CryoSPARC¶
CryoSPARC is a state of the art scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.
There are two main approaches to running CryoSPARC on HiPerGator.
Standalone Install¶
Do not run CryoSPARC on a login node. Only run it in a SLURM job / OOD session!
An individual approach to running CryoSPARC on HiPerGator is to install it in a 'standalone' mode into a personal directory tree in /blue. Once installed, you can run it inside a SLURM job while accessing its web front-end from a browser in Open OnDemand or via an ssh tunnel from your local computer.
An example of a standalone install on HPG can be found in the standalone cryosparc build article.
You must have access to an NGU allocation to run cryosparc because some of its tools require GPU use.
Group Web Interface¶
Our web application hosting platform allows a HPG group or groups using the same allocation run an always on CryoSPARC web interface integrated with HPG compute and storage and accessible at a stable url like https://cryosparc-mygroup.rc.ufl.edu from the UF network or with UF VPN.
Summary of steps to procure a long-running CryoSPARC setup.
- Purchase or request a trial of a PrivApps web hosting instance.
- Open a support request to request privapps CryoSPARC setup.
- Request a free academic CryoSPARC LICENSE_ID and forward the resulting email to RC support or post the id into the support ticket.
- List one or more group members whose accounts we should create to be the group's admin users. We will create admin cryosparc account(s) and email the registration token necessary to set the initial password to respective users by email.
Once the above information is provided in the ticket we will setup a cryosparc server install integrated with HiPErGator.
See the cryosparc server update article for more details.
CryoSPARC install maintenance¶
For standalone installations it's up to you to update your cryosparc install
For private cryosparc servers cluster integration requires that the worker code is updated manually. See the cryosparc server update article for more details.
Categories¶
cryo-em