cryosparcm reference (v5.0+)

How to use the cryosparcm utility for starting and stopping the CryoSPARC instance, checking status or logs, managing users and using CryoSPARC's command-line interface.

Access the CryoSPARC command line utility, `cryosparcm`

The CryoSPARC master node hosts the web server and manages job resource allocation.

Workstations or master nodes with a cryosparc_master installation have access to cryosparcm, CryoSPARC's built-in command-line utility for all administrative, management and advanced usage tasks.

To use it, log into the machine onto which CryoSPARC was installed. Open a Terminal running a shell (such as bash) and enter any of the commands described below.

If CryoSPARC was installed without adding CryoSPARC’s bin path to the shell’s path configuration, navigate to the cryosparc_master installation directory and run ./bin/cryosparcm instead of cryosparcm.

For help with a specific command, run:

cryosparcm COMMAND --help

For example, for help starting CryoSPARC, run:

cryosparcm start --help

`cryosparcm`

Usage:

$ cryosparcm [OPTIONS] COMMAND [ARGS]...

Options:

--install-completion: Install completion for the current shell.
--show-completion: Show completion for the current shell, to copy it or customize the installation.
--help: Show this message and exit.

All available cryosparcm commands are listed and documented in the sections below.

Instance Status and Management

Always run instance management commands in this section from the UNIX user account that owns the CryoSPARC installation, and always on the same machine on the network that cryosparc_master was installed on. If these conditions are not met, you may see the following message:

$ cryosparcm status
────────────────────────────────────────────────────────────────────────────────
CryoSPARC System master node installed at
/home/cryosparcuser/cryosparc_master
Current CryoSPARC version: develop
────────────────────────────────────────────────────────────────────────────────

✕ UnauthorizedException: This command must run on the CryoSPARC master host, but
there is a mismatch between the $CRYOSPARC_MASTER_HOSTNAME definition
(example.edu) and the configured hostname of this host (gpu.example.xyz).

If, and only if, the command ran on the CryoSPARC master host, but the host is
configured with a different hostname, consider the appropriate intervention for
your circumstances:

 1 Ensure $CRYOSPARC_MASTER_HOSTNAME and the output of command hostname -f
   match. CRYOSPARC_MASTER_HOSTNAME may be defined inside
   cryosparc_master/config.sh. Restart CryoSPARC after this change.
 2 Or: re-run this command with the environment variable
   CRYOSPARC_FORCE_HOSTNAME="true". This setting bypasses an important safety
   check and may disrupt CryoSPARC function if used inappropriately.

You can temporarily force cryosparcm to ignore the current hostname or user by specifying the CRYOSPARC_FORCE_HOSTNAME or CRYOSPARC_FORCE_USER variables just before calling the command:

$ CRYOSPARC_FORCE_HOSTNAME=true cryosparcm status

If you see the above error message, but the hostname it reports is incorrect (i.e., the hostname specified in the error message is actually the same host, just a different identifier), you can set CRYOSPARC_MASTER_HOSTNAME in cryosparc_master/config.sh to the correct hostname. You can also set CRYOSPARC_FORCE_HOSTNAME or CRYOSPARC_FORCE_USER in this file to permanently suppress this message.

`cryosparcm status`

Show system status, including the status of all individual processes (database, app, api, etc.). Also shows configuration environment variables.

Usage:

$ cryosparcm status [OPTIONS]

Options:

--help: Show this message and exit.

`cryosparcm version`

Show CryoSPARC version.

Usage:

$ cryosparcm version [OPTIONS]

Options:

--help: Show this message and exit.

`cryosparcm start`

Start CryoSPARC or one of its services.

All processes start in the background, including all jobs and the web interface; the command line may be closed after running start. Provide an optional service name to only start that specific service.

Usage:

$ cryosparcm start [OPTIONS] [SERVICE]:[app|database|cache|api|scheduler|command_vis|app_api]

Arguments:

[SERVICE]:[app|database|cache|api|scheduler|command_vis|app_api]

Options:

--systemd / --no-systemd: [default: no-systemd]
--startup / --no-startup: [default: startup]
--app / --no-app: [default: app]
--help: Show this message and exit.

Always run this command from the same host and UNIX user account originally used to install CryoSPARC.

`cryosparcm stop`

Stop CryoSPARC or one of its services.

Provide an optional service name to only start that specific service.

Usage:

$ cryosparcm stop [OPTIONS] [SERVICE]:[app|database|cache|api|scheduler|command_vis|app_api]

Arguments:

[SERVICE]:[app|database|cache|api|scheduler|command_vis|app_api]

Options:

--help: Show this message and exit.

Always run this command from the same host and UNIX user account originally used to install CryoSPARC.

`cryosparcm restart`

Stop and start CryoSPARC or one of its services.

Usage:

$ cryosparcm restart [OPTIONS] [SERVICE]:[app|database|cache|api|scheduler|command_vis|app_api]

Arguments:

[SERVICE]:[app|database|cache|api|scheduler|command_vis|app_api]

Options:

--help: Show this message and exit.

Always run this command from the same host and UNIX user account originally used to install CryoSPARC.

`cryosparcm maintenancemode`

Enable, disable or check maintenance mode. While enabled, prevents queued jobs from running while allowing running jobs to finish. Improves user experience user experience while CryoSPARC is undergoing maintenance, for example during restart, patch, or update.

See Guide: Maintenance Mode and Configurable User Facing Messages for full details.

Usage:

$ cryosparcm maintenancemode [OPTIONS] COMMAND:{status|on|off}

Arguments:

COMMAND:{status|on|off}: [required]

Options:

--help: Show this message and exit.

`cryosparcm resources`

Print a formatted table of available scheduler targets and their properties.

Usage:

$ cryosparcm resources [OPTIONS] [LANE_NAME]

Arguments:

[LANE_NAME]: Only show target information for a specific lane

Options:

--help: Show this message and exit.

`cryosparcm changeport`

Change instance base port.

Usage:

$ cryosparcm changeport [OPTIONS] PORT

Arguments:

PORT: [required]

Options:

-y, --yes: Confirm without prompting
--help: Show this message and exit.

Always run this command from the same host and UNIX user account originally used to install CryoSPARC.

`cryosparcm asset-stats`

Show asset storage statistics.

Usage:

$ cryosparcm asset-stats [OPTIONS]

Options:

--help: Show this message and exit.

`cryosparcm recover`

Restore instance configuration and recover projects from an exported instance configuration file. Should only run when the database has no projects. For full instructions, see Instance Recovery.

Usage:

$ cryosparcm recover [OPTIONS]

Options:

-f, --file FILE: Path to input file [required]
--claim-project-ownership: Take over projects locked to other instances
-y, --yes: Confirm without prompting
--help: Show this message and exit.

Instance Setup

`cryosparcm update`

Install the latest CryoSPARC update. See Software Updates for full details.

Usage:

$ cryosparcm update [OPTIONS]

Options:

--version TEXT: Version to update to [default: latest]
--list: List available versions
--check: Check for update
--download: Download only
--install: Install previous download
--force: Force install the latest or specified version
--help: Show this message and exit.

Always run this command from the same host and UNIX user account originally used to install CryoSPARC.

`cryosparcm patch`

Download and install the latest patch for this version.

Usage:

$ cryosparcm patch [OPTIONS] [PATCH_NAME]

Arguments:

[PATCH_NAME]: Name of patch to download

Options:

--check: Check to see if a patch is available
--download: Download patches for manual installation
--install: Manually install a downloaded patch file
-f, --force: Force install or re-install latest patch
-y, --yes: Confirm patch installation without prompt
--help: Show this message and exit.

Frequently used commands:

cryosparcm patch: Automatically install the latest patches on workstations or master node and connected workers. Not recommended for clusters: Use the --download and --install flags instead.
cryosparcm patch --force: Reinstall the latest patches in case something went wrong with a previous attempt
cryosparcm patch --check: Show information about the latest patches without installing
cryosparcm patch --download: Download the latest patches without installing them. Follow the resulting instructions to install the master and worker patches
cryosparcm patch --install: Run this command immediately after a --download to install the patch on the master node.

Always run this command from the same host and UNIX user account originally used to install CryoSPARC.

`cryosparcm worker`

Worker management commands.

Ensure CryoSPARC is running before running worker management commands.

Usage:

$ cryosparcm worker [OPTIONS] COMMAND [ARGS]...

Options:

--help: Show this message and exit.

Commands:

update: Install a cryosparc worker update on all connected workers.
patch: Install a cryosparc worker patch on all connected workers.
connect: Connect a worker node that jobs can be scheduled on.
disconnect: Remove a worker node from the scheduler.

`cryosparcm worker update`

Install a cryosparc worker update on all workers or the given worker.

Usage:

Arguments:

[WORKER]: Target name. Applies to all targets if not specified

Options:

--file FILE: [default: cryosparc_worker.tar.gz]
--force
--help: Show this message and exit.

Always run this command from the same host and UNIX user account originally used to install CryoSPARC.

`cryosparcm worker patch`

Install a cryosparc worker patch on all workers or the given worker.

Usage:

$ cryosparcm worker patch [OPTIONS] [WORKER]

Arguments:

[WORKER]: Target name. Applies to all targets if not specified

Options:

--file FILE: [default: cryosparc_worker_patch.tar.gz]
--force
--help: Show this message and exit.

Always run this command from the same host and UNIX user account originally used to install CryoSPARC.

`cryosparcm worker connect`

Connect a worker node that jobs can be scheduled on, or update an existing worker configuration.

Usage:

$ cryosparcm worker connect [OPTIONS]

Options:

--path TEXT: Path to cryosparc_worker folder [required]
--worker TEXT: Name of worker. Defaults to $(hostname) if not specified.
--lane TEXT: Scheduler lane for worker (create if does not exist). [default: default]
--sshstr TEXT: SSH login string to access worker, required if the worker's hostname or UNIX user differs when connecting from master, or to specify additional SSH flags. Defaults to "$(whoami)@worker".
--cpus INTEGER RANGE: Number of CPU cores to enable for jobs. Enable all cores if not specified. [x>=1]
--rams INTEGER RANGE: Number of 8GiB RAM slots to enable for jobs. Enable all RAM if not specified. [x>=1]
--gpus TEXT: Comma-separated list of GPU device IDs, e.g., '0,1,2'. Selects all GPUs if not specified. Cannot be specified with --no-gpu.
--gpu / --no-gpu: Do not attempt to select any GPUs. Don't specify both --no-gpu and --gpus flag. [default: gpu]
--ssdpath TEXT: Local SSD scratch path. Strongly recommended.
--ssdquota INTEGER: Maximum amount of SSD space to use for caching, in megabytes (MB).
--ssdreserve INTEGER: Minimum amount free space to leave on the SSD, in megabytes (MB). [default: 10000]
--help: Show this message and exit.

Always run this command from the same host and UNIX user account originally used to install CryoSPARC.

`cryosparcm worker disconnect`

Remove a worker node from the scheduler.

Usage:

$ cryosparcm worker disconnect [OPTIONS]

Options:

--worker TEXT: Name of worker. Defaults to $(hostname) if not specified. [required]
--help: Show this message and exit.

Always run this command from the same host and UNIX user account originally used to install CryoSPARC.

`cryosparcm cluster`

Cluster management commands. See the Download and Installation page for full details.

Ensure CryoSPARC is running before running cluster management commands.

Usage:

$ cryosparcm cluster [OPTIONS] COMMAND [ARGS]...

Options:

--help: Show this message and exit.

Commands:

connect: Create or update a cluster with...
dump: Write cluster configuration and script to...
validate
remove: Remove a cluster from the scheduler.
example: Write example cluster configuration and...

`cryosparcm cluster example`

Write example cluster configuration (cluster_info.json) and script (cluster_script.sh) to a directory.

Examples are available for Portable Batch System (cryosparcm cluster example pbs) and SLURM (cryosparcm cluster example slurm) schedulers. Other systems are similar; run one of the two cluster example commands and modify the output files accordingly.

Usage:

$ cryosparcm cluster example [OPTIONS] TYPE:{pbs|slurm}

Arguments:

TYPE:{pbs|slurm}: Any cluster scheduler is supported but may require a custom submission script. [required]

Options:

-o, --output-dir DIRECTORY: Path to output directory [default: .]
--help: Show this message and exit.

`cryosparcm cluster connect`

Create or update a cluster with cluster_info.json and cluster_script.sh.

Usage:

$ cryosparcm cluster connect [OPTIONS]

Options:

--info FILE: [default: cluster_info.json]
--script FILE: [default: cluster_script.sh]
--help: Show this message and exit.

`cryosparcm cluster dump`

Write cluster configuration and script to a directory.

Usage:

$ cryosparcm cluster dump [OPTIONS] NAME

Arguments:

NAME: Cluster target name [required]

Options:

o, --output-dir DIRECTORY: Path to output directory [default: .]
--help: Show this message and exit.

`cryosparcm cluster remove`

Remove a cluster from the scheduler.

Usage:

$ cryosparcm cluster remove [OPTIONS] NAME

Arguments:

NAME: Cluster target name [required]

Options:

--help: Show this message and exit.

`cryosparcm deps`

Install Python and external dependencies. Specify --force to install even if they haven't changed.

Usage:

$ cryosparcm deps [OPTIONS]

Options:

--force
--help: Show this message and exit.

`cryosparcm test`

Verifies the instance has been correctly installed by running several tests. Provides a report upon completion. For more information, see Guide: Installation Testing with cryosparcm test.

Ensure CryoSPARC is running before running worker management commands.

Usage:

$ cryosparcm test [OPTIONS] COMMAND [ARGS]...

Options:

--help: Show this message and exit.

Commands:

license: Verify that your CryoSPARC license is valid
install: Test all installation components
i: Alias for install
workers: Test worker installation
w: Alias for workers

`cryosparcm test license`

Verify that your CryoSPARC license is valid and that CryoSPARC can verify job runs with the license server at get.cryosparc.com.

Usage:

$ cryosparcm test license [OPTIONS]

Options:

-l, --long
--help: Show this message and exit.

`cryosparcm test install`

Tests the core installation components of CryoSPARC (HTTP connections, licensing, workers, etc.) that are required to start running jobs. Provides information on the status of the CryoSPARC instance (e.g., which version is running, whether a patch is available, etc.).

Usage:

$ cryosparcm test install [OPTIONS]

Options:

--help: Show this message and exit.

Always run this command from the same host and UNIX user account originally used to install CryoSPARC.

`cryosparcm test i`

Alias for cryosparcm test install

`cryosparcm test workers`

Test workers by running validation jobs in the specified project.

Usage:

$ cryosparcm test workers [OPTIONS] PROJECT

Arguments:

PROJECT: [required]

Options:

--test [all|launch|ssd|gpu]: Specify either the launch, ssd or gpu test [required]
-t, --target TEXT: Specify one or more targets to run tests on, tests all if not specified
--test-pytorch / --no-test-pytorch: Test if worker(s) can launch PyTorch jobs on all enabled GPUs [default: no-test-pytorch]
--help: Show this message and exit.

`cryosparcm test w`

Alias for cryosparcm test workers

Logs

`cryosparcm log`

Show a service output log from the most recent entries. The log is live-updated while the command-line remains open and new data is added to the log. To stop live updates and return to the shell, press ctrl C on your keyboard followed by q.

Usage:

$ cryosparcm log [OPTIONS] SERVICE:{app|database|cache|api|scheduler|command_vis|app_api|supervisord}

Arguments:

SERVICE:{app|database|cache|api|scheduler|command_vis|app_api|supervisord}: [required]

Options:

--help: Show this message and exit.

To save the full log, redirect the output to a file. Example:

cryosparcm log api > api.log

To show only the last xx lines of the log, pipe to tail. For example, to see the last 1000 lines of the log:

Copy

cryosparcm log api | tail -n 1000

`cryosparcm filterlog`

Show a filtered service output log.

Usage:

$ cryosparcm filterlog [OPTIONS] SERVICE:{app|database|cache|api|scheduler|command_vis|app_api|supervisord}

Arguments:

SERVICE:{app|database|cache|api|scheduler|command_vis|app_api|supervisord}: [required]

Options:

-d, --days INTEGER RANGE: Show logs within previous N days [default: 30; x>=0]
-D, --date [%Y-%m-%d]: Show logs on date
-m, --max-lines INTEGER RANGE: Max lines to show [x>=0]
-t, --tail: Continuously follow this log
--help: Show this message and exit.

Note that only database, api, scheduler and command_vis services support date and days filters.

`cryosparcm snaplogs`

Create an archive with all current master service logs.

Usage:

$ cryosparcm snaplogs [OPTIONS]

Options:

-o, --output-dir DIRECTORY: Path to output directory [default: .]
--help: Show this message and exit.

`cryosparcm errorreport`

Generate a diagnostic information bundle. For more information, see Guide: Download Error Reports.

Usage:

$ cryosparcm errorreport [OPTIONS]

Options:

-o, --output-dir DIRECTORY: Path to output directory [default: .]
-d, --days INTEGER RANGE: Show logs within previous N days [default: 30; x>=0]
-D, --date [%Y-%m-%d]: Show logs on date
-m, --max-lines INTEGER RANGE: Max lines to show [x>=0]
--offline / --no-offline: Skip database and worker data [default: no-offline]
--skip-workers / --no-skip-workers: Skip worker data [default: no-skip-workers]
--help: Show this message and exit.

`cryosparcm get-workspace-report`

Download HTML workspace report from the CryoSPARC app.

Usage:

$ cryosparcm get-workspace-report [OPTIONS]

Options:

--project TEXT: [required]
--workspace TEXT: [required]
-o, --path PATH: Path to output file or directory [default: .]
--help: Show this message and exit.

User Management

Functions provided by these commands are also available from the web interface. For more details, see the Admin Panel guide.

`cryosparcm user`

User management commands.

Usage:

$ cryosparcm user [OPTIONS] COMMAND [ARGS]...

Options:

--help: Show this message and exit.

Commands:

list: Show a table of available user accounts
exists: Check if user exists
create: Create a new user account
update: Update user account information
resetpassword: Reset a user account's password

`cryosparcm user list`

Show a table of available user accounts, including their names, email address and admin status.

Usage:

$ cryosparcm user list [OPTIONS]

Options:

--help: Show this message and exit.

`cryosparcm user exists`

Check if user exists. Command exits with status 0 if user exists, 1 otherwise. Shows an “exists” or “does not exist” message in either case.

Usage:

$ cryosparcm user exists [OPTIONS]

Options:

--email TEXT: Email [required]
--help: Show this message and exit.

`cryosparcm user create`

Create a new user account. Call without arguments to create interactively.

Usage:

$ cryosparcm user create [OPTIONS]

Options:

--email TEXT: Login email [required]
--password TEXT: Password [required]
--username TEXT: User name [required]
--firstname TEXT: First or given name [required]
--lastname TEXT: Last or surname [required]
--role [user|admin]: User role [default: user]
--help: Show this message and exit.

<aside> 💡

If any required options are not specified, an input prompt will be provided.

</aside>

`cryosparcm user update`

Update user account information and access, providing the email and password to verify. To change the password, use cryosparcm users resetpassword. Note that the user's email cannot be changed with this command.

Usage:

$ cryosparcm user update [OPTIONS]

Options:

--email TEXT: Email [required]
--password TEXT: Password [required]
--username TEXT: New user name
--firstname TEXT: New first or given name
--lastname TEXT: New last or surname
--role [user|admin]: New user role
--help: Show this message and exit.

<aside> 💡

If any required options are not specified, an input prompt will be provided.

</aside>

Other than for the first user account created, new users do not have administrative privileges by default. After creating the first user account, other accounts can also be created through the user interface if preferred.

`cryosparcm user resetpassword`

Reset a user account's password.

Usage:

$ cryosparcm user resetpassword [OPTIONS]

Options:

--email TEXT: Email [required]
--password TEXT: Password [required]
--help: Show this message and exit.

If any required options are not specified, an input prompt will be provided.

Job Management

`cryosparcm job`

Job management commands.

Usage:

$ cryosparcm job [OPTIONS] COMMAND [ARGS]...

Options:

--help: Show this message and exit.

Commands:

status: Show a summary of queued and active jobs
queue: Queue a job
clear: Clear a job
kill: Kill a job
log: Show job standard output and error log
events: Show job event log

`cryosparcm job status`

Show a summary of queued and active jobs.

Usage:

$ cryosparcm job status [OPTIONS]

Options:

--help: Show this message and exit.

`cryosparcm job queue`

Queue a job. Specify either --lane or --hostname, except for interactive jobs. One or more --gpu options may be specified with --hostname.

Usage:

$ cryosparcm job queue [OPTIONS] PROJECT_UID JOB_UID

Arguments:

PROJECT_UID: [required]
JOB_UID: [required]

Options:

-l, --lane TEXT: Scheduler lane to queue to
-h, --hostname TEXT: Worker node to queue to
-g, --gpu INTEGER: Specify one or more GPUs to queue to, --hostname must also be specified
--check-inputs-ready / --no-check-inputs-ready: If disabled, job will run even if parent input jobs are incomplete [default: check-inputs-ready]
--help: Show this message and exit.

`cryosparcm job clear`

Clear a job.

Usage:

$ cryosparcm job clear [OPTIONS] PROJECT_UID JOB_UID

Arguments:

PROJECT_UID: [required]
JOB_UID: [required]

Options:

--help: Show this message and exit.

`cryosparcm job kill`

Kill a job by its project UID and job UID.

Usage:

$ cryosparcm job kill [OPTIONS] PROJECT_UID JOB_UID

Arguments:

PROJECT_UID: [required]
JOB_UID: [required]

Options:

--help: Show this message and exit.

`cryosparcm job log`

Show job standard output and error log.

Usage:

$ cryosparcm job log [OPTIONS] PROJECT_UID JOB_UID

Arguments:

PROJECT_UID: [required]
JOB_UID: [required]

Options:

--help: Show this message and exit.

`cryosparcm job events`

Show job event log.

Usage:

$ cryosparcm job events [OPTIONS] PROJECT_UID JOB_UID

Arguments:

PROJECT_UID: [required]
JOB_UID: [required]

Options:

-c, --checkpoint INTEGER: Show events from this checkpoint up until the next one. Shows all events if not provided. Specify -1 to show everything after the last checkpoint.
--help: Show this message and exit.

Database Management

`cryosparcm database`

Database management commands.

Usage:

$ cryosparcm database [OPTIONS] COMMAND [ARGS]...

Options:

--help: Show this message and exit.

Commands:

check: Check that the database is running correctly.
configure: Prepare the database for running.
fixport: Update expected database port.
backup: Make a backup copy of the database.
restore: Restore the database from a backup file.
compact: Attempt to reduce database size.
export: Export the contents of the database.
import: Import a collection from an exported .json file
export-instance-config: Export instance configuration and project information.
import-instance-config: Import instance configuration from an exported file.

`cryosparcm database check`

Check that the database is running with the correct host configuration.

Usage:

$ cryosparcm database check [OPTIONS]

Options:

--quiet / --no-quiet: [default: no-quiet]
--help: Show this message and exit.

Always run this command from the same host and UNIX user account originally used to install CryoSPARC.

`cryosparcm database configure`

Prepare the database for running. Automatically runs during start, manual invocation not typically required.

Usage:

$ cryosparcm database configure [OPTIONS]

Options:

-v, --verbose
--help: Show this message and exit.

Always run this command from the same host and UNIX user account originally used to install CryoSPARC.

`cryosparcm database fixport`

Update expected database port so that it matches the configured port following a change to CRYOSPARC_BASE_PORT in config.sh.

Usage:

$ cryosparcm database fixport [OPTIONS]

Options:

--help: Show this message and exit.

Always run this command from the same host and UNIX user account originally used to install CryoSPARC.

`cryosparcm database backup`

Make a backup copy of the database with mongodump.

By default, and saves the backup as an .archive file to the current working directory, with the current date and time in in the filename, e.g., cryosparc_backup_2021_06_14_11h27.archive

Do not allow the backup to fill up the filesystem on which the database is stored. If needed, specify a custom alternative path where the backup will be written.

Usage:

$ cryosparcm database backup [OPTIONS]

Options:

-o, --output PATH: Path to output file or directory [default: .]
-c, --collection TEXT
--help: Show this message and exit.

CryoSPARC can be running when cryosparcm database backup is run, but the backup will impact the performance of your running database (source).

Once CryoSPARC projects or jobs are created, deleted, or otherwise modified during or after the backup, a database restored from the resulting backup file will no longer be compatible with the modified project directories.

Use the cryosparcm recover command to avoid this issue.

Always run this command from the same host and UNIX user account originally used to install CryoSPARC.

`cryosparcm database restore`

Restore the database from a backup file.

A database backup becomes outdated and incompatible with project directories as soon as CryoSPARC projects or jobs are created, deleted or modified following a database backup. Do not restore an outdated database backup. Restoration of an outdated database backup and subsequent use with CryoSPARC is likely to corrupt CryoSPARC projects.

Use the cryosparcm recover command to avoid this issue.

CryoSPARC must be installed and but not started before running this command.

Usage:

$ cryosparcm database restore [OPTIONS]

Options:

-f, --file FILE: Path to input file [required]
-c, --collection TEXT
--help: Show this message and exit.

Always run this command from the same host and UNIX user account originally used to install CryoSPARC.

`cryosparcm database compact`

Attempt to reduce database size.

Usage:

$ cryosparcm database compact [OPTIONS]

Options:

--help: Show this message and exit.

Always run this command from the same host and UNIX user account originally used to install CryoSPARC.

`cryosparcm database export`

Export the contents of a database collection to a .json file.

Usage:

$ cryosparcm database export [OPTIONS] COLLECTION_NAME

Arguments:

COLLECTION_NAME: [required]

Options:

-o, --output-dir DIRECTORY: Path to output directory [default: .]
--help: Show this message and exit.

Always run this command from the same host and UNIX user account originally used to install CryoSPARC.

`cryosparcm database import`

Import a collection from an exported .json file. Overwrites existing data in that collection.

Usage:

$ cryosparcm database import [OPTIONS] COLLECTION_NAME

Arguments:

COLLECTION_NAME: [required]

Options:

-f, --file FILE: Path to input file [required]
--help: Show this message and exit.

Always run this command from the same host and UNIX user account originally used to install CryoSPARC.

`cryosparcm database export-instance-config`

Export instance configuration and project information to a .tar file.

Usage:

$ cryosparcm database export-instance-config [OPTIONS]

Options:

-o, --output-dir DIRECTORY: Path to output directory [default: .]
--help: Show this message and exit.

Always run this command from the same host and UNIX user account originally used to install CryoSPARC.

`cryosparcm database import-instance-config`

Imports instance configuration from an exported instance configuration .tar file.

Usage:

$ cryosparcm database import-instance-config [OPTIONS]

Options:

-f, --file FILE: Path to input file [required]
-y, --yes: Confirm without prompting
--help: Show this message and exit.

Always run this command from the same host and UNIX user account originally used to install CryoSPARC.

Command Line Utilities

`cryosparcm env`

Export environment variables used by CryoSPARC.

Usage:

$ cryosparcm env [OPTIONS]

Options:

--help: Show this message and exit.

Run this command with eval to define the variables output by the env command.

eval $(cryosparcm env)

`cryosparcm call`

Run any command with the CryoSPARC environment. For example:

cryosparcm call python -c "import sys; print(sys.path)"

Usage:

$ cryosparcm call [COMMAND] [ARGS]...

Equivalent to running eval $(cryosparcm env) followed by the command.

`cryosparcm python`

Run python command with the CryoSPARC environment. For example:

cryosparcm python -c "import sys; print(sys.path)"

Usage:

$ cryosparcm python [OPTIONS] [ARGS]...

`cryosparcm ipython`

Run an interactive python shell with the CryoSPARC environment.

Usage:

$ cryosparcm ipython [OPTIONS]

`cryosparcm cli`

Interact with CryoSPARC from the command line with Python expressions. See cryosparcm cli reference for full details.

Usage:

$ cryosparcm cli [OPTIONS] EXPRESSION

Arguments:

EXPRESSION: [required] Python expression

Options:

--help: Show this message and exit.

`cryosparcm icli`

Interact with CryoSPARC from an ipython shell. Can use api object in Python commands. See cryosparcm cli reference for full details.

Usage:

$ cryosparcm icli [OPTIONS] [ARGS]...

`cryosparcm downloadtest`

Download a test dataset. For use with the T20S Introductory Tutorial or Installation Testing or Performance benchmarking.

Usage:

$ cryosparcm downloadtest [OPTIONS]

Options:

-o, --output-dir DIRECTORY: Path to output directory [default: .]
--dataset TEXT: Which dataset to download. One of '10025', '10305', or 'PERFORMANCE_BENCHMARK_DATA' [default: 10025]
--help: Show this message and exit.

`cryosparcm mongo`

Start a mongo shell for CryoSPARC’s local MongoDB database service.

Usage:

$ cryosparcm mongo [OPTIONS] [ARGS]...

Always run this command from the same host and UNIX user account originally used to install CryoSPARC.

`cryosparcm redis`

Start a redis-cli prompt for command line access to the Redis cache service.

Usage:

$ cryosparcm redis [OPTIONS] [ARGS]...

Always run this command from the same host and UNIX user account originally used to install CryoSPARC.

Deprecated Commands

These commands were present in CryoSPARC v4 and remain in CryoSPARC v5 but should no longer be used; instead, the corresponding commands above should be used.

`cryosparcm checkdb` (Deprecated)

Use cryosparcm database check instead.

Usage:

$ cryosparcm checkdb [OPTIONS]

Options:

--help: Show this message and exit.

`cryosparcm configuredb` (Deprecated)

Use cryosparcm database configure instead.

Usage:

$ cryosparcm configuredb [OPTIONS]

Options:

--help: Show this message and exit.

`cryosparcm fixdbport` (Deprecated)

Use cryosparcm database fixport instead.

Usage:

$ cryosparcm fixdbport [OPTIONS]

Options:

--help: Show this message and exit.

`cryosparcm backup` (Deprecated)

Use cryosparcm database backup instead.

Usage:

$ cryosparcm backup [OPTIONS]

Options:

--help: Show this message and exit.

`cryosparcm restore` (Deprecated)

Use cryosparcm database restore instead.

Usage:

$ cryosparcm restore [OPTIONS]

Options:

--help: Show this message and exit.

`cryosparcm compact` (Deprecated)

Use cryosparcm database compact instead.

Usage:

$ cryosparcm compact [OPTIONS]

Options:

--help: Show this message and exit.

`cryosparcm listusers` (Deprecated)

Use cryosparcm user list instead.

Usage:

$ cryosparcm listusers [OPTIONS]

Options:

--help: Show this message and exit.

`cryosparcm createuser` (Deprecated)

Use cryosparcm user create instead.

Usage:

$ cryosparcm createuser [OPTIONS]

Options:

--email TEXT: [required]
--password TEXT: [required]
--username TEXT: [required]
--firstname TEXT: [required]
--lastname TEXT: [required]
--role [user|admin]: [default: user]
--help: Show this message and exit.

`cryosparcm updateuser` (Deprecated)

Use cryosparcm user update instead.

Usage:

$ cryosparcm updateuser [OPTIONS]

Options:

--email TEXT: [required]
--password TEXT: [required]
--username TEXT
--firstname TEXT
--lastname TEXT
--admin [true|false]
--help: Show this message and exit.

`cryosparcm resetpassword` (Deprecated)

Use cryosparcm user resetpassword instead.

Usage:

$ cryosparcm resetpassword [OPTIONS]

Options:

--email TEXT: [required]
--password TEXT: [required]
--help: Show this message and exit.

`cryosparcm jobstatus` (Deprecated)

Use cryosparcm jobstatus instead.

Usage:

$ cryosparcm jobstatus [OPTIONS]

Options:

--help: Show this message and exit.

`cryosparcm joblog` (Deprecated)

Use cryosparcm job log instead.

Usage:

$ cryosparcm joblog [OPTIONS] PROJECT JOB

Arguments:

PROJECT: [required]
JOB: [required]

Options:

--help: Show this message and exit.

`cryosparcm eventlog` (Deprecated)

Use cryosparcm job events instead.

Usage:

$ cryosparcm eventlog [OPTIONS] PROJECT JOB

Arguments:

PROJECT: [required]
JOB: [required]

Options:

--help: Show this message and exit.

`cryosparcm licensestatus` (Deprecated)

Use cryosparcm test license instead.

Usage:

$ cryosparcm licensestatus [OPTIONS]

Options:

--help: Show this message and exit.

`cryosparcm cluster validate` (Deprecated)

Use cryosparcm test workers instead.

Usage:

$ cryosparcm cluster validate [OPTIONS] NAME

Arguments:

NAME: Cluster target name [required]

Options:

--projects-dir TEXT: Absolute path to projects directory [required]
--help: Show this message and exit.

PreviousEnvironment Variables (v5.0+)Nextcryosparcm cli reference (v5.0+)

Last updated 1 day ago

hashtagAccess the CryoSPARC command line utility, cryosparcm

hashtagcryosparcm

hashtagInstance Status and Management

hashtagcryosparcm status

hashtagcryosparcm version

hashtagcryosparcm start

hashtagcryosparcm stop

hashtagcryosparcm restart

hashtagcryosparcm maintenancemode

hashtagcryosparcm resources

hashtagcryosparcm changeport

hashtagcryosparcm asset-stats

hashtagcryosparcm recover

hashtagInstance Setup

hashtagcryosparcm update

hashtagcryosparcm patch

hashtagcryosparcm worker

hashtagcryosparcm worker update

hashtagcryosparcm worker patch

hashtagcryosparcm worker connect

hashtagcryosparcm worker disconnect

hashtagcryosparcm cluster

hashtagcryosparcm cluster example

hashtagcryosparcm cluster connect

hashtagcryosparcm cluster dump

hashtagcryosparcm cluster remove

hashtagcryosparcm deps

hashtagcryosparcm test

hashtagcryosparcm test license

hashtagcryosparcm test install

hashtagcryosparcm test i

hashtagcryosparcm test workers

hashtagcryosparcm test w

hashtagLogs

hashtagcryosparcm log

hashtagcryosparcm filterlog

hashtagcryosparcm snaplogs

hashtagcryosparcm errorreport

hashtagcryosparcm get-workspace-report

hashtagUser Management

hashtagcryosparcm user

hashtagcryosparcm user list

hashtagcryosparcm user exists

hashtagcryosparcm user create

hashtagcryosparcm user update

hashtagcryosparcm user resetpassword

hashtagJob Management

hashtagcryosparcm job

hashtagcryosparcm job status

hashtagcryosparcm job queue

hashtagcryosparcm job clear

hashtagcryosparcm job kill

hashtagcryosparcm job log

hashtagcryosparcm job events

hashtagDatabase Management

hashtagcryosparcm database

hashtagcryosparcm database check

hashtagcryosparcm database configure

hashtagcryosparcm database fixport

hashtagcryosparcm database backup

hashtagcryosparcm database restore

hashtagcryosparcm database compact

hashtagcryosparcm database export

hashtagcryosparcm database import

hashtagcryosparcm database export-instance-config

hashtagcryosparcm database import-instance-config

hashtagCommand Line Utilities

hashtagcryosparcm env

hashtagcryosparcm call

hashtagcryosparcm python

hashtagcryosparcm ipython

hashtagcryosparcm cli

hashtagcryosparcm icli

hashtagcryosparcm downloadtest

hashtagcryosparcm mongo

hashtagcryosparcm redis

hashtagDeprecated Commands

hashtagcryosparcm checkdb (Deprecated)

hashtagcryosparcm configuredb (Deprecated)

hashtagcryosparcm fixdbport (Deprecated)

Access the CryoSPARC command line utility, `cryosparcm`

`cryosparcm`

Instance Status and Management

`cryosparcm status`

`cryosparcm version`

`cryosparcm start`

`cryosparcm stop`

`cryosparcm restart`

`cryosparcm maintenancemode`

`cryosparcm resources`

`cryosparcm changeport`

`cryosparcm asset-stats`

`cryosparcm recover`

Instance Setup

`cryosparcm update`

`cryosparcm patch`

`cryosparcm worker`

`cryosparcm worker update`

`cryosparcm worker patch`

`cryosparcm worker connect`

`cryosparcm worker disconnect`

`cryosparcm cluster`

`cryosparcm cluster example`

`cryosparcm cluster connect`

`cryosparcm cluster dump`

`cryosparcm cluster remove`

`cryosparcm deps`

`cryosparcm test`

`cryosparcm test license`

`cryosparcm test install`

`cryosparcm test i`

`cryosparcm test workers`

`cryosparcm test w`

Logs

`cryosparcm log`

`cryosparcm filterlog`

`cryosparcm snaplogs`

`cryosparcm errorreport`

`cryosparcm get-workspace-report`

User Management

`cryosparcm user`

`cryosparcm user list`

`cryosparcm user exists`

`cryosparcm user create`

`cryosparcm user update`

`cryosparcm user resetpassword`

Job Management

`cryosparcm job`

`cryosparcm job status`

`cryosparcm job queue`

`cryosparcm job clear`

`cryosparcm job kill`

`cryosparcm job log`

`cryosparcm job events`

Database Management

`cryosparcm database`

`cryosparcm database check`

`cryosparcm database configure`

`cryosparcm database fixport`

`cryosparcm database backup`

`cryosparcm database restore`

`cryosparcm database compact`

`cryosparcm database export`

`cryosparcm database import`

`cryosparcm database export-instance-config`

`cryosparcm database import-instance-config`

Command Line Utilities

`cryosparcm env`

`cryosparcm call`

`cryosparcm python`

`cryosparcm ipython`

`cryosparcm cli`

`cryosparcm icli`

`cryosparcm downloadtest`

`cryosparcm mongo`

`cryosparcm redis`

Deprecated Commands

`cryosparcm checkdb` (Deprecated)

`cryosparcm configuredb` (Deprecated)

`cryosparcm fixdbport` (Deprecated)