OSError: for command_core (OSError #98)

[jiangq9992003]

Today when I restarted cryoSPARC I had the following error.
command_core : ERROR (spawn error). The details in log seem to point to OSError: Address already in use. It is a bit strange because it had been running for more than 3 weeks. I will reboot the system to test it. I wonder if the following message would be informative.

cryosparc_user@dhcp-128-205-48-236 ~]$ cryosparcm log command_core | tail -40

2022-08-12 10:04:15,028 COMMAND.MAIN start INFO | === STARTED ===
2022-08-12 10:04:15,029 COMMAND.BG_WORKER background_worker INFO | === STARTED ===
2022-08-12 10:04:15,029 COMMAND.CORE run INFO | === STARTED TASKS WORKER ===

• 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
  Traceback (most recent call last):
  File “”, line 1, in
  File “/home/cryosparc_user/cryosparc3.3/cryosparc_master/cryosparc_command/command_core/init.py”, line 277, in start
  app.run(host=“0.0.0.0”, port=port, threaded=True, passthrough_errors=False)
  File “/home/cryosparc_user/cryosparc3.3/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/flask/app.py”, line 990, in run
  run_simple(host, port, self, **options)
  File “/home/cryosparc_user/cryosparc3.3/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/werkzeug/serving.py”, line 1052, in run_simple
  inner()
  File “/home/cryosparc_user/cryosparc3.3/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/werkzeug/serving.py”, line 1005, in inner
  fd=fd,
  File “/home/cryosparc_user/cryosparc3.3/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/werkzeug/serving.py”, line 848, in make_server
  host, port, app, request_handler, passthrough_errors, ssl_context, fd=fd
  File “/home/cryosparc_user/cryosparc3.3/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/werkzeug/serving.py”, line 740, in init
  HTTPServer.init(self, server_address, handler)
  File “/home/cryosparc_user/cryosparc3.3/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/socketserver.py”, line 452, in init
  self.server_bind()
  File “/home/cryosparc_user/cryosparc3.3/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/http/server.py”, line 137, in server_bind
  socketserver.TCPServer.server_bind(self)
  File “/home/cryosparc_user/cryosparc3.3/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/socketserver.py”, line 466, in server_bind
  self.socket.bind(self.server_address)
  OSError: [Errno 98] Address already in use

[wtempel]

Does this question concern the same problem mentioned in

Error when updating from v3.3.1 to v3.3.2

Thanks for your suggestions. The error happened when I started the upgrading online. I did not do the database backup the way you suggested. I reinstalled v3.3.2 and then move the database directory directly. It worked with the old database. Today I encountered a different error when I tried to shut down and restart cryoSPARC after running for 3 weeks. command_core: ERROR (spawn error). Is there anything to do with the “out-of-memory” errors I have encountered in the past two days in 2D class…

?

[jiangq9992003]

It is a different one. I realized it and started a new topic. Thanks.

[wtempel]

@jiangq9992003

After rebooting of the workstation, the problems went away.

If this topic is not resolved by the reboot mentioned, you may try the solution proposed in the following post:

Cryosparc starting error

Hi @KSJ, this looks like there are some zombie cryoSPARC services still running that were somehow disconnected from the supervisor process that manages them. To fix this you may either restart the machine with hostname local02 or kill the processes manually. Enter these commands in a terminal while logged into that machine: ps -ax | grep supervisord ps -ax | grep cryosparc Look for the process ID of processes related to cryoSPARC at the beginning of each line of output. Kill them with the k…

[jiangq9992003]

Problem solved by rebooting. It was likely due to the zombie processes accumulated when there were multiple out-of-memory errors in the previous two days. Thanks.