Hey,
We have an issue with our cryoSPARC database. CryoSPARC is currently running, and I can access it through the web interface. However, I cannot restart or manually back up cryoSPARC. I get the following errors:
Backup:
(base) em7@em7:~$ cryosparcm backup --dir=/media/thor/cryoSPARC_backup/em7_20260127
Backing up to /media/thor/cryoSPARC_backup/em7_20260127/cryosparc_backup_2026_01_27_21h21.archive
CryoSPARC is not already running.
Starting the database in case it's not already running.
Starting CryoSPARC database
database: ERROR (spawn error)
Restarting cryoSPARC (It kept running and still works through the web interface):
(base) em7@em7:~$ cryosparcm restart
CryoSPARC is running.
Stopping cryoSPARC
Shut down
Starting CryoSPARC System master process...
CryoSPARC is not already running.
configuring database...
Warning: Could not get database status (attempt 1/3)
Warning: Could not get database status (attempt 2/3)
Warning: Could not get database status (attempt 3/3)
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/home/em7/Software/cryosparc/cryosparc_master/cryosparc_compute/database_management.py", line 47, in configure_mongo
initialize_replica_set()
File "/home/em7/Software/cryosparc/cryosparc_master/cryosparc_compute/database_management.py", line 84, in initialize_replica_set
admin_db = try_get_pymongo_db(mongo_client)
File "/home/em7/Software/cryosparc/cryosparc_master/cryosparc_compute/database_management.py", line 251, in try_get_pymongo_db
admin_db.command(({'serverStatus': 1}))
File "/home/em7/Software/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/pymongo/_csot.py", line 108, in csot_wrapper
return func(self, *args, **kwargs)
File "/home/em7/Software/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/pymongo/database.py", line 897, in command
return self._command(
File "/home/em7/Software/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/pymongo/database.py", line 737, in _command
return conn.command(
File "/home/em7/Software/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/pymongo/helpers.py", line 342, in inner
return func(*args, **kwargs)
File "/home/em7/Software/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/pymongo/pool.py", line 989, in command
return command(
File "/home/em7/Software/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/pymongo/network.py", line 212, in command
helpers._check_command_response(
File "/home/em7/Software/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/pymongo/helpers.py", line 248, in _check_command_response
raise OperationFailure(errmsg, code, response, max_wire_version)
pymongo.errors.OperationFailure: there are no users authenticated, full error: {'operationTime': Timestamp(1769545368, 1), 'ok': 0.0, 'errmsg': 'there are no users authenticated', 'code': 13, 'codeName': 'Unauthorized', '$clusterTime': {'clusterTime': Timestamp(1769545368, 1), 'signature': {'hash': b'L\x1b~\xa6\x1e\xa8?\xb9\xbe\x02I]\xadX\xcb6\x16\xb2\x9e\x83', 'keyId': 7567315140954030082}}}
[2026-01-27T21:22:51+01:00] Error configuring database. Most recent database log lines:
2026-01-27T21:22:38.321+0100 I STORAGE [initandlisten] exception in initAndListen: DBPathInUse: Unable to lock the lock file: /home/em7/Software/cryosparc/cryosparc_database/mongod.lock (Resource temporarily unavailable). Another mongod instance is already running on the /home/em7/Software/cryosparc/cryosparc_database directory, terminating
2026-01-27T21:22:38.321+0100 I CONTROL [initandlisten] now exiting
2026-01-27T21:22:38.321+0100 I CONTROL [initandlisten] shutting down with code:100
2026-01-27T21:22:41.314+0100 I NETWORK [listener] connection accepted from 127.0.0.1:44430 #19861 (178 connections now open)
2026-01-27T21:22:41.314+0100 I NETWORK [conn19861] received client metadata from 127.0.0.1:44430 conn19861: { driver: { name: "PyMongo", version: "4.8.0" }, os: { type: "Linux", name: "Linux", architecture: "x86_64", version: "6.14.0-35-generic" }, platform: "CPython 3.10.18.final.0" }
2026-01-27T21:22:41.315+0100 I NETWORK [listener] connection accepted from 127.0.0.1:44446 #19862 (179 connections now open)
2026-01-27T21:22:41.315+0100 I NETWORK [conn19862] received client metadata from 127.0.0.1:44446 conn19862: { driver: { name: "PyMongo", version: "4.8.0" }, os: { type: "Linux", name: "Linux", architecture: "x86_64", version: "6.14.0-35-generic" }, platform: "CPython 3.10.18.final.0" }
2026-01-27T21:22:51.327+0100 I ACCESS [conn19862] Unauthorized: not authorized on admin to execute command { endSessions: [ { id: UUID("b8386791-4f16-4d36-9c05-d12242b7735b") } ], $clusterTime: { clusterTime: Timestamp(1769545368, 1), signature: { hash: BinData(0, 4C1B7EA61EA83FB9BE02495DAD58CB3616B29E83), keyId: 7567315140954030082 } }, $db: "admin", $readPreference: { mode: "primaryPreferred" } }
2026-01-27T21:22:51.327+0100 I NETWORK [conn19861] end connection 127.0.0.1:44430 (178 connections now open)
2026-01-27T21:22:51.327+0100 I NETWORK [conn19862] end connection 127.0.0.1:44446 (177 connections now open)
I also checked the status of cryoSPARC:
(base) em7@em7:~$ cryosparcm status
----------------------------------------------------------------------------
CryoSPARC System master node installed at
/home/em7/Software/cryosparc/cryosparc_master
Current cryoSPARC version: v4.7.1-cuda12+250814
----------------------------------------------------------------------------
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
----------------------------------------------------------------------------
License is valid
----------------------------------------------------------------------------
global config variables:
export CRYOSPARC_LICENSE_ID="There is a license I just removed it"
export CRYOSPARC_MASTER_HOSTNAME="em7"
export CRYOSPARC_DB_PATH="/home/em7/Software/cryosparc/cryosparc_database"
export CRYOSPARC_BASE_PORT=39000
export CRYOSPARC_DB_CONNECTION_TIMEOUT_MS=20000
export CRYOSPARC_INSECURE=false
export CRYOSPARC_DB_ENABLE_AUTH=true
export CRYOSPARC_CLUSTER_JOB_MONITOR_INTERVAL=10
export CRYOSPARC_CLUSTER_JOB_MONITOR_MAX_RETRIES=1000000
export CRYOSPARC_PROJECT_DIR_PREFIX='CS-'
export CRYOSPARC_DEVELOP=false
export CRYOSPARC_CLICK_WRAP=true
We are currently running v4.7.1-cuda12+250814, Ubuntu 24.04.3 LTS, and we haven’t had any recent issues with crashing systems.
I would be very happy about help!
Best,
Ole