Hi -
I was about to update from v 4.02 to 4.1. Before doing it, as I stopped and re-started Cryosparc, I got an “pymongo.errors.OperationFailure: there are no users authenticated, full error:” which I solved thanks to another post by stopping cryosparc and killing an orphan mongod job.
then, I managed to re-start cryosparc, but notice the status below:
$ cryosparcm status
----------------------------------------------------------------------------
CryoSPARC System master node installed at
/gpfs/data/bhabhaekiertlabs/local_software/CryoSparc/cryosparc2_master
Current cryoSPARC version: v4.0.2
----------------------------------------------------------------------------
CryoSPARC process status:
app EXITED Jan 12 08:50 AM
app_api STARTING
app_api_dev STOPPED Not started
app_legacy STOPPED Not started
app_legacy_dev STOPPED Not started
command_core FATAL Exited too quickly (process log may have details)
command_rtp RUNNING pid 2948, uptime 0:00:02
command_vis RUNNING pid 2862, uptime 0:00:07
database RUNNING pid 2147, uptime 0:01:05
----------------------------------------------------------------------------
License is valid
----------------------------------------------------------------------------
when running cryosparcm log command_core, I see:
File "/gpfs/data/bhabhaekiertlabs/local_software/CryoSparc/cryosparc2_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 "/gpfs/data/bhabhaekiertlabs/local_software/CryoSparc/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/werkzeug/serving.py", line 1052, in run_simple
inner()
File "/gpfs/data/bhabhaekiertlabs/local_software/CryoSparc/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/werkzeug/serving.py", line 1005, in inner
fd=fd,
File "/gpfs/data/bhabhaekiertlabs/local_software/CryoSparc/cryosparc2_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 "/gpfs/data/bhabhaekiertlabs/local_software/CryoSparc/cryosparc2_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 "/gpfs/data/bhabhaekiertlabs/local_software/CryoSparc/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/socketserver.py", line 452, in __init__
self.server_bind()
File "/gpfs/data/bhabhaekiertlabs/local_software/CryoSparc/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/http/server.py", line 137, in server_bind
socketserver.TCPServer.server_bind(self)
File "/gpfs/data/bhabhaekiertlabs/local_software/CryoSparc/cryosparc2_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
2023-01-12 08:50:30,345 COMMAND.STARTUP startup INFO | CryoSPARC instance ID: f2b48e65-83de-47b5-b69c-2dd8cc7d36ea
2023-01-12 08:50:30,345 COMMAND.SCHEDULER get_gpu_info INFO | UPDATING WORKER GPU INFO
2023-01-12 08:50:30,345 COMMAND.JOBS update_all_job_sizes INFO | UPDATING ALL JOB SIZES IN 10s
2023-01-12 08:50:30,345 COMMAND.DATA export_all_projects INFO | EXPORTING ALL PROJECTS IN 60s...
2023-01-12 08:50:32,956 COMMAND.MAIN start INFO | === STARTED ===
2023-01-12 08:50:32,956 COMMAND.BG_WORKER background_worker INFO | === STARTED ===
2023-01-12 08:50:32,956 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 "<string>", line 1, in <module>
File "/gpfs/data/bhabhaekiertlabs/local_software/CryoSparc/cryosparc2_master/cryosparc_command/command_core/__init__.py", line 209, in start
app.run(host="0.0.0.0", port=port, threaded=True, passthrough_errors=False)
File "/gpfs/data/bhabhaekiertlabs/local_software/CryoSparc/cryosparc2_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 "/gpfs/data/bhabhaekiertlabs/local_software/CryoSparc/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/werkzeug/serving.py", line 1052, in run_simple
inner()
File "/gpfs/data/bhabhaekiertlabs/local_software/CryoSparc/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/werkzeug/serving.py", line 1005, in inner
fd=fd,
File "/gpfs/data/bhabhaekiertlabs/local_software/CryoSparc/cryosparc2_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 "/gpfs/data/bhabhaekiertlabs/local_software/CryoSparc/cryosparc2_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 "/gpfs/data/bhabhaekiertlabs/local_software/CryoSparc/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/socketserver.py", line 452, in __init__
self.server_bind()
File "/gpfs/data/bhabhaekiertlabs/local_software/CryoSparc/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/http/server.py", line 137, in server_bind
socketserver.TCPServer.server_bind(self)
File "/gpfs/data/bhabhaekiertlabs/local_software/CryoSparc/cryosparc2_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
Before moving forward with the update, I’d like to know what happened and if anything should / could be done to deal with this “FATAL” status of the command_core?
Thanks,
Best,
Nicolas