Environment variables
(Advanced) Specify additional environment variables in the configuration files to augment CryoSPARC's low-level behaviour.
To set or change one of these environment settings, add a new line to one the config.sh
files with the following format (substitute VARIABLE
and VALUE
as indicated in the next sections):
Or set the value based on a different environment variable provided by the system:
Which config.sh
file you use depends on which variable you need to change. The variables available for each file are described below.
cryosparc_master/config.sh
Note: Restart CryoSPARC with cryosparcm restart
after changing this file.
Variable | Description | Default Value |
---|---|---|
| How many seconds to wait for network requests between CryoSPARC master/master processes before timing out with an error |
|
| The amount of time to wait (in seconds) in between status updates for cluster jobs. |
|
| The maximum amount of retries for cluster job status updates. |
|
| The amount of time to wait (in milliseconds) for the database to respond when starting it. |
|
| In master/worker or cluster modes, Import Jobs always run on the default master node. Set this to |
|
| In master/worker or cluster modes, |
|
|
|
|
| Override the installed master hostname when checking that | - |
| When checking that job directory is empty before running a job, set to |
|
| Override CryoSPARC license server address. Use for systems that require access through a proxy. |
|
| Set to |
|
| The path to a bash script that runs every time a session's data management status changes: See Live Session Data Management Tutorial. Use this to perform archive or deletion processes specific to your system (e.g., move archive data to an S3 bucket). The script is given arguments for the project UID, session UID, the datatype that changed ( | - |
| How much RAM to allocate for MongoDB database query cache, in GB |
|
| How many CPU cores to allocate for each GPU used in Patch, Full-frame and Local Motion Correction jobs |
|
| How much RAM (in MB) to allocate for each GPU used in Patch, Full-frame and Local Motion Correction jobs |
|
| The prefix to add to a project directory name on the filesystem when it is created. |
|
| If set, CryoSPARC makes an HTTP request to this URL each time a job's status changes with some job metadata encoded in JSON | - |
| Whenever a job requires SSD cache, it automatically checks for and removes files that haven't been accessed in more than the number of days specified by this variable. Note: Files may remain on the SSD for longer than this amount since they only get cleaned up when a job runs |
|
| Set to | - |
| May be required for connection to the CryoSPARC license verification server on systems with outdated Certificate-Authority files or that filter HTTPS requests through a proxy. Specify a path to a file or folder that contains the certificates. | - |
| CryoSPARC jobs running on worker nodes regularly report their status to the master command server to indicate that they are still running and active. If a job fails to report for more than this number of seconds (e.g., due to stalling, a slow network or a silent error), CryoSPARC marks the job as failed. Increase for very busy/low-resource worker nodes or slow/unreliable connections between the master and worker nodes. Increasing may reduce heartbeat-related job failures. |
|
Note: This file includes the following environment variables that are specified at installation time:
CRYOSPARC_LICENSE_ID
CRYOSPARC_MASTER_HOSTNAME
CRYOSPARC_DB_PATH
CRYOSPARC_BASE_PORT
cryosparc_worker/config.sh
No restart is required after changing this file.
Variable | Description | Default Value |
---|---|---|
| (v4.3+) Number of threads to use during caching when copying particle |
|
| (v4.5+) Distributed locking strategy to use when multiple running jobs access the SSD cache simultaneously. Set to |
|
| How many seconds to wait for network requests between CryoSPARC worker/master processes before timing out with an error |
|
| Use the new, more reliable SSD cache system (v4.4+) |
|
| By default, CryoSPARC uses the CUDA driver's |
|
| Set this variable to override the SSD cache path provided when you installed the worker. Useful if the SSD cache path is generated by your cluster as an environment variable when the job is scheduled | - |
| When reading TIFF or EER movie files, CryoSPARC reads the entire file into memory before decompressing. This significantly improves performance on some networked file systems but uses more memory. Set to |
|
Note: This file includes the following environment variables that are specified at installation time:
CRYOSPARC_LICENSE_ID
CRYOSPARC_CUDA_PATH
CRYOSPARC_USE_GPU
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