I was in the process of trying to upgrade from Centos 7 to 8. I wasn’t able to complete the upgrade and now Cryosparc is not connecting to the database. Here is what happens when I try to start CryoSPARC:
[cryosparc_user@X ~]$ cryosparcm start
Starting cryoSPARC System master process..
CryoSPARC is not already running.
configuring database
configuration complete
database: started
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)
checkdb error - could not get replica set status; please reconfigure the database with `cryosparcm configuredb`
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/home/cryosparc_user/software/cryosparc/cryosparc_master/cryosparc_compute/database_management.py", line 268, in check_mongo
admin_db = try_get_pymongo_admin_db(mongo_client)
File "/home/cryosparc_user/software/cryosparc/cryosparc_master/cryosparc_compute/database_management.py", line 249, in try_get_pymongo_admin_db
admin_db.command(({'serverStatus': 1}))
File "/home/cryosparc_user/software/cryosparc/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/software/cryosparc/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/software/cryosparc/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/software/cryosparc/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/software/cryosparc/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/software/cryosparc/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/software/cryosparc/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: defcon2.bio.uci.edu:39001: [Errno 113] No route to host, Timeout: 20.0s, Topology Description: <TopologyDescription id: 646278909ed7920fe7478880, topology_type: Unknown, servers: [<ServerDescription ('defcon2.bio.uci.edu', 39001) server_type: Unknown, rtt: None, error=AutoReconnect('defcon2.bio.uci.edu:39001: [Errno 113] No route to host')>]>
[2023-05-15T11:24:23-0700] Error checking database. Most recent database log lines:
2023-05-15T11:23:10.427-0700 I REPL [replexec-0] Starting replication reporter thread
2023-05-15T11:23:10.428-0700 I REPL [rsSync] transition to SECONDARY from RECOVERING
2023-05-15T11:23:10.428-0700 I REPL [rsSync] conducting a dry run election to see if we could be elected. current term: 108
2023-05-15T11:23:10.428-0700 I REPL [replexec-0] dry election run succeeded, running for election in term 109
2023-05-15T11:23:10.433-0700 I REPL [replexec-0] election succeeded, assuming primary role in term 109
2023-05-15T11:23:10.433-0700 I REPL [replexec-0] transition to PRIMARY from SECONDARY
2023-05-15T11:23:10.433-0700 I REPL [replexec-0] Resetting sync source to empty, which was :27017
2023-05-15T11:23:10.433-0700 I REPL [replexec-0] Entering primary catch-up mode.
2023-05-15T11:23:10.433-0700 I REPL [replexec-0] Exited primary catch-up mode.
2023-05-15T11:23:12.429-0700 I REPL [rsSync] transition to primary complete; database writes are now permitted
[cryosparc_user@defcon2 ~]$ cd /home/cryosparc_user/software/cryosparc/cryosparc_worker/
[cryosparc_user@X cryosparc_worker]$ ls
bin check_install_deps.sh config.sh cryosparc_compute cryosparc_tools deps deps_bundle deps_bundle_hashes deps_hashes environment.yml install.sh version
[cryosparc_user@X cryosparc_worker]$ ls ../cryosparc_master/cryosparc_worker.tar.gz
../cryosparc_master/cryosparc_worker.tar.gz
[cryosparc_user@X cryosparc_worker]$ ln -s ../cryosparc_master/cryosparc_worker.tar.gz
[cryosparc_user@X cryosparc_worker]$ ./bin/cryosparcw update
Updating... checking versions
Current version v4.2.1 - New version v4.2.1
Already up to date
[cryosparc_user@X cryosparc_worker]$