Timeout when connecting to MongoDB Atlas

FireWorks
1

Dear developers and users,

I have tested the mongo shell and the direct use of pymongo, they both worked. But it failed when I tested the lpad -l test.yaml get_wflows.

I installed all updated versions.

Traceback (most recent call last): File “/Users/jyxu/miniconda3/envs/fireworks/bin/lpad”, line 10, in sys.exit(lpad()) File “/Users/jyxu/miniconda3/envs/fireworks/lib/python3.8/site-packages/fireworks/scripts/lpad_run.py”, line 1209, in lpad args.func(args) File “/Users/jyxu/miniconda3/envs/fireworks/lib/python3.8/site-packages/fireworks/scripts/lpad_run.py”, line 322, in get_wfs ids = lp.get_wf_ids(query, sort, args.max, count_only=args.display_format == ‘count’) File “/Users/jyxu/miniconda3/envs/fireworks/lib/python3.8/site-packages/fireworks/core/launchpad.py”, line 767, in get_wf_ids for fw in self.workflows.find(criteria, {“nodes”: True}, File “/Users/jyxu/miniconda3/envs/fireworks/lib/python3.8/site-packages/pymongo/cursor.py”, line 1207, in next if len(self.__data) or self._refresh(): File “/Users/jyxu/miniconda3/envs/fireworks/lib/python3.8/site-packages/pymongo/cursor.py”, line 1100, in _refresh self.__session = self.__collection.database.client._ensure_session() File “/Users/jyxu/miniconda3/envs/fireworks/lib/python3.8/site-packages/pymongo/mongo_client.py”, line 1816, in _ensure_session return self.__start_session(True, causal_consistency=False) File “/Users/jyxu/miniconda3/envs/fireworks/lib/python3.8/site-packages/pymongo/mongo_client.py”, line 1766, in __start_session server_session = self._get_server_session() File “/Users/jyxu/miniconda3/envs/fireworks/lib/python3.8/site-packages/pymongo/mongo_client.py”, line 1802, in _get_server_session return self._topology.get_server_session() File “/Users/jyxu/miniconda3/envs/fireworks/lib/python3.8/site-packages/pymongo/topology.py”, line 490, in get_server_session self._select_servers_loop( File “/Users/jyxu/miniconda3/envs/fireworks/lib/python3.8/site-packages/pymongo/topology.py”, line 215, in _select_servers_loop raise ServerSelectionTimeoutError( pymongo.errors.ServerSelectionTimeoutError: connection closed,connection closed,connection closed, Timeout: 30s, Topology Description: <TopologyDescription id: 600b6bf32381c9b1f0cb72d5, topology_type: ReplicaSetNoPrimary, servers: [<ServerDescription (‘fireworks-shard-00-00.d4nzu.mongodb.net’, 27017) server_type: Unknown, rtt: None, error=AutoReconnect(‘connection closed’)>, <ServerDescription (‘fireworks-shard-00-01.d4nzu.mongodb.net’, 27017) server_type: Unknown, rtt: None, error=AutoReconnect(‘connection closed’)>, <ServerDescription (‘fireworks-shard-00-02.d4nzu.mongodb.net’, 27017) server_type: Unknown, rtt: None, error=AutoReconnect(‘connection closed’)>]>

2

I failed the test as well, have you solved this problem?

3

I ran into the same issue when I was trying to set up atomate a few months ago. In the atomate setup, I found that adding "authsource":"admin" to the end of my db.json file and then both ssl: True and authsource: admin to the end of the my_launchpad.yaml file made it work. In your case, you may just need to add those two lines to the end of your test.yaml file.