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.

cryoSPARC's installation script adds the location of cryosparcm to the $PATH environment variable via ~/.bashrc for the <cryosparcuser> UNIX user account (see Prerequisites & System Requirements for details).

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.

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.

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 remove <name>

Removes a cluster configuration from the scheduler.

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:

Error message shown when a core command is not executed on the master node

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"

cryosparcm status

Prints out current status of the cryoSPARC master system, including the status of all individual processes (database, webapp, command_core, etc). Also prints out configuration environment variables.

cryosparcm start

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.

cryosparcm stop

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 restart

Equivalent to running cryosparcm stop && cryosparcm start

cryosparcm jobstatus

Show a summary of how many jobs are active

cryosparcm backup

Backs up cryoSPARC database. By default, creates a file in cryosparc_master/run/db_backups/ with the current timestamp in its name.

To change the output location, specify the --dir or --file flag.

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

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>

Shows the output log of the master node process denoted by <process> which can be one of the following:

  • command_core

  • command_vis

  • database

  • webapp

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

To show only the last xx lines of the log, use tail

cryosparcm log command_core | tail -n 1000

This show the last 1000 lines of the log.

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

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>" \
--password "<new password>" \
--username "<login username>" \
--firstname "<given name>"\
--lastname "<surname>"

cryosparcm resetpassword

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

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

cryosparcm updateuser

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

cryosparcm updateuser \
--email "<email address>" \
--password "<current password>" \
--name "<new name>" \
--admin "<'true' or 'false'>"

The --name and --admin flags are optional.

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:

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.

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 $(cryosparc env) followed by another shell command.