How to recover from Database Spawn error

My CS database crashed giving me a SPWAN ERROR ever since CS crashed (most possibly due to HDD ran out of space).
I removed the *.sock files from /tmp and also removed the .lock files, however, the error stays.
Steps performed so far:

  1. kill all running instances of CS
  2. Repair process as I found in earlier thread:
    `[user@c101030 cryosparc2_database]$ eval $(cryosparcm env)

[user@c101030 cryosparc2_database]$ mongod --dbpath ./ --repair
2020-12-02T10:55:45.014-0800 I CONTROL [initandlisten] MongoDB starting : pid=40043 port=27017 dbpath=./ 64-bit host=c101030.localdomain
2020-12-02T10:55:45.014-0800 I CONTROL [initandlisten] db version v3.4.10-4-g67ee356c6b
2020-12-02T10:55:45.014-0800 I CONTROL [initandlisten] git version: 67ee356c6be377cda547d16423daef5beb4e8377
2020-12-02T10:55:45.014-0800 I CONTROL [initandlisten] OpenSSL version: OpenSSL 1.0.2p 14 Aug 2018
2020-12-02T10:55:45.014-0800 I CONTROL [initandlisten] allocator: tcmalloc
2020-12-02T10:55:45.014-0800 I CONTROL [initandlisten] modules: none
2020-12-02T10:55:45.014-0800 I CONTROL [initandlisten] build environment:
2020-12-02T10:55:45.015-0800 I CONTROL [initandlisten] distarch: x86_64
2020-12-02T10:55:45.015-0800 I CONTROL [initandlisten] target_arch: x86_64
2020-12-02T10:55:45.015-0800 I CONTROL [initandlisten] options: { repair: true, storage: { dbPath: “./” } }
2020-12-02T10:55:45.047-0800 I - [initandlisten] Detected data files in ./ created by the ‘wiredTiger’ storage engine, so setting the active storage engine to ‘wiredTiger’.
2020-12-02T10:55:45.047-0800 I STORAGE [initandlisten]
2020-12-02T10:55:45.047-0800 I STORAGE [initandlisten] ** WARNING: Using the XFS filesystem is strongly recommended with the WiredTiger storage engine
2020-12-02T10:55:45.047-0800 I STORAGE [initandlisten] ** See
2020-12-02T10:55:45.047-0800 I STORAGE [initandlisten] wiredtiger_open config: create,cache_size=257340M,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),checkpoint=(wait=60,log_size=2GB),statistics_log=(wait=0),log=(enabled=false),
2020-12-02T10:55:45.061-0800 E STORAGE [initandlisten] WiredTiger error (13) [1606935345:61959][40043:0x7f16d1a1dd40], file:WiredTiger.wt, connection: .//WiredTiger.turtle: handle-open: open: Permission denied
2020-12-02T10:55:45.062-0800 I - [initandlisten] Assertion: 28595:13: Permission denied src/mongo/db/storage/wiredtiger/wiredtiger_kv_engine.cpp 276
2020-12-02T10:55:45.062-0800 I STORAGE [initandlisten] exception in initAndListen: 28595 13: Permission denied, terminating
2020-12-02T10:55:45.062-0800 I NETWORK [initandlisten] shutdown: going to close listening sockets…
2020-12-02T10:55:45.062-0800 I NETWORK [initandlisten] removing socket file: /tmp/mongodb-27017.sock
2020-12-02T10:55:45.062-0800 I NETWORK [initandlisten] shutdown: going to flush diaglog…
2020-12-02T10:55:45.062-0800 I CONTROL [initandlisten] now exiting
2020-12-02T10:55:45.062-0800 I CONTROL [initandlisten] shutting down with code:100`

After this when I go for cryosparcm start it gives the same error as below:
Starting cryoSPARC System master process.. CryoSPARC is not already running. database: ERROR (spawn error) Traceback (most recent call last): File "<string>", line 1, in <module> File "/home/cryoSPARC_v2/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/", line 1149, in database_names "listDatabases")["databases"]] File "/home/cryoSPARC_v2/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/", line 491, in command with client._socket_for_reads(read_preference) as (sock_info, slave_ok): File "/home/cryoSPARC_v2/cryosparc2_master/deps/anaconda/lib/python2.7/", line 17, in __enter__ return File "/home/cryoSPARC_v2/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/", line 859, in _socket_for_reads with self._get_socket(read_preference) as sock_info: File "/home/cryoSPARC_v2/cryosparc2_master/deps/anaconda/lib/python2.7/", line 17, in __enter__ return File "/home/cryoSPARC_v2/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/", line 823, in _get_socket server = self._get_topology().select_server(selector) File "/home/cryoSPARC_v2/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/", line 214, in select_server address)) File "/home/cryoSPARC_v2/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/", line 189, in select_servers self._error_message(selector)) pymongo.errors.ServerSelectionTimeoutError: localhost:39001: [Errno 111] Connection refused

I don’t think the repair process or removing .sock or .lock get any help for me.
Please suggest how to recover from this Spawn Error .


Is it possible to disconnect the database from CS and then import non-faulty jobs again to create a new database ?
Please suggest if there’s a work around here.