in Portal PLGrid.
To get access to cryoSPARC installation at Prometheus cluster
- Apply for membership in
plggcryospar
team in Portal PLGrid and ask for registration in Cyfronet's internal cryoSPARC users' database and a dedicated port for access to cryoSPARC master through Helpdesk PLGrid. Log in to the Prometheus login node.
Log into Prometheus login nodessh <login>@pro.cyfronet.pl
Load cryoSPARC module using command
Set cryoSPARC environmentmodule add plgrid/apps/cryosparc
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 theplgrid-gpu
partition for GPU jobs andprometheus-gpu-v100
forplgrid-gpu-v100
partition. Both lanes are going to useplgrid
partition for CPU-only jobs. As an argument for script pass license id, your e-mail and password (they will be used to login to the cryoSPARC web app), and your first and last name.Configure cryoSPARCcryosparc_configuration --license <XXXX> --email <your-email> --password <password> --firstname <Givenname> --lastname <Surname>
Access problems
In the case of "
cryosparc_configuration: command not found
" error run in terminalnewgrp plggcryospar
to start a new subshell with permissions of
plggcryospar
team.Access to GPU partitions
To use GPUs on the Promehteus cluster, you must apply for GPU resources at Portal PLGrid in your computational grant. At Prometheus, there are two kinds of GPGPUs available - Nvidia Tesla K40 XL in
plgrid-gpu
partition and Nvidia Telsa V100 inplgrid-gpu-v100
partition, and you have to describe in your grant which would you like to use.To check whether you have access to the partition on the Prometheus login node, run the below command and check whether your PLGrid computational grants are on AllowAccounts list
partition
plgrid-gpu
scontrol show partition plgrid-gpu | grep Accounts | grep <PLGrid grant name>
partition
plgrid-gpu-v100
scontrol show partition plgrid-gpu-v100 | grep Accounts | grep <PLGrid grant name>
If you do not have access to one or both of the above partitions, check your PLGrid computational grant details at Portal PLGrid. If your grant lists GPU resources and access to the required queue or queues is impossible, don't hesitate to contact Helpdesk at https://helpdesk.plgrid.pl.
- Your cryoSPARC master setup is already done. All crypoSPARC master instances should be run in batch jobs.
cryoSPARC master job
cryoSPARC master process must not be run on login nodes of the Prometheus cluster. It should be run using plgrid-servicies
partition through the SLURM job described below.
Automated cryoSPARK master in batch job
cryoSPARC master could be started through the batch job.
#!/bin/bash #SBATCH --partition plgrid-services #SBATCH --nodes 1 #SBATCH --ntasks-per-node 4 #SBATCH --mem 10GB #SBATCH --time 14-0 #SBATCH -C localfs #SBATCH --dependency=singleton #SBATCH --job-name cryosparc-master #SBATCH --output cryosparc-master-log-%J.txt #SBATCH --signal=B:2@240 ## Load environment for cryoSPARC module add plgrid/apps/cryosparc ## get tunneling info ipnport=$CRYOSPARC_BASE_PORT ipnip=$(hostname -i) user=$USER ## print tunneling instructions to cryosparc-master-log-<JobID>.txt echo -e " Copy/Paste this in your local terminal to ssh tunnel with remote ----------------------------------------------------------------- ssh -o ServerAliveInterval=300 -N -L $ipnport:$ipnip:$ipnport ${user}@pro.cyfronet.pl ----------------------------------------------------------------- Then open a browser on your local machine to the following address ------------------------------------------------------------------ localhost:$ipnport ------------------------------------------------------------------ " ## start a cryoSPARC master server cryosparcm restart ## loop which keep job running till "scancel --batch --signal=2 <JobID>" by user or automatic kill by SLURM at end of requested walltime source $CRYOSPARC_GLOBAL_ADDITIONAL_FILES_DIR/cryosparc_additional_bash_functions.sh loop-and-stop
The above script is located at $CRYOSPARC_ADDITIONAL_FILES_DIR/cryosparc-master.slurm
. The $CRYOSPARC_ADDITIONAL_FILES_DIR
variable is available when cryoSPARC module is loaded into the environment. You could copy it into your working folder.
cp $CRYOSPARC_ADDITIONAL_FILES_DIR/cryosparc-master.slurm .
Submit job
job submisionsbatch cryosparc-master.slurm
cryoSPARC master job
There should be only one job which runs cryoSPARC master in
plgrid-servicies
partition per user.Check whether the job was started.
jobs statussqueue -j <JobID>
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 is waiting for them to become ready for use (e.g. booting). On PrometheusCF
state could last for up to 8 minutes in a 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.
Make a tunnel
In your directory cat job log file:
Listing of job's logcat cryosparc-master-log-<JobID>.txt
where `
XXXXXXX
` is your batch job id which is displayed after you run it f.e. `cat cryosparc-master-log-49145683.txt
`It will show you something like this:
Example of job logCopy/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 ------------------------------------------------------------------
Exec in another shell at your local computer given the command to make a tunnel:
Tunnelingssh -o ServerAliveInterval=300 -N -L 40100:172.20.68.193:40100 plgusername@pro.cyfronet.pl
- Log into cryoSPARC web application - open in browser: `
localhost:40100
` To gracefully stop cryoSPARC master in a batch job, send signal "2" using
scancel --batch --signal=2 <JobID>
command.Ending master jobscancel --batch --signal=2 <JobID>
In case when job won't be stopped by a user through
scancel
it is going to be ended gracefully by sending signal "2" just before maximal time (it is done through#SBATCH --signal=B:2@240
command in the script).
Adding optional lanes
You could create additional lanes for other maximal duration of SLURM job:
Start interactive job using command
Interactive jobsrun -p plgrid-services --nodes=1 --ntasks=1 --mem=5GB --time=0-1 --pty bash
Load cryoSPARC environment using modules
Load cryoSPARC environmentmodule add plgrid/apps/cryosparc
Copy cluster config
cluster_info.json
and script templatecluster_script.sh
from$CRYOSPARC_ADDITIONAL_FILES_DIR
directory to your working directoryCopy filescp $CRYOSPARC_ADDITIONAL_FILES_DIR/cluster_info.json . cp $CRYOSPARC_ADDITIONAL_FILES_DIR/cluster_script.sh .
- Modify files accordingly
- in config
cluster_info.json
change the name of lane/cluster to avoid overwriting default prometheus* lanes - in
cluster_script.sh
change--time
,--partition
or other parts of the script template accordingly
- in config
Start cryoSPARC master
cryoSPARC master job
There should be only one job which runs cryoSPARC master per user. Therefore you should stop the job with cryoSPARC master before this step.
run cryoSPARC mastercryosparcm restart
run command
cryosparcm cluster connect <name-of-cluster-form-cluster_info.json>
to add lane/clusteradd linecryosparcm cluster connect
- Repeat the above points to create another lane if necessary
Stop cryoSPARC master
run cryoSPARC mastercryosparcm stop
End interactive job
end interactive jobexit
Upgrading to a newer version
cryoSPARC is updated frequently with updates and patches (see https://cryosparc.com/updates). For each new version, a new module plgrid/apps/cryosparc/<version>
is created, which is made default after testing (among other tests also with standard benchmark). To upgrade to a new version, one has to
- End all running cryoSPARC jobs.
- Update
cryosparc-master.slurm
script (or check that it uses the default cryoSPARC module). - Manually update all lanes created (those created during configuration and added later). Script described in Known problems and issues section could be used to automate this process.
- Restart cryoSPARC master server.