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: 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
Powered by GitBook
On this page
  • Software updates
  • New versions
  • Patches
  • Before you update or downgrade
  • 1. Complete or `kill` running jobs
  • 2. Create a backup of the database
  • 3. Completely shutdown CryoSPARC (with confirmation)
  • Checking for updates
  • Installing automatic updates
  • Manual Cluster Updates
  • Update or roll back/downgrade to a specific version
  • Forced update
  • Skip Downloading Update Packages During Update
  • Manually Download Update Packages
  • Verify successful update or installation (optional)
  • Apply Patches
  1. Setup, Configuration and Management

Software Updates and Patches

How to get the latest CryoSPARC features and fixes or roll back to a previous version.

PreviousUsing CryoSPARC with Cluster Management SoftwareNextManagement and Monitoring

Last updated 1 year ago

Software updates

New versions

When we release a new version of CryoSPARC, the Dashboard will display an update notification.

In CryoSPARC v4.0+, the update notification is displayed at the top of the Dashboard:

In CryoSPARC v3, the update notification is displayed in the footer:

Patches

Before you update or downgrade

1. Complete or `kill` running jobs

Before you update your instance, wait for all presently running jobs to complete, or kill them from the Resource Manager. We also highly recommend making a backup of your database as described below.

In CryoSPARC v4.0+, you can use the Maintenance Mode feature to pause new jobs during an update:

2. Create a backup of the database

3. Completely shutdown CryoSPARC (with confirmation)

Checking for updates

Unless otherwise noted:

  • Log in to the workstation or remote node where cryosparc_master is installed.

  • Use the same non-root UNIX user account that runs the cryoSPARC process and was used to install cryoSPARC.

  • Run all commands on this page in a terminal running bash

Run this command to check for CryoSPARC updates.

cryosparcm update --check

This checks online for available updates and indicates whether an update is available.

$ cryosparcm update --check

CryoSPARC current version v2.15.0
          update starting on Wed Mar 18 12:09:52 EDT 2020

  current version v2.15.0
      new version v3.0.0

Update available!

You can also use cryosparcm update --list to get a full list of available versions (including old versions in case you would like to downgrade).

$ cryosparcm update --list

CryoSPARC current version v4.1.0
          update starting on Wed Mar 18 12:11:42 EDT 2020

Available versions:

v2.0.18
v2.0.20
v2.0.23
...
v4.0.2
v4.0.3
v4.1.0

To install a specific version, use 
    $ cryosparcm update --version=vXX.YY.ZZ[-branchname]

Installing automatic updates

Perform the following actions when installing the latest version of CryoSPARC.

To begin automatic master and non-cluster worker updates with the newest available version of CryoSPARC, run

cryosparcm update

Cluster workers are not updated automatically. See the "Manual Cluster Updates" section below

This commands executes the following:

1. Runs an automatic master update

  • Downloads the new master (cryosparc_master.tar.gz) and worker (cryosparc_worker.tar.gz) update packages if --skip-download was not specified

  • Shuts down the running CryoSPARC instance

  • Extracts and installs the master release

  • If dependencies have changed, automatically re-installs these

CryoSPARC releases include many compressed files; the extraction step may take several minutes on slower disks.

2. Runs automatic worker updates

Once the master update is complete, master starts up and automatically updates registered workers:

  • Transfers the worker release cryosparc_worker.tar.gz to each worker node via scp

  • Extracts and installs the worker release

  • Updates dependencies

If multiple standalone worker nodes are registered that all share the same worker installation, the update is only applied once.

Manual Cluster Updates

Cluster installations do not update automatically because not all clusters have internet access on worker nodes.

Once the automatic update above is complete, navigate to the CryoSPARC master installation directory via command-line. Look for the latest downloaded worker release, named cryosparc_worker.tar.gz orcryosparc2_worker.tar.gz

Copy this file (via scp) to cluster worker's installation directory. It should be in the same directory as the bin and deps folders. Navigate to the installation directory and run

If you're updating from cryoSPARC v2 to v3, the downloaded file is calledcryosparc2_worker.tar.gz. Do not change this file name when you copy it into the worker directory.

bin/cryosparcw update

This updates the worker at the current location with the given release file.

cryoSPARC does not allow running mismatched versions of master and worker releases. If you see this error:

Version mismatch! Worker and master versions are not the same. Please update.

Then re-install your cryoSPARC master and worker and check they are on the same version.

Update or roll back/downgrade to a specific version

Follow this section to install or update/downgrade to a specific release of CryoSPARC.

Steps are as described above, but with this command instead

cryosparcm update --version=vX.Y.Z

Use cryosparcm update --list to see the list of available versions. Substitute the vX.Y.Z in the command above with one of the results.

For instructions on updating an existing CryoSPARC v3.x instance to v4.0, please see: Guide: Updating to CryoSPARC v4

Forced update

This removes CryoSPARC and installs the latest available version, bypassing all file and dependency checks.

On the master node run

cryosparcm update --override

Then on each worker node run

bin/cryosparcw update --override

You cannot specify a version to install when overriding the update manager. Only the latest version of cryoSPARC will be installed.

Skip Downloading Update Packages During Update

Use the command line flag --skip-download with the cryosparcm update command to perform a full update of CryoSPARC using the update packages already inside the cryosparc_master directory. This command can be run after manually downloading the update packages using cryosparcm update --download-only.

For example:

cryosparcm update --skip-download

Manually Download Update Packages

Use the command line flag --download-only with the cryosparcm update command to only download the update packages and not perform a full update of CryoSPARC. This can be helpful if your internet connection is slow, and you'd like to limit CryoSPARC's downtime. This option can be used to download any version of CryoSPARC available (use cryosparcm update --list to see the list of available versions).

You can then use cryosparcm update --skip-download to perform a full update using the downloaded update packages.

For example:

cryosparcm update --download-only # downloads the latest update packages

cryosparcm update --version=v4.1.0 --download-only # downloads the update packages corresponding to v4.1.0

Verify successful update or installation (optional)

CryoSPARC provides two methods of verifying that all components of an installation are correctly working and set up.

The first method is to run cryosparcm test install and cryosparcm test workers via the command line. For more information, see Guide: Installation Testing with cryosparcm test

  • CryoSPARC system and license installation

  • Worker/Cluster configuration

  • GPU and CUDA driver installation

  • SSD caching

Apply Patches

Patches for a specific CryoSPARC version are cumulative:

  • One may apply the latest patch without having applied earlier patches.

  • After application of the latest patch, application of an earlier patch is not needed and should not be attempted.

To check for available patches, run

cryosparcm patch --check

Before applying patches, ensure CryoSPARC is running:

cryosparcm start

Apply the patch with one of the following strategies (table):

If a cluster is connected, use the cluster installation instructions even if CryoSPARC was initially installed in workstation or master/worker mode

Automatically install all patches:

cryosparcm patch

Automatically install patches on the master and connected dedicated worker nodes

cryosparcm patch

From the master node, run

cryosparcm patch --download

This downloads master and worker tarballs to the cryosparc_master installation directory. Follow the resulting set of instructions for installing both patch files.

The instructions will involve the following:

  • Install the master patch file with cryosparcm patch --install

  • Copy or upload the downloaded cryosparc_worker_patch.tar.gz patch into the cryosparc_worker directory

  • Inside the cryosparc_worker directory, run bin/cryosparcw patch

Depending on your cluster setup, either install the patch once in the cryosparc_worker directory shared by all cluster nodes or repeatedly for each cluster node that hosts an independent cryosparc_worker directory.

Finally, restart CryoSPARC:

cryosparcm restart

You can to receive an email when we release a new update or patch.

We also periodically release patch updates for CryoSPARC, to address issues outside of normal updates. To learn more about patches, see:

IMPORTANT. Before you update your instance, we recommend making a

IMPORTANT. Before you update your instance, we recommend making a

Incomplete shutdown of the CryoSPARC instance during updates is a known cause for update failures. Follow the sequence for a of the CryoSPARC instance.

Please see .

If your CryoSPARC instance is running v4.0.0 and later, the oldest version of CryoSPARC you can downgrade to is v3.4.0. For more information, see

Follow this section when a cryoSPARC install or update process fails part-way, or if CryoSPARC cannot start after following the steps.

The second method is to run the Extensive Workflow job.

This automatic workflow executes all steps in the and verifies the following system components:

We periodically releases patches for specific versions of CryoSPARC to fix bugs which do not require a full formal software update. to receive an email when we release a patch.

sign up for the newsletter
https://guide.cryosparc.com/setup-configuration-and-management/software-updates#apply-patches
backup of your database.
Guide: Maintenance Mode and Configurable User Facing Messages
backup of your database.
Troubleshooting
See the Extensive Workflow guide here.
T20S Introductory Tutorial
Subscribe to the CryoSPARC Newsletter
Before you update or downgrade
LogoSoftware UpdatesCryoSPARC Guide
Downgrading from v4​
Look for the new version notification in the bottom status bar of the cryoSPARC dashboard.
complete shutdown