Software Updates and Patches
How to get the latest CryoSPARC features and fixes or roll back to a previous version.
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.
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
Before installing an update or downgrading to a previous version, 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:
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
You can also use
cryosparcm update --listto get a full list of available versions (including old versions in case you would like to downgrade).
$ cryosparcm update --list
CryoSPARC current version v2.14.0
update starting on Wed Mar 18 12:11:42 EDT 2020
To install a specific version, use
$ cryosparcm update --version=vXX.YY.ZZ[-branchname]
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
This commands executes the following:
- Shuts down the running CryoSPARC instance
- Downloads new the master (
cryosparc_master.tar.gz) and worker (
- 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.
Once the master update is complete, master starts up and automatically updates registered workers:
- Transfers the worker release
cryosparc_worker.tar.gzto each worker node via
- 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.
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
Copy this file (via
scp) to cluster worker's installation directory. It should be in the same directory as the
depsfolders. Navigate to the installation directory and run
This updates the worker at the current location with the given release file.
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
cryosparcm update --listto see the list of available versions. Substitute the
vX.Y.Zin the command above with one of the results.
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
CryoSPARC provides two methods of verifying that all components of an installation are correctly working and set up.
- CryoSPARC system and license installation
- Worker/Cluster configuration
- GPU and CUDA driver installation
- SSD caching
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.
To check for available patches, run
cryosparcm patch --check
Before applying patches, ensure CryoSPARC is running:
Apply the patch with one of the following strategies (table):
Automatically install all patches:
Automatically install patches on the master and connected dedicated worker nodes
From the master node, run
cryosparcm patch --download
This downloads master and worker tarballs to the
cryosparc_masterinstallation 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.gzpatch into the
- Inside the
Depending on your cluster setup, either install the patch once in the
cryosparc_workerdirectory shared by all cluster nodes or repeatedly for each cluster node that hosts an independent
Finally, reload CryoSPARC and refresh job types:
cryosparcm cli "reload()"
cryosparcm cli "refresh_job_types()"