After I moved the database from a 100% full disk to a new location by
rsync -r --links /home/cryosparc_user/cryosparc_database /data/sparc/
cryosparc does not start
cryosparcm start
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 “”, line 1, in
File “/home/cryosparc_user/cryosparc_master/cryosparc_compute/database_management.py”, line 49, in configure_mongo
initialize_replica_set()
File “/home/cryosparc_user/cryosparc_master/cryosparc_compute/database_management.py”, line 88, in initialize_replica_set
admin_db = try_get_pymongo_db(mongo_client)
File “/home/cryosparc_user/cryosparc_master/cryosparc_compute/database_management.py”, line 251, in try_get_pymongo_db
admin_db.command(({‘serverStatus’: 1}))
File “/home/cryosparc_user/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.8/site-packages/pymongo/database.py”, line 827, in command
with self.__client._socket_for_reads(read_preference, session) as (sock_info, secondary_ok):
File “/home/cryosparc_user/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.8/contextlib.py”, line 113, in enter
return next(self.gen)
File “/home/cryosparc_user/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.8/site-packages/pymongo/mongo_client.py”, line 1478, in _socket_for_reads
server = self._select_server(read_preference, session)
File “/home/cryosparc_user/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.8/site-packages/pymongo/mongo_client.py”, line 1436, in _select_server
server = topology.select_server(server_selector)
File “/home/cryosparc_user/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.8/site-packages/pymongo/topology.py”, line 250, in select_server
return random.choice(self.select_servers(selector, server_selection_timeout, address))
File “/home/cryosparc_user/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.8/site-packages/pymongo/topology.py”, line 211, in select_servers
server_descriptions = self._select_servers_loop(selector, server_timeout, address)
File “/home/cryosparc_user/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.8/site-packages/pymongo/topology.py”, line 226, in _select_servers_loop
raise ServerSelectionTimeoutError(
pymongo.errors.ServerSelectionTimeoutError: localhost:39001: [Errno 111] Connection refused, Timeout: 20.0s, Topology Description: <TopologyDescription id: 66156a50df82c3da4d5d510a, topology_type: Single, servers: [<ServerDescription (‘localhost’, 39001) server_type: Unknown, rtt: None, error=AutoReconnect(‘localhost:39001: [Errno 111] Connection refused’)>]>
[2024-04-09T12:19:35-0400] Error configuring database. Most recent database log lines:
mongod(wiredtiger_open+0x1BBA) [0x563c29656c8a]
mongod(_ZN5mongo18WiredTigerKVEngineC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_PNS_11ClockSourceES8_mmbbbb+0x8D6) [0x563c29623cf6]
mongod(+0xA25AEC) [0x563c29605aec]
mongod(_ZN5mongo20ServiceContextMongoD29initializeGlobalStorageEngineEv+0x266) [0x563c29815fb6]
mongod(+0xA025B8) [0x563c295e25b8]
mongod(ZN5mongo11mongoDbMainEiPPcS1+0x26C) [0x563c295e563c]
mongod(main+0x9) [0x563c2956bbc9]
libc.so.6(__libc_start_main+0xF5) [0x7f6c1be333d5]
mongod(+0x9ED741) [0x563c295cd741]
----- END BACKTRACE -----
Please advise.
Thank you,
Yehuda