Hi,
I’ve been trying to install cryoSPARC master on a cluster node, but keep getting this error after I do “cryosparcm start”:
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 "/scratch/users/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/mongo_client.py", line 1149, in database_names
"listDatabases")["databases"]]
File "/scratch/users/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/database.py", line 491, in command
with client._socket_for_reads(read_preference) as (sock_info, slave_ok):
File "/scratch/users/cryosparc2_master/deps/anaconda/lib/python2.7/contextlib.py", line 17, in __enter__
return self.gen.next()
File "/scratch/users/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/mongo_client.py", line 859, in _socket_for_reads
with self._get_socket(read_preference) as sock_info:
File "/scratch/users/cryosparc2_master/deps/anaconda/lib/python2.7/contextlib.py", line 17, in __enter__
return self.gen.next()
File "/scratch/users/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/mongo_client.py", line 823, in _get_socket
server = self._get_topology().select_server(selector)
File "/scratch/users/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/topology.py", line 214, in select_server
address))
File "/scratch/users/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/topology.py", line 189, in select_servers
self._error_message(selector))
pymongo.errors.ServerSelectionTimeoutError: localhost:39001: [Errno 111] Connection refuse
So I checked the “log database”:
2019-12-08T13:21:22.713-0600 I CONTROL [initandlisten] options: { net: { port: 39001 }, replication: { oplogSizeMB: 64, replSet: "meteor" }, storage: { dbPath: "/home/ql8/scratch", journal: { enabled: false }, wiredTiger: { engineConfig: { cacheSizeGB: 4.0 } } } }
2019-12-08T13:21:22.747-0600 I STORAGE [initandlisten] wiredtiger_open config: create,cache_size=4096M,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),
2019-12-08T13:21:22.756-0600 E STORAGE [initandlisten] WiredTiger error (2) [1575832882:756539][13025:0x2ae463d75cc0], file:WiredTiger.wt, connection: /home/ql8/scratch/WiredTiger.wt: handle-open: open: No such file or directory
2019-12-08T13:21:22.757-0600 I - [initandlisten] Assertion: 28595:2: No such file or directory src/mongo/db/storage/wiredtiger/wiredtiger_kv_engine.cpp 276
2019-12-08T13:21:22.757-0600 I STORAGE [initandlisten] exception in initAndListen: 28595 2: No such file or directory, terminating
2019-12-08T13:21:22.757-0600 I NETWORK [initandlisten] shutdown: going to close listening sockets...
2019-12-08T13:21:22.757-0600 I NETWORK [initandlisten] removing socket file: /tmp/mongodb-39001.sock
2019-12-08T13:21:22.757-0600 I NETWORK [initandlisten] shutdown: going to flush diaglog...
2019-12-08T13:21:22.757-0600 I CONTROL [initandlisten] now exiting
2019-12-08T13:21:22.757-0600 I CONTROL [initandlisten] shutting down with code:100
2019-12-08T13:21:24.823-0600 I CONTROL [initandlisten] MongoDB starting : pid=13038 port=39001 dbpath=/home/ql8/scratch 64-bit host=golubh3.campuscluster.illinois.edu
2019-12-08T13:21:24.823-0600 I CONTROL [initandlisten] db version v3.4.10-4-g67ee356c6b
2019-12-08T13:21:24.823-0600 I CONTROL [initandlisten] git version: 67ee356c6be377cda547d16423daef5beb4e8377
2019-12-08T13:21:24.823-0600 I CONTROL [initandlisten] OpenSSL version: OpenSSL 1.0.2p 14 Aug 2018
2019-12-08T13:21:24.824-0600 I CONTROL [initandlisten] allocator: tcmalloc
2019-12-08T13:21:24.824-0600 I CONTROL [initandlisten] modules: none
2019-12-08T13:21:24.824-0600 I CONTROL [initandlisten] build environment:
2019-12-08T13:21:24.824-0600 I CONTROL [initandlisten] distarch: x86_64
2019-12-08T13:21:24.824-0600 I CONTROL [initandlisten] target_arch: x86_64
2019-12-08T13:21:24.824-0600 I CONTROL [initandlisten] options: { net: { port: 39001 },
> replication: { oplogSizeMB: 64, replSet: "meteor" }, storage: { dbPath: "/home/ql8/scratch", journal: { enabled: false }, wiredTiger: { engineConfig: { cacheSizeGB: 4.0 } } } }
2019-12-08T13:21:24.860-0600 I STORAGE [initandlisten] wiredtiger_open config: create,cache_size=4096M,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),
2019-12-08T13:21:24.869-0600 E STORAGE [initandlisten] WiredTiger error (2) [1575832884:869324][13038:0x2ac674d26cc0], file:WiredTiger.wt, connection: /home/ql8/scratch/WiredTiger.wt: handle-open: open: No such file or directory
2019-12-08T13:21:24.869-0600 I - [initandlisten] Assertion: 28595:2: No such file or directory src/mongo/db/storage/wiredtiger/wiredtiger_kv_engine.cpp 276
2019-12-08T13:21:24.870-0600 I STORAGE [initandlisten] exception in initAndListen: 28595 2: No such file or directory, terminating
2019-12-08T13:21:24.870-0600 I NETWORK [initandlisten] shutdown: going to close listening sockets...
2019-12-08T13:21:24.870-0600 I NETWORK [initandlisten] removing socket file: /tmp/mongodb-39001.sock
2019-12-08T13:21:24.870-0600 I NETWORK [initandlisten] shutdown: going to flush diaglog...
2019-12-08T13:21:24.870-0600 I CONTROL [initandlisten] now exiting
2019-12-08T13:21:24.870-0600 I CONTROL [initandlisten] shutting down with code:100
2019-12-08T13:21:27.935-0600 I CONTROL [initandlisten] MongoDB starting : pid=13044 port=39001 dbpath=/home/ql8/scratch 64-bit host=golubh3.campuscluster.illinois.edu
2019-12-08T13:21:27.935-0600 I CONTROL [initandlisten] db version v3.4.10-4-g67ee356c6b
2019-12-08T13:21:27.935-0600 I CONTROL [initandlisten] git version: 67ee356c6be377cda547d16423daef5beb4e8377
2019-12-08T13:21:27.936-0600 I CONTROL [initandlisten] OpenSSL version: OpenSSL 1.0.2p 14 Aug 2018
2019-12-08T13:21:27.936-0600 I CONTROL [initandlisten] allocator: tcmalloc
2019-12-08T13:21:27.936-0600 I CONTROL [initandlisten] modules: none
2019-12-08T13:21:27.936-0600 I CONTROL [initandlisten] build environment:
2019-12-08T13:21:27.936-0600 I CONTROL [initandlisten] distarch: x86_64
2019-12-08T13:21:27.936-0600 I CONTROL [initandlisten] target_arch: x86_64
2019-12-08T13:21:27.936-0600 I CONTROL [initandlisten] options: { net: { port: 39001 }, replication: { oplogSizeMB: 64, replSet: "meteor" }, storage: { dbPath: "/home/ql8/scratch", journal: { enabled: false }, wiredTiger: { engineConfig: { cacheSizeGB: 4.0 } } } }
2019-12-08T13:21:27.970-0600 I STORAGE [initandlisten] wiredtiger_open config: create,cache_size=4096M,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),
2019-12-08T13:21:27.979-0600 E STORAGE [initandlisten] WiredTiger error (2) [1575832887:979476][13044:0x2b636e04acc0], file:WiredTiger.wt, connection: /home/ql8/scratch/WiredTiger.wt: handle-open: open: No such file or directory
2019-12-08T13:21:27.980-0600 I - [initandlisten] Assertion: 28595:2: No such file or directory src/mongo/db/storage/wiredtiger/wiredtiger_kv_engine.cpp 276
2019-12-08T13:21:27.980-0600 I STORAGE [initandlisten] exception in initAndListen: 28595 2: No such file or directory, terminating
2019-12-08T13:21:27.980-0600 I NETWORK [initandlisten] shutdown: going to close listening sockets...
2019-12-08T13:21:27.980-0600 I NETWORK [initandlisten] removing socket file: /tmp/mongodb-39001.sock
2019-12-08T13:21:27.980-0600 I NETWORK [initandlisten] shutdown: going to flush diaglog...
2019-12-08T13:21:27.980-0600 I CONTROL [initandlisten] now exiting
2019-12-08T13:21:27.980-0600 I CONTROL [initandlisten] shutting down with code:100
2019-12-10T17:09:53.357-0600 I CONTROL [initandlisten] MongoDB starting : pid=33453 port=39001 dbpath=/home/ql8/scratch 64-bit host=golubh3.campuscluster.illinois.edu
2019-12-10T17:09:53.358-0600 I CONTROL [initandlisten] db version v3.4.10-4-g67ee356c6b
2019-12-10T17:09:53.358-0600 I CONTROL [initandlisten] git version: 67ee356c6be377cda547d16423daef5beb4e8377
2019-12-10T17:09:53.358-0600 I CONTROL [initandlisten] OpenSSL version: OpenSSL 1.0.2p 14 Aug 2018
2019-12-10T17:09:53.358-0600 I CONTROL [initandlisten] allocator: tcmalloc
2019-12-10T17:09:53.358-0600 I CONTROL [initandlisten] modules: none
2019-12-10T17:09:53.358-0600 I CONTROL [initandlisten] build environment:
2019-12-10T17:09:53.358-0600 I CONTROL [initandlisten] distarch: x86_64
2019-12-10T17:09:53.358-0600 I CONTROL [initandlisten] target_arch: x86_64
2019-12-10T17:09:53.358-0600 I CONTROL [initandlisten] options: { net: { port: 39001 }, replication: { oplogSizeMB: 64, replSet: "meteor" }, storage: { dbPath: "/home/ql8/scratch", journal: { enabled: false }, wiredTiger: { engineConfig: { cacheSizeGB: 4.0 } } } }
2019-12-10T17:09:53.394-0600 I STORAGE [initandlisten] wiredtiger_open config: create,cache_size=4096M,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),
2019-12-10T17:09:53.406-0600 E STORAGE [initandlisten] WiredTiger error (2) [1576019393:406553][33453:0x2ac167398cc0], file:WiredTiger.wt, connection: /home/ql8/scratch/WiredTiger.wt: handle-open: open: No such file or directory
2019-12-10T17:09:53.407-0600 I - [initandlisten] Assertion: 28595:2: No such file or directory src/mongo/db/storage/wiredtiger/wiredtiger_kv_engine.cpp 276
2019-12-10T17:09:53.407-0600 I STORAGE [initandlisten] exception in initAndListen: 28595 2: No such file or directory, terminating
2019-12-10T17:09:53.407-0600 I NETWORK [initandlisten] shutdown: going to close listening sockets...
2019-12-10T17:09:53.407-0600 I NETWORK [initandlisten] removing socket file: /tmp/mongodb-39001.sock
2019-12-10T17:09:53.407-0600 I NETWORK [initandlisten] shutdown: going to flush diaglog...
2019-12-10T17:09:53.408-0600 I CONTROL [initandlisten] now exiting
2019-12-10T17:09:53.408-0600 I CONTROL [initandlisten] shutting down with code:100
2019-12-10T17:09:54.472-0600 I CONTROL [initandlisten] MongoDB starting : pid=33463 port=39001 dbpath=/home/ql8/scratch 64-bit host=golubh3.campuscluster.illinois.edu
2019-12-10T17:09:54.472-0600 I CONTROL [initandlisten] db version v3.4.10-4-g67ee356c6b
2019-12-10T17:09:54.472-0600 I CONTROL [initandlisten] git version: 67ee356c6be377cda547d16423daef5beb4e8377
2019-12-10T17:09:54.472-0600 I CONTROL [initandlisten] OpenSSL version: OpenSSL 1.0.2p 14 Aug 2018
2019-12-10T17:09:54.472-0600 I CONTROL [initandlisten] allocator: tcmalloc
2019-12-10T17:09:54.472-0600 I CONTROL [initandlisten] modules: none
2019-12-10T17:09:54.472-0600 I CONTROL [initandlisten] build environment:
2019-12-10T17:09:54.472-0600 I CONTROL [initandlisten] distarch: x86_64
2019-12-10T17:09:54.472-0600 I CONTROL [initandlisten] target_arch: x86_64
2019-12-10T17:09:54.472-0600 I CONTROL [initandlisten] options: { net: { port: 39001 }, replication: { oplogSizeMB: 64, replSet: "meteor" }, storage: { dbPath: "/home/ql8/scratch", journal: { enabled: false }, wiredTiger: { engineConfig: { cacheSizeGB: 4.0 } } } }
2019-12-10T17:09:54.509-0600 I STORAGE [initandlisten] wiredtiger_open config: create,cache_size=4096M,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),
2019-12-10T17:09:54.518-0600 E STORAGE [initandlisten] WiredTiger error (2) [1576019394:518663][33463:0x2b5ce9438cc0], file:WiredTiger.wt, connection: /home/ql8/scratch/WiredTiger.wt: handle-open: open: No such file or directory
2019-12-10T17:09:54.519-0600 I - [initandlisten] Assertion: 28595:2: No such file or directory src/mongo/db/storage/wiredtiger/wiredtiger_kv_engine.cpp 276
2019-12-10T17:09:54.519-0600 I STORAGE [initandlisten] exception in initAndListen: 28595 2: No such file or directory, terminating
2019-12-10T17:09:54.519-0600 I NETWORK [initandlisten] shutdown: going to close listening sockets...
2019-12-10T17:09:54.519-0600 I NETWORK [initandlisten] removing socket file: /tmp/mongodb-39001.sock
2019-12-10T17:09:54.519-0600 I NETWORK [initandlisten] shutdown: going to flush diaglog...
2019-12-10T17:09:54.519-0600 I CONTROL [initandlisten] now exiting
2019-12-10T17:09:54.519-0600 I CONTROL [initandlisten] shutting down with code:100
2019-12-10T17:09:56.583-0600 I CONTROL [initandlisten] MongoDB starting : pid=33468 port=39001 dbpath=/home/ql8/scratch 64-bit host=golubh3.campuscluster.illinois.edu
2019-12-10T17:09:56.583-0600 I CONTROL [initandlisten] db version v3.4.10-4-g67ee356c6b
2019-12-10T17:09:56.583-0600 I CONTROL [initandlisten] git version: 67ee356c6be377cda547d16423daef5beb4e8377
2019-12-10T17:09:56.583-0600 I CONTROL [initandlisten] OpenSSL version: OpenSSL 1.0.2p 14 Aug 2018
2019-12-10T17:09:56.583-0600 I CONTROL [initandlisten] allocator: tcmalloc
2019-12-10T17:09:56.583-0600 I CONTROL [initandlisten] modules: none
2019-12-10T17:09:56.583-0600 I CONTROL [initandlisten] build environment:
2019-12-10T17:09:56.583-0600 I CONTROL [initandlisten] distarch: x86_64
2019-12-10T17:09:56.583-0600 I CONTROL [initandlisten] target_arch: x86_64
2019-12-10T17:09:56.583-0600 I CONTROL [initandlisten] options: { net: { port: 39001 }, replication: { oplogSizeMB: 64, replSet: "meteor" }, storage: { dbPath: "/home/ql8/scratch", journal: { enabled: false }, wiredTiger: { engineConfig: { cacheSizeGB: 4.0 } } } }
2019-12-10T17:09:56.619-0600 I STORAGE [initandlisten] wiredtiger_open config: create,cache_size=4096M,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),
2019-12-10T17:09:56.629-0600 E STORAGE [initandlisten] WiredTiger error (2) [1576019396:629385][33468:0x2b14b9fb9cc0], file:WiredTiger.wt, connection: /home/ql8/scratch/WiredTiger.wt: handle-open: open: No such file or directory
2019-12-10T17:09:56.629-0600 I - [initandlisten] Assertion: 28595:2: No such file or directory src/mongo/db/storage/wiredtiger/wiredtiger_kv_engine.cpp 276
2019-12-10T17:09:56.630-0600 I STORAGE [initandlisten] exception in initAndListen: 28595 2: No such file or directory, terminating
2019-12-10T17:09:56.630-0600 I NETWORK [initandlisten] shutdown: going to close listening sockets...
2019-12-10T17:09:56.630-0600 I NETWORK [initandlisten] removing socket file: /tmp/mongodb-39001.sock
2019-12-10T17:09:56.630-0600 I NETWORK [initandlisten] shutdown: going to flush diaglog...
2019-12-10T17:09:56.630-0600 I CONTROL [initandlisten] now exiting
2019-12-10T17:09:56.630-0600 I CONTROL [initandlisten] shutting down with code:100
2019-12-10T17:09:59.695-0600 I CONTROL [initandlisten] MongoDB starting : pid=33473 port=39001 dbpath=/home/ql8/scratch 64-bit host=golubh3.campuscluster.illinois.edu
2019-12-10T17:09:59.695-0600 I CONTROL [initandlisten] db version v3.4.10-4-g67ee356c6b
2019-12-10T17:09:59.695-0600 I CONTROL [initandlisten] git version: 67ee356c6be377cda547d16423daef5beb4e8377
2019-12-10T17:09:59.695-0600 I CONTROL [initandlisten] OpenSSL version: OpenSSL 1.0.2p 14 Aug 2018
2019-12-10T17:09:59.695-0600 I CONTROL [initandlisten] allocator: tcmalloc
2019-12-10T17:09:59.695-0600 I CONTROL [initandlisten] modules: none
2019-12-10T17:09:59.695-0600 I CONTROL [initandlisten] build environment:
2019-12-10T17:09:59.695-0600 I CONTROL [initandlisten] distarch: x86_64
2019-12-10T17:09:59.695-0600 I CONTROL [initandlisten] target_arch: x86_64
2019-12-10T17:09:59.695-0600 I CONTROL [initandlisten] options: { net: { port: 39001 }, replication: { oplogSizeMB: 64, replSet: "meteor" }, storage: { dbPath: "/home/ql8/scratch", journal: { enabled: false }, wiredTiger: { engineConfig: { cacheSizeGB: 4.0 } } } }
2019-12-10T17:09:59.731-0600 I STORAGE [initandlisten] wiredtiger_open config: create,cache_size=4096M,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),
2019-12-10T17:09:59.741-0600 E STORAGE [initandlisten] WiredTiger error (2) [1576019399:741326][33473:0x2b38c841fcc0], file:WiredTiger.wt, connection: /home/ql8/scratch/WiredTiger.wt: handle-open: open: No such file or directory
2019-12-10T17:09:59.741-0600 I - [initandlisten] Assertion: 28595:2: No such file or directory src/mongo/db/storage/wiredtiger/wiredtiger_kv_engine.cpp 276
2019-12-10T17:09:59.742-0600 I STORAGE [initandlisten] exception in initAndListen: 28595 2: No such file or directory, terminating
2019-12-10T17:09:59.742-0600 I NETWORK [initandlisten] shutdown: going to close listening sockets...
2019-12-10T17:09:59.742-0600 I NETWORK [initandlisten] removing socket file: /tmp/mongodb-39001.sock
2019-12-10T17:09:59.742-0600 I NETWORK [initandlisten] shutdown: going to flush diaglog...
2019-12-10T17:09:59.742-0600 I CONTROL [initandlisten] now exiting
2019-12-10T17:09:59.742-0600 I CONTROL [initandlisten] shutting down with code:100
2019-12-10T17:18:14.050-0600 I CONTROL [initandlisten] MongoDB starting : pid=35089 port=39001 dbpath=/home/ql8/scratch 64-bit host=golubh3.campuscluster.illinois.edu
2019-12-10T17:18:14.050-0600 I CONTROL [initandlisten] db version v3.4.10-4-g67ee356c6b
2019-12-10T17:18:14.050-0600 I CONTROL [initandlisten] git version: 67ee356c6be377cda547d16423daef5beb4e8377
2019-12-10T17:18:14.050-0600 I CONTROL [initandlisten] OpenSSL version: OpenSSL 1.0.2p 14 Aug 2018
2019-12-10T17:18:14.050-0600 I CONTROL [initandlisten] allocator: tcmalloc
2019-12-10T17:18:14.050-0600 I CONTROL [initandlisten] modules: none
2019-12-10T17:18:14.050-0600 I CONTROL [initandlisten] build environment:
2019-12-10T17:18:14.050-0600 I CONTROL [initandlisten] distarch: x86_64
2019-12-10T17:18:14.050-0600 I CONTROL [initandlisten] target_arch: x86_64
2019-12-10T17:18:14.050-0600 I CONTROL [initandlisten] options: { net: { port: 39001 }, replication: { oplogSizeMB: 64, replSet: "meteor" }, storage: { dbPath: "/home/ql8/scratch", journal: { enabled: false }, wiredTiger: { engineConfig: { cacheSizeGB: 4.0 } } } }
2019-12-10T17:18:14.072-0600 I STORAGE [initandlisten] wiredtiger_open config: create,cache_size=4096M,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),
2019-12-10T17:18:14.079-0600 E STORAGE [initandlisten] WiredTiger error (2) [1576019894:79953][35089:0x2b37460a4cc0], file:WiredTiger.wt, connection: /home/ql8/scratch/WiredTiger.wt: handle-open: open: No such file or directory
2019-12-10T17:18:14.080-0600 I - [initandlisten] Assertion: 28595:2: No such file or directory src/mongo/db/storage/wiredtiger/wiredtiger_kv_engine.cpp 276
2019-12-10T17:18:14.080-0600 I STORAGE [initandlisten] exception in initAndListen: 28595 2: No such file or directory, terminating
2019-12-10T17:18:14.080-0600 I NETWORK [initandlisten] shutdown: going to close listening sockets...
2019-12-10T17:18:14.080-0600 I NETWORK [initandlisten] removing socket file: /tmp/mongodb-39001.sock
2019-12-10T17:18:14.080-0600 I NETWORK [initandlisten] shutdown: going to flush diaglog...
2019-12-10T17:18:14.080-0600 I CONTROL [initandlisten] now exiting
2019-12-10T17:18:14.080-0600 I CONTROL [initandlisten] shutting down with code:100
2019-12-10T17:18:15.142-0600 I CONTROL [initandlisten] MongoDB starting : pid=35093 port=39001 dbpath=/home/ql8/scratch 64-bit host=golubh3.campuscluster.illinois.edu
2019-12-10T17:18:15.142-0600 I CONTROL [initandlisten] db version v3.4.10-4-g67ee356c6b
2019-12-10T17:18:15.142-0600 I CONTROL [initandlisten] git version: 67ee356c6be377cda547d16423daef5beb4e8377
2019-12-10T17:18:15.142-0600 I CONTROL [initandlisten] OpenSSL version: OpenSSL 1.0.2p 14 Aug 2018
2019-12-10T17:18:15.142-0600 I CONTROL [initandlisten] allocator: tcmalloc
2019-12-10T17:18:15.142-0600 I CONTROL [initandlisten] modules: none
2019-12-10T17:18:15.142-0600 I CONTROL [initandlisten] build environment:
2019-12-10T17:18:15.143-0600 I CONTROL [initandlisten] distarch: x86_64
2019-12-10T17:18:15.143-0600 I CONTROL [initandlisten] target_arch: x86_64
2019-12-10T17:18:15.143-0600 I CONTROL [initandlisten] options: { net: { port: 39001 }, replication: { oplogSizeMB: 64, replSet: "meteor" }, storage: { dbPath: "/home/ql8/scratch", journal: { enabled: false }, wiredTiger: { engineConfig: { cacheSizeGB: 4.0 } } } }
2019-12-10T17:18:15.174-0600 I STORAGE [initandlisten] wiredtiger_open config: create,cache_size=4096M,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),
2019-12-10T17:18:15.183-0600 E STORAGE [initandlisten] WiredTiger error (2) [1576019895:183411][35093:0x2b3b85915cc0], file:WiredTiger.wt, connection: /home/ql8/scratch/WiredTiger.wt: handle-open: open: No such file or directory
2019-12-10T17:18:15.183-0600 I - [initandlisten] Assertion: 28595:2: No such file or directory src/mongo/db/storage/wiredtiger/wiredtiger_kv_engine.cpp 276
2019-12-10T17:18:15.184-0600 I STORAGE [initandlisten] exception in initAndListen: 28595 2: No such file or directory, terminating
2019-12-10T17:18:15.184-0600 I NETWORK [initandlisten] shutdown: going to close listening sockets...
2019-12-10T17:18:15.184-0600 I NETWORK [initandlisten] removing socket file: /tmp/mongodb-39001.sock
2019-12-10T17:18:15.184-0600 I NETWORK [initandlisten] shutdown: going to flush diaglog...
2019-12-10T17:18:15.184-0600 I CONTROL [initandlisten] now exiting
2019-12-10T17:18:15.184-0600 I CONTROL [initandlisten] shutting down with code:100
2019-12-10T17:18:17.250-0600 I CONTROL [initandlisten] MongoDB starting : pid=35104 port=39001 dbpath=/home/ql8/scratch 64-bit host=golubh3.campuscluster.illinois.edu
2019-12-10T17:18:17.250-0600 I CONTROL [initandlisten] db version v3.4.10-4-g67ee356c6b
2019-12-10T17:18:17.250-0600 I CONTROL [initandlisten] git version: 67ee356c6be377cda547d16423daef5beb4e8377
2019-12-10T17:18:17.250-0600 I CONTROL [initandlisten] OpenSSL version: OpenSSL 1.0.2p 14 Aug 2018
2019-12-10T17:18:17.250-0600 I CONTROL [initandlisten] allocator: tcmalloc
2019-12-10T17:18:17.250-0600 I CONTROL [initandlisten] modules: none
2019-12-10T17:18:17.250-0600 I CONTROL [initandlisten] build environment:
2019-12-10T17:18:17.250-0600 I CONTROL [initandlisten] distarch: x86_64
2019-12-10T17:18:17.250-0600 I CONTROL [initandlisten] target_arch: x86_64
2019-12-10T17:18:17.250-0600 I CONTROL [initandlisten] options: { net: { port: 39001 }, replication: { oplogSizeMB: 64, replSet: "meteor" }, storage: { dbPath: "/home/ql8/scratch", journal: { enabled: false }, wiredTiger: { engineConfig: { cacheSizeGB: 4.0 } } } }
2019-12-10T17:18:17.283-0600 I STORAGE [initandlisten] wiredtiger_open config: create,cache_size=4096M,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),
2019-12-10T17:18:17.292-0600 E STORAGE [initandlisten] WiredTiger error (2) [1576019897:292731][35104:0x2ac19f1c9cc0], file:WiredTiger.wt, connection: /home/ql8/scratch/WiredTiger.wt: handle-open: open: No such file or directory
2019-12-10T17:18:17.293-0600 I - [initandlisten] Assertion: 28595:2: No such file or directory src/mongo/db/storage/wiredtiger/wiredtiger_kv_engine.cpp 276
2019-12-10T17:18:17.293-0600 I STORAGE [initandlisten] exception in initAndListen: 28595 2: No such file or directory, terminating
2019-12-10T17:18:17.293-0600 I NETWORK [initandlisten] shutdown: going to close listening sockets...
2019-12-10T17:18:17.293-0600 I NETWORK [initandlisten] removing socket file: /tmp/mongodb-39001.sock
2019-12-10T17:18:17.293-0600 I NETWORK [initandlisten] shutdown: going to flush diaglog...
2019-12-10T17:18:17.293-0600 I CONTROL [initandlisten] now exiting
2019-12-10T17:18:17.293-0600 I CONTROL [initandlisten] shutting down with code:100
2019-12-10T17:18:20.359-0600 I CONTROL [initandlisten] MongoDB starting : pid=35112 port=39001 dbpath=/home/ql8/scratch 64-bit host=golubh3.campuscluster.illinois.edu
2019-12-10T17:18:20.359-0600 I CONTROL [initandlisten] db version v3.4.10-4-g67ee356c6b
2019-12-10T17:18:20.359-0600 I CONTROL [initandlisten] git version: 67ee356c6be377cda547d16423daef5beb4e8377
2019-12-10T17:18:20.359-0600 I CONTROL [initandlisten] OpenSSL version: OpenSSL 1.0.2p 14 Aug 2018
2019-12-10T17:18:20.359-0600 I CONTROL [initandlisten] allocator: tcmalloc
2019-12-10T17:18:20.359-0600 I CONTROL [initandlisten] modules: none
2019-12-10T17:18:20.359-0600 I CONTROL [initandlisten] build environment:
2019-12-10T17:18:20.359-0600 I CONTROL [initandlisten] distarch: x86_64
2019-12-10T17:18:20.359-0600 I CONTROL [initandlisten] target_arch: x86_64
2019-12-10T17:18:20.359-0600 I CONTROL [initandlisten] options: { net: { port: 39001 }, replication: { oplogSizeMB: 64, replSet: "meteor" }, storage: { dbPath: "/home/ql8/scratch", journal: { enabled: false }, wiredTiger: { engineConfig: { cacheSizeGB: 4.0 } } } }
2019-12-10T17:18:20.395-0600 I STORAGE [initandlisten] wiredtiger_open config: create,cache_size=4096M,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),
2019-12-10T17:18:20.404-0600 E STORAGE [initandlisten] WiredTiger error (2) [1576019900:404633][35112:0x2adf37b19cc0], file:WiredTiger.wt, connection: /home/ql8/scratch/WiredTiger.wt: handle-open: open: No such file or directory
2019-12-10T17:18:20.405-0600 I - [initandlisten] Assertion: 28595:2: No such file or directory src/mongo/db/storage/wiredtiger/wiredtiger_kv_engine.cpp 276
2019-12-10T17:18:20.405-0600 I STORAGE [initandlisten] exception in initAndListen: 28595 2: No such file or directory, terminating
2019-12-10T17:18:20.405-0600 I NETWORK [initandlisten] shutdown: going to close listening sockets...
2019-12-10T17:18:20.405-0600 I NETWORK [initandlisten] removing socket file: /tmp/mongodb-39001.sock
2019-12-10T17:18:20.405-0600 I NETWORK [initandlisten] shutdown: going to flush diaglog...
2019-12-10T17:18:20.405-0600 I CONTROL [initandlisten] now exiting
2019-12-10T17:18:20.405-0600 I CONTROL [initandlisten] shutting down with code:100
I also tried to stop it and checked by “ps -ax | grep supervisord” and made sure there’s no other cryoSPARC jobs running and then restarted it, but it still won’t start properly.
Does anyone have any idea how to fix this?
Thanks!