cryosparcm reference
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 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.
For systems that do not support this, navigate to the cryosparc_master
installation directory and run ./bin/cryosparcm
instead of cryosparcm
Instance Setup
cryosparcm update
cryosparcm update
See Software Updates for details.
Software Updates and PatchesThis command can only be run by the UNIX user that owns the CryoSPARC installation directory.
cryosparcm patch
cryosparcm patch
Apply the latest patches available for your installed version of CryoSPARC without doing a full version update.
Specify the --help
flag to see full usage
Frequently used commands:
cryosparcm patch
: Automatically installs 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
: Reinstalls the latest patches in case something went wrong with a previous attemptcryosparcm patch --check
: Shows information about the latest patches without installingcryosparcm patch --download
: Downloads the latest patches without installing them. Follow the resulting instructions to install the master and worker patchescryosparcm patch --install
: Run this command immediately after a--download
to install the patch on the master node.
Some patches require restarting CryoSPARC. After running cryosparcm patch
, when prompted restart with cryosparcm restart
.
This command can only be run by the UNIX user that owns the CryoSPARC installation directory.
cryosparcm cluster
cryosparcm cluster
Configures cluster installation. See the Download and Installation page for details.
Downloading and Installing CryoSPARCUse with one of the following sub-commands.
cryosparcm cluster example <cluster_type>
cryosparcm cluster example <cluster_type>
Writes config and script template files to current working directory, cluster_info.json
and cluster_script.sh
respectively.
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.
cryosparcm cluster dump <name>
cryosparcm cluster dump <name>
Outputs the existing config and script to current working directory for the cluster with the given name.
cryosparcm cluster connect
cryosparcm cluster connect
Reads cluster_info.json
and cluster_script.sh
from the current directory. Connects a new or updates an existing cluster configuration using the name from cluster_info.json
.
cryosparcm cluster validate <name> --projects_dir </abs/path/to/project/dir>
cryosparcm cluster validate <name> --projects_dir </abs/path/to/project/dir>
Validate the cluster configuration specified by submitting test jobs. For more information on cluster validation, see Guide: Cluster Integration Validation
cryosparcm cluster remove <name>
cryosparcm cluster remove <name>
Removes a cluster configuration from the scheduler.
cryosparcm test
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
Specify the --help
flag to see full usage
cryosparcm test install
Tests the core components of CryoSPARC (HTTP connections, licensing, workers, etc.) that are required to start running jobs and provides information on the status of the CryoSPARC instance (e.g., which version is running, whether a patch is available, etc.).
cryosparcm test workers <project_uid>
Tests workers connected to CryoSPARC to ensure they can correctly run CryoSPARC jobs by testing if the worker can launch jobs, cache particles to an SSD (if an SSD is configured), and utilize the GPU correctly.
Instance Status and Management
The following commands are only allowed to be executed by <cryosparcuser>
(the user that installed CryoSPARC), and can only be executed on the master node. If these conditions are not met, you may see the following error:
You can mitigate errors temporarily by specifying the CRYOSPARC_FORCE_HOSTNAME
variable just before calling the command:
If this error message is incorrect (the hostname specified in the error message is actually the same host, just a different identifier), you can set the hostname that the management script will use to compare by adding the variable CRYOSPARC_HOSTNAME_CHECK
to cryosparc_master/config.sh
. You can also set CRYOSPARC_FORCE_HOSTNAME
in this file to permanently suppress this error.
Available CryoSPARC Services
app
app_api
app_legacy
command_core
command_rtp
command_vis
database
cryosparcm status
cryosparcm status
Prints out current status of the CryoSPARC master system, including the status of all individual processes (database
, app
, command_core
, etc). Also prints out configuration environment variables.
This command can only be run by the UNIX user that owns the CryoSPARC installation directory.
cryosparcm start [<service name>]
cryosparcm start [<service name>]
Starts the CryoSPARC instance if stopped, including the database, the command server, the web interface, etc.
All processes start in the background, including all jobs and the web interface; the command line may be closed after running start
.
Providing an optional service name will only start that specific service. For a list of all available services, see Available CryoSPARC Services.
In v4.0.0, app_legacy
(the original web application, formerly "webapp
") is not started by default, but can be at any time.
This command can only be run by the UNIX user that owns the CryoSPARC installation directory.
cryosparcm stop [<service name>]
cryosparcm stop [<service name>]
Stops the CryoSPARC instance if running. This will gracefully kill all the master processes, and will cause any running jobs (potentially on other nodes) to fail.
Providing an optional service name will only stop that specific service. For a list of all available services, see Available CryoSPARC Services.
This command can only be run by the UNIX user that owns the CryoSPARC installation directory.
cryosparcm restart [<service name>]
cryosparcm restart [<service name>]
Equivalent to running cryosparcm stop && cryosparcm start
Providing an optional service name will only restart that specific service. For a list of all available services, see Available CryoSPARC Services.
Stops the CryoSPARC instance if running. This will gracefully kill all the master processes, and will cause any running jobs (potentially on other nodes) to fail.
cryosparcm jobstatus
cryosparcm jobstatus
Show a summary of how many jobs are active.
cryosparcm backup
cryosparcm backup
Backs up the CryoSPARC MongoDB database using mongodump
. By default, the function creates a folder named backup
inside the database path specified by the CRYOSPARC_DB_PATH
environment variable in cryosparc_master/config.sh
(e.g., /u/cryosparcuser/cryosparc_db/backup
) and saves the backup as an .archive
file with the current date and time in its path (e.g., cryosparc_backup_2021_06_14_11h27.archive
) inside this folder.
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.
To change the directory the backup will be written to, specify the --dir
flag. To change the name of the backup file, specify the --file
flag.
CryoSPARC can be running when cryosparcm backup
is run, but the backup will impact the performance of your running database. (source).
Moreover, and perhaps more importantly, if CryoSPARC projects or jobs are created, deleted, or otherwise modified during the backup, a database restored from the resulting backup file will no longer be compatible with the modified project directories.
Creating a cron job to backup the CryoSPARC database automatically on a schedule
You can create a cron
job to execute the cryosparcm backup
command on a schedule, ensuring you always have a recent copy of the database that you can restore in case anything goes wrong.
For example, adding the following cron
job using crontab -e
(more information here):
Will run the backup command every day at 4:10 AM. The argument --file=database_backup_$(date +"%A").archive
will simulate a rolling-window backup, as a backup file will be created with the day of the week in the file path (e.g., database_backup_Friday.archive
). This allows you to keep a one-week buffer for the backup while limiting how much space the backups take, since future backups will overwrite a file if they are made on the same day.
This command can only be run by the UNIX user that owns the CryoSPARC installation directory.
cryosparcm restore
cryosparcm restore
Restore your database from a backup file (see cryosparcm 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.
CryoSPARC must be turned off before running this command.
The database directory (CRYOSPARC_DB_PATH
found in cryosparc_master/config.sh
) must exist and be empty before running this command.
This command can only be run by the UNIX user that owns the CryoSPARC installation directory.
cryosparcm changeport <port>
cryosparcm changeport <port>
Change CryoSPARC's base port to something else. Use the --yes
or -y
flag to proceed without confirmation.
This command can only be run by the UNIX user that owns the CryoSPARC installation directory.
cryosparcm checkdb
cryosparcm checkdb
Ensure the database is running with the correct host configuration
cryosparcm fixdbport
cryosparcm fixdbport
Run this command after manually changing CryoSPARC's base port number to ensure the Mongo database registers the change.
cryosparcm licensestatus
cryosparcm licensestatus
Check configured CryoSPARC license ID to see if there are any issues with verifying it.
cryosparcm maintenancemode [on|off|status]
cryosparcm maintenancemode [on|off|status]
Stops queued jobs from running while allowing running jobs to finish. Can be used to facilitate a better user experience while CryoSPARC is undergoing maintenance, for example during restart, patch, or update. For more information, see Guide: Maintenance Mode and Configurable User Facing Messages
cryosparcm test
cryosparcm test
Run cryosparcm test --help
for usage information.
Test all components of a CryoSPARC instance to confirm it is working properly. For more information, see Guide: Installation Testing with cryosparcm test
Logs
The CryoSPARC system maintains several log files for its various processes that help with debugging any components of the CryoSPARC system that are not working.
cryosparcm log <process>
cryosparcm log <process>
Tails the output log of the master node process denoted by <process>
which can be one of the following:
command_core
command_rtp
command_vis
database
app
app_legacy
app_api
For example
The log is live and automatically updates while the command-line remains open and new data is added to the log. To stop live updates and return to the shell, press control C
on your keyboard, and then q
.
To save the full log, redirect the output to a file
To show only the last lines of the log, use tail
. For example, to see the last 1000 lines of the log:
cryosparcm filterlog <process>
cryosparcm filterlog <process>
Shows the output log of the master node process denoted by <process>
which can be one of the following:
command_core
command_rtp
command_vis
database
app
app_legacy
app_api
For example
The log is live and automatically updates while the command-line remains open and new data is added to the log. To stop live updates and return to the shell, press control C
on your keyboard.
Additional Arguments
To see cryosparcm filterlog
usage, run cryosparcm filterlog -h
:
Please note that only command_core
, command_rtp
and command_vis
support the following arguments with the exception of database
, which also supports the date filter.
--days|-d N
Show last N days worth of logs
--date|-D YYYY-MM-DD
Show only logs from the given date
--max_lines|-m MAX_LINES
the maximum number of lines to return
--name|-n NAME
Show only logs with the given log name as a prefix (before dots). For example:
cryosparcm filterlog command_core -n COMMAND.SCHEDULER
--func|-f FUNCTION
Show only logs from the given log function. For example
cryosparcm filterlog command_core -f get_gpu_info_run
--level|-l LEVEL
Show only logs with the given level. For example:
cryosparcm filterlog command_core -l ERROR
--tail|-t
Will tail the log with the filters applied. To stop live updates and return to the shell, press
control C.
cryosparcm joblog PX JXX
cryosparcm joblog PX JXX
Shows a live output log for job JXX
in project PX
. Includes the standard input and error from the python process for the job.
For example, to show the output of Job 123 in Project 3, run the following
joblog
shows the full stdout
for the job, which is more comprehensive than the job log in the web interface and is more helpful for debugging.
To stop logging, save the full log or view only the last few log lines, see instructions for cryosparcm log
cryosparcm eventlog PX JXX
cryosparcm eventlog PX JXX
Prints the text of the processing log for job JXX
in project PX
to stdout.
For example, to write text components of the processing log for CryoSPARC job J123 in project P3 to a file in the current working directory, run:
cryosparcm eventlog P3 J123 > P3_J123_events.log
cryosparcm snaplogs
cryosparcm snaplogs
Compresses all .log
files in the cryosparc_master/run
folder into a .tgz
file inside cryosparc_master/run
.
cryosparcm errorreport
cryosparcm errorreport
Run cryosparcm errorreport --help
for usage information.
Create a CryoSPARC error report which includes diagnostic information and CryoSPARC instance logs. For more information, see Guide: Download Error Reports
User Management
cryosparcm listusers
cryosparcm listusers
Outputs a table of users registered with the system, including their names, email addresses and admin status.
cryosparcm createuser
cryosparcm createuser
Creates a new user account for log in through the web interface. Full use:
If the--password
argument is not specified, a silent input prompt is provided.
This command can only be run by the UNIX user that owns the CryoSPARC installation directory.
cryosparcm resetpassword
cryosparcm resetpassword
Resets the password for indicated user with the new <password>
provided. Full use:
If the --password
argument is not specified, a silent input prompt is provided.
This command can only be run by the UNIX user that owns the CryoSPARC installation directory.
cryosparcm updateuser
cryosparcm updateuser
Updates a user profile to change the user name or set admin privileges. Full use:
If the --password
argument is not specified, a silent input prompt is provided.
--email
is required and can not be changed with this command.
--username
, --firstname
, --lastname
are used for display and do not otherwise affect CryoSPARC function.
Other than for the first-created user account, new users do not have administrative privileges applied by default. Following creation of the first-created user account, other accounts can also be created through the user interface if preferred:
Guide: User ManagementThis command can only be run by the UNIX user that owns the CryoSPARC installation directory.
Command-Line Interface
cryosparcm env
cryosparcm env
Prints a list of environment variables for use in a command-line shell to replicate the exact environment used to when running CryoSPARC processes.
Run this command with eval
to define the variables output by the env
command.
This may be used to, for example, run the Python distribution that ships with CryoSPARC.
cryosparcm cli
cryosparcm cli
Runs a command using with cryoSPARC's command-line interface
See the full command reference
cryosparcm cli referencecryosparcm icli
cryosparcm icli
Runs an an interactive cryosparc shell that connects to the master processes. Use this to interactively run Python commands in the same environment as CryoSPARC.
cryosparcm rtpcli
cryosparcm rtpcli
Similar to cryosparcm cli
, but for running interactive commands with CryoSPARC Live.
Additional details coming soon.
See our guide on Managing a CryoSPARC Live Session from the CLI:
cryosparcm downloadtest
cryosparcm downloadtest
Download test data (subset of 20 movies from the EMPIAR-10025 dataset) to the current working directory for use with the T20S Introductory Tutorial.
cryosparcm help
cryosparcm help
Prints a help message
cryosparcm mongo
cryosparcm mongo
Starts a mongo
shell for CryoSPARC's local mongoDB instance.
cryosparcm call <command>
cryosparcm call <command>
Execute a shell command in CryoSPARC's shell environment, such as Python. Equivalent to calling:
eval $(cryosparcm env)
followed by another shell command.
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