Cannot start CryoSPARC `pymongo.errors.OperationFailure: there are no users authenticated`


I recently updated to version 4.0.1. For a while, everything was fine. However, recently the master process stopped. When I try to restart it, however, I get the following error:

Starting cryoSPARC System master process..
CryoSPARC is not already running.
configuring database
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/apps/cryosparc/cryosparc_master/cryosparc_compute/", line 41, in configure_mongo
  File "/apps/cryosparc/cryosparc_master/cryosparc_compute/", line 82, in initializeReplicaSet
    admin_db.command(({'serverStatus': 1}))
  File "/apps/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/", line 761, in command
    codec_options, session=session, **kwargs)
  File "/apps/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/", line 652, in _command
  File "/apps/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/", line 721, in command
  File "/apps/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/", line 163, in command
  File "/apps/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/", line 167, in _check_command_response
    raise OperationFailure(errmsg, code, response, max_wire_version)
pymongo.errors.OperationFailure: there are no users authenticated, full error: {'operationTime': Timestamp(1666580760, 1), 'ok': 0.0, 'errmsg': 'there are no users authenticated', 'code': 13, 'codeName': 'Unauthorized', '$clusterTime': {'clusterTime': Timestamp(1666580760, 1), 'signature': {'hash': b'\xd2\xb4\x12|\xa4\xa7\x9b\xf4\t\xac8K\x82\xee\xb1\xd0\xa1\tR\xfa', 'keyId': 7153128110043430913}}}

Any idea what is going on? It seems that a similar error was reported here for version 4.0:

But I have verified that I have 4.0.1 on both master and worker.

Thanks a lot in advance

Hi @Rafa,

Could you please try the following and see if it resolves the issue:

Check that no MongoDB zombie processes are running on the master node. First stop the running CryoSPARC instance:

cryosparcm stop

On the CryoSPARC master node, list all processes associated with MongoDB with the following command:

ps -aux | grep mongo

If you see any processes that appear associated with MongoDB launched by a previous instance of CryoSPARC, kill them with the command kill <PID> , where <PID> is the process ID number at the beginning of each line.

Then start CryoSPARC on the master note or workstation:

cryosparcm start

Hi @nwong ,

Thanks a lot, this has indeed worked and I have been able to restart cryoSPARC!

Best wishes,


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