Jobs hang after update: no module `cryosparc_compute`

Install, Configure and Update
1

Job are not running after I recently updated cryosparc on our workstation from v3 to the newest v4.1.2.

The status of all jobs are stuck at “Launched” but don’t progress. The logs report the following:


Traceback (most recent call last):
  File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'cryosparc_compute'

Output of cryosparcm status:

----------------------------------------------------------------------------
CryoSPARC System master node installed at
/opt/cryosparc/cryosparc2_master
Current cryoSPARC version: v4.1.2
----------------------------------------------------------------------------

CryoSPARC process status:

app                              RUNNING   pid 267226, uptime 0:10:12
app_api                          RUNNING   pid 267260, uptime 0:10:10
app_api_dev                      STOPPED   Not started
app_legacy                       STOPPED   Not started
app_legacy_dev                   STOPPED   Not started
command_core                     RUNNING   pid 266937, uptime 0:10:26
command_rtp                      RUNNING   pid 267100, uptime 0:10:18
command_vis                      RUNNING   pid 267068, uptime 0:10:20
database                         RUNNING   pid 266794, uptime 0:10:29

----------------------------------------------------------------------------
License is valid
----------------------------------------------------------------------------
2

Two issues:

  1. Is not finding the cryosparc_compute dir blocking my jobs from launching?

  2. If 1 is yes, cryosparc is able to see cryosparc_compute during initialization but not when running jobs. I am not sure how to update the cryosparc paths to find cryosparc_compute. My python path has this dir included:

echo $PYTHONPATH
/opt/cryosparc/cryosparc2_master/
3

Welcome to the forum @Max.
The worker portion of the update may have failed.
What are the outputs of

ls -l /opt/cryosparc/cryosparc2_worker
cat /opt/cryosparc/cryosparc2_worker/version

?
Are there any error messages inside
/opt/cryosparc/cryosparc2_master/run/update.log
?

4

Thanks for the reply!

Looks like you’re onto something! Worker version still says 3.2.0. I tried rerunning the update again as a fix, so it looks like that has overwritten any error messages that might have occurred between v3 and v4. Is there a way I can update the worker to version 4 independently?

ls -l /opt/cryosparc/cryosparc2_worker

drwxr-xr-x+ 2 cryosparc cryosparc         42 May 13  2020 bin
-rwxr-xr-x+ 1 cryosparc cryosparc       5417 May 13  2020 check_install_deps.sh
-rw-rw-r--+ 1 cryosparc cryosparc        179 May  2  2020 config.sh
drwxr-xr-x+ 9 cryosparc cryosparc       4096 May 15  2020 cryosparc2_compute
-rw-rw-r--+ 1 cryosparc cryosparc  654398576 May 13  2020 cryosparc2_worker.tar.gz
-rw-rw-r--+ 1 cryosparc cryosparc 1895278500 Aug 25  2021 cryosparc_worker.tar.gz
drwxrwxr-x+ 4 cryosparc cryosparc         38 May  2  2020 deps
drwxrwxr-x+ 4 cryosparc cryosparc         36 May 13  2020 deps_bundle
drwxr-xr-x+ 4 cryosparc cryosparc         36 May 13  2020 deps_bundle_hashes
drwxrwxr-x+ 4 cryosparc cryosparc         36 May  2  2020 deps_hashes
-rwxr-xr-x+ 1 cryosparc cryosparc       9638 May 13  2020 install.sh
-rw-rw-r--+ 1 spadm     spadm              7 Mar 29  2021 version

cat /opt/cryosparc/cryosparc2_worker/version

v3.2.0

cat /opt/cryosparc/cryosparc2_master/run/update.log

Update at 2023-02-09T22:20:09-06:00
CryoSPARC current version v4.1.2
          update starting on Thu Feb  9 22:20:10 CST 2023

No version specified - updating to latest version.

Already up to date: current version v4.1.2 new version v4.1.2

Update at 2023-02-09T22:42:45-06:00
CryoSPARC current version v4.1.2
          update starting on Thu Feb  9 22:42:46 CST 2023

No version specified - updating to latest version.

Already up to date: current version v4.1.2 new version v4.1.2
5

There is, usually exercised for cluster workers, but you may try this method in your situation also.

6

That worked! Thanks for the help!