Hi everyone,
I seems to have run into cryosparc database issue on my single workstation cryoSPARC. The app is very much alive, jobs can still be sent and run to completion, but when I switch to Tree viewing, the page starts to freeze after 5 seconds. Then I try seeing if my instance is still alive with ‘cryosparcm status’. The first time it returns this
CryoSPARC System master node installed at
/home/cryosparcuser/cryosparc/cryosparc_master
Current cryoSPARC version: v4.6.0
----------------------------------------------------------------------------
CryoSPARC is not running.
----------------------------------------------------------------------------
global config variables:
export CRYOSPARC_LICENSE_ID="XXXXXXXXXXX"
export CRYOSPARC_MASTER_HOSTNAME="10.xxxxxxxx"
export CRYOSPARC_FORCE_HOSTNAME=true
export CRYOSPARC_DB_PATH="/home/cryosparcuser/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
Which is weird because all the usual “cryosparc process status” are not showing. I tried “cryosparcm restart” then this pops out
CryoSPARC is not already running.
If you would like to restart, use cryosparcm restart
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/cryosparcuser/cryosparc/cryosparc_master/cryosparc_compute/database_manageme nt.py", line 47, in configure_mongo
initialize_replica_set()
File "/home/cryosparcuser/cryosparc/cryosparc_master/cryosparc_compute/database_manageme nt.py", line 84, in initialize_replica_set
admin_db = try_get_pymongo_db(mongo_client)
File "/home/cryosparcuser/cryosparc/cryosparc_master/cryosparc_compute/database_manageme nt.py", line 251, in try_get_pymongo_db
admin_db.command(({'serverStatus': 1}))
File "/home/cryosparcuser/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/cryosparcuser/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/cryosparcuser/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/cryosparcuser/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/cryosparcuser/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/cryosparcuser/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/cryosparcuser/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master _env/lib/python3.10/site-packages/pymongo/helpers.py", line 248, in _check_command_respons e
raise OperationFailure(errmsg, code, response, max_wire_version)
pymongo.errors.OperationFailure: there are no users authenticated, full error: {'operation Time': Timestamp(1733972676, 1), 'ok': 0.0, 'errmsg': 'there are no users authenticated', 'code': 13, 'codeName': 'Unauthorized', '$clusterTime': {'clusterTime': Timestamp(17339726 76, 1), 'signature': {'hash': b'E\xe2\xad#\x02\x9ej\xdb\\\x17"\x9a\xb8\x95\x816\x1f\x18\x1 2\xed', 'keyId': 7401057373537697799}}}
[2024-12-12T11:04:41+08:00] Error configuring database. Most recent database log lines:
2024-12-12T11:04:28.282+0800 I STORAGE [initandlisten] exception in initAndListen: DBPath InUse: Unable to lock the lock file: /home/cryosparcuser/cryosparc/cryosparc_database/mong od.lock (Resource temporarily unavailable). Another mongod instance is already running on the /home/cryosparcuser/cryosparc/cryosparc_database directory, terminating
2024-12-12T11:04:28.282+0800 I CONTROL [initandlisten] now exiting
2024-12-12T11:04:28.282+0800 I CONTROL [initandlisten] shutting down with code:100
2024-12-12T11:04:31.253+0800 I NETWORK [listener] connection accepted from 127.0.0.1:3672 0 #682 (135 connections now open)
2024-12-12T11:04:31.253+0800 I NETWORK [conn682] received client metadata from 127.0.0.1: 36720 conn682: { driver: { name: "PyMongo", version: "4.8.0" }, os: { type: "Linux", name: "Linux", architecture: "x86_64", version: "5.14.0-362.13.1.el9_3.x86_64" }, platform: "CP ython 3.10.14.final.0" }
2024-12-12T11:04:31.254+0800 I NETWORK [listener] connection accepted from 127.0.0.1:3673 0 #683 (136 connections now open)
2024-12-12T11:04:31.254+0800 I NETWORK [conn683] received client metadata from 127.0.0.1: 36730 conn683: { driver: { name: "PyMongo", version: "4.8.0" }, os: { type: "Linux", name: "Linux", architecture: "x86_64", version: "5.14.0-362.13.1.el9_3.x86_64" }, platform: "CP ython 3.10.14.final.0" }
2024-12-12T11:04:41.269+0800 I ACCESS [conn683] Unauthorized: not authorized on admin to execute command { endSessions: [ { id: UUID("3e3fcfbd-dcd9-4366-a78f-90291ef748dc") } ], $clusterTime: { clusterTime: Timestamp(1733972676, 1), signature: { hash: BinData(0, 45E2A D23029E6ADB5C17229AB89581361F1812ED), keyId: 7401057373537697799 } }, $db: "admin", $readP reference: { mode: "primaryPreferred" } }
2024-12-12T11:04:41.270+0800 I NETWORK [conn683] end connection 127.0.0.1:36730 (135 conn ections now open)
2024-12-12T11:04:41.270+0800 I NETWORK [conn682] end connection 127.0.0.1:36720 (134 conn ections now open)
I’m not sure what is currently happening. Can someone help me?
Thanks and kind regards,
Khoa.