Dear all,
We recently rebuilt our machines with CUDA 10.1 and Ubuntu 20.04 and I have redownloaded and reinstalled cryosparc.
The installation went smoothly, but I have encountered this error when I start/restart cryosparcm:
CryoSPARC is not already running.
database: ERROR (spawn error)
Traceback (most recent call last):
File “”, line 1, in
File “/home/esrf/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/mongo_client.py”, line 1149, in database_names
“listDatabases”)[“databases”]]
File “/home/esrf/cryosparc/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 “/home/esrf/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/contextlib.py”, line 17, in enter
return self.gen.next()
File “/home/esrf/cryosparc/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 “/home/esrf/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/contextlib.py”, line 17, in enter
return self.gen.next()
File “/home/esrf/cryosparc/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 “/home/esrf/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/topology.py”, line 214, in select_server
address))
File “/home/esrf/cryosparc/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 refused
I have been reading the topics on this matter and have deleted the /tmp .sock file checked that there are no zombie processes.
The command cryosparcm log database gives me this:
cryosparcm log database
2020-10-29T13:07:24.163+0100 I STORAGE [initandlisten] exception in initAndListen: 98 Unable to lock file: /home/esrf/cryosparc/database/mongod.lock Resource temporarily unavailable. Is a mongod instance already running?, terminating
2020-10-29T13:07:24.163+0100 I NETWORK [initandlisten] shutdown: going to close listening sockets…
2020-10-29T13:07:24.163+0100 I NETWORK [initandlisten] shutdown: going to flush diaglog…
2020-10-29T13:07:24.163+0100 I CONTROL [initandlisten] now exiting
2020-10-29T13:07:24.163+0100 I CONTROL [initandlisten] shutting down with code:100
2020-10-29T13:07:27.241+0100 I CONTROL [initandlisten] MongoDB starting : pid=3068559 port=39001 dbpath=/home/esrf/cryosparc/database 64-bit host=cmproc1
2020-10-29T13:07:27.241+0100 I CONTROL [initandlisten] db version v3.4.10-4-g67ee356c6b
2020-10-29T13:07:27.241+0100 I CONTROL [initandlisten] git version: 67ee356c6be377cda547d16423daef5beb4e8377
2020-10-29T13:07:27.241+0100 I CONTROL [initandlisten] OpenSSL version: OpenSSL 1.0.2p 14 Aug 2018
2020-10-29T13:07:27.241+0100 I CONTROL [initandlisten] allocator: tcmalloc
2020-10-29T13:07:27.241+0100 I CONTROL [initandlisten] modules: none
2020-10-29T13:07:27.241+0100 I CONTROL [initandlisten] build environment:
2020-10-29T13:07:27.241+0100 I CONTROL [initandlisten] distarch: x86_64
2020-10-29T13:07:27.241+0100 I CONTROL [initandlisten] target_arch: x86_64
2020-10-29T13:07:27.241+0100 I CONTROL [initandlisten] options: { net: { port: 39001 }, replication: { oplogSizeMB: 64, replSet: “meteor” }, storage: { dbPath: “/home/esrf/cryosparc/database”, journal: { enabled: false }, wiredTiger: { engineConfig: { cacheSizeGB: 4.0 } } } }
How can I get the program up and running again?
Thank you very much in advance,
David