Upgrade v4 to v5

Install, Configure and Update
1

Hi team,

When updating from CryoSPARC v4 to v5, we noticed this:

" CryoSPARC v5 includes new database validation checks that ensure consistency. For this reason, when updating from v4 to v5, a database upgrade step will be automatically performed during the update process."

However, one of our use cases involves allowing our users to bind their existing database directories and configuration files in pre-built containers with different CryoSPARC versions. Consequently, users are able to go between versions without having to run cryosparcm update.

My questions are:

  • Is there another way to run this database validation done during the update?

  • Does this validation is run when starting CryoSPARC v5 with a database used in v4?

  • Will users have issues with starting v5 with an unaltered v4 database?

Kind regards and thanks!

2

Hi @vatese,

To run the upgrade step manually, you can run the following commands before you start a newly-updated v5 installation with an existing database:

cryosparcm start database
cryosparcm start cache
cryosparcm upgrade
cryosparcm restart

Note also that the upgrade command has some prompts, which you may confirm manually or by adding the -y flag. This may take a long time depending on the size of the database, so we recommend running this only once per version update, if possible.

Disclaimer for any others reading this thread in future: This is not an update mechanism that we officially recommend. In future versions, it may not work.

To help us with future development, could you share any details about your setup? Including anything you can say about why it has to be this way and what your deployment strategy looks like. Is it to avoid users having to manage their own CryoSPARC installation?

3

Hi @nfrasser,

Thank you for the reply.

Our users work in an HPC environment with specific firewall rules and limited storage quotas. A CryoSPARC installation consumes quite a bit of space and would take a lot of their storage allocation. Additionally, some of our users are not technical with Linux, so we need to make the process of launching a CryoSPARC instance easier (they just need to input their licence and DB directory for it to start). This is why we need to find a process to update their current databases from v4 to v5 without having them do a full installation/update.

Cheers.

4

Hi @vatese thank you for the information! I’ll take this to my team for consideration in future improvements. Please also let me know if the instructions I provided are sufficient for you to proceed with the v5 update.

5

Hi @nfrasser

Thank you!

It indeed ended up working with these:

cryosparcm start database
cryosparcm start cache
cryosparcm upgrade -y

Please note cryosparcm update --help does not list -y as an available flag.

Kind regards,

1 Like
6

Ah yes, my mistake for the upgrade command! Revised the original message.