Mongo error after upgrade from 4.1.0 to 4.1.1

Install, Configure and Update
1

After the last upgrade I receive this error on startup:

configuring database
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/share/sw/cryoSPARC/cryosparc_master/cryosparc_compute/database_management.py", line 41, in configure_mongo
    initializeReplicaSet()
  File "/share/sw/cryoSPARC/cryosparc_master/cryosparc_compute/database_management.py", line 83, in initializeReplicaSet
    admin_db.command(({'serverStatus': 1}))
  File "/share/sw/cryoSPARC/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/database.py", line 758, in command
    read_preference, session) as (sock_info, secondary_ok):
  File "/share/sw/cryoSPARC/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/contextlib.py", line 112, in __enter__
    return next(self.gen)
  File "/share/sw/cryoSPARC/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/mongo_client.py", line 1387, in _socket_for_reads
    server = self._select_server(read_preference, session)
  File "/share/sw/cryoSPARC/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/mongo_client.py", line 1346, in _select_server
    server = topology.select_server(server_selector)
  File "/share/sw/cryoSPARC/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/topology.py", line 246, in select_server
    address))
  File "/share/sw/cryoSPARC/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/topology.py", line 203, in select_servers
    selector, server_timeout, address)
  File "/share/sw/cryoSPARC/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/topology.py", line 220, in _select_servers_loop
    (self._error_message(selector), timeout, self.description))
pymongo.errors.ServerSelectionTimeoutError: localhost:39001: [Errno 111] Connection refused, Timeout: 20.0s, Topology Description: <TopologyDescription id: 63b5aa87b154de4c396f3364, topology_type: Single, servers: [<ServerDescription ('localhost', 39001) server_type: Unknown, rtt: None, error=AutoReconnect('localhost:39001: [Errno 111] Connection refused')>]>

the logfile has an ever repeating entry since update:

2022-12-25T01:59:30.775+0100 I COMMAND [LogicalSessionCacheRefresh] command config.$cmd command: update { update: "system.sessions", ordered: false, allowImplicitCollectionCreation: false, writeConcern: { w: "majority", wtimeout: 15000 }, $db: "config" } numYields:0 reslen:229 locks:{ Global: { acquireCount: { r: 6, w: 6 } }, Database: { acquireCount: { w: 6 } }, Collection: { acquireCount: { w: 3 } }, oplog: { acquireCount: { w: 3 } } } protocol:op_msg 103ms

the config looks like this:

cryosparcm status
CryoSPARC System master node installed at
/share/sw/cryoSPARC/cryosparc_master
Current cryoSPARC version: v4.1.0

global config variables:
export CRYOSPARC_LICENSE_ID="?????"
export CRYOSPARC_MASTER_HOSTNAME="crunchy.???.???"
export CRYOSPARC_DB_PATH="/share/cryosparcuser/cryosparc_database"
export CRYOSPARC_BASE_PORT=39000
export CRYOSPARC_DEVELOP=false
export CRYOSPARC_INSECURE=false
export CRYOSPARC_CLICK_WRAP=true
export CRYOSPARC_HEARTBEAT_SECONDS=180

I have incremental rsync backups from the cryosparc database and recreated an older version from before the update, but the same error appears. I also tried downgrading to 4.1.0, no effect. Any suggestions?

Thanks,
Michael

2

The output of the following commands, after running
cryosparcm stop, may help in narrowing down the cause of the error:

  1. df -h /share/cryosparcuser/cryosparc_database
  2. ls -al /share/cryosparcuser/cryosparc_database
  3. ps axuww | grep mongo
  4. ls -al /tmp/*sock
3

I tried removing the .sock file in temp but the same error persists on startup. Michael

4

@torreypines Have you since found a workaround, or are you still stuck at this point? If (and only if) it’s the latter, please try the procedure described under

and update us on any problems you encounter.

5

Did all the steps til 8. then

(base) cryosparcuser@?????:/share/sw/cryoSPARC/cryosparc_master$ 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 "<string>", line 1, in <module>
  File "/share/sw/cryoSPARC/cryosparc_master/cryosparc_compute/database_management.py", line 41, in configure_mongo
    initialize_replica_set()
  File "/share/sw/cryoSPARC/cryosparc_master/cryosparc_compute/database_management.py", line 80, in initialize_replica_set
    admin_db = try_get_pymongo_admin_db(mongo_client)
  File "/share/sw/cryoSPARC/cryosparc_master/cryosparc_compute/database_management.py", line 242, in try_get_pymongo_admin_db
    admin_db.command(({'serverStatus': 1}))
  File "/share/sw/cryoSPARC/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/database.py", line 758, in command
    read_preference, session) as (sock_info, secondary_ok):
  File "/share/sw/cryoSPARC/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/contextlib.py", line 112, in __enter__
    return next(self.gen)
  File "/share/sw/cryoSPARC/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/mongo_client.py", line 1387, in _socket_for_reads
    server = self._select_server(read_preference, session)
  File "/share/sw/cryoSPARC/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/mongo_client.py", line 1346, in _select_server
    server = topology.select_server(server_selector)
  File "/share/sw/cryoSPARC/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/topology.py", line 246, in select_server
    address))
  File "/share/sw/cryoSPARC/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/topology.py", line 203, in select_servers
    selector, server_timeout, address)
  File "/share/sw/cryoSPARC/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/topology.py", line 220, in _select_servers_loop
    (self._error_message(selector), timeout, self.description))
pymongo.errors.ServerSelectionTimeoutError: localhost:39001: [Errno 111] Connection refused, Timeout: 20.0s, Topology Description: <TopologyDescription id: 63c1e473b19959671c369b17, topology_type: Single, servers: [<ServerDescription ('localhost', 39001) server_type: Unknown, rtt: None, error=AutoReconnect('localhost:39001: [Errno 111] Connection refused')>]>
[2023-01-14T00:09:46+01:00] Error configuring database. Most recent database log lines:
 mongod(_ZN5mongo20WiredTigerSizeStorerC1EP15__wt_connectionRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEbb+0x2DE) [0x5600bf2a6c9e]
 mongod(_ZN5mongo18WiredTigerKVEngineC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_PNS_11ClockSourceES8_mmbbbb+0xE14) [0x5600bf28c234]
 mongod(+0xA25AEC) [0x5600bf26daec]
 mongod(_ZN5mongo20ServiceContextMongoD29initializeGlobalStorageEngineEv+0x266) [0x5600bf47dfb6]
 mongod(+0xA025B8) [0x5600bf24a5b8]
 mongod(_ZN5mongo11mongoDbMainEiPPcS1_+0x26C) [0x5600bf24d63c]
 mongod(main+0x9) [0x5600bf1d3bc9]
 libc.so.6(__libc_start_main+0xEB) [0x7f56a429609b]
 mongod(+0x9ED741) [0x5600bf235741]
-----  END BACKTRACE  -----

still seems to be the same error. Thank you, Michael

6

I reinstalled 4.1.1. now on an recently updated Debian 11 server. Needed to fix the known ipv6 error and switch to conda version 11.7 to make it work. With conda 12.0 there were the known pyconda compile errors. Anyway, thanks for your help.