I updated cryosparc from 3.3 to 4.4.1 lately. When I tried starting it up, this error shows up.
Traceback (most recent call last):
File “”, line 1, in
File “/home/software/CryoSPARC/cryosparc_master/cryosparc_compute/init.py”, line 10, in
from . import dataset # noqa
File “/home/software/CryoSPARC/cryosparc_master/cryosparc_compute/dataset.py”, line 34, in
from cryosparc_tools.cryosparc.dataset import Dataset, Row, Spool
File “/home/software/CryoSPARC/cryosparc_master/cryosparc_tools/cryosparc/dataset.py”, line 47, in
from typing_extensions import Literal, SupportsIndex
ModuleNotFoundError: No module named ‘typing_extensions’
Traceback (most recent call last):
File “”, line 1, in
File “/home/software/CryoSPARC/cryosparc_master/cryosparc_compute/init.py”, line 10, in
from . import dataset # noqa
File “/home/software/CryoSPARC/cryosparc_master/cryosparc_compute/dataset.py”, line 34, in
from cryosparc_tools.cryosparc.dataset import Dataset, Row, Spool
File “/home/software/CryoSPARC/cryosparc_master/cryosparc_tools/cryosparc/dataset.py”, line 47, in
from typing_extensions import Literal, SupportsIndex
ModuleNotFoundError: No module named ‘typing_extensions’
Starting cryoSPARC System master process…
CryoSPARC is not already running.
Traceback (most recent call last):
File “”, line 1, in
File “/home/software/CryoSPARC/cryosparc_master/cryosparc_compute/init.py”, line 10, in
from . import dataset # noqa
File “/home/software/CryoSPARC/cryosparc_master/cryosparc_compute/dataset.py”, line 34, in
from cryosparc_tools.cryosparc.dataset import Dataset, Row, Spool
File “/home/software/CryoSPARC/cryosparc_master/cryosparc_tools/cryosparc/dataset.py”, line 47, in
from typing_extensions import Literal, SupportsIndex
ModuleNotFoundError: No module named ‘typing_extensions’
[2024-01-05T19:35:17+0800] Error configuring database. Most recent database log lines:
2024-01-05T16:59:28.701+0800 I REPL [signalProcessingThread] Stopping replication reporter thread
2024-01-05T16:59:28.701+0800 I REPL [signalProcessingThread] Stopping replication fetcher thread
2024-01-05T16:59:28.701+0800 I REPL [signalProcessingThread] Stopping replication applier thread
2024-01-05T16:59:29.377+0800 I REPL [signalProcessingThread] Stopping replication storage threads
2024-01-05T16:59:29.378+0800 I FTDC [signalProcessingThread] Shutting down full-time diagnostic data capture
2024-01-05T16:59:29.395+0800 I STORAGE [signalProcessingThread] WiredTigerKVEngine shutting down
2024-01-05T16:59:29.523+0800 I STORAGE [signalProcessingThread] shutdown: removing fs lock…
2024-01-05T16:59:29.527+0800 I CONTROL [signalProcessingThread] now exiting
2024-01-05T16:59:29.527+0800 I CONTROL [signalProcessingThread] shutting down with code:0
2024-01-05T16:59:29.527+0800 I CONTROL [initandlisten] shutting down with code:0
I’ve tried installing typing_extensions via pip and restarting the master node but that didn’t work. Here’s what cryosparcm status gave:
CryoSPARC System master node installed at
/home/software/CryoSPARC/cryosparc_master
Current cryoSPARC version: v4.4.1
CryoSPARC process status:
app STOPPED Not started
app_api STOPPED Not started
app_api_dev STOPPED Not started
command_core STOPPED Not started
command_rtp STOPPED Not started
command_vis STOPPED Not started
database STOPPED Not started
An error ocurred while checking license status
Could not get license verification status. Are all CryoSPARC processes RUNNING?
Is it possible to fix this issue? I just took over the task of managing the cluster so the very last thing I would like to try is re-installing the instance.