CryoSPARC v5.0.6 upgraded from v4.7.0: job parameter edits / workspace rename-delete not persisting

Install, Configure and Update
1

Hello CryoSPARC Support,

We upgraded an existing CryoSPARC instance from “v4.7.0” to “v5.0.6”. After the upgrade, the system starts normally and all services report as running, but we are seeing a serious issue where some UI operations appear successful but are not actually persisted.

Environment

- CryoSPARC version: “v5.0.6”

- Upgraded from: “v4.7.0”

- OS: “Ubuntu 20.04”

- NVIDIA driver: “580.126.09”

- GPUs: “4 × NVIDIA GeForce RTX 4080 SUPER”

bserved behavior

We can:

- create new projects

- create new workspaces

- create new jobs

However, we cannot successfully persist update/delete actions:

- editing job parameters does not take effect

- renaming existing workspaces does not take effect

- deleting existing workspaces shows success feedback in the UI, but the workspace is not actually removed

- modifying existing workspace names also shows success feedback, but the changes are not saved

Example symptom

We created a new **Import Micrographs** job successfully, but when trying to enqueue it, the job fails validation because required parameters are still missing, which suggests that the parameter edits made in the UI were never saved.

Relevant API log excerpt:

- Job creation succeeds:

  • `POST /projects/P23/workspaces/W1/jobs?type=import_micrographs` → “201”

- Enqueue fails:

  • `POST /projects/P23/jobs/J1:enqueue?lane=default` → “422”

Validation error from the log:

- `spec.params.blob_paths` → Field required

- `spec.params.psize_A` → Field required

- `spec.params.accel_kv` → Field required

- `spec.params.cs_mm` → Field required

- `spec.params.total_dose_e_per_A2` → Field required

This strongly suggests that the job object is created, but later parameter updates from the UI are not being persisted.

Additional observations

- Workspace delete preview is generated successfully, but actual deletion does not persist.

- `cryosparcm status` shows all services as RUNNING.

- We have already restarted CryoSPARC and the browser.

- We also upgraded the NVIDIA driver, but this does not appear to be a GPU/CUDA issue.

Service status

All key services are running:

- api

- app

- app_api

- cache

- command_vis

- database

- scheduler

Database log observation

We also noticed repeated MongoDB log messages like:

`recv(): message msgLen 100729622 is invalid. Min 16 Max: 48000000`

We are not sure whether this is related, but we wanted to mention it.

Our current suspicion

This looks like an “upgrade-related instance state/schema issue”, where create operations still work, but update/delete mutations are not actually persisted after upgrading from v4.7.0 to v5.0.6.

Could you please advise:

1. whether this is a known issue for upgrades from v4.7.0 to v5.0.6

2. whether any database repair, migration re-run, or recovery step is recommended

3. what additional logs or diagnostics you would like us to provide

Thank you very much.

Best regards,

Zhang Jie

2

Welcome to the forum @Jie .

Please can you confirm that you updated to v5.0.6
using the cryosparcm update command, which would have included essential database validation and upgrade steps?

3

Hello,

We followed the official downgrade/upgrade procedure and now have a clearer result.

What we did

  1. Downgraded from v5.0.6 to v4.7.1 using:

    cryosparcm update --version v4.7.1

  2. Confirmed that the instance behaved normally again in v4.7.1

  3. Upgraded again to v5.0.6 using the official update process

  4. After the upgrade, the same problem returned

We now have the full terminal output from the installation/update process and can provide it if useful.

Please let us know what logs or diagnostic information you would like us to send next.

Best regards,
Jie

Additional information:

lab2@lab2:/software/cryosparc/cryosparc_master/bin$ ./cryosparcm update

CryoSPARC current version v4.7.1update starting on 2026年 07月 29日 星期三 17:02:33 CST

No version specified - updating to latest version.

=============================
Updating to version v5.0.6.

Removing previous downloads…
Downloading master update…
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:–:-- 0:00:03 --:–:-- 0
100 609M 100 609M 0 0 9.9M 0 0:01:01 0:01:01 --:–:-- 11.1M
Downloading worker update…
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:–:-- 0:00:01 --:–:-- 0
100 4080M 100 4080M 0 0 9340k 0 0:07:27 0:07:27 --:–:-- 10.5M
Done.

Update will now be applied to the master installation,
followed by worker installations on other nodes.

CryoSPARC is not already running.
If you would like to restart, use cryosparcm restart
Deleting old files…
Extracting…
Done.
─────────────────────────────────────────────────────────────────────────────────────
Installing dependencies…
─────────────────────────────────────────────────────────────────────────────────────
Checking python dependency…
Installing python dependency…
Extracting all packages…
tar: 102389760 (98MiB, 121MiB/s)
tar: 204789760 (196MiB, 124MiB/s)
tar: 307189760 (293MiB, 125MiB/s)
tar: 409589760 (391MiB, 129MiB/s)
tar: 511989760 (489MiB, 132MiB/s)
tar: 614389760 (586MiB, 131MiB/s)
tar: 716789760 (684MiB, 134MiB/s)
tar: 819189760 (782MiB, 137MiB/s)
tar: 921589760 (879MiB, 139MiB/s)
tar: 1023989760 (977MiB, 140MiB/s)
tar: 1126389760 (1.1GiB, 139MiB/s)

Python packages installation successful.
python installation completed.
─────────────────────────────────────────────────────────────────────────────────────
Checking mongodb dependency…
Installing mongodb dependency…
mongodb 4.0.28 installation successful.
mongodb installation completed.
─────────────────────────────────────────────────────────────────────────────────────
Dependencies installed.
Successfully updated master installation files to version v5.0.6.
─────────────────────────────────────────────────────────────────────────────────────
Attempting initial startup of database and core services…
Starting CryoSPARC master services…
CryoSPARC is not already running.
Configuring database… OK
database: started
Checking database… OK
cache: started
✓ cache connection succeeded
api:0: started
api:1: started
api:2: started
✓ api connection succeeded
command_vis: started
Successfully started database and core services.
─────────────────────────────────────────────────────────────────────────────────────
Attempting database upgrade…
Pre-upgrade task: updating database indexes…
Pre-upgrade task: database migration…
✓ Pre-upgrade tasks complete.
Validating database contents…
Validating users ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 0:00:00
✓ All users validated successfully!
Validating targets
✓ All targets validated successfully!
Validating lanes
✓ All lanes validated successfully!
Validating projects ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 0:00:00
17 projects passed validation.
✓ All projects validated successfully!
Database validation succeeded.
Continuing with upgrade…
Upgrading users ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 0:00:00
✓ All users upgraded successfully!
Upgrading targets
✓ Upgraded all targets
Upgrading lanes
✓ Upgraded all lanes
Upgrading projects ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 0:00:00
✓ All 17 projects upgraded successfully!
Successfully completed database upgrade.
─────────────────────────────────────────────────────────────────────────────────────
Attempting to restart database and all services…
Stopping CryoSPARC …
api:2: stopped
cache: stopped
api:0: stopped
api:1: stopped
command_vis: stopped
database: stopped
Shut down
Starting CryoSPARC master services…
CryoSPARC is not already running.
Configuring database… OK
database: started
Checking database… OK
cache: started
✓ cache connection succeeded
api:0: started
api:1: started
api:2: started
✓ api connection succeeded
✓ api startup succeeded
scheduler: started
command_vis: started
app: started
app_api: started
───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────

CryoSPARC master started.
From this machine, access CryoSPARC and CryoSPARC Live at
http://localhost:xxxxx

From other machines on the network, access CryoSPARC and CryoSPARC Live at
http://lb2:40000

Successfully restarted database and all services.
Master installation update to v5.0.6 complete.
─────────────────────────────────────────────────────────────────────────────────────
Now updating workers.
─────────────────────────────────────────────────────────────────────────────────────
Installing update on 1 worker(s):
lab2
───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Installing update on worker node lab2
Copying /software/cryosparc/cryosparc_master/cryosparc_worker.tar.gz to lab2:/software/cryosparc/cryosparc_worker/cryosparc_worker.tar.gz…
Updating… checking versions
Current version v4.7.1 - New version v5.0.6

Updating worker…

Deleting old files…
Extracting…
Cleaning up…
Done.
Updating dependencies…
─────────────────────────────────────────────────────────────────────────────────────
Installing dependencies…
─────────────────────────────────────────────────────────────────────────────────────
Checking python dependency…
Installing python dependency…
Extracting all packages…
tar: 102389760 (98MiB, 124MiB/s)
tar: 204789760 (196MiB, 124MiB/s)
tar: 307189760 (293MiB, 124MiB/s)
tar: 409589760 (391MiB, 134MiB/s)
tar: 511989760 (489MiB, 143MiB/s)
tar: 614389760 (586MiB, 133MiB/s)
tar: 716789760 (684MiB, 130MiB/s)
tar: 819189760 (782MiB, 129MiB/s)
tar: 921589760 (879MiB, 130MiB/s)
tar: 1023989760 (977MiB, 132MiB/s)
tar: 1126389760 (1.1GiB, 131MiB/s)
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tar: 7372789760 (6.9GiB, 124MiB/s)

Python packages installation successful.
python installation completed.
─────────────────────────────────────────────────────────────────────────────────────
Checking ctffind dependency…
ctffind dependency has not changed.
─────────────────────────────────────────────────────────────────────────────────────
Checking gctf dependency…
gctf dependency has not changed.
─────────────────────────────────────────────────────────────────────────────────────
Dependencies installed.

Successfully updated.

───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✓ Successfully installed update on all workers
─────────────────────────────────────────────────────────────────────────────────────
Installation complete.

4

Hello,

Here is an update.

We upgraded the server from Ubuntu 20.04 to Ubuntu 22.04.5 LTS and confirmed that the system and NVIDIA driver are working normally (nvidia-smi is normal, driver 580.173.02, 4× RTX 4080 SUPER).

We then repeated the test:

  • downgrade to CryoSPARC v4.7.0 → works normally
  • upgrade again to v5.0.6 → same problem returns

In v5.0.6, we can still create jobs, but we cannot modify job parameters or delete jobs. The UI may show normal feedback, but the changes are not actually saved/applied. Previously we also observed the same behavior for workspace rename/delete.

So the issue still reproduces even on Ubuntu 22.04.5, which suggests that this is not caused by the OS version or NVIDIA driver environment, but is specific to v5.0.6 or the v4 → v5 upgrade result for this instance.

Please let me know what additional logs or diagnostics would be most useful.

Best regards,
Jie

5

Thanks @Jie for these details. Please can you

  1. post the project and job IDs of an example job where you observed and the project on workspace IDs of a workspace where
  2. email us the tgz file created by the
    cryosparcm snaplogs command. I will send you a PM with the email address.
6

Dear Wolfram Tempel,

Sorry for the delayed reply — I was away attending a conference and could not respond sooner.

I have now collected the requested information.

Example workspace where rename/delete does not persist

  • Project ID: P1 (zhangjie)
  • Workspace ID: W44 (test-260804)

Example job where parameters cannot be modified and the job cannot be deleted

  • Project ID: P1 (zhangjie)
  • Workspace ID: W44 (test-260804)
  • Job ID: J4238

I will also generate the cryosparcm snaplogs .tgz file and send it to the email address you provided by PM.

Best regards,
Jie

7

Thanks @Jie . Please can you try if the issue is resolved either

?

8

Dear Wolfram Tempel,

Thank you for the suggestion.

I tested this in Google Chrome after clearing the browser cache, and I also logged into CryoSPARC using a new incognito window. However, the issue still persists:

  • I still cannot modify job parameters
  • I still cannot successfully create/run a new job

I would also like to provide an additional observation that may be helpful:

On the same CryoSPARC instance, there is another regular user account. That user is able to modify job parameters and successfully create/run jobs. However, that user is also unable to delete jobs.

Examples of jobs that this user was able to run successfully:

  • Project ID: P17
  • Workspace ID: W6
  • Job IDs: J2504（2D classification with GPU running） and J2495（Local Resolution Estimation）

So at the moment, the behavior appears to differ by user:

  • for my account, I cannot modify parameters or successfully create/run jobs
  • for the other regular user, parameter modification and job creation/running work, but job deletion still does not work

I have also sent the snaplogs.tgz file to the email address you provided.

I hope this information is helpful. Thank you very much for your assistance.

Best regards,
Jie

9

Dear Wolfram Tempel,

I would like to add an important new observation.

The API log I posted above was not from the original upgraded instance. We also installed a fresh new CryoSPARC v5.0.6 instance in a new directory, and we are seeing a similar issue there as well.

In this newly installed v5.0.6 instance, even the initial License Agreement dialog cannot be accepted properly — the Accept button is visible, but clicking it does nothing.

So this issue does not appear to be limited to the original upgraded v4 → v5 instance. We now see similar behavior even in a fresh v5.0.6 installation, which suggests that the problem may not be caused only by upgrade/database migration state.

I have also included the snaplogs from the newly installed v5.0.6 instance in the email.

We would greatly appreciate your reply and hope this issue can be resolved soon so that we can start using CryoSPARC v5 normally.

Best regards,
Jie

10

Thanks @Jie For the additional information. Please can you also

  1. describe web bowser type(s), version(s) and browser OS platform on which you observed the problem

  2. describe the host where cryosparc_master services are running:

    • OS and OS version
    • amount of RAM
    • OS installed on bare metal or inside a virtual machine or container?

  3. Send us UI error logging output that you would record when attempting failing operations, like changing a job parameter or clicking the Accept button on the license confirmation page.

11

Hello,

Sorry for the delayed reply over the past 3 days.

Thank you for the follow-up.

Below is the information for the host running cryosparc_master:

  • OS: Ubuntu 22.04.5 LTS
  • RAM: 1024 GB
  • Deployment type: bare metal (installed directly on physical hardware, not in a virtual machine or container)
    • CPU: 2 × Intel Xeon Gold 6326
  • GPU: 4 × NVIDIA GeForce RTX 4080 SUPER

Browser information from one of the systems where the issue was observed:

  • Browser: Google Chrome
  • Version: 151.0.7922.76 (64-bit)
  • Browser OS platform: Windows 11

Regarding the UI error logging output, at the moment I have already downgraded CryoSPARC back to v4.7.0 in order to continue running jobs normally. Therefore, I am not able to immediately reproduce the failing v5.0.6 operations right now.

I will need some time before I can switch back to v5.0.6 again and capture the browser UI error logging output (for example from the browser developer tools while reproducing operations such as changing a job parameter or clicking the Accept button on the license confirmation page).

I will provide that information as soon as I am able to reproduce the issue again.

Best regards,
Jie

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