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Hi @jesseyoder,
Is it possible if you can provide the logs of database, command_core and command_vis?
cryosparcm log database
cryosparcm log command_core
cryosparcm log command_vis
We’ve seen issues with dependencies on CentOS before, but it seems like you’ve tried most of the solutions. I’d suggest to try installing a fresh version of cryoSPARC v2.9, and making sure ports 39000-39010 are open before you install.
cryosparcm log command_core
[cryosparc_user@Anfinsen cryosparc2_master]$ cryosparcm log command_core
Traceback (most recent call last):
File "cryosparc2_command/command_core/__init__.py", line 106, in wrapper
res = func(*args, **kwargs)
File "cryosparc2_command/command_core/__init__.py", line 372, in set_config_var
mongo.db[colname].update_one({'name' : name}, {op : {'name' : name, 'value' : value}}, upsert=True)
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/collection.py", line 890, in update_one
with self._socket_for_writes() as sock_info:
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/contextlib.py", line 17, in __enter__
return self.gen.next()
File "/home/cryosparc_user/software/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/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/topology.py", line 214, in select_server
address))
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/topology.py", line 189, in select_servers
self._error_message(selector))
ServerSelectionTimeoutError: anfinsen:39001: [Errno -2] Name or service not known
-----------------------------------------------------
[2019-06-26 11:20:35,846] ERROR in app: Exception on /startup [GET]
Traceback (most recent call last):
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/flask/app.py", line 1982, in wsgi_app
response = self.full_dispatch_request()
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/flask/app.py", line 1614, in full_dispatch_request
rv = self.handle_user_exception(e)
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/flask/app.py", line 1517, in handle_user_exception
reraise(exc_type, exc_value, tb)
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/flask/app.py", line 1612, in full_dispatch_request
rv = self.dispatch_request()
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/flask/app.py", line 1598, in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
File "cryosparc2_command/command_core/__init__.py", line 238, in startup
set_config_var('running_version', versionfile.read().strip())
File "cryosparc2_command/command_core/__init__.py", line 115, in wrapper
raise e
ServerSelectionTimeoutError: anfinsen:39001: [Errno -2] Name or service not known
[JSONRPC ERROR 2019-06-26 11:20:40.871644 at get_config_var ]
-----------------------------------------------------
Traceback (most recent call last):
File "cryosparc2_command/command_core/__init__.py", line 106, in wrapper
res = func(*args, **kwargs)
File "cryosparc2_command/command_core/__init__.py", line 350, in get_config_var
res = mongo.db[colname].find_one({'name' : name})
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/collection.py", line 1102, in find_one
for result in cursor.limit(-1):
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/cursor.py", line 1114, in next
if len(self.__data) or self._refresh():
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/cursor.py", line 1036, in _refresh
self.__collation))
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/cursor.py", line 873, in __send_message
**kwargs)
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/mongo_client.py", line 888, in _send_message_with_response
server = topology.select_server(selector)
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/topology.py", line 214, in select_server
address))
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/topology.py", line 189, in select_servers
self._error_message(selector))
ServerSelectionTimeoutError: anfinsen:39001: [Errno -2] Name or service not known
-----------------------------------------------------
[JSONRPC ERROR 2019-06-26 11:20:40.872924 at get_scheduler_lanes ]
-----------------------------------------------------
Traceback (most recent call last):
File "cryosparc2_command/command_core/__init__.py", line 106, in wrapper
res = func(*args, **kwargs)
File "cryosparc2_command/command_core/__init__.py", line 690, in get_scheduler_lanes
return get_config_var('lanes', 'sched_config', fail_notset=False, default=[])
File "cryosparc2_command/command_core/__init__.py", line 115, in wrapper
raise e
ServerSelectionTimeoutError: anfinsen:39001: [Errno -2] Name or service not known
-----------------------------------------------------
Traceback (most recent call last):
File "cryosparc2_command/command_core/__init__.py", line 175, in background_worker
scheduler_run_core() # sets last run time
File "cryosparc2_command/command_core/__init__.py", line 1215, in scheduler_run_core
lanes = get_scheduler_lanes()
File "cryosparc2_command/command_core/__init__.py", line 115, in wrapper
raise e
ServerSelectionTimeoutError: anfinsen:39001: [Errno -2] Name or service not known
Traceback (most recent call last):
File "cryosparc2_command/command_core/__init__.py", line 180, in background_worker
check_heartbeats()
File "cryosparc2_command/command_core/__init__.py", line 1373, in check_heartbeats
'heartbeat_at' : {'$lt' : deadline} }, {'project_uid' : 1, 'uid' : 1}))
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/cursor.py", line 1114, in next
if len(self.__data) or self._refresh():
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/cursor.py", line 1036, in _refresh
self.__collation))
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/cursor.py", line 873, in __send_message
**kwargs)
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/mongo_client.py", line 888, in _send_message_with_response
server = topology.select_server(selector)
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/topology.py", line 214, in select_server
address))
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/topology.py", line 189, in select_servers
self._error_message(selector))
ServerSelectionTimeoutError: anfinsen:39001: [Errno -2] Name or service not known
****** Scheduler Failed ****
****** Heartbeat check failed ****
[JSONRPC ERROR 2019-06-26 11:21:42.434804 at get_config_var ]
-----------------------------------------------------
Traceback (most recent call last):
File "cryosparc2_command/command_core/__init__.py", line 106, in wrapper
res = func(*args, **kwargs)
File "cryosparc2_command/command_core/__init__.py", line 350, in get_config_var
res = mongo.db[colname].find_one({'name' : name})
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/collection.py", line 1102, in find_one
for result in cursor.limit(-1):
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/cursor.py", line 1114, in next
if len(self.__data) or self._refresh():
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/cursor.py", line 1036, in _refresh
self.__collation))
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/cursor.py", line 873, in __send_message
**kwargs)
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/mongo_client.py", line 888, in _send_message_with_response
server = topology.select_server(selector)
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/topology.py", line 214, in select_server
address))
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/topology.py", line 189, in select_servers
self._error_message(selector))
ServerSelectionTimeoutError: anfinsen:39001: [Errno -2] Name or service not known
-----------------------------------------------------
[JSONRPC ERROR 2019-06-26 11:21:42.435358 at get_scheduler_lanes ]
-----------------------------------------------------
Traceback (most recent call last):
File "cryosparc2_command/command_core/__init__.py", line 106, in wrapper
res = func(*args, **kwargs)
File "cryosparc2_command/command_core/__init__.py", line 690, in get_scheduler_lanes
return get_config_var('lanes', 'sched_config', fail_notset=False, default=[])
File "cryosparc2_command/command_core/__init__.py", line 115, in wrapper
raise e
ServerSelectionTimeoutError: anfinsen:39001: [Errno -2] Name or service not known
-----------------------------------------------------
Traceback (most recent call last):
File "cryosparc2_command/command_core/__init__.py", line 175, in background_worker
scheduler_run_core() # sets last run time
File "cryosparc2_command/command_core/__init__.py", line 1215, in scheduler_run_core
lanes = get_scheduler_lanes()
File "cryosparc2_command/command_core/__init__.py", line 115, in wrapper
raise e
ServerSelectionTimeoutError: anfinsen:39001: [Errno -2] Name or service not known
Traceback (most recent call last):
File "cryosparc2_command/command_core/__init__.py", line 180, in background_worker
check_heartbeats()
File "cryosparc2_command/command_core/__init__.py", line 1373, in check_heartbeats
'heartbeat_at' : {'$lt' : deadline} }, {'project_uid' : 1, 'uid' : 1}))
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/cursor.py", line 1114, in next
if len(self.__data) or self._refresh():
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/cursor.py", line 1036, in _refresh
self.__collation))
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/cursor.py", line 873, in __send_message
**kwargs)
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/mongo_client.py", line 888, in _send_message_with_response
server = topology.select_server(selector)
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/topology.py", line 214, in select_server
address))
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/topology.py", line 189, in select_servers
self._error_message(selector))
ServerSelectionTimeoutError: anfinsen:39001: [Errno -2] Name or service not known
****** Scheduler Failed ****
****** Heartbeat check failed ****
[JSONRPC ERROR 2019-06-26 11:22:43.814760 at get_config_var ]
-----------------------------------------------------
Traceback (most recent call last):
File "cryosparc2_command/command_core/__init__.py", line 106, in wrapper
res = func(*args, **kwargs)
File "cryosparc2_command/command_core/__init__.py", line 350, in get_config_var
res = mongo.db[colname].find_one({'name' : name})
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/collection.py", line 1102, in find_one
for result in cursor.limit(-1):
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/cursor.py", line 1114, in next
if len(self.__data) or self._refresh():
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/cursor.py", line 1036, in _refresh
self.__collation))
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/cursor.py", line 873, in __send_message
**kwargs)
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/mongo_client.py", line 888, in _send_message_with_response
server = topology.select_server(selector)
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/topology.py", line 214, in select_server
address))
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/topology.py", line 189, in select_servers
self._error_message(selector))
ServerSelectionTimeoutError: anfinsen:39001: [Errno -2] Name or service not known
-----------------------------------------------------
[JSONRPC ERROR 2019-06-26 11:22:43.815348 at get_scheduler_lanes ]
-----------------------------------------------------
Traceback (most recent call last):
File "cryosparc2_command/command_core/__init__.py", line 106, in wrapper
res = func(*args, **kwargs)
File "cryosparc2_command/command_core/__init__.py", line 690, in get_scheduler_lanes
return get_config_var('lanes', 'sched_config', fail_notset=False, default=[])
File "cryosparc2_command/command_core/__init__.py", line 115, in wrapper
raise e
ServerSelectionTimeoutError: anfinsen:39001: [Errno -2] Name or service not known
-----------------------------------------------------
Traceback (most recent call last):
File "cryosparc2_command/command_core/__init__.py", line 175, in background_worker
scheduler_run_core() # sets last run time
File "cryosparc2_command/command_core/__init__.py", line 1215, in scheduler_run_core
lanes = get_scheduler_lanes()
File "cryosparc2_command/command_core/__init__.py", line 115, in wrapper
raise e
ServerSelectionTimeoutError: anfinsen:39001: [Errno -2] Name or service not known
Traceback (most recent call last):
File "cryosparc2_command/command_core/__init__.py", line 180, in background_worker
check_heartbeats()
File "cryosparc2_command/command_core/__init__.py", line 1373, in check_heartbeats
'heartbeat_at' : {'$lt' : deadline} }, {'project_uid' : 1, 'uid' : 1}))
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/cursor.py", line 1114, in next
if len(self.__data) or self._refresh():
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/cursor.py", line 1036, in _refresh
self.__collation))
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/cursor.py", line 873, in __send_message
**kwargs)
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/mongo_client.py", line 888, in _send_message_with_response
server = topology.select_server(selector)
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/topology.py", line 214, in select_server
address))
File "/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/topology.py", line 189, in select_servers
self._error_message(selector))
ServerSelectionTimeoutError: anfinsen:39001: [Errno -2] Name or service not known
****** Scheduler Failed ****
****** Heartbeat check failed ****Problem resolved!
The hostname (Anfinsen) was not listed in /etc/hosts. After adding the name to 127.0.0.1 I was able to start cryosparc successfully.
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