ood-cryosparc

This OnDemand CryoSPARC app launches CryoSPARC (both master and worker processes) on a single compute node.

The CryoSPARC master can be accessed via a web browser in an OOD Remote Desktop, or local web browser with SSH port forwarding.

Prerequisites

• Slurm cluster
• Apptainer or SingularityCE
• CryoSPARC license
  • https://cryosparc.com/download

Install

1. After obtaining a CryoSPARC license, download the master and worker tarballs:

version=4.7.1
license_id=...CRYOSPARC_LICENSE_ID...
curl -o cryosparc-master_v${version}.tar.gz -L https://get.cryosparc.com/download/master-v${version}/${license_id} 
curl -o cryosparc-worker_v${version}.tar.gz -L https://get.cryosparc.com/download/worker-v${version}/${license_id} 

2. Build the SIF image (from the same working directory as the CryoSPARC master/worker tarballs):

   singularity build --fakeroot cryosparc.sif Singularity.def

Site-specific modifications

• form.yml.erb - replace odyssey3 with a valid cluster OOD cluster configuration name
• template/script.sh.erb - replace ${HOME}/cryosparc.sif with the path to the cryosparc.sif built in Install step 2
• template/before.sh.erb - (if necessary) replace find_port localhost 7000 11000 with valid port range in your environment

Testing

1. Download the test data set to a filesystem accessible from all compute nodes:

singularity exec --env CRYOSPARC_DB_PATH=/ --env CRYOSPARC_BASE_PORT=1 cryosparc.sif cryosparcm downloadtest
tar -xf empiar_10025_subset.tar

2. Launch the CryoSPARC OOD batch app.

   • The CryoSPARC database path should be on a shared filesystem for persistence after the OOD job terminates.
   • Many CryoSPARC jobs require least 1 GPU.

3. After CryoSPARC is ready, instructions on connecting to the CryoSPARC master from an OOD Remote Desktop or local web browser (with SSH tunneling) will be shown.

4. Verify the CryoSPARC Installation with the Extensive Validation Job

   • In the "Path to Dataset Data" textbox, enter the absolute path to the empiar_10025_subset directory extracted in step 1

Credits

Kevin Dalton, Milson Munakami, Nathan Weeks