Mongod (spawn error)

jflanagan01 · May 30, 2017, 3:29pm

Hi
I have been unable to get cryosparc to start mongod. It not clear what is happening.Traceback (most recent call last):
File “”, line 1, in
File “/srv/home/johnf/cryosparc/anaconda2/lib/python2.7/site-packages/pymongo/mongo_client.py”, line 1088, in database_names
“listDatabases”)[“databases”]]
File “/srv/home/johnf/cryosparc/anaconda2/lib/python2.7/site-packages/pymongo/database.py”, line 478, in command
with client._socket_for_reads(read_preference) as (sock_info, slave_ok):
File “/srv/home/johnf/cryosparc/anaconda2/lib/python2.7/contextlib.py”, line 17, in enter
return self.gen.next()
File “/srv/home/johnf/cryosparc/anaconda2/lib/python2.7/site-packages/pymongo/mongo_client.py”, line 798, in _socket_for_reads
with self._get_socket(read_preference) as sock_info:
File “/srv/home/johnf/cryosparc/anaconda2/lib/python2.7/contextlib.py”, line 17, in enter
return self.gen.next()
File “/srv/home/johnf/cryosparc/anaconda2/lib/python2.7/site-packages/pymongo/mongo_client.py”, line 762, in _get_socket
server = self._get_topology().select_server(selector)
File “/srv/home/johnf/cryosparc/anaconda2/lib/python2.7/site-packages/pymongo/topology.py”, line 210, in select_server
address))
File “/srv/home/johnf/cryosparc/anaconda2/lib/python2.7/site-packages/pymongo/topology.py”, line 186, in select_servers
self._error_message(selector))
pymongo.errors.ServerSelectionTimeoutError: localhost:38001: [Errno 111] Connection refused

Any thoughts?

apunjani · May 30, 2017, 4:22pm

Hi @jflanagan01,

At what point do you see this error? Is this after calling cryosparc start?
What does cryosparc status report as the status of the mongod process?
Are there any errors reported in the cryosparc/run/mongod.stdout log file?

Thanks,
Ali

jflanagan01 · May 30, 2017, 4:26pm

Yes, just after I do cryosparc start. The cryosparc is looking at the port but no mongod running.

jflanagan01 · May 30, 2017, 4:30pm

2017-05-30T11:25:41.196-0400 I CONTROL [initandlisten] build environment:
2017-05-30T11:25:41.196-0400 I CONTROL [initandlisten] distarch: x86_64
2017-05-30T11:25:41.196-0400 I CONTROL [initandlisten] target_arch: x86_64
2017-05-30T11:25:41.196-0400 I CONTROL [initandlisten] options: { net: { port: 38001 }, replication: { oplogSizeMB: 64, replSet: “meteor” }, storage: { dbPath: “/srv/home/johnf/cryosparc/run/db”, journal: { enabled: false } } }
2017-05-30T11:25:41.220-0400 I - [initandlisten] Detected data files in /srv/home/johnf/cryosparc/run/db created by the ‘wiredTiger’ storage engine, so setting the active storage engine to ‘wiredTiger’.
2017-05-30T11:25:41.220-0400 I STORAGE [initandlisten] wiredtiger_open config: create,cache_size=74G,session_max=20000,eviction=(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),
2017-05-30T11:25:41.226-0400 E STORAGE [initandlisten] WiredTiger (13) [1496157941:226691][1479:0x7fb07318dcc0], file:WiredTiger.wt, connection: /srv/home/johnf/cryosparc/run/db/WiredTiger.turtle: handle-open: open: Permission denied
2017-05-30T11:25:41.227-0400 I - [initandlisten] Assertion: 28595:13: Permission denied
2017-05-30T11:25:41.227-0400 I STORAGE [initandlisten] exception in initAndListen: 28595 13: Permission denied, terminating
2017-05-30T11:25:41.227-0400 I CONTROL [initandlisten] dbexit: rc: 100
johnf@dilbert:~$ tail -100 cryosparc/run/mongod.stdout
2017-05-30T11:24:09.451-0400 I CONTROL [initandlisten] build environment:
2017-05-30T11:24:09.451-0400 I CONTROL [initandlisten] distarch: x86_64
2017-05-30T11:24:09.451-0400 I CONTROL [initandlisten] target_arch: x86_64
2017-05-30T11:24:09.451-0400 I CONTROL [initandlisten] options: { net: { port: 38001 }, replication: { oplogSizeMB: 64, replSet: “meteor” }, storage: { dbPath: “/srv/home/johnf/cryosparc/run/db”, journal: { enabled: false } } }
2017-05-30T11:24:09.475-0400 I - [initandlisten] Detected data files in /srv/home/johnf/cryosparc/run/db created by the ‘wiredTiger’ storage engine, so setting the active storage engine to ‘wiredTiger’.
2017-05-30T11:24:09.475-0400 I STORAGE [initandlisten] wiredtiger_open config: create,cache_size=74G,session_max=20000,eviction=(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),
2017-05-30T11:24:09.481-0400 E STORAGE [initandlisten] WiredTiger (13) [1496157849:481439][1371:0x7f6e3868fcc0], file:WiredTiger.wt, connection: /srv/home/johnf/cryosparc/run/db/WiredTiger.turtle: handle-open: open: Permission denied
2017-05-30T11:24:09.481-0400 I - [initandlisten] Assertion: 28595:13: Permission denied
2017-05-30T11:24:09.481-0400 I STORAGE [initandlisten] exception in initAndListen: 28595 13: Permission denied, terminating
2017-05-30T11:24:09.481-0400 I CONTROL [initandlisten] dbexit: rc: 100
2017-05-30T11:24:11.512-0400 I CONTROL [initandlisten] MongoDB starting : pid=1377 port=38001 dbpath=/srv/home/johnf/cryosparc/run/db 64-bit host=dilbert
2017-05-30T11:24:11.512-0400 I CONTROL [initandlisten] db version v3.2.9
2017-05-30T11:24:11.512-0400 I CONTROL [initandlisten] git version: 22ec9e93b40c85fc7cae7d56e7d6a02fd811088c
2017-05-30T11:24:11.512-0400 I CONTROL [initandlisten] allocator: tcmalloc
2017-05-30T11:24:11.512-0400 I CONTROL [initandlisten] modules: none
2017-05-30T11:24:11.512-0400 I CONTROL [initandlisten] build environment:
2017-05-30T11:24:11.512-0400 I CONTROL [initandlisten] distarch: x86_64
2017-05-30T11:24:11.512-0400 I CONTROL [initandlisten] target_arch: x86_64
2017-05-30T11:24:11.512-0400 I CONTROL [initandlisten] options: { net: { port: 38001 }, replication: { oplogSizeMB: 64, replSet: “meteor” }, storage: { dbPath: “/srv/home/johnf/cryosparc/run/db”, journal: { enabled: false } } }
2017-05-30T11:24:11.536-0400 I - [initandlisten] Detected data files in /srv/home/johnf/cryosparc/run/db created by the ‘wiredTiger’ storage engine, so setting the active storage engine to ‘wiredTiger’.
2017-05-30T11:24:11.536-0400 I STORAGE [initandlisten] wiredtiger_open config: create,cache_size=74G,session_max=20000,eviction=(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),
2017-05-30T11:24:11.543-0400 E STORAGE [initandlisten] WiredTiger (13) [1496157851:543845][1377:0x7f12ee9e3cc0], file:WiredTiger.wt, connection: /srv/home/johnf/cryosparc/run/db/WiredTiger.turtle: handle-open: open: Permission denied
2017-05-30T11:24:11.544-0400 I - [initandlisten] Assertion: 28595:13: Permission denied
2017-05-30T11:24:11.544-0400 I STORAGE [initandlisten] exception in initAndListen: 28595 13: Permission denied, terminating
2017-05-30T11:24:11.544-0400 I CONTROL [initandlisten] dbexit: rc: 100
2017-05-30T11:24:14.574-0400 I CONTROL [initandlisten] MongoDB starting : pid=1379 port=38001 dbpath=/srv/home/johnf/cryosparc/run/db 64-bit host=dilbert
2017-05-30T11:24:14.574-0400 I CONTROL [initandlisten] db version v3.2.9
2017-05-30T11:24:14.574-0400 I CONTROL [initandlisten] git version: 22ec9e93b40c85fc7cae7d56e7d6a02fd811088c
2017-05-30T11:24:14.574-0400 I CONTROL [initandlisten] allocator: tcmalloc
2017-05-30T11:24:14.574-0400 I CONTROL [initandlisten] modules: none
2017-05-30T11:24:14.574-0400 I CONTROL [initandlisten] build environment:
2017-05-30T11:24:14.574-0400 I CONTROL [initandlisten] distarch: x86_64
2017-05-30T11:24:14.574-0400 I CONTROL [initandlisten] target_arch: x86_64
2017-05-30T11:24:14.574-0400 I CONTROL [initandlisten] options: { net: { port: 38001 }, replication: { oplogSizeMB: 64, replSet: “meteor” }, storage: { dbPath: “/srv/home/johnf/cryosparc/run/db”, journal: { enabled: false } } }
2017-05-30T11:24:14.598-0400 I - [initandlisten] Detected data files in /srv/home/johnf/cryosparc/run/db created by the ‘wiredTiger’ storage engine, so setting the active storage engine to ‘wiredTiger’.
2017-05-30T11:24:14.598-0400 I STORAGE [initandlisten] wiredtiger_open config: create,cache_size=74G,session_max=20000,eviction=(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),
2017-05-30T11:24:14.605-0400 E STORAGE [initandlisten] WiredTiger (13) [1496157854:605538][1379:0x7f62d32facc0], file:WiredTiger.wt, connection: /srv/home/johnf/cryosparc/run/db/WiredTiger.turtle: handle-open: open: Permission denied
2017-05-30T11:24:14.605-0400 I - [initandlisten] Assertion: 28595:13: Permission denied
2017-05-30T11:24:14.606-0400 I STORAGE [initandlisten] exception in initAndListen: 28595 13: Permission denied, terminating
2017-05-30T11:24:14.606-0400 I CONTROL [initandlisten] dbexit: rc: 100
2017-05-30T11:25:35.020-0400 I CONTROL [initandlisten] MongoDB starting : pid=1469 port=38001 dbpath=/srv/home/johnf/cryosparc/run/db 64-bit host=dilbert
2017-05-30T11:25:35.020-0400 I CONTROL [initandlisten] db version v3.2.9
2017-05-30T11:25:35.020-0400 I CONTROL [initandlisten] git version: 22ec9e93b40c85fc7cae7d56e7d6a02fd811088c
2017-05-30T11:25:35.020-0400 I CONTROL [initandlisten] allocator: tcmalloc
2017-05-30T11:25:35.020-0400 I CONTROL [initandlisten] modules: none
2017-05-30T11:25:35.020-0400 I CONTROL [initandlisten] build environment:
2017-05-30T11:25:35.020-0400 I CONTROL [initandlisten] distarch: x86_64
2017-05-30T11:25:35.020-0400 I CONTROL [initandlisten] target_arch: x86_64
2017-05-30T11:25:35.020-0400 I CONTROL [initandlisten] options: { net: { port: 38001 }, replication: { oplogSizeMB: 64, replSet: “meteor” }, storage: { dbPath: “/srv/home/johnf/cryosparc/run/db”, journal: { enabled: false } } }
2017-05-30T11:25:35.043-0400 I - [initandlisten] Detected data files in /srv/home/johnf/cryosparc/run/db created by the ‘wiredTiger’ storage engine, so setting the active storage engine to ‘wiredTiger’.
2017-05-30T11:25:35.043-0400 I STORAGE [initandlisten] wiredtiger_open config: create,cache_size=74G,session_max=20000,eviction=(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),
2017-05-30T11:25:35.049-0400 E STORAGE [initandlisten] WiredTiger (13) [1496157935:49583][1469:0x7fdc16840cc0], file:WiredTiger.wt, connection: /srv/home/johnf/cryosparc/run/db/WiredTiger.turtle: handle-open: open: Permission denied
2017-05-30T11:25:35.049-0400 I - [initandlisten] Assertion: 28595:13: Permission denied
2017-05-30T11:25:35.049-0400 I STORAGE [initandlisten] exception in initAndListen: 28595 13: Permission denied, terminating
2017-05-30T11:25:35.049-0400 I CONTROL [initandlisten] dbexit: rc: 100
2017-05-30T11:25:36.077-0400 I CONTROL [initandlisten] MongoDB starting : pid=1475 port=38001 dbpath=/srv/home/johnf/cryosparc/run/db 64-bit host=dilbert
2017-05-30T11:25:36.077-0400 I CONTROL [initandlisten] db version v3.2.9
2017-05-30T11:25:36.077-0400 I CONTROL [initandlisten] git version: 22ec9e93b40c85fc7cae7d56e7d6a02fd811088c
2017-05-30T11:25:36.077-0400 I CONTROL [initandlisten] allocator: tcmalloc
2017-05-30T11:25:36.077-0400 I CONTROL [initandlisten] modules: none
2017-05-30T11:25:36.077-0400 I CONTROL [initandlisten] build environment:
2017-05-30T11:25:36.077-0400 I CONTROL [initandlisten] distarch: x86_64
2017-05-30T11:25:36.077-0400 I CONTROL [initandlisten] target_arch: x86_64
2017-05-30T11:25:36.077-0400 I CONTROL [initandlisten] options: { net: { port: 38001 }, replication: { oplogSizeMB: 64, replSet: “meteor” }, storage: { dbPath: “/srv/home/johnf/cryosparc/run/db”, journal: { enabled: false } } }
2017-05-30T11:25:36.100-0400 I - [initandlisten] Detected data files in /srv/home/johnf/cryosparc/run/db created by the ‘wiredTiger’ storage engine, so setting the active storage engine to ‘wiredTiger’.
2017-05-30T11:25:36.100-0400 I STORAGE [initandlisten] wiredtiger_open config: create,cache_size=74G,session_max=20000,eviction=(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),
2017-05-30T11:25:36.108-0400 E STORAGE [initandlisten] WiredTiger (13) [1496157936:108353][1475:0x7f504540ecc0], file:WiredTiger.wt, connection: /srv/home/johnf/cryosparc/run/db/WiredTiger.turtle: handle-open: open: Permission denied
2017-05-30T11:25:36.108-0400 I - [initandlisten] Assertion: 28595:13: Permission denied
2017-05-30T11:25:36.108-0400 I STORAGE [initandlisten] exception in initAndListen: 28595 13: Permission denied, terminating
2017-05-30T11:25:36.108-0400 I CONTROL [initandlisten] dbexit: rc: 100
2017-05-30T11:25:38.137-0400 I CONTROL [initandlisten] MongoDB starting : pid=1477 port=38001 dbpath=/srv/home/johnf/cryosparc/run/db 64-bit host=dilbert
2017-05-30T11:25:38.137-0400 I CONTROL [initandlisten] db version v3.2.9
2017-05-30T11:25:38.137-0400 I CONTROL [initandlisten] git version: 22ec9e93b40c85fc7cae7d56e7d6a02fd811088c
2017-05-30T11:25:38.137-0400 I CONTROL [initandlisten] allocator: tcmalloc
2017-05-30T11:25:38.137-0400 I CONTROL [initandlisten] modules: none
2017-05-30T11:25:38.137-0400 I CONTROL [initandlisten] build environment:
2017-05-30T11:25:38.137-0400 I CONTROL [initandlisten] distarch: x86_64
2017-05-30T11:25:38.137-0400 I CONTROL [initandlisten] target_arch: x86_64
2017-05-30T11:25:38.137-0400 I CONTROL [initandlisten] options: { net: { port: 38001 }, replication: { oplogSizeMB: 64, replSet: “meteor” }, storage: { dbPath: “/srv/home/johnf/cryosparc/run/db”, journal: { enabled: false } } }
2017-05-30T11:25:38.160-0400 I - [initandlisten] Detected data files in /srv/home/johnf/cryosparc/run/db created by the ‘wiredTiger’ storage engine, so setting the active storage engine to ‘wiredTiger’.
2017-05-30T11:25:38.160-0400 I STORAGE [initandlisten] wiredtiger_open config: create,cache_size=74G,session_max=20000,eviction=(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),
2017-05-30T11:25:38.167-0400 E STORAGE [initandlisten] WiredTiger (13) [1496157938:167678][1477:0x7f2c48617cc0], file:WiredTiger.wt, connection: /srv/home/johnf/cryosparc/run/db/WiredTiger.turtle: handle-open: open: Permission denied
2017-05-30T11:25:38.168-0400 I - [initandlisten] Assertion: 28595:13: Permission denied
2017-05-30T11:25:38.168-0400 I STORAGE [initandlisten] exception in initAndListen: 28595 13: Permission denied, terminating
2017-05-30T11:25:38.168-0400 I CONTROL [initandlisten] dbexit: rc: 100
2017-05-30T11:25:41.196-0400 I CONTROL [initandlisten] MongoDB starting : pid=1479 port=38001 dbpath=/srv/home/johnf/cryosparc/run/db 64-bit host=dilbert
2017-05-30T11:25:41.196-0400 I CONTROL [initandlisten] db version v3.2.9
2017-05-30T11:25:41.196-0400 I CONTROL [initandlisten] git version: 22ec9e93b40c85fc7cae7d56e7d6a02fd811088c
2017-05-30T11:25:41.196-0400 I CONTROL [initandlisten] allocator: tcmalloc
2017-05-30T11:25:41.196-0400 I CONTROL [initandlisten] modules: none
2017-05-30T11:25:41.196-0400 I CONTROL [initandlisten] build environment:
2017-05-30T11:25:41.196-0400 I CONTROL [initandlisten] distarch: x86_64
2017-05-30T11:25:41.196-0400 I CONTROL [initandlisten] target_arch: x86_64
2017-05-30T11:25:41.196-0400 I CONTROL [initandlisten] options: { net: { port: 38001 }, replication: { oplogSizeMB: 64, replSet: “meteor” }, storage: { dbPath: “/srv/home/johnf/cryosparc/run/db”, journal: { enabled: false } } }
2017-05-30T11:25:41.220-0400 I - [initandlisten] Detected data files in /srv/home/johnf/cryosparc/run/db created by the ‘wiredTiger’ storage engine, so setting the active storage engine to ‘wiredTiger’.
2017-05-30T11:25:41.220-0400 I STORAGE [initandlisten] wiredtiger_open config: create,cache_size=74G,session_max=20000,eviction=(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),
2017-05-30T11:25:41.226-0400 E STORAGE [initandlisten] WiredTiger (13) [1496157941:226691][1479:0x7fb07318dcc0], file:WiredTiger.wt, connection: /srv/home/johnf/cryosparc/run/db/WiredTiger.turtle: handle-open: open: Permission denied
2017-05-30T11:25:41.227-0400 I - [initandlisten] Assertion: 28595:13: Permission denied
2017-05-30T11:25:41.227-0400 I STORAGE [initandlisten] exception in initAndListen: 28595 13:

jflanagan01 · May 30, 2017, 4:32pm

Running CryoSPARC Tool at /srv/home/johnf/cryosparc
Current cryoSPARC version: v0.4.0

Process status:

meteor STOPPED Not started
mongod FATAL Exited too quickly (process log may have details)
webapp STOPPED Not started

Config variables:

CUDA Setup

export PATH="/usr/local/cuda/bin":$PATH
export LD_LIBRARY_PATH="/usr/local/cuda/lib64":$LD_LIBRARY_PATH

export PYTHONPATH=""

export CRYOSPARC_ROOT_DIR="/srv/home/johnf/cryosparc"
export CRYOSPARC_LICENSE_ID=“xxxx”
export CRYOSPARC_REGISTER_DONE=true
export CRYOSPARC_METEOR_BINDIR=""
export CRYOSPARC_NODEJS_BINDIR="/srv/home/johnf/cryosparc/nodejs/bin"
export CRYOSPARC_MONGODB_BINDIR="/srv/home/johnf/cryosparc/mongodb/bin"
export CRYOSPARC_ANACONDA_BINDIR="/srv/home/johnf/cryosparc/anaconda2/bin"
export CRYOSPARC_HTTP_PORT=38000
export CRYOSPARC_MONGO_PORT=38001
export CRYOSPARC_MASTER_HOSTNAME=“dilbert.med.virginia.edu”
export CRYOSPARC_INSTALL_TYPE=master
export CRYOSPARC_DEVELOP=false
export METEOR_SETTINGS="{“public”:{“webinstance”:false, “instancename”:“dilbert.med.virginia.edu”, “instancetype”:“academicbeta”}}"
export CRYOSPARC_SUPERVISOR_SOCK_FILE=/tmp/supervisor-8694678123667752252.sock

export CRYOSPARC_CACHE_CUSHION=10240.0
export CRYOSPARC_CUDA_DEVS=“0,1”
export CRYOSPARC_RAM_SLOTS=“16”

export CRYOSPARC_RESULTS_MIGRATION_DONE=true

apunjani · May 31, 2017, 4:27am

Hi @jflanagan01,

Thanks for reporting further.
It looks like there is a permissions issue with the database files - any chance you’re running cryoSPARC as a user other than the user that installed it?
Can you check with ls -l that the files inside /srv/home/johnf/cryosparc/run/db are all owned/writable by the current user?

Ali

jflanagan01 · May 31, 2017, 1:04pm

Hi
I was the user that installed it on dilbert. This has been a problem on the other two installations in the lab. I will take a look at it more closely. What I did notice is that things were pointing to Ali’s home directory, one of the other users, and that had given a problem before this issue. There are only two files not owned by johnf, WiredTigerLAS.wt and WiredTiger.Turtle. Interesting names, these are assigned to root. One question, I set up this installation and ran previously on a different disk, but since the current data is on a the /srv/cluster/johnf disk could that be the problem. There are cryrosparc files on my other disk /d3/johnf and that was where things were set up. My guess is that Ali started his cryosparc runs from data on /srv/cluster/ali. Assuming that this is the problem, is there any way around this?

Cheers
John

ms4392 · September 22, 2017, 12:22am

Hi I have the same mongod ERROR (spawn error) here. I tried the following things. However, neither worked. Any inputs are much appreciated. (1) restarted the computer, (2) restarted cryosparc (3) make sure folder is accessbile to my own account as well as cryosparc account (4) the port (Centos7) is correct (5) updated cryosparc to the latest version & previous version. Many thanks in advance

jianhaoc · October 19, 2017, 2:20am

I have similar problem, But when I check the mongod.stdout, it seems the problem of run/db/mongod.lock
I deleted the mongod.lock, but still failed. Someone suggested me to change the path to mongod.lock, but I don’t know the way to change that.

Any other way to solved that? Thanks!

mongod.stdout:

2017-10-17T19:46:46.120+0800 I CONTROL [initandlisten] MongoDB starting : pid=12933 port=38001 dbpath=/home/jianhaoc/s/cs/run/db 64-bit host=brain4
2017-10-17T19:46:46.120+0800 I CONTROL [initandlisten] db version v3.2.9
2017-10-17T19:46:46.120+0800 I CONTROL [initandlisten] git version: 22ec9e93b40c85fc7cae7d56e7d6a02fd811088c
2017-10-17T19:46:46.120+0800 I CONTROL [initandlisten] allocator: tcmalloc
2017-10-17T19:46:46.120+0800 I CONTROL [initandlisten] modules: none
2017-10-17T19:46:46.120+0800 I CONTROL [initandlisten] build environment:
2017-10-17T19:46:46.120+0800 I CONTROL [initandlisten] distarch: x86_64
2017-10-17T19:46:46.120+0800 I CONTROL [initandlisten] target_arch: x86_64
2017-10-17T19:46:46.120+0800 I CONTROL [initandlisten] options: { net: { port: 38001 }, replication: { oplogSizeMB: 64, replSet: “meteor” }, storage: { dbPath: “/home/jianhaoc/s/cs/run/db”, journal: { enabled: false } } }
2017-10-17T19:46:46.152+0800 I STORAGE [initandlisten] exception in initAndListen: 98 Unable to lock file: /home/jianhaoc/s/cs/run/db/mongod.lock errno:38 Function not implemented. Is a mongod instance already running?, terminating
2017-10-17T19:46:46.153+0800 I CONTROL [initandlisten] dbexit: rc: 100

ScarabMonkey · March 16, 2018, 11:42am

I had exactly this problem because someone had accidentally run cryosparc as root!
'Chown’ed everything in the installation directory and now sorted.

rdrighetto · August 15, 2018, 10:13am

This fixed it for me too. Thanks for sharing!

spunjani · October 11, 2018, 7:48pm