when i install cryosparc(not the first time), i can’t start service,there is install information, thanks!
dd@dong:~/cc2/cryosparc_master$ ./install.sh --standalone --license $–worker_path /home/dd/cc2/cryosparc_worker --cudapath /usr/local/cuda --ssdpath /home/dd --initial_email "@.edu.cn" --initial_password “00000000000” --initial_username “" --initial_firstname "" --initial_lastname "” --port 61000
************ CRYOSPARC SYSTEM: MASTER INSTALLER **************
Installation Settings:
License ID : **
Root Directory : /home/dd/cc2/cryosparc_master
Master Hostname : dong.lan
Database Directory : /home/dd/cc2/cryosparc_database
Base HTTP Port Number : 61000
Developer Install : false
Operating System : Linux
Insecure Install : false
Standalone Install : true
Worker Root Directory : /home/dd/cc2/cryosparc_worker
Initial User Email : **
Initial User Password : **
Initial User Name : **
Initial First Name : **
Initial Last Name : **
CUDA Path : /usr/local/cuda
SSD : true
SSD Path : /home/dd
Version : v3.2.0
The cryoSPARC System master installation will host a database,
web application, and command layer for cryoSPARC, but will not
perform processing jobs.
Please read and confirm the above settings. The cryoSPARC database
will be stored at the database directory which is relative to the
root directory, unless provided as an absolute path.
You can change the database directory now by passing the --dbapth
parameter to this installer, or later via the command line.
Are the above settings correct?
- Yes
- No
#? 1
Continuing.
Setting up hard-coded config.sh environment variables
Installing all dependencies.
Checking dependencies…
Dependencies for python have not changed.
Currently checking hash for mongodb
Dependencies for mongodb have not changed.
Completed dependency check.
************ CRYOSPARC MASTER INSTALLATION COMPLETE **************
CryoSPARC System master has now been installed.
Add bin directory to your ~/.bashrc ?
- Yes
- No
#? 1
The following lines were appended to your ~/.bashrc:
export PATH=/home/dd/cc2/cryosparc_master/bin:$PATH
************ CRYOSPARC SYSTEM: STANDALONE INSTALLER **************
The installer will now download, install and connect the worker
package on this machine. The worker package will allow cryoSPARC
to run compute jobs.
Starting cryoSPARC…
Starting cryoSPARC System master process…
CryoSPARC is not already running.
database: started
command_core: started
run_old(*args, **kw)
File “/home/dd/cc2/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/threading.py”, line 870, in run
self._target(*self._args, **self._kwargs)
File “/home/dd/cc2/cryosparc_master/cryosparc_command/command_core/init.py”, line 208, in background_worker
last_audit_date = get_config_var(‘audit’, fail_notset=False, default={})
File “/home/dd/cc2/cryosparc_master/cryosparc_command/command_core/init.py”, line 140, in wrapper
raise e
File “/home/dd/cc2/cryosparc_master/cryosparc_command/command_core/init.py”, line 131, in wrapper
res = func(*args, **kwargs)
File “/home/dd/cc2/cryosparc_master/cryosparc_command/command_core/init.py”, line 550, in get_config_var
res = mongo.db[colname].find_one({‘name’ : name})
File “/home/dd/cc2/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/collection.py”, line 1319, in find_one
for result in cursor.limit(-1):
File “/home/dd/cc2/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/cursor.py”, line 1207, in next
if len(self.__data) or self._refresh():
File “/home/dd/cc2/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/cursor.py”, line 1124, in _refresh
self.__send_message(q)
File “/home/dd/cc2/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/cursor.py”, line 1001, in __send_message
address=self.__address)
File “/home/dd/cc2/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/mongo_client.py”, line 1372, in _run_operation_with_response
exhaust=exhaust)
File “/home/dd/cc2/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/mongo_client.py”, line 1471, in _retryable_read
return func(session, server, sock_info, slave_ok)
File “/home/dd/cc2/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/mongo_client.py”, line 1366, in _cmd
unpack_res)
File “/home/dd/cc2/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/server.py”, line 137, in run_operation_with_response
first, sock_info.max_wire_version)
File “/home/dd/cc2/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/helpers.py”, line 140, in _check_command_response
raise NotMasterError(errmsg, response)
pymongo.errors.NotMasterError: node is not in primary or recovering state, full error: {‘ok’: 0.0, ‘errmsg’: ‘node is not in primary or recovering state’, ‘code’: 13436, ‘codeName’: ‘NotMasterOrSecondary’}
COMMAND CORE STARTED === 2021-10-07 00:52:22.222267 ==========================
*** BG WORKER START
- Serving Flask app “command_core” (lazy loading)
- Environment: production
WARNING: This is a development server. Do not use it in a production deployment.
Use a production WSGI server instead. - Debug mode: off
[JSONRPC ERROR 2021-10-07 00:52:27.233927 at get_config_var ]
Traceback (most recent call last):
File “/home/dd/cc2/cryosparc_master/cryosparc_command/command_core/init.py”, line 131, in wrapper
res = func(*args, **kwargs)
File “/home/dd/cc2/cryosparc_master/cryosparc_command/command_core/init.py”, line 550, in get_config_var
res = mongo.db[colname].find_one({‘name’ : name})
File “/home/dd/cc2/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/collection.py”, line 1319, in find_one
for result in cursor.limit(-1):
File “/home/dd/cc2/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/cursor.py”, line 1207, in next
if len(self.__data) or self._refresh():
File “/home/dd/cc2/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/cursor.py”, line 1124, in _refresh
self.__send_message(q)
File “/home/dd/cc2/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/cursor.py”, line 1001, in __send_message
address=self.__address)
File “/home/dd/cc2/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/mongo_client.py”, line 1372, in _run_operation_with_response
exhaust=exhaust)
File “/home/dd/cc2/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/mongo_client.py”, line 1471, in _retryable_read
return func(session, server, sock_info, slave_ok)
File “/home/dd/cc2/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/mongo_client.py”, line 1366, in _cmd
unpack_res)
File “/home/dd/cc2/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/server.py”, line 137, in run_operation_with_response
first, sock_info.max_wire_version)
File “/home/dd/cc2/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/helpers.py”, line 140, in _check_command_response
raise NotMasterError(errmsg, response)
pymongo.errors.NotMasterError: node is not in primary or recovering state, full error: {‘ok’: 0.0, ‘errmsg’: ‘node is not in primary or recovering state’, ‘code’: 13436, ‘codeName’: ‘NotMasterOrSecondary’}
**custom thread exception hook caught something
**** handle exception rc
Traceback (most recent call last):
File “/home/dd/cc2/cryosparc_master/cryosparc_compute/jobs/runcommon.py”, line 1790, in run_with_except_hook
run_old(*args, **kw)
File “/home/dd/cc2/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/threading.py”, line 870, in run
self._target(*self._args, **self._kwargs)
File “/home/dd/cc2/cryosparc_master/cryosparc_command/command_core/init.py”, line 208, in background_worker
last_audit_date = get_config_var(‘audit’, fail_notset=False, default={})
File “/home/dd/cc2/cryosparc_master/cryosparc_command/command_core/init.py”, line 140, in wrapper
raise e
File “/home/dd/cc2/cryosparc_master/cryosparc_command/command_core/init.py”, line 131, in wrapper
res = func(*args, **kwargs)
File “/home/dd/cc2/cryosparc_master/cryosparc_command/command_core/init.py”, line 550, in get_config_var
res = mongo.db[colname].find_one({‘name’ : name})
File “/home/dd/cc2/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/collection.py”, line 1319, in find_one
for result in cursor.limit(-1):
File “/home/dd/cc2/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/cursor.py”, line 1207, in next
if len(self.__data) or self._refresh():
File “/home/dd/cc2/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/cursor.py”, line 1124, in _refresh
self.__send_message(q)
File “/home/dd/cc2/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/cursor.py”, line 1001, in __send_message
address=self.__address)
File “/home/dd/cc2/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/mongo_client.py”, line 1372, in _run_operation_with_response
exhaust=exhaust)
File “/home/dd/cc2/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/mongo_client.py”, line 1471, in _retryable_read
return func(session, server, sock_info, slave_ok)
File “/home/dd/cc2/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/mongo_client.py”, line 1366, in _cmd
unpack_res)
File “/home/dd/cc2/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/server.py”, line 137, in run_operation_with_response
first, sock_info.max_wire_version)
File “/home/dd/cc2/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/helpers.py”, line 140, in _check_command_response
raise NotMasterError(errmsg, response)
pymongo.errors.NotMasterError: node is not in primary or recovering state, full error: {‘ok’: 0.0, ‘errmsg’: ‘node is not in primary or recovering state’, ‘code’: 13436, ‘codeName’: ‘NotMasterOrSecondary’}