unresponsive web server galaxy local

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1

Hi there,

Initially, after loading galaxy local for the first time I am able to access the web server and create an account. I then cancel galaxy and edit the galaxy.yml file to make me an admin and try to log in, the web browser is unresponsive, it completely freezes and I am unable to load or work galaxy. Why might this be?

Prior to the http link, there are many DEBUG lines (far to many to copy and paste here), so I take it something still some issue underlying this.

any help would be greatly appreciated!

2 Likes
2

I don’t know why this might be, but you could try to start galaxy with the command:

sh run.sh --daemon

And you can stop galaxy with:

sh run.sh --stop-daemon

By default this writes the log output to galaxy/galaxy.log maybe you can do this and scroll trough this file and maybe see some clear errors. It is also possible the yml format of the config file is wrong now because you added something.

My admin email line looks like something like:
admin_users: 'adminname@fakeemail.com, secondadmin@fakeemail.com'

1 Like
3

thanks @gbbio
I have now tried your suggestion and this is what is shown in the galaxy/galaxy.log file:

writing pidfile to galaxy.pid
*** uWSGI is running in multiple interpreter mode ***
spawned uWSGI master process (pid: 775)
spawned uWSGI worker 1 (pid: 776, cores: 4)
spawned 2 offload threads for uWSGI worker 1
spawned uWSGI http 1 (pid: 777)
running “unix_signal:2 gracefully_kill_them_all” (master-start)…
running “unix_signal:15 gracefully_kill_them_all” (master-start)…
Exception ignored in: <function _after_at_fork_child_reinit_locks at 0x1028528c0>
Traceback (most recent call last):
File “/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/lib/python3.7/logging/init.py”, line 258, in _after_at_fork_child_reinit_locks
_releaseLock() # Acquired by os.register_at_fork(before=.
File “/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/lib/python3.7/logging/init.py”, line 226, in _releaseLock
_lock.release()
RuntimeError: cannot release un-acquired lock
galaxy.web_stack DEBUG 2020-04-10 14:10:21,878 [p:776,w:1,m:0] [MainThread] Calling postfork function: <bound method ApplicationStack.set_postfork_server_name of <galaxy.web_stack.UWSGIApplicationStack object at 0x11004c4d0>>
galaxy.web_stack DEBUG 2020-04-10 14:10:21,927 [p:776,w:1,m:0] [MainThread] server_name set to: main.web.1
galaxy.web_stack DEBUG 2020-04-10 14:10:21,927 [p:776,w:1,m:0] [MainThread] Calling postfork function: <bound method Thread.start of <Thread(LocalRunner.work_thread-0, stopped daemon)>>
galaxy.web_stack DEBUG 2020-04-10 14:10:21,928 [p:776,w:1,m:0] [MainThread] Calling postfork function: <bound method Thread.start of <Thread(LocalRunner.work_thread-1, stopped daemon)>>
galaxy.web_stack DEBUG 2020-04-10 14:10:21,929 [p:776,w:1,m:0] [MainThread] Calling postfork function: <bound method Thread.start of <Thread(LocalRunner.work_thread-2, stopped daemon)>>
galaxy.web_stack DEBUG 2020-04-10 14:10:21,929 [p:776,w:1,m:0] [MainThread] Calling postfork function: <bound method Thread.start of <Thread(LocalRunner.work_thread-3, stopped daemon)>>
galaxy.web_stack DEBUG 2020-04-10 14:10:21,929 [p:776,w:1,m:0] [MainThread] Calling postfork function: <bound method Monitors.start_monitoring of <galaxy.jobs.handler.JobHandlerQueue object at 0x1126a6b50>>
galaxy.web_stack DEBUG 2020-04-10 14:10:21,930 [p:776,w:1,m:0] [MainThread] Calling postfork function: <bound method Monitors.start_monitoring of <galaxy.jobs.handler.JobHandlerStopQueue object at 0x111e439d0>>
galaxy.web_stack DEBUG 2020-04-10 14:10:21,930 [p:776,w:1,m:0] [MainThread] Calling postfork function: <bound method JobManager.start of <galaxy.jobs.manager.JobManager object at 0x112659250>>
galaxy.jobs.handler DEBUG 2020-04-10 14:10:21,930 [p:776,w:1,m:0] [MainThread] Handler queue starting for jobs assigned to handler: main.web.1
galaxy.web_stack.message DEBUG 2020-04-10 14:10:21,961 [p:776,w:1,m:0] [MainThread] Bound default message handler ‘JobHandlerMessage.default_handler’ to <bound method TaskMessage.default_handler of <galaxy.jobs.handler.JobHandlerQueue object at 0x1126a6b50>>
galaxy.jobs.handler INFO 2020-04-10 14:10:21,964 [p:776,w:1,m:0] [MainThread] job handler queue started
galaxy.jobs.handler INFO 2020-04-10 14:10:21,967 [p:776,w:1,m:0] [MainThread] job handler stop queue started
galaxy.web_stack DEBUG 2020-04-10 14:10:21,968 [p:776,w:1,m:0] [MainThread] Calling postfork function: <bound method Monitors.start_monitoring of <galaxy.workflow.scheduling_manager.WorkflowRequestMonitor object at 0x1126e8d90>>
galaxy.web_stack DEBUG 2020-04-10 14:10:21,968 [p:776,w:1,m:0] [MainThread] Calling postfork function: <bound method WorkflowRequestMonitor.start of <galaxy.workflow.scheduling_manager.WorkflowRequestMonitor object at 0x1126e8d90>>
galaxy.web_stack DEBUG 2020-04-10 14:10:21,969 [p:776,w:1,m:0] [MainThread] Calling postfork function: <bound method DatabaseHeartbeat.start of <galaxy.model.database_heartbeat.DatabaseHeartbeat object at 0x1126bd390>>
galaxy.web_stack DEBUG 2020-04-10 14:10:21,971 [p:776,w:1,m:0] [MainThread] Calling postfork function: <bound method UWSGIApplicationStack.start of <galaxy.web_stack.UWSGIApplicationStack object at 0x11004c4d0>>
galaxy.web_stack DEBUG 2020-04-10 14:10:21,973 [p:776,w:1,m:0] [MainThread] Calling postfork function:
galaxy.web_stack DEBUG 2020-04-10 14:10:21,975 [p:776,w:1,m:0] [MainThread] Calling postfork function: <function postfork_setup at 0x11002b3b0>
galaxy.queue_worker INFO 2020-04-10 14:10:21,976 [p:776,w:1,m:0] [MainThread] Binding and starting galaxy control worker for main.web.1
galaxy.web_stack INFO 2020-04-10 14:10:21,987 [p:776,w:1,m:0] [MainThread] Galaxy server instance ‘main.web.1’ is running

galaxy.model.database_heartbeat DEBUG 2020-04-10 14:10:22,052 [p:776,w:1,m:0] [database_heartbeart_main.web.1.thread] main.web.1 is config watcher
/Volumes/My_Book/Galaxy/galaxy/.venv/lib/python3.7/site-packages/sqlalchemy/sql/sqltypes.py:666: SAWarning: Dialect sqlite+pysqlite does not support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage.
“storage.” % (dialect.name, dialect.driver

I have no idea what any of this means?

I have also checked the galaxy.yml file and my email address is listed as your example.

4

@Lauren which Galaxy release is that? Are you running it under Linux?

5

hi @bjoern.gruening its the latest, 20.01 and I am installing it on my Mac with Catalina OS

6

I am having the same sqlite error, I’m running on windows subsystem for linux. I tried rolling back to an earlier stable version of my database and that didn’t solve the problem. In the meantime, the only changes I can think of are a few characters in existing custom tools (i.e. things like changing the filtering metric from 3->4).