Software Updates
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.
IMPORTANT. Before you update your instance, we recommend making a backup of your database.
Unless otherwise noted:
Log in to the workstation or remote node where
cryosparc_masteris 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 --checkCryoSPARC current version v2.15.0update starting on Wed Mar 18 12:09:52 EDT 2020current version v2.15.0new version v3.0.0Update 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...v2.14.2v2.15.0v3.0.0To 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
cryosparcm update
Cluster workers are not updated automatically. See the "Manual Cluster Updates" section below
This commands executes the following:
Shuts down the running cryoSPARC instance
Downloads new the master (
cryosparc_master.tar.gz) and worker (cryosparc_worker.tar.gz) releasesExtracts 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 viascpExtracts 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 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.
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.
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.
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
Worker/Cluster configuration
GPU and CUDA driver installation
SSD caching
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:
cryosparcm start
Apply the patch with one of the following strategies:
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 a set of instructions for installing both patch files.
The instructions will involve the following:
Install the master patch file with
cryosparcm patch --installUpload the downloaded patch to worker nodes
From each worker node, run
bin/cryosparcw patch
Finally, reload cryoSPARC and refresh job types:
cryosparcm cli "reload()"cryosparcm cli "refresh_job_types()"
