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.

cryosparcuser@emserver1:~$ cryosparcm status
----------------------------------------------------------------------------
CryoSPARC System master node installed at
/home/cryosparcuser/sw/cryosparc_master
Current cryoSPARC version: v4.3.1
----------------------------------------------------------------------------

CryoSPARC process status:

app                              RUNNING   pid 1599310, uptime 0:30:11
app_api                          RUNNING   pid 1599643, uptime 0:30:10
app_api_dev                      STOPPED   Not started
app_legacy                       STOPPED   Not started
app_legacy_dev                   STOPPED   Not started
command_core                     RUNNING   pid 1593955, uptime 0:30:26
command_rtp                      RUNNING   pid 1595620, uptime 0:30:16
command_vis                      RUNNING   pid 1594923, uptime 0:30:17
database                         RUNNING   pid 1593553, uptime 0:30:29

----------------------------------------------------------------------------
License is valid
----------------------------------------------------------------------------

global config variables:
export CRYOSPARC_LICENSE_ID="xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx"
export CRYOSPARC_MASTER_HOSTNAME=emserver1.internal
export CRYOSPARC_DB_PATH="/home/cryosparcuser/sw/cryosparc_db_61561"
export CRYOSPARC_BASE_PORT=61560
export CRYOSPARC_DB_CONNECTION_TIMEOUT_MS=20000
export CRYOSPARC_INSECURE=false
export CRYOSPARC_DB_ENABLE_AUTH=true
export CRYOSPARC_CLUSTER_JOB_MONITOR_INTERVAL=10
export CRYOSPARC_CLUSTER_JOB_MONITOR_MAX_RETRIES=1000000
export CRYOSPARC_PROJECT_DIR_PREFIX='CS-'
export CRYOSPARC_DEVELOP=false
export CRYOSPARC_CLICK_WRAP=true

cryosparcuser@emserver1:~$

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

See Software Updates for details.

This command can only be run by the UNIX user that owns the CryoSPARC installation directory.

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

$ cryosparcm patch --help
usage: cryosparcm patch [-h] [-f] [-y] [--check] [--download] [--install]

Download and apply cryoSPARC patches. Run cryosparcm patch to automatically
install the latest patches on master and worker nodes

optional arguments:
  -h, --help   show this help message and exit
  -f, --force  install latest patch again even if already installed
  -y, --yes    confirm patch installation without prompt
  --check      check to see if a patch is available
  --download   download master and worker patches for manual installation
  --install    manually install a downloaded patch file

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 attempt

  • cryosparcm patch --check: Shows information about the latest patches without installing

  • cryosparcm patch --download: Downloads 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.

See also cryosparcw patch

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

Configures cluster installation. See the Download and Installation page for details.

Use with one of the following sub-commands.

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>

Outputs the existing config and script to current working directory for the cluster with the given name.

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>

Validate the cluster configuration specified by submitting test jobs. For more information on cluster validation, see Guide: Cluster Integration Validation

cryosparcm cluster remove <name>

Removes a cluster configuration from the scheduler.

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:

cryosparcuser@wrong.server:~$ CRYOSPARC_FORCE_HOSTNAME="true"
cryosparcuser@wrong.server:~$ cryosparcm status
----------------------------------------------------------------------------
CryoSPARC System master node installed at
/home/cryosparcuser/cryosparc/cryosparc_master
----------------------------------------------------------------------------

cryosparcm process status:
...

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.

File: /home/cryosparcuser/cryosparc/cryosparc_master/config.sh                          

export CRYOSPARC_LICENSE_ID="xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx"
export CRYOSPARC_MASTER_HOSTNAME="uoft"
export CRYOSPARC_DB_PATH="/home/cryosparcuser/cryosparc/cryosparc_master"
export CRYOSPARC_BASE_PORT=61000
export CRYOSPARC_HOSTNAME_CHECK="uoft"

Available CryoSPARC Services

  • app

  • app_api

  • app_legacy

  • command_core

  • command_rtp

  • command_vis

  • database

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>]

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>]

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>]

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

Show a summary of how many jobs are active.

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.

cryosparcm backup \
    --dir=/path/to/backups \
    --file=custombackupfile

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):

10 4 * * * /u/cryosparcuser/cryosparc_master/bin/cryosparcm backup --dir=/remote_volume/cryosparc_db_backup --file=database_backup_$(date +"%A").archive >> /remote_volume/cryosparc_db_backup/backuplog

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

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.

cryosparcm restore --file=/path/to/backups/backupfile

This command can only be run by the UNIX user that owns the CryoSPARC installation directory.

cryosparcm changeport <port>

Change CryoSPARC's base port to something else. Use the --yes or -y flag to proceed without confirmation.

cryosparcm changeport 40000

This command can only be run by the UNIX user that owns the CryoSPARC installation directory.

cryosparcm checkdb

Ensure the database is running with the correct host configuration

cryosparcm fixdbport

Run this command after manually changing CryoSPARC's base port number to ensure the Mongo database registers the change.

cryosparcm licensestatus

Check configured CryoSPARC license ID to see if there are any issues with verifying it.

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

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>

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

cryosparcm log command_core

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

cryosparcm log command_core > command_core.log
cryosparcm log command_core | tail -n 1000

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

cryosparcm filterlog command_core

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:

Usage:
    cryosparcm filterlog SERVICE
    cryosparcm filterlog [--days|-d N] [--date|-D YYYY-MM-DD] [--max_lines|-m MAX_LINES] [--name|-n NAME] [--func|-f FUNCTION] [--level|-l LEVEL] [--tail|-t] SERVICE
Where SERVICE is one of:
    app
    app_legacy
    app_api
    command_core
    command_rtp
    command_vis
    database
Some flags not available for all services.

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

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

cryosparcm joblog P3 J123

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

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

Compresses all .log files in the cryosparc_master/run folder into a .tgz file inside cryosparc_master/run.

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

Outputs a table of users registered with the system, including their names, email addresses and admin status.

cryosparcm createuser

Creates a new user account for log in through the web interface. Full use:

cryosparcm createuser \
    --email "<email address>" \
    --username "<login username>" \
    --firstname "<given name>"\
    --lastname "<surname>" \
    [--password "<new password>"]

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

Resets the password for indicated user with the new <password> provided. Full use:

cryosparcm resetpassword \
    --email "<email address>" \
    [--password "<new password>"]

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

Updates a user profile to change the user name or set admin privileges. Full use:

cryosparcm updateuser \
  --email "<email associated with cryoSPARC account>" \
  --username "<new username for that user>" \
  --firstname "<new first name(s) for that user>" \
  --lastname "<new last name(s) for that user>" \
  --admin "<true|false>" \
  [--password "<corresponding cryoSPARC password>"]

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:

This command can only be run by the UNIX user that owns the CryoSPARC installation directory.

Command-Line Interface

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.

eval $(cryosparcm env)

This may be used to, for example, run the Python distribution that ships with CryoSPARC.

cryosparcm cli

Runs a command using with cryoSPARC's command-line interface

cryosparcm cli <command>

See the full command reference

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

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

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

Prints a help message

cryosparcm mongo

Starts a mongo shell for CryoSPARC's local mongoDB instance.

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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