Software Updates and Patches

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

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:

Look for the new version notification in the bottom status bar of the cryoSPARC dashboard.

You can sign up for the newsletter to receive an email when we release a new update or patch.

Patches

We also periodically release patch updates for CryoSPARC, to address issues outside of normal updates. To learn more about patches, see: https://guide.cryosparc.com/setup-configuration-and-management/software-updates#apply-patches

Software UpdatesCryoSPARC Guide

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.

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

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

pageGuide: Maintenance Mode and Configurable User Facing Messages

2. Create a backup of the database

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

3. Completely shutdown CryoSPARC (with confirmation)

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

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.

Please see Before you update or downgrade.

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

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 Downgrading from v4​

Forced update

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

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

The second method is to run the Extensive Workflow job. See the Extensive Workflow guide here.

This automatic workflow executes all steps in the T20S Introductory Tutorial and verifies the following system components:

• CryoSPARC system and license installation

• Worker/Cluster configuration

• GPU and CUDA driver installation

• SSD caching

Apply Patches

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

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

Single Workstation

Automatically install all patches:

cryosparcm patch

Master Node

Automatically install patches on the master and connected dedicated worker nodes

cryosparcm patch

Cluster

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