Last night, I tried to update cryosparc v5.0.1 to v5.0.4, some error happened. I tried clean stop cryosparc jobs and check the /tmp/.sock files, but it still does not work? Could anyone help this?
cryosparc@jyh3c:/home/jy_lab$ cryosparcm update --version=v5.0.4
----------------------
CryoSPARC update to v5.0.4
Starting on 2026? 04? 06? ??? 22:57:14 CST
----------------------
Removing previous downloads...
Downloading master update...
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 99 0 0 100 99 0 69 0:00:01 0:00:01 --:--:-- 69
100 609M 100 609M 0 0 50186 0 3:32:07 3:32:07 --:--:-- 439k
Downloading worker update...
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 99 0 0 100 99 0 20 0:00:04 0:00:04 --:--:-- 20
100 4080M 100 4080M 0 0 2650k 0 0:26:16 0:26:16 --:--:-- 4236k
Done.
Update will now be applied to the master installation,
followed by any connected workers.
CryoSPARC is not already running.
Deleting old files...
Extracting...
Done.
----------------------------
Installing dependencies...
----------------------------
Checking python dependency...
Installing python dependency...
Extracting all packages...
tar: 102389760 (98MiB, 1.8MiB/s)
tar: 204789760 (196MiB, 2.7MiB/s)
tar: 307189760 (293MiB, 3.7MiB/s)
tar: 409589760 (391MiB, 4.8MiB/s)
tar: 511989760 (489MiB, 2.4MiB/s)
tar: 614389760 (586MiB, 2.1MiB/s)
tar: 716789760 (684MiB, 2.5MiB/s)
tar: 819189760 (782MiB, 2.8MiB/s)
tar: 921589760 (879MiB, 3.1MiB/s)
tar: 1023989760 (977MiB, 2.9MiB/s)
tar: 1126389760 (1.1GiB, 2.7MiB/s)
Python packages installation successful.
python installation completed.
-------------------------------------
Checking mongodb dependency...
mongodb dependency has not changed.
-------------------------------------
Dependencies installed.
Successfully updated master installation files to version v5.0.4.
-------------------------------------
Attempting initial startup of database and core services...
Starting CryoSPARC master services...
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)
OK
database: started
Checking database...
??????????????????????? Traceback (most recent call last) ???????????????????????
? /data3/cryosp_projs/cryosparc/cryosparc_master/cli/database.py:46 in check ?
? ?
? 43 ? ? out.log("Checking database... ", end="") ?
? 44 ? logfile = core.settings.run_dir / "database.log" ?
? 45 ? try: ?
? ? 46 ? ? database_management.check_mongo() ?
? 47 ? except Exception: ?
? 48 ? ? if not quiet: ?
? 49 ? ? ? err.log() ?
? ?
? /data3/cryosp_projs/cryosparc/cryosparc_master/core/database_management.py:28 ?
? 8 in check_mongo ?
? ?
? 285 ? ?
? 286 ? try: ?
? 287 ? ? # check replset ?
? ? 288 ? ? admin_db = try_get_pymongo_db(mongo_client) ?
? 289 ? ? replset_status = admin_db.command("replSetGetStatus") ?
? 290 ? ? members = replset_status.get("members") ?
? 291 ? ? if not members or not members[0]: ?
? ?
? /data3/cryosp_projs/cryosparc/cryosparc_master/core/database_management.py:26 ?
? 2 in try_get_pymongo_db ?
? ?
? 259 ? ? tries += 1 ?
? 260 ? ? try: ?
? 261 ? ? ? admin_db = mongo_client.get_database(db_name) ?
? ? 262 ? ? ? admin_db.command(({"serverStatus": 1})) ?
? 263 ? ? ? return admin_db ?
? 264 ? ? except Exception: ?
? 265 ? ? ? print(f"Warning: Could not get database status (attempt {tr ?
? ?
? /data3/cryosp_projs/cryosparc/cryosparc_master/.pixi/envs/master/lib/python3. ?
? 12/site-packages/pymongo/_csot.py:119 in csot_wrapper ?
? ?
? 116 ? ? ? ? if timeout is not None: ?
? 117 ? ? ? ? ? with _TimeoutContext(timeout): ?
? 118 ? ? ? ? ? ? return func(self, *args, **kwargs) ?
? ? 119 ? ? ? return func(self, *args, **kwargs) ?
? 120 ? ?
? 121 ? return cast(F, csot_wrapper) ?
? 122 ?
? ?
? /data3/cryosp_projs/cryosparc/cryosparc_master/.pixi/envs/master/lib/python3. ?
? 12/site-packages/pymongo/synchronous/database.py:926 in command ?
? ?
? 923 ? ? ?
? 924 ? ? if read_preference is None: ?
? 925 ? ? ? read_preference = (session and session._txn_read_preferenc ?
? ? 926 ? ? with self._client._conn_for_reads(read_preference, session, op ?
? 927 ? ? ? connection, ?
? 928 ? ? ? read_preference, ?
? 929 ? ? ): ?
? ?
? /data3/cryosp_projs/cryosparc/cryosparc_master/.pixi/envs/master/lib/python3. ?
? 12/site-packages/pymongo/synchronous/mongo_client.py:1701 in _conn_for_reads ?
? ?
? 1698 ? ? operation: str, ?
? 1699 ? ) -> ContextManager[tuple[Connection, _ServerMode]]: ?
? 1700 ? ? assert read_preference is not None, "read_preference must not ?
? ? 1701 ? ? server = self._select_server(read_preference, session, operati ?
? 1702 ? ? return self._conn_from_server(read_preference, server, session ?
? 1703 ? ?
? 1704 ? @_csot.apply ?
? ?
? /data3/cryosp_projs/cryosparc/cryosparc_master/.pixi/envs/master/lib/python3. ?
? 12/site-packages/pymongo/synchronous/mongo_client.py:1649 in _select_server ?
? ?
? 1646 ? ? ? ? if not server: ?
? 1647 ? ? ? ? ? raise AutoReconnect("server %s:%s no longer availa ?
? 1648 ? ? ? else: ?
? ? 1649 ? ? ? ? server = topology.select_server( ?
? 1650 ? ? ? ? ? server_selector, ?
? 1651 ? ? ? ? ? operation, ?
? 1652 ? ? ? ? ? deprioritized_servers=deprioritized_servers, ?
? ?
? /data3/cryosp_projs/cryosparc/cryosparc_master/.pixi/envs/master/lib/python3. ?
? 12/site-packages/pymongo/synchronous/topology.py:398 in select_server ?
? ?
? 395 ? ? operation_id: Optional[int] = None, ?
? 396 ? ) -> Server: ?
? 397 ? ? """Like select_servers, but choose a random server if several ?
? ? 398 ? ? server = self._select_server( ?
? 399 ? ? ? selector, ?
? 400 ? ? ? operation, ?
? 401 ? ? ? server_selection_timeout, ?
? ?
? /data3/cryosp_projs/cryosparc/cryosparc_master/.pixi/envs/master/lib/python3. ?
? 12/site-packages/pymongo/synchronous/topology.py:376 in _select_server ?
? ?
? 373 ? ? deprioritized_servers: Optional[list[Server]] = None, ?
? 374 ? ? operation_id: Optional[int] = None, ?
? 375 ? ) -> Server: ?
? ? 376 ? ? servers = self.select_servers( ?
? 377 ? ? ? selector, operation, server_selection_timeout, address, op ?
? 378 ? ? ) ?
? 379 ? ? servers = _filter_servers(servers, deprioritized_servers) ?
? ?
? /data3/cryosp_projs/cryosparc/cryosparc_master/.pixi/envs/master/lib/python3. ?
? 12/site-packages/pymongo/synchronous/topology.py:283 in select_servers ?
? ?
? 280 ? ? ? server_timeout = server_selection_timeout ?
? 281 ? ? ?
? 282 ? ? with self._lock: ?
? ? 283 ? ? ? server_descriptions = self._select_servers_loop( ?
? 284 ? ? ? ? selector, server_timeout, operation, operation_id, add ?
? 285 ? ? ? ) ?
? 286 ?
? ?
? /data3/cryosp_projs/cryosparc/cryosparc_master/.pixi/envs/master/lib/python3. ?
? 12/site-packages/pymongo/synchronous/topology.py:333 in _select_servers_loop ?
? ?
? 330 ? ? ? ? ? ? clientId=self.description._topology_settings._ ?
? 331 ? ? ? ? ? ? failure=self._error_message(selector), ?
? 332 ? ? ? ? ? ) ?
? ? 333 ? ? ? ? raise ServerSelectionTimeoutError( ?
? 334 ? ? ? ? ? f"{self._error_message(selector)}, Timeout: {timeo ?
? 335 ? ? ? ? ) ?
? 336 ?
--------------------------------
ServerSelectionTimeoutError: jyh3c:39001: [Errno 111] Connection refused
(configured timeouts: socketTimeoutMS: 20000.0ms, connectTimeoutMS: 20000.0ms),
Timeout: 30.0s, Topology Description: <TopologyDescription id:
69d405313268109c026468f2, topology_type: Unknown, servers: [<ServerDescription
('jyh3c', 39001) server_type: Unknown, rtt: None,
error=AutoReconnect('jyh3c:39001: [Errno 111] Connection refused (configured
timeouts: socketTimeoutMS: 20000.0ms, connectTimeoutMS: 20000.0ms)')>]>
2026-04-07T03:12:22.096977 Error checking database; could not get replica set
status. Please reconfigure the database with `cryosparcm database configure`.
Most recent database log lines:
2026-04-07T03:10:40.637+0800 I STORAGE [initandlisten]
2026-04-07T03:10:40.637+0800 I STORAGE [initandlisten] ** WARNING: Using the XFS filesystem is strongly recommended with the WiredTiger storage engine
2026-04-07T03:10:40.637+0800 I STORAGE [initandlisten] ** See http://dochub.mongodb.org/core/prodnotes-filesystem
2026-04-07T03:10:40.637+0800 I STORAGE [initandlisten] wiredtiger_open config: create,cache_size=4096M,cache_overflow=(file_max=0M),session_max=20000,eviction=(threads_min=4,threads_max=4),config_base=false,statistics=(fast),log=(enabled=true,archive=true,path=journal,compressor=snappy),file_manager=(close_idle_time=100000),statistics_log=(wait=0),verbose=(recovery_progress),
2026-04-07T03:10:42.848+0800 I STORAGE [initandlisten] WiredTiger message [1775502642:848307][1936425:0x79cd952f7a40], txn-recover: Main recovery loop: starting at 17116/896 to 17117/256
2026-04-07T03:10:42.902+0800 I STORAGE [initandlisten] WiredTiger message [1775502642:902978][1936425:0x79cd952f7a40], txn-recover: Recovering log 17116 through 17117
2026-04-07T03:10:43.864+0800 I STORAGE [initandlisten] WiredTiger message [1775502643:864970][1936425:0x79cd952f7a40], txn-recover: Recovering log 17117 through 17117
2026-04-07T03:10:43.893+0800 I STORAGE [initandlisten] WiredTiger message [1775502643:893268][1936425:0x79cd952f7a40], txn-recover: Set global recovery timestamp: 0
2026-04-07T03:10:49.657+0800 I RECOVERY [initandlisten] WiredTiger recoveryTimestamp. Ts: Timestamp(0, 0)
2026-04-07T03:10:49.658+0800 I STORAGE [initandlisten] Starting to check the table logging settings for existing WiredTiger tables
2026-04-07T03:10:53.512+0800 I STORAGE [initandlisten] Starting OplogTruncaterThread local.oplog.rs
2026-04-07T03:10:53.512+0800 I STORAGE [initandlisten] The size storer reports that the oplog contains 15712 records totaling to 62219025 bytes
2026-04-07T03:10:53.512+0800 I STORAGE [initandlisten] Sampling the oplog to determine where to place markers for truncation
2026-04-07T03:10:53.514+0800 I STORAGE [initandlisten] Sampling from the oplog between Apr 5 18:08:48:2 and Apr 7 03:08:44:4 to determine where to place markers for truncation
2026-04-07T03:10:53.514+0800 I STORAGE [initandlisten] Taking 92 samples and assuming that each section of oplog contains approximately 1695 records totaling to 6712146 bytes
2026-04-07T03:10:53.518+0800 I STORAGE [initandlisten] Placing a marker at optime Apr 6 12:10:53:1
2026-04-07T03:10:53.518+0800 I STORAGE [initandlisten] Placing a marker at optime Apr 6 12:59:26:1
2026-04-07T03:10:53.518+0800 I STORAGE [initandlisten] Placing a marker at optime Apr 6 13:36:28:1
2026-04-07T03:10:53.518+0800 I STORAGE [initandlisten] Placing a marker at optime Apr 6 14:25:02:1
2026-04-07T03:10:53.518+0800 I STORAGE [initandlisten] Placing a marker at optime Apr 6 15:01:34:2
2026-04-07T03:10:53.518+0800 I STORAGE [initandlisten] Placing a marker at optime Apr 6 15:38:36:1
2026-04-07T03:10:53.518+0800 I STORAGE [initandlisten] Placing a marker at optime Apr 6 16:27:10:2
2026-04-07T03:10:53.518+0800 I STORAGE [initandlisten] Placing a marker at optime Apr 6 17:04:12:2
2026-04-07T03:10:53.518+0800 I STORAGE [initandlisten] Placing a marker at optime Apr 6 17:52:19:13
2026-04-07T03:10:53.518+0800 I STORAGE [initandlisten] WiredTiger record store oplog processing took 5ms
2026-04-07T03:11:08.886+0800 I CONTROL [initandlisten]
2026-04-07T03:11:08.886+0800 I CONTROL [initandlisten] ** WARNING: You are running on a NUMA machine.
2026-04-07T03:11:08.886+0800 I CONTROL [initandlisten] ** We suggest launching mongod like this to avoid performance problems:
2026-04-07T03:11:08.886+0800 I CONTROL [initandlisten] ** numactl --interleave=all mongod [other options]
2026-04-07T03:11:08.886+0800 I CONTROL [initandlisten]
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)
cryosparcm ERROR: Startup failed! Please address the above error and retry installation with:
cryosparcm stop
cryosparcm install
cryosparc@jyh3c:/home/jy_lab$ cryosparcm stop
Stopping CryoSPARC ...
database: stopped
Shut down
cryosparc@jyh3c:/home/jy_lab$ cryosparcm status
-----------------------------------------
CryoSPARC System master node installed at
/data3/cryosp_projs/cryosparc/cryosparc_master
Current CryoSPARC version: v5.0.4
-----------------------------------------
CryoSPARC is not running.
-----------------------------------------
? License is valid
-----------------------------------------
global config variables:
export CRYOSPARC_LICENSE_ID="36038a70-48ec-11ef-ace8-d79aea7fa0e5"
export CRYOSPARC_MASTER_HOSTNAME="jyh3c"
export CRYOSPARC_DB_PATH="/data3/cryosp_projs/cryosparc/cryosparc_database"
export CRYOSPARC_BASE_PORT=39000
export CRYOSPARC_DB_CONNECTION_TIMEOUT_MS=30000
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
export CRYOSPARC_SSD_CACHE_LIFETIME_DAYS=5
export CRYOSPARC_FORCE_USER=true
cryosparc@jyh3c:/home/jy_lab$ ps -eo user,pid,ppid,start,command | grep -e cryosparc_ -e mongo
cryospa+ 1936887 1934104 09:53:50 grep --color=auto -e cryosparc_ -e mongo
cryosparc@jyh3c:/home/jy_lab$ ls -l /tmp/mongo*.sock /tmp/cryosparc*.sock
ls: cannot access '/tmp/mongo*.sock': No such file or directory
ls: cannot access '/tmp/cryosparc*.sock': No such file or directory
cryosparc@jyh3c:/home/jy_lab$ cryosparcm log database | tail -n 60
2026-04-07T03:12:33.536+0800 I REPL [rsSync-0] Starting oplog application
2026-04-07T03:12:33.537+0800 I REPL [rsSync-0] transition to SECONDARY from RECOVERING
2026-04-07T03:12:33.537+0800 I REPL [rsSync-0] conducting a dry run election to see if we could be elected. current term: 93
2026-04-07T03:12:33.537+0800 I NETWORK [listener] connection accepted from 127.0.0.1:49724 #2 (1 connection now open)
2026-04-07T03:12:33.537+0800 I REPL [replexec-0] dry election run succeeded, running for election in term 94
2026-04-07T03:12:33.538+0800 I REPL [replexec-0] election succeeded, assuming primary role in term 94
2026-04-07T03:12:33.538+0800 I REPL [replexec-0] transition to PRIMARY from SECONDARY
2026-04-07T03:12:33.538+0800 I REPL [replexec-0] Resetting sync source to empty, which was :27017
2026-04-07T03:12:33.538+0800 I REPL [replexec-0] Entering primary catch-up mode.
2026-04-07T03:12:33.538+0800 I REPL [replexec-0] Exited primary catch-up mode.
2026-04-07T03:12:33.538+0800 I REPL [replexec-0] Stopping replication producer
2026-04-07T03:12:33.538+0800 I REPL [ReplBatcher] Oplog buffer has been drained in term 94
2026-04-07T03:12:33.538+0800 I NETWORK [conn2] received client metadata from 127.0.0.1:49724 conn2: { driver: { name: "NetworkInterfaceTL", version: "4.0.28" }, os: { type: "Linux", name: "Ubuntu", architecture: "x86_64", version: "22.04" } }
2026-04-07T03:12:33.538+0800 W NETWORK [LogicalSessionCacheRefresh] Unable to reach primary for set meteor
2026-04-07T03:12:33.539+0800 I REPL [rsSync-0] transition to primary complete; database writes are now permitted
2026-04-07T03:12:34.039+0800 I NETWORK [LogicalSessionCacheRefresh] localhost:39001 detected as new replica set primary for meteor; Old primary was :27017
2026-04-07T03:12:34.040+0800 I NETWORK [listener] connection accepted from 127.0.0.1:49730 #5 (2 connections now open)
2026-04-07T03:12:34.040+0800 I NETWORK [listener] connection accepted from 127.0.0.1:49738 #6 (3 connections now open)
2026-04-07T03:12:34.041+0800 I NETWORK [conn5] received client metadata from 127.0.0.1:49730 conn5: { driver: { name: "MongoDB Internal Client", version: "4.0.28" }, os: { type: "Linux", name: "Ubuntu", architecture: "x86_64", version: "22.04" } }
2026-04-07T03:12:34.041+0800 I NETWORK [conn6] received client metadata from 127.0.0.1:49738 conn6: { driver: { name: "MongoDB Internal Client", version: "4.0.28" }, os: { type: "Linux", name: "Ubuntu", architecture: "x86_64", version: "22.04" } }
2026-04-07T03:12:34.041+0800 I NETWORK [LogicalSessionCacheRefresh] Successfully connected to localhost:39001 (1 connections now open to localhost:39001 with a 0 second timeout)
2026-04-07T03:12:34.041+0800 I NETWORK [LogicalSessionCacheReap] Successfully connected to localhost:39001 (2 connections now open to localhost:39001 with a 0 second timeout)
2026-04-07T03:12:34.172+0800 I COMMAND [LogicalSessionCacheReap] command config.transactions command: find { find: "transactions", filter: { lastWriteDate: { $lt: new Date(1775500953535) } }, projection: { _id: 1 }, sort: { _id: 1 }, $db: "config" } planSummary: IXSCAN { _id: 1 } keysExamined:0 docsExamined:0 cursorExhausted:1 numYields:0 nreturned:0 reslen:233 locks:{ Global: { acquireCount: { r: 1 } }, Database: { acquireCount: { r: 1 } }, Collection: { acquireCount: { r: 1 } } } storage:{} protocol:op_msg 130ms
2026-04-07T03:12:34.654+0800 I STORAGE [WTJournalFlusher] Triggering the first stable checkpoint. Initial Data: Timestamp(1775502524, 4) PrevStable: Timestamp(0, 0) CurrStable: Timestamp(1775502753, 2)
2026-04-07T03:17:34.039+0800 I CONNPOOL [ReplicaSetMonitor-TaskExecutor] Dropping all pooled connections to localhost:39001 due to NetworkInterfaceExceededTimeLimit: Connection pool has been idle for longer than the host timeout
2026-04-07T03:17:34.042+0800 I NETWORK [conn2] end connection 127.0.0.1:49724 (2 connections now open)
2026-04-07T09:49:51.674+0800 I CONTROL [signalProcessingThread] got signal 15 (Terminated), will terminate after current cmd ends
2026-04-07T09:49:51.674+0800 I CONTROL [signalProcessingThread] Shutdown started
2026-04-07T09:49:51.674+0800 I CONTROL [signalProcessingThread] Shutting down the LogicalSessionCache
2026-04-07T09:49:51.675+0800 I NETWORK [signalProcessingThread] shutdown: going to close listening sockets...
2026-04-07T09:49:51.675+0800 I NETWORK [signalProcessingThread] removing socket file: /tmp/mongodb-39001.sock
2026-04-07T09:49:51.675+0800 I NETWORK [signalProcessingThread] Shutting down the global connection pool
2026-04-07T09:49:51.675+0800 I STORAGE [signalProcessingThread] Shutting down the PeriodicThreadToAbortExpiredTransactions
2026-04-07T09:49:51.675+0800 I REPL [signalProcessingThread] Shutting down the ReplicationCoordinator
2026-04-07T09:49:51.675+0800 I REPL [signalProcessingThread] shutting down replication subsystems
2026-04-07T09:49:51.675+0800 I REPL [signalProcessingThread] Stopping replication reporter thread
2026-04-07T09:49:51.675+0800 I REPL [signalProcessingThread] Stopping replication fetcher thread
2026-04-07T09:49:51.676+0800 I REPL [signalProcessingThread] Stopping replication applier thread
2026-04-07T09:49:51.676+0800 I REPL [rsBackgroundSync] Stopping replication producer
2026-04-07T09:49:51.915+0800 I REPL [rsSync-0] Finished oplog application
2026-04-07T09:49:51.916+0800 I REPL [signalProcessingThread] Stopping replication storage threads
2026-04-07T09:49:51.916+0800 I ASIO [RS] Killing all outstanding egress activity.
2026-04-07T09:49:51.916+0800 I ASIO [RS] Killing all outstanding egress activity.
2026-04-07T09:49:51.917+0800 I ASIO [Replication] Killing all outstanding egress activity.
2026-04-07T09:49:51.917+0800 I SHARDING [signalProcessingThread] Shutting down the ShardingInitializationMongoD
2026-04-07T09:49:51.917+0800 I COMMAND [signalProcessingThread] Killing all open transactions
2026-04-07T09:49:51.917+0800 I - [signalProcessingThread] Killing all operations for shutdown
2026-04-07T09:49:51.917+0800 I NETWORK [signalProcessingThread] Shutting down the ReplicaSetMonitor
2026-04-07T09:49:51.917+0800 I ASIO [ReplicaSetMonitor-TaskExecutor] Killing all outstanding egress activity.
2026-04-07T09:49:51.918+0800 I REPL [signalProcessingThread] Shutting down the LogicalTimeValidator
2026-04-07T09:49:51.918+0800 I CONTROL [signalProcessingThread] Shutting down free monitoring
2026-04-07T09:49:51.918+0800 I FTDC [signalProcessingThread] Shutting down full-time data capture
2026-04-07T09:49:51.918+0800 I FTDC [signalProcessingThread] Shutting down full-time diagnostic data capture
2026-04-07T09:49:51.924+0800 I STORAGE [signalProcessingThread] Shutting down the HealthLog
2026-04-07T09:49:51.924+0800 I STORAGE [signalProcessingThread] Shutting down the storage engine
2026-04-07T09:49:51.924+0800 I STORAGE [WTOplogJournalThread] oplog journal thread loop shutting down
2026-04-07T09:49:51.924+0800 I STORAGE [signalProcessingThread] WiredTigerKVEngine shutting down
2026-04-07T09:49:51.925+0800 I STORAGE [signalProcessingThread] Shutting down session sweeper thread
2026-04-07T09:49:51.925+0800 I STORAGE [signalProcessingThread] Finished shutting down session sweeper thread
2026-04-07T09:49:55.288+0800 I STORAGE [signalProcessingThread] Downgrading WiredTiger datafiles.
cryosparc@jyh3c:/home/jy_lab$ cryosparcm log command_core | tail -n 40
Usage: cryosparcm log [OPTIONS] SERVICE:{app|database|cache|api|scheduler|comm
and_vis|app_api|supervisord}
Try 'cryosparcm log --help' for help.
?? Error ????????????????????????????????????????????????????????????????????????????????????????????????????????
? Invalid value for 'SERVICE:{app|database|cache|api|scheduler|command_vis|app_api|supervisord}': ?
? 'command_core' is not one of 'app', 'database', 'cache', 'api', 'scheduler', 'command_vis', 'app_api', ?
? 'supervisord'. ?
?????????????????????????????????????????????????????????????????????????????????????????????????????????????????
cryosparc@jyh3c:/home/jy_lab$ cryosparcm log supervisord | tail -n 40
2026-04-06 20:47:02,255 INFO Creating socket tcp://0.0.0.0:39002
2026-04-06 20:47:02,255 INFO Closing socket tcp://0.0.0.0:39002
2026-04-06 20:47:02,257 INFO RPC interface 'supervisor' initialized
2026-04-06 20:47:02,260 INFO daemonizing the supervisord process
2026-04-06 20:47:02,261 INFO supervisord started with pid 1932359
2026-04-06 21:17:37,536 INFO Creating socket tcp://0.0.0.0:39002
2026-04-06 21:17:37,536 INFO Closing socket tcp://0.0.0.0:39002
2026-04-06 21:17:37,539 INFO RPC interface 'supervisor' initialized
2026-04-06 21:17:37,540 INFO daemonizing the supervisord process
2026-04-06 21:17:37,541 INFO supervisord started with pid 1932460
2026-04-06 21:27:54,387 INFO Creating socket tcp://0.0.0.0:39002
2026-04-06 21:27:54,387 INFO Closing socket tcp://0.0.0.0:39002
2026-04-06 21:27:54,389 INFO RPC interface 'supervisor' initialized
2026-04-06 21:27:54,391 INFO daemonizing the supervisord process
2026-04-06 21:27:54,392 INFO supervisord started with pid 1932915
2026-04-06 21:32:12,704 WARN received SIGTERM indicating exit request
2026-04-06 21:32:29,061 INFO Creating socket tcp://0.0.0.0:39002
2026-04-06 21:32:29,061 INFO Closing socket tcp://0.0.0.0:39002
2026-04-06 21:32:29,063 INFO RPC interface 'supervisor' initialized
2026-04-06 21:32:29,066 INFO daemonizing the supervisord process
2026-04-06 21:32:29,067 INFO supervisord started with pid 1932975
2026-04-06 22:11:12,851 INFO Creating socket tcp://0.0.0.0:39002
2026-04-06 22:11:12,851 INFO Closing socket tcp://0.0.0.0:39002
2026-04-06 22:11:12,853 INFO RPC interface 'supervisor' initialized
2026-04-06 22:11:12,855 INFO daemonizing the supervisord process
2026-04-06 22:11:12,857 INFO supervisord started with pid 1935599
2026-04-07 03:07:20,109 INFO Creating socket tcp://0.0.0.0:39002
2026-04-07 03:07:20,109 INFO Closing socket tcp://0.0.0.0:39002
2026-04-07 03:07:20,111 INFO RPC interface 'supervisor' initialized
2026-04-07 03:07:20,113 INFO daemonizing the supervisord process
2026-04-07 03:07:20,114 INFO supervisord started with pid 1936350
2026-04-07 03:10:40,612 INFO spawned: 'database' with pid 1936425
2026-04-07 03:10:41,638 INFO success: database entered RUNNING state, process has stayed up for > than 1 seconds (startsecs)
2026-04-07 09:49:51,674 INFO waiting for database to stop
2026-04-07 09:49:53,927 INFO waiting for database to stop
2026-04-07 09:49:56,290 INFO waiting for database to stop
2026-04-07 09:49:58,293 INFO waiting for database to stop
2026-04-07 09:50:00,296 INFO waiting for database to stop
2026-04-07 09:50:01,729 WARN killing 'database' (1936425) with SIGKILL
2026-04-07 09:50:01,861 WARN stopped: database (terminated by SIGKILL)
cryosparc@jyh3c:/home/jy_lab$ cryosparcm env | grep -v LICENSE_ID
export CONDA_DEFAULT_ENV=base
export CONDA_EXE=/home/jy_lab/anaconda3/bin/conda
export CONDA_PREFIX=/data3/cryosp_projs/cryosparc/cryosparc_master/.pixi/envs/master
export CONDA_PROMPT_MODIFIER='(base) '
export CONDA_PYTHON_EXE=/home/jy_lab/anaconda3/bin/python
export CONDA_SHLVL=1
export CRYOSPARC_BASE_PORT=39000
export CRYOSPARC_CLICK_WRAP=true
export CRYOSPARC_CLUSTER_JOB_MONITOR_INTERVAL=10
export CRYOSPARC_CLUSTER_JOB_MONITOR_MAX_RETRIES=1000000
export CRYOSPARC_DB_CONNECTION_TIMEOUT_MS=30000
export CRYOSPARC_DB_ENABLE_AUTH=true
export CRYOSPARC_DB_PATH=/data3/cryosp_projs/cryosparc/cryosparc_database
export CRYOSPARC_DEVELOP=false
export CRYOSPARC_FORCE_HOSTNAME=false
export CRYOSPARC_FORCE_USER=true
export CRYOSPARC_INSECURE=false
export CRYOSPARC_LICENSE_SERVER_ADDR=https://get.cryosparc.com
export CRYOSPARC_MASTER_HOSTNAME=jyh3c
export CRYOSPARC_PROJECT_DIR_PREFIX=CS-
export CRYOSPARC_ROOT_DIR=/data3/cryosp_projs/cryosparc/cryosparc_master
export CRYOSPARC_SSD_CACHE_LIFETIME_DAYS=5
export LD_PRELOAD=/data3/cryosp_projs/cryosparc/cryosparc_master/.pixi/envs/master/lib/libpython3.12.so
export PATH=/data3/cryosp_projs/cryosparc/cryosparc_master/deps/external/mongodb/bin:/data3/cryosp_projs/cryosparc/cryosparc_master/bin:/data3/cryosp_projs/cryosparc/cryosparc_master/.pixi/envs/master/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/data3/cryosp_projs/cryosparc/cryosparc_master/bin:/data3/cryosp_projs/cryosparc/cryosparc_worker/bin
export PYTHONPATH=/data3/cryosp_projs/cryosparc/cryosparc_master