We release new updates to cryoSPARC approximately every 6-8 weeks. The cryoSPARC Dashboard shows update notifications:
You can also sign up for the newsletter to receive update notifications with an overview of new features.
Before installing an update, wait for all presently running jobs to complete, or kill them from the Resource Manager.
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 --checkCryoSPARC current version v2.14.0update starting on Wed Mar 18 12:09:52 EDT 2020current version v2.14.0new version v2.14.2Update 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 --listCryoSPARC current version v2.14.0update starting on Wed Mar 18 12:11:42 EDT 2020Available versions:v2.0.18v2.0.20v2.0.23...v2.13.2v2.14.0v2.14.2To 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 (
cryosparc2_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
cryosparc2_worker.tar.gz to each worker node via
Extracts and installs the worker release
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
deps folders. 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 --list to see the list of available versions. Substitute the
vX.Y.Z in the command above with one of the results.
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
CryoSPARC provides a method of verifying that all components of an installation are correctly working and set up. 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
GPU and CUDA driver installation
The cryoSPARC team periodically releases patches for specific versions of cryoSPARC that fix bugs which do not require a full formal software update.
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:
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
cryosparc2_master installation directory. Follow the resulting a set of instructions for installing both patch files.
The instructions will involve the following:
Install the master patch file with
cryosparcm patch --install
Upload the downloaded patch to worker nodes
From each worker node, run
Finally, reload cryoSPARC and refresh job types:
cryosparcm cli "reload()"cryosparcm cli "refresh_job_types()"