Closed maikenp closed 1 year ago
Can you look at the logs ?
I don't know what the tutorial uses as service name, but systemctl
should list the service
Also for development this is way too complicated ./run.sh
will work fine and be much easier to manage.
Thanks, so the problem shows up in nginx, while galaxy-gunicorn seems to be ok:
[root@galaxy-arc-test ~]# systemctl status galaxy-gunicorn
● galaxy-gunicorn.service - Galaxy gunicorn
Loaded: loaded (/etc/systemd/system/galaxy-gunicorn.service; disabled; preset: disabled)
Active: active (running) since Fri 2023-08-11 09:56:35 CEST; 25s ago
Main PID: 26656 (gunicorn)
Tasks: 1 (limit: 50188)
Memory: 216.4M
CPU: 4.780s
CGroup: /system.slice/galaxy-gunicorn.service
└─26656 /storage/srv/galaxy/venv/bin/python3 /storage/srv/galaxy/venv/bin/gunicorn "galaxy.webapps.galaxy.fast_factory:factory()" --timeout 300 --pythonpath lib -k galaxy.webapps.galaxy.workers.Worke>
Aug 11 09:56:41 galaxy-arc-test.itf.uiocloud.no galaxyctl[26656]: galaxy.tool_util.toolbox.base DEBUG 2023-08-11 09:56:41,277 [pN:main,p:26656,tN:MainThread] Loaded tool id: hello_arc, version: 1.0.0 into tool pa>
Aug 11 09:56:41 galaxy-arc-test.itf.uiocloud.no galaxyctl[26656]: galaxy.tool_util.toolbox.base DEBUG 2023-08-11 09:56:41,277 [pN:main,p:26656,tN:MainThread] Loading tool panel finished (0.206 ms)
Aug 11 09:56:41 galaxy-arc-test.itf.uiocloud.no galaxyctl[26656]: galaxy.tool_util.toolbox.base DEBUG 2023-08-11 09:56:41,279 [pN:main,p:26656,tN:MainThread] Loaded tool id: upload1, version: 1.1.7 into tool pane>
Aug 11 09:56:41 galaxy-arc-test.itf.uiocloud.no galaxyctl[26656]: galaxy.tool_util.toolbox.base DEBUG 2023-08-11 09:56:41,279 [pN:main,p:26656,tN:MainThread] Loaded tool id: hello_arc, version: 1.0.0 into tool pa>
Aug 11 09:56:41 galaxy-arc-test.itf.uiocloud.no galaxyctl[26656]: galaxy.tool_util.toolbox.views.edam DEBUG 2023-08-11 09:56:41,279 [pN:main,p:26656,tN:MainThread] Loading EDAM tool panel finished (1.032 ms)
Aug 11 09:56:41 galaxy-arc-test.itf.uiocloud.no galaxyctl[26656]: galaxy.tool_util.toolbox.base DEBUG 2023-08-11 09:56:41,279 [pN:main,p:26656,tN:MainThread] Loaded tool id: upload1, version: 1.1.7 into tool pane>
Aug 11 09:56:41 galaxy-arc-test.itf.uiocloud.no galaxyctl[26656]: galaxy.tool_util.toolbox.base DEBUG 2023-08-11 09:56:41,279 [pN:main,p:26656,tN:MainThread] Loaded tool id: hello_arc, version: 1.0.0 into tool pa>
Aug 11 09:56:41 galaxy-arc-test.itf.uiocloud.no galaxyctl[26656]: galaxy.tool_util.toolbox.views.edam DEBUG 2023-08-11 09:56:41,279 [pN:main,p:26656,tN:MainThread] Loading EDAM tool panel finished (0.836 ms)
Aug 11 09:56:41 galaxy-arc-test.itf.uiocloud.no galaxyctl[26656]: galaxy.tool_util.toolbox.integrated_panel DEBUG 2023-08-11 09:56:41,280 [pN:main,p:26656,tN:MainThread] Writing integrated tool panel config file >
Aug 11 09:56:41 galaxy-arc-test.itf.uiocloud.no galaxyctl[26656]: galaxy.tool_util.deps DEBUG 2023-08-11 09:56:41,282 [pN:main,p:26656,tN:MainThread] Unable to find config file '/storage/srv/galaxy/config/depende>
[root@galaxy-arc-test ~]# systemctl status nginx
● nginx.service - The nginx HTTP and reverse proxy server
Loaded: loaded (/usr/lib/systemd/system/nginx.service; enabled; preset: disabled)
Active: active (running) since Thu 2023-08-10 22:36:23 CEST; 11h ago
Main PID: 1008 (nginx)
Tasks: 3 (limit: 50188)
Memory: 6.8M
CPU: 638ms
CGroup: /system.slice/nginx.service
├─1008 "nginx: master process /usr/sbin/nginx"
├─1009 "nginx: worker process"
└─1010 "nginx: worker process"
Aug 11 09:56:49 galaxy-arc-test.itf.uiocloud.no nginx[1010]: galaxy-arc-test.itf.uiocloud.no nginx: 2023/08/11 09:56:49 [crit] 1010#1010: *3166 connect() to unix:/storage/srv/galaxy/var/config/gunicorn.sock faile>
Aug 11 09:56:49 galaxy-arc-test.itf.uiocloud.no nginx[1010]: galaxy-arc-test.itf.uiocloud.no nginx: 193.157.183.31 - - [11/Aug/2023:09:56:49 +0200] "GET /api/entry_points?running=true HTTP/1.1" 502 157 "https://g>
Aug 11 09:56:57 galaxy-arc-test.itf.uiocloud.no nginx[1010]: galaxy-arc-test.itf.uiocloud.no nginx: 2023/08/11 09:56:57 [crit] 1010#1010: *3166 connect() to unix:/storage/srv/galaxy/var/config/gunicorn.sock faile>
Aug 11 09:56:57 galaxy-arc-test.itf.uiocloud.no nginx[1010]: galaxy-arc-test.itf.uiocloud.no nginx: 193.157.183.31 - - [11/Aug/2023:09:56:57 +0200] "GET /history/current_history_json?since=2023-08-10T21:01:30.079>
Aug 11 09:56:58 galaxy-arc-test.itf.uiocloud.no nginx[1010]: galaxy-arc-test.itf.uiocloud.no nginx: 2023/08/11 09:56:58 [crit] 1010#1010: *3166 connect() to unix:/storage/srv/galaxy/var/config/gunicorn.sock faile>
Aug 11 09:56:58 galaxy-arc-test.itf.uiocloud.no nginx[1010]: galaxy-arc-test.itf.uiocloud.no nginx: 193.157.183.31 - - [11/Aug/2023:09:56:58 +0200] "GET /api/entry_points?running=true HTTP/1.1" 502 157 "https://g>
Aug 11 09:56:59 galaxy-arc-test.itf.uiocloud.no nginx[1010]: galaxy-arc-test.itf.uiocloud.no nginx: 2023/08/11 09:56:59 [crit] 1010#1010: *3166 connect() to unix:/storage/srv/galaxy/var/config/gunicorn.sock faile>
Aug 11 09:56:59 galaxy-arc-test.itf.uiocloud.no nginx[1010]: galaxy-arc-test.itf.uiocloud.no nginx: 193.157.183.31 - - [11/Aug/2023:09:56:59 +0200] "GET /api/entry_points?running=true HTTP/1.1" 502 157 "https://g>
Aug 11 09:56:59 galaxy-arc-test.itf.uiocloud.no nginx[1010]: galaxy-arc-test.itf.uiocloud.no nginx: 2023/08/11 09:56:59 [crit] 1010#1010: *3166 connect() to unix:/storage/srv/galaxy/var/config/gunicorn.sock faile>
Aug 11 09:56:59 galaxy-arc-test.itf.uiocloud.no nginx[1010]: galaxy-arc-test.itf.uiocloud.no nginx: 193.157.183.31 - - [11/Aug/2023:09:56:59 +0200] "GET /api/entry_points?running=true HTTP/1.1" 502 157 "https://g>
[root@galaxy-arc-test ~]# /usr/local/bin/galaxyctl status
Dynamic handlers are configured in Gravity but Galaxy is not configured to assign jobs to handlers dynamically, so these handlers will not handle jobs. Set the job handler assignment method in the Galaxy job configuration to `db-skip-locked` or `db-transaction-isolation` to fix this.
UNIT LOAD ACTIVE SUB DESCRIPTION
galaxy-celery-beat.service loaded active running Galaxy celery-beat
galaxy-celery.service loaded active running Galaxy celery
galaxy-gunicorn.service loaded active running Galaxy gunicorn
galaxy-handler@0.service loaded active running Galaxy handler (process 0)
galaxy-handler@1.service loaded active running Galaxy handler (process 1)
galaxy.target loaded active active Galaxy
LOAD = Reflects whether the unit definition was properly loaded.
ACTIVE = The high-level unit activation state, i.e. generalization of SUB.
SUB = The low-level unit activation state, values depend on unit type.
6 loaded units listed.
To show all installed unit files use 'systemctl list-unit-files'.
The list of all services running:
[root@galaxy-arc-test ~]# systemctl list-units --type=service
UNIT LOAD ACTIVE SUB DESCRIPTION
auditd.service loaded active running Security Auditing Service
chronyd.service loaded active running NTP client/server
cloud-config.service loaded active exited Apply the settings specified in cloud-config
cloud-final.service loaded active exited Execute cloud user/final scripts
cloud-init-local.service loaded active exited Initial cloud-init job (pre-networking)
cloud-init.service loaded active exited Initial cloud-init job (metadata service crawler)
crond.service loaded active running Command Scheduler
dbus-broker.service loaded active running D-Bus System Message Bus
dracut-shutdown.service loaded active exited Restore /run/initramfs on shutdown
galaxy-celery-beat.service loaded active running Galaxy celery-beat
galaxy-celery.service loaded active running Galaxy celery
galaxy-gunicorn.service loaded active running Galaxy gunicorn
galaxy-handler@0.service loaded active running Galaxy handler (process 0)
galaxy-handler@1.service loaded active running Galaxy handler (process 1)
getty@tty1.service loaded active running Getty on tty1
gssproxy.service loaded active running GSSAPI Proxy Daemon
irqbalance.service loaded active running irqbalance daemon
kmod-static-nodes.service loaded active exited Create List of Static Device Nodes
mariadb.service loaded active running MariaDB 10.5 database server
munge.service loaded active running MUNGE authentication service
NetworkManager-wait-online.service loaded active exited Network Manager Wait Online
NetworkManager.service loaded active running Network Manager
nginx.service loaded active running The nginx HTTP and reverse proxy server
nis-domainname.service loaded active exited Read and set NIS domainname from /etc/sysconfig/network
polkit.service loaded active running Authorization Manager
postgresql-15.service loaded active running PostgreSQL 15 database server
qemu-guest-agent.service loaded active running QEMU Guest Agent
rpc-statd-notify.service loaded active exited Notify NFS peers of a restart
rpcbind.service loaded active running RPC Bind
rsyslog.service loaded active running System Logging Service
serial-getty@ttyS0.service loaded active running Serial Getty on ttyS0
slurmctld.service loaded active running Slurm controller daemon
slurmdbd.service loaded active running Slurm DBD accounting daemon
sshd.service loaded active running OpenSSH server daemon
systemd-boot-update.service loaded active exited Automatic Boot Loader Update
systemd-fsck@dev-disk-by\x2duuid-D33D\x2dDD3C.service loaded active exited File System Check on /dev/disk/by-uuid/D33D-DD3C
systemd-journal-flush.service loaded active exited Flush Journal to Persistent Storage
systemd-journald.service loaded active running Journal Service
systemd-logind.service loaded active running User Login Management
systemd-modules-load.service loaded active exited Load Kernel Modules
systemd-network-generator.service loaded active exited Generate network units from Kernel command line
systemd-random-seed.service loaded active exited Load/Save Random Seed
systemd-remount-fs.service loaded active exited Remount Root and Kernel File Systems
systemd-sysctl.service loaded active exited Apply Kernel Variables
systemd-tmpfiles-setup-dev.service loaded active exited Create Static Device Nodes in /dev
systemd-tmpfiles-setup.service loaded active exited Create Volatile Files and Directories
systemd-udev-trigger.service loaded active exited Coldplug All udev Devices
systemd-udevd.service loaded active running Rule-based Manager for Device Events and Files
systemd-update-utmp.service loaded active exited Record System Boot/Shutdown in UTMP
systemd-user-sessions.service loaded active exited Permit User Sessions
tuned.service loaded active running Dynamic System Tuning Daemon
user-runtime-dir@1000.service loaded active exited User Runtime Directory /run/user/1000
user@1000.service loaded active running User Manager for UID 1000
LOAD = Reflects whether the unit definition was properly loaded.
ACTIVE = The high-level unit activation state, i.e. generalization of SUB.
SUB = The low-level unit activation state, values depend on unit type.
53 loaded units listed. Pass --all to see loaded but inactive units, too.
To show all installed unit files use 'systemctl list-unit-files'.
About the ./run.sh - I used that initially actually, but was not sure if that was the required way of doing things, so I turned to the ansible playbook instead. In addition to having some issues also with run.sh on this system (forgot what they were right now).
Can you include the whole startup sequence for Galaxy ?
(the fact that the log ends in the middle of the startup sequence probably means galaxy wasn't able to start up fully and is being restarted)
The log output from the startup?
the galaxy logs are truncated, it doesn't include the start and the messages are also truncated ... there must be a journalctl option to get the full logs, but I can never remember and I don't use systemd.
alternatively you can use journalctl -fu galaxy-gunicorn.service
and wait until it restarts ... just before that there will be a reason given for why Galaxy can't start.
It's not done booting at this point, is the process still alive, and if yes, what is it doing ? (you can check with https://pypi.org/project/py-spy/, py-spy dump --pid <pid>
)
I stopped galaxy with galaxyctl stop
Checked that all galaxy-related processes were gone
[root@galaxy-arc-test ~]# ps aux | grep galaxy
root 27342 0.0 0.0 3876 2040 pts/1 S+ 10:31 0:00 grep --color=auto galaxy
Then restarted with "restart"
And this is then what I have
[root@galaxy-arc-test ~]# ps aux | grep galaxy
root 27347 0.2 0.5 232696 47348 pts/0 S+ 10:32 0:00 journalctl -fu galaxy-*
galaxy 27351 19.5 2.5 429508 207080 ? Ss 10:32 0:02 /storage/srv/galaxy/venv/bin/python3 /storage/srv/galaxy/venv/bin/celery --app galaxy.celery beat --loglevel DEBUG --schedule /storage/srv/galaxy/var/gravity/celery-beat-schedule
galaxy 27352 20.1 2.6 455404 212436 ? Ss 10:32 0:02 /storage/srv/galaxy/venv/bin/python3 /storage/srv/galaxy/venv/bin/celery --app galaxy.celery worker --concurrency 2 --loglevel DEBUG --pool threads --queues celery,galaxy.internal,galaxy.external
galaxy 27353 39.0 3.2 510904 267148 ? Ss 10:32 0:05 /storage/srv/galaxy/venv/bin/python3 /storage/srv/galaxy/venv/bin/gunicorn galaxy.webapps.galaxy.fast_factory:factory() --timeout 300 --pythonpath lib -k galaxy.webapps.galaxy.workers.Worker -b unix:/storage/srv/galaxy/var/config/gunicorn.sock --workers=2 --config python:galaxy.web_stack.gunicorn_config --preload --forwarded-allow-ips=*
galaxy 27354 37.2 3.2 504808 262076 ? Ss 10:32 0:04 /storage/srv/galaxy/venv/bin/python ./lib/galaxy/main.py -c /storage/srv/galaxy/config/galaxy.yml --server-name=handler_0 --attach-to-pool=job-handlers --attach-to-pool=workflow-schedulers
galaxy 27355 37.0 3.2 504808 262124 ? Ss 10:32 0:04 /storage/srv/galaxy/venv/bin/python ./lib/galaxy/main.py -c /storage/srv/galaxy/config/galaxy.yml --server-name=handler_1 --attach-to-pool=job-handlers --attach-to-pool=workflow-schedulers
galaxy 27374 0.2 0.1 12900 10956 ? S 10:32 0:00 /storage/srv/galaxy/venv/bin/python3 -c from multiprocessing.resource_tracker import main;main(7)
postgres 27376 0.1 0.2 211900 18900 ? Ss 10:32 0:00 postgres: galaxy galaxy [local] idle
postgres 27378 13.6 0.2 213848 23684 ? Ss 10:32 0:00 postgres: galaxy galaxy [local] idle
postgres 27380 13.8 0.2 213848 23688 ? Ss 10:32 0:00 postgres: galaxy galaxy [local] idle
postgres 27382 13.6 0.2 213848 23684 ? Ss 10:32 0:00 postgres: galaxy galaxy [local] idle
root 27387 0.0 0.0 3876 2024 pts/1 S+ 10:32 0:00 grep --color=auto galaxy
[root@galaxy-arc-test ~]# systemctl status galaxy-gunicorn^C
[root@galaxy-arc-test ~]# /usr/local/bin/py-spy dump --pid 27351
Process 27351: /storage/srv/galaxy/venv/bin/python3 /storage/srv/galaxy/venv/bin/celery --app galaxy.celery beat --loglevel DEBUG --schedule /storage/srv/galaxy/var/gravity/celery-beat-schedule
Python v3.9.16 (/usr/bin/python3.9)
Thread 27351 (idle): "MainThread"
start (celery/beat.py:649)
start_scheduler (celery/apps/beat.py:105)
run (celery/apps/beat.py:77)
beat (celery/bin/beat.py:72)
caller (celery/bin/base.py:134)
new_func (click/decorators.py:33)
invoke (click/core.py:783)
invoke (click/core.py:1434)
invoke (click/core.py:1688)
main (click/core.py:1078)
__call__ (click/core.py:1157)
main (celery/bin/celery.py:217)
main (celery/__main__.py:15)
<module> (celery:8)
[root@galaxy-arc-test ~]# /usr/local/bin/py-spy dump --pid 27352
Process 27352: /storage/srv/galaxy/venv/bin/python3 /storage/srv/galaxy/venv/bin/celery --app galaxy.celery worker --concurrency 2 --loglevel DEBUG --pool threads --queues celery,galaxy.internal,galaxy.external
Python v3.9.16 (/usr/bin/python3.9)
Thread 27352 (idle): "MainThread"
drain_events (kombu/transport/virtual/base.py:976)
drain_events (kombu/connection.py:316)
synloop (celery/worker/loops.py:130)
start (celery/worker/consumer/consumer.py:628)
start (celery/bootsteps.py:116)
start (celery/worker/consumer/consumer.py:332)
start (celery/bootsteps.py:365)
start (celery/bootsteps.py:116)
start (celery/worker/worker.py:203)
worker (celery/bin/worker.py:351)
caller (celery/bin/base.py:134)
new_func (click/decorators.py:33)
invoke (click/core.py:783)
invoke (click/core.py:1434)
invoke (click/core.py:1688)
main (click/core.py:1078)
__call__ (click/core.py:1157)
main (celery/bin/celery.py:217)
main (celery/__main__.py:15)
<module> (celery:8)
[root@galaxy-arc-test ~]# /usr/local/bin/py-spy dump --pid 27353
Process 27353: /storage/srv/galaxy/venv/bin/python3 /storage/srv/galaxy/venv/bin/gunicorn galaxy.webapps.galaxy.fast_factory:factory() --timeout 300 --pythonpath lib -k galaxy.webapps.galaxy.workers.Worker -b unix:/storage/srv/galaxy/var/config/gunicorn.sock --workers=2 --config python:galaxy.web_stack.gunicorn_config --preload --forwarded-allow-ips=*
Python v3.9.16 (/usr/bin/python3.9)
Thread 27353 (idle): "MainThread"
acquire (galaxy/util/filelock.py:50)
__enter__ (galaxy/util/filelock.py:68)
ensure_installed (galaxy/tool_util/deps/installable.py:67)
__init__ (galaxy/tool_util/deps/resolvers/conda.py:152)
__load_plugins_from_dicts (galaxy/util/plugin_config.py:129)
load_plugins (galaxy/util/plugin_config.py:59)
__parse_resolver_conf_plugins (galaxy/tool_util/deps/__init__.py:362)
__init__ (galaxy/tool_util/deps/__init__.py:146)
build_dependency_manager (galaxy/tool_util/deps/__init__.py:105)
_init_dependency_manager (galaxy/tools/__init__.py:609)
__init__ (galaxy/tools/__init__.py:418)
_configure_toolbox (galaxy/app.py:307)
__init__ (galaxy/app.py:683)
app_pair (galaxy/webapps/galaxy/buildapp.py:59)
factory (galaxy/webapps/galaxy/fast_factory.py:63)
import_app (gunicorn/util.py:424)
load_wsgiapp (gunicorn/app/wsgiapp.py:48)
load (gunicorn/app/wsgiapp.py:58)
wsgi (gunicorn/app/base.py:67)
setup (gunicorn/arbiter.py:118)
__init__ (gunicorn/arbiter.py:58)
run (gunicorn/app/base.py:72)
run (gunicorn/app/base.py:236)
run (gunicorn/app/wsgiapp.py:67)
<module> (gunicorn:8)
[root@galaxy-arc-test ~]# /usr/local/bin/py-spy dump --pid 27354
Process 27354: /storage/srv/galaxy/venv/bin/python ./lib/galaxy/main.py -c /storage/srv/galaxy/config/galaxy.yml --server-name=handler_0 --attach-to-pool=job-handlers --attach-to-pool=workflow-schedulers
Python v3.9.16 (/usr/bin/python3.9)
Thread 27354 (idle): "MainThread"
acquire (galaxy/util/filelock.py:50)
__enter__ (galaxy/util/filelock.py:68)
ensure_installed (galaxy/tool_util/deps/installable.py:67)
__init__ (galaxy/tool_util/deps/resolvers/conda.py:152)
__load_plugins_from_dicts (galaxy/util/plugin_config.py:129)
load_plugins (galaxy/util/plugin_config.py:59)
__parse_resolver_conf_plugins (galaxy/tool_util/deps/__init__.py:362)
__init__ (galaxy/tool_util/deps/__init__.py:146)
build_dependency_manager (galaxy/tool_util/deps/__init__.py:105)
_init_dependency_manager (galaxy/tools/__init__.py:609)
__init__ (galaxy/tools/__init__.py:418)
_configure_toolbox (galaxy/app.py:307)
__init__ (galaxy/app.py:683)
load_galaxy_app (galaxy/main.py:91)
app_loop (galaxy/main.py:112)
main (galaxy/main.py:255)
<module> (galaxy/main.py:259)
[root@galaxy-arc-test ~]# /usr/local/bin/py-spy dump --pid 27355
Process 27355: /storage/srv/galaxy/venv/bin/python ./lib/galaxy/main.py -c /storage/srv/galaxy/config/galaxy.yml --server-name=handler_1 --attach-to-pool=job-handlers --attach-to-pool=workflow-schedulers
Python v3.9.16 (/usr/bin/python3.9)
Thread 27355 (idle): "MainThread"
acquire (galaxy/util/filelock.py:50)
__enter__ (galaxy/util/filelock.py:68)
ensure_installed (galaxy/tool_util/deps/installable.py:67)
__init__ (galaxy/tool_util/deps/resolvers/conda.py:152)
__load_plugins_from_dicts (galaxy/util/plugin_config.py:129)
load_plugins (galaxy/util/plugin_config.py:59)
__parse_resolver_conf_plugins (galaxy/tool_util/deps/__init__.py:362)
__init__ (galaxy/tool_util/deps/__init__.py:146)
build_dependency_manager (galaxy/tool_util/deps/__init__.py:105)
_init_dependency_manager (galaxy/tools/__init__.py:609)
__init__ (galaxy/tools/__init__.py:418)
_configure_toolbox (galaxy/app.py:307)
__init__ (galaxy/app.py:683)
load_galaxy_app (galaxy/main.py:91)
app_loop (galaxy/main.py:112)
main (galaxy/main.py:255)
<module> (galaxy/main.py:259)
[root@galaxy-arc-test ~]# /usr/local/bin/py-spy dump --pid 27374
Process 27374: /storage/srv/galaxy/venv/bin/python3 -c from multiprocessing.resource_tracker import main;main(7)
Python v3.9.16 (/usr/bin/python3.9)
Thread 27374 (idle): "MainThread"
main (multiprocessing/resource_tracker.py:189)
<module> (<string>:1)
It's waiting for a filelock to perform the conda setup. I think the training playbook has a separate task to set up conda. You can sidestep this and install conda manually at the right location, or set conda_auto_init: false
in the galaxy config if you don't need conda right away.
Ah right, thanks. I omitted the conda installation in fact as I had issues with the installation. I will try with the conda_auto_init setting, thanks!
That did it!
Thanks a lot!
Describe the bug
When using the ansible-galaxy playbook and following: https://training.galaxyproject.org/training-material/topics/admin/tutorials/ansible-galaxy/tutorial.html but setting
galaxy_commit_id: dev
instead of
release_23
the gunicorn.sock is not created.
Aug 10 23:28:54 galaxy-arc-test.itf.uiocloud.no nginx[1010]: galaxy-arc-test.itf.uiocloud.no nginx: 2023/08/10 23:28:54 [crit] 1010#1010: *386 connect() to unix:/storage/srv/galaxy/var/config/gunicorn.sock failed (2: No such file or directory) while connecting to upstream, client: 86.62.155.78, server: galaxy-arc-test.itf.uiocloud.no, request: "GET /api/entry_points?running=true HTTP/1.1", upstream: "http://unix:/storage/srv/galaxy/var/config/gunicorn.sock:/api/entry_points?running=true", host: "galaxy-arc-test.itf.uiocloud.no", referrer: "https://galaxy-arc-test.itf.uiocloud.no/admin"
If I instead install
release_23
everything works as expected and gunicorn.sock is created. And I can use the galaxy server and submit jobs.Galaxy Version and/or server at which you observed the bug dev branch of https://github.com/galaxyproject/galaxy
Installed on a test galaxy-server running almalinux 9. selinux is turned off for testing purposes.
To Reproduce Steps to reproduce the behavior:
Expected behavior Galaxy server should start as normal.