CryoSPARC tips

CryoSPARC job documents
https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc

https://cryosparc.com/docs/reference/jobs#manually-curate-exposures

Deleting cache
The location of the cache directory is set in the cryosparcw start command in "--ssdpath /SSD_disk". The name of the cache folder is usually "instance_MachineName:39001".

The contents in the cache can be safely deleted to release disk space, when no job is running. If deleted when jobs are running, only the running job may quit because the cached data it is using no longer exists. Finished jobs do not have any result directed to the cache folder.

Changing Database location
https://discuss.cryosparc.com/t/how-to-change-database-directory-in-cryosparc-v2/2068/6

An example cryoSPARC2 start script (single workstation)
cryoSPARC2.sh: Run the above script as:

For freshly installed cryosparc2 there may not be a lane already. The above worker startup command should be changed to:

Fixing "ERROR: This hostname is already registered! Remove it first."
1 Delete the current lane (assuming that it is "default": 2 Restart cryosparcm 3 create a new lane

Removing cryoSPARC from $PATH
The cryoSPARC dependencies (anaconda python, mongodb, supervisord) do not need to exits in the path. Deleting them from .bashrc is completely safe.

With a minor modification to the cryosparcm and cryosparcw scripts, even the cryoSPARC_master/bin and cryoSPARC_master/bin directories can be removed from $PATH: to

Changing CUDA version
The cryosparcw script needs to be able to find the pip of the anaconda isntallation in the "deps" dir.



If after this cryoSPARC2 can not run 2D classification, it is likely the Nvidia driver needs update.

listing documents in a collection
for example:

Backing up and restoring database
Eqivalent to:

Eqivalent to:

"cryosparcm cli" commands
https://guide.cryosparc.com/setup-configuration-and-management/management-and-monitoring/cli

The "cryosparcm cli" commands allow directly calling internal control functions.

Turning off automatic caching on job start
Source: https://discuss.cryosparc.com/t/how-to-clear-the-cache-in-v2/2161/12

Getting job information
This returns the mongodb entry of the job as a dictionary. The "kwargs" can be a list of keywords of interest, such as "running_at", "job_type", "_id", "job_dir", "output_results", "input_slot_groups", etc.. To find all keys, use this command: