What is CryoSPARC?
CryoSPARC is a state of the art scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.
📘 Local cryosparc_user account on HPC
CryoSPARC requires a local user account named cryosparc_user that is used to control needed CryoSPARC resources and job allocations.
When looking to run CryoSPARC jobs, a user would need to connect/login into HPC as the cryosparc_user account.
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Submit an interactive SLURM job:
srun --partition=general-gpu -N 1 -n 62 --gres=gpu:1 --time=00:30:00 --pty bash
Once a node is assigned to the interactive SLURM srun job, start the Cryosparc Master process:
cryosparcm start
cd /home/cryosparc_user/cryosparc/cryosparc2_worker/bin
./cryosparcw connect --worker $(hostname) --master $(hostname) --port 39000 --nossd --lane default --newlane
Open a local web browser to assigned GPU node IP address, view IP information with the following command:
ip a
https://IPaddressOfGPUnode:39000/
Login screen for CryoSparc should show up, login using CryoSparc account details, launch CryoSparc job to gpu node that was assigned to the interactive SLURM srun job in previous step.
If there is a network interruption, the CryoSparc Master process on the gpu node will crash. There is a /tmp/ cryosparc .sock file that would need to be removed to refresh and allow cryosparc to continue running on a node that had the brief interruption.