CryoSPARC Guide
  • About CryoSPARC
  • Current Version
  • Licensing
    • Non-commercial license agreement
  • Setup, Configuration and Management
    • CryoSPARC Architecture and System Requirements
    • CryoSPARC Installation Prerequisites
    • How to Download, Install and Configure
      • Obtaining A License ID
      • Downloading and Installing CryoSPARC
      • CryoSPARC Cluster Integration Script Examples
      • Accessing the CryoSPARC User Interface
    • Deploying CryoSPARC on AWS
      • Performance Benchmarks
    • Using CryoSPARC with Cluster Management Software
    • Software Updates and Patches
    • Management and Monitoring
      • Environment variables
      • (Optional) Hosting CryoSPARC Through a Reverse Proxy
      • cryosparcm reference
      • cryosparcm cli reference
      • cryosparcw reference
    • Software System Guides
      • Guide: Updating to CryoSPARC v4
      • Guide: Installation Testing with cryosparcm test
      • Guide: Verify CryoSPARC Installation with the Extensive Validation Job (v4.3+)
      • Guide: Verify CryoSPARC Installation with the Extensive Workflow (≤v4.2)
      • Guide: Performance Benchmarking (v4.3+)
      • Guide: Download Error Reports
      • Guide: Maintenance Mode and Configurable User Facing Messages
      • Guide: User Management
      • Guide: Multi-user Unix Permissions and Data Access Control
      • Guide: Lane Assignments and Restrictions
      • Guide: Queuing Directly to a GPU
      • Guide: Priority Job Queuing
      • Guide: Configuring Custom Variables for Cluster Job Submission Scripts
      • Guide: SSD Particle Caching in CryoSPARC
      • Guide: Data Management in CryoSPARC (v4.0+)
      • Guide: Data Cleanup (v4.3+)
      • Guide: Reduce Database Size (v4.3+)
      • Guide: Data Management in CryoSPARC (≤v3.3)
      • Guide: CryoSPARC Live Session Data Management
      • Guide: Manipulating .cs Files Created By CryoSPARC
      • Guide: Migrating your CryoSPARC Instance
      • Guide: EMDB-friendly XML file for FSC plots
    • Troubleshooting
  • Application Guide (v4.0+)
    • A Tour of the CryoSPARC Interface
    • Browsing the CryoSPARC Instance
    • Projects, Workspaces and Live Sessions
    • Jobs
    • Job Views: Cards, Tree, and Table
    • Creating and Running Jobs
    • Low Level Results Interface
    • Filters and Sorting
    • View Options
    • Tags
    • Flat vs Hierarchical Navigation
    • File Browser
    • Blueprints
    • Workflows
    • Inspecting Data
    • Managing Jobs
    • Interactive Jobs
    • Upload Local Files
    • Managing Data
    • Downloading and Exporting Data
    • Instance Management
    • Admin Panel
  • Cryo-EM Foundations
    • Image Formation
      • Contrast in Cryo-EM
      • Waves as Vectors
      • Aliasing
  • Expectation Maximization in Cryo-EM
  • Processing Data in cryoSPARC
    • Get Started with CryoSPARC: Introductory Tutorial (v4.0+)
    • Tutorial Videos
    • All Job Types in CryoSPARC
      • Import
        • Job: Import Movies
        • Job: Import Micrographs
        • Job: Import Particle Stack
        • Job: Import 3D Volumes
        • Job: Import Templates
        • Job: Import Result Group
        • Job: Import Beam Shift
      • Motion Correction
        • Job: Patch Motion Correction
        • Job: Full-Frame Motion Correction
        • Job: Local Motion Correction
        • Job: MotionCor2 (Wrapper) (BETA)
        • Job: Reference Based Motion Correction (BETA)
      • CTF Estimation
        • Job: Patch CTF Estimation
        • Job: Patch CTF Extraction
        • Job: CTFFIND4 (Wrapper)
        • Job: Gctf (Wrapper) (Legacy)
      • Exposure Curation
        • Job: Micrograph Denoiser (BETA)
        • Job: Micrograph Junk Detector (BETA)
        • Interactive Job: Manually Curate Exposures
      • Particle Picking
        • Interactive Job: Manual Picker
        • Job: Blob Picker
        • Job: Template Picker
        • Job: Filament Tracer
        • Job: Blob Picker Tuner
        • Interactive Job: Inspect Particle Picks
        • Job: Create Templates
      • Extraction
        • Job: Extract from Micrographs
        • Job: Downsample Particles
        • Job: Restack Particles
      • Deep Picking
        • Guideline for Supervised Particle Picking using Deep Learning Models
        • Deep Network Particle Picker
          • T20S Proteasome: Deep Particle Picking Tutorial
          • Job: Deep Picker Train and Job: Deep Picker Inference
        • Topaz (Bepler, et al)
          • T20S Proteasome: Topaz Particle Picking Tutorial
          • T20S Proteasome: Topaz Micrograph Denoising Tutorial
          • Job: Topaz Train and Job: Topaz Cross Validation
          • Job: Topaz Extract
          • Job: Topaz Denoise
      • Particle Curation
        • Job: 2D Classification
        • Interactive Job: Select 2D Classes
        • Job: Reference Based Auto Select 2D (BETA)
        • Job: Reconstruct 2D Classes
        • Job: Rebalance 2D Classes
        • Job: Class Probability Filter (Legacy)
        • Job: Rebalance Orientations
        • Job: Subset Particles by Statistic
      • 3D Reconstruction
        • Job: Ab-Initio Reconstruction
      • 3D Refinement
        • Job: Homogeneous Refinement
        • Job: Heterogeneous Refinement
        • Job: Non-Uniform Refinement
        • Job: Homogeneous Reconstruction Only
        • Job: Heterogeneous Reconstruction Only
        • Job: Homogeneous Refinement (Legacy)
        • Job: Non-uniform Refinement (Legacy)
      • CTF Refinement
        • Job: Global CTF Refinement
        • Job: Local CTF Refinement
        • Job: Exposure Group Utilities
      • Conformational Variability
        • Job: 3D Variability
        • Job: 3D Variability Display
        • Job: 3D Classification
        • Job: Regroup 3D Classes
        • Job: Reference Based Auto Select 3D (BETA)
        • Job: 3D Flexible Refinement (3DFlex) (BETA)
      • Postprocessing
        • Job: Sharpening Tools
        • Job: DeepEMhancer (Wrapper)
        • Job: Validation (FSC)
        • Job: Local Resolution Estimation
        • Job: Local Filtering
        • Job: ResLog Analysis
        • Job: ThreeDFSC (Wrapper) (Legacy)
      • Local Refinement
        • Job: Local Refinement
        • Job: Particle Subtraction
        • Job: Local Refinement (Legacy)
      • Helical Reconstruction
        • Helical symmetry in CryoSPARC
        • Job: Helical Refinement
        • Job: Symmetry search utility
        • Job: Average Power Spectra
      • Utilities
        • Job: Exposure Sets Tool
        • Job: Exposure Tools
        • Job: Generate Micrograph Thumbnails
        • Job: Cache Particles on SSD
        • Job: Check for Corrupt Particles
        • Job: Particle Sets Tool
        • Job: Reassign Particles to Micrographs
        • Job: Remove Duplicate Particles
        • Job: Symmetry Expansion
        • Job: Volume Tools
        • Job: Volume Alignment Tools
        • Job: Align 3D maps
        • Job: Split Volumes Group
        • Job: Orientation Diagnostics
      • Simulations
        • Job: Simulate Data (GPU)
        • Job: Simulate Data (Legacy)
    • CryoSPARC Tools
    • Data Processing Tutorials
      • Case study: End-to-end processing of a ligand-bound GPCR (EMPIAR-10853)
      • Case Study: DkTx-bound TRPV1 (EMPIAR-10059)
      • Case Study: Pseudosymmetry in TRPV5 and Calmodulin (EMPIAR-10256)
      • Case Study: End-to-end processing of an inactive GPCR (EMPIAR-10668)
      • Case Study: End-to-end processing of encapsulated ferritin (EMPIAR-10716)
      • Case Study: Discrete and Continuous Heterogeneity in FaNaC1 (EMPIAR-11631 and -11632)
      • Case Study: Picking-induced Orientation Bias in HA Trimer (EMPIAR-10096 and -10097)
      • Case Study: Exploratory data processing by Oliver Clarke
      • Tutorial: Tips for Membrane Protein Structures
      • Tutorial: Common CryoSPARC Plots
      • Tutorial: Negative Stain Data
      • Tutorial: Phase Plate Data
      • Tutorial: EER File Support
      • Tutorial: EPU AFIS Beam Shift Import
      • Tutorial: Patch Motion and Patch CTF
      • Tutorial: Float16 Support
      • Tutorial: Particle Picking Calibration
      • Tutorial: Blob Picker Tuner
      • Tutorial: Helical Processing using EMPIAR-10031 (MAVS)
      • Tutorial: Maximum Box Sizes for Refinement
      • Tutorial: CTF Refinement
      • Tutorial: Ewald Sphere Correction
      • Tutorial: Symmetry Relaxation
      • Tutorial: Orientation Diagnostics
      • Tutorial: BILD files in CryoSPARC v4.4+
      • Tutorial: Mask Creation
      • Case Study: Yeast U4/U6.U5 tri-snRNP
      • Tutorial: 3D Classification
      • Tutorial: 3D Variability Analysis (Part One)
      • Tutorial: 3D Variability Analysis (Part Two)
      • Tutorial: 3D Flexible Refinement
        • Installing 3DFlex Dependencies (v4.1–v4.3)
      • Tutorial: 3D Flex Mesh Preparation
    • Webinar Recordings
  • Real-time processing in cryoSPARC Live
    • About CryoSPARC Live
    • Prerequisites and Compute Resources Setup
    • How to Access cryoSPARC Live
    • UI Overview
    • New Live Session: Start to Finish Guide
    • CryoSPARC Live Tutorial Videos
    • Live Jobs and Session-Level Functions
    • Performance Metrics
    • Managing a CryoSPARC Live Session from the CLI
    • FAQs and Troubleshooting
  • Guides for v3
    • v3 User Interface Guide
      • Dashboard
      • Project and Workspace Management
      • Create and Build Jobs
      • Queue Job, Inspect Job and Other Job Actions
      • View and Download Results
      • Job Relationships
      • Resource Manager
      • User Management
    • Tutorial: Job Builder
    • Get Started with CryoSPARC: Introductory Tutorial (v3)
    • Tutorial: Manually Curate Exposures (v3)
  • Resources
    • Questions and Support
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On this page
  • Access the command line utility, cryosparcm
  • Instance Setup
  • cryosparcm update
  • cryosparcm patch
  • cryosparcm cluster
  • cryosparcm test
  • Instance Status and Management
  • Available CryoSPARC Services
  • cryosparcm status
  • cryosparcm start [<service name>]
  • cryosparcm stop [<service name>]
  • cryosparcm restart [<service name>]
  • cryosparcm jobstatus
  • cryosparcm backup
  • cryosparcm restore
  • cryosparcm changeport <port>
  • cryosparcm checkdb
  • cryosparcm fixdbport
  • cryosparcm licensestatus
  • cryosparcm maintenancemode [on|off|status]
  • cryosparcm test
  • Logs
  • cryosparcm log <process>
  • cryosparcm filterlog <process>
  • cryosparcm joblog PX JXX
  • cryosparcm eventlog PX JXX
  • cryosparcm snaplogs
  • cryosparcm errorreport
  • User Management
  • cryosparcm listusers
  • cryosparcm createuser
  • cryosparcm resetpassword
  • cryosparcm updateuser
  • Command-Line Interface
  • cryosparcm env
  • cryosparcm cli
  • cryosparcm icli
  • cryosparcm rtpcli
  • cryosparcm downloadtest
  • cryosparcm help
  • cryosparcm mongo
  • cryosparcm call <command>
  1. Setup, Configuration and Management
  2. Management and Monitoring

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.

Previous(Optional) Hosting CryoSPARC Through a Reverse ProxyNextcryosparcm cli reference

Last updated 2 months ago

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 utility for all administrative, management and advanced usage tasks.

To use it, log into the machine onto which . 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

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.

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

cryosparcm cluster

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.

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.

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.

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.

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

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.

Moreover, and perhaps more importantly, 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.

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

cryosparcm restore

A database backup becomes outdated and incompatible with project directories as soon as CryoSPARC projects or jobs are created, deleted or modified following the the 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.

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.

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)

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

Additional details coming soon.

See our guide on Managing a CryoSPARC Live Session from the CLI:

cryosparcm downloadtest

cryosparcm help

Prints a help message

cryosparcm mongo

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.

See for details.

Some patches require restarting CryoSPARC. After running cryosparcm patch, when prompted restart with .

Configures cluster installation. See the page for details.

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

Providing an optional service name will only start that specific service. For a list of all available services, see .

Providing an optional service name will only stop that specific service. For a list of all available services, see .

Providing an optional service name will only restart that specific service. For a list of all available services, see .

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

Restore your database from a backup file (see ).

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

To stop logging, save the full log or view only the last few log lines, see instructions for

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

Similar to , but for running interactive commands with CryoSPARC Live.

Download test data (subset of 20 movies from the EMPIAR-10025 dataset) to the current working directory for use with the .

Starts a for CryoSPARC's local mongoDB instance.

command-line
CryoSPARC was installed
Software Updates
Software Updates and Patches
Download and Installation
Downloading and Installing CryoSPARC
Portable Batch System
SLURM
source
Guide: User Management
Python
cryosparcm cli reference
cryosparcm cli reference
mongo shell
cryosparcm restart
Available CryoSPARC Services
Available CryoSPARC Services
Available CryoSPARC Services
cryosparcm backup
cryosparcm log
See also cryosparcw patch
cryosparcm cli
T20S Introductory Tutorial
Managing a CryoSPARC Live Session from the CLICryoSPARC Guide
https://guide.cryosparc.com/live/how-to-access-cryosparc-live/managing-a-cryosparc-live-session-from-the-cli#setup
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Error message shown when a core command is not executed on the master node