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Fix #5994: make etc/run-jupyterhub.sh work again #5995

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merged 7 commits into from
Jun 27, 2023
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  • notebook must now be installed explicitly
  • serverextension call is no longer needed with the version of notebook we install
  • jupyterhub_debug was removed in favor of feature_config.debug but this needed to be cascaded in the jupyterhub conf jinja

- notebook must now be installed explicitly
- serverextension call is no longer needed with the version of notebook we install
- jupyterhub_debug was removed in favor of feature_config.debug but this
needed to be cascaded in the jupyterhub conf jinja
@e-carlin e-carlin requested a review from rorour June 20, 2023 22:45
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@rorour ping

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rorour commented Jun 27, 2023

Not working for me. I keep getting "error: jupyterlab-server: not installed run pip install jupyterlab-server==2.8.2" which i've already run. Here is the full output.

[py3;@v sirepo]$ bash etc/run-jupyterhub.sh
nginx: [alert] could not open error log file: open() "/var/log/nginx/error.log" failed (13: Permission denied)
2023/06/26 20:21:35 [warn] 242217#242217: could not build optimal types_hash, you should increase either types_hash_max_size: 2048 or types_hash_bucket_size: 64; ignoring types_hash_bucket_size
2023/06/26 20:21:35 [notice] 242217#242217: using the "epoll" event method
2023/06/26 20:21:35 [notice] 242217#242217: nginx/1.24.0
2023/06/26 20:21:35 [notice] 242217#242217: OS: Linux 6.2.10-100.fc36.x86_64
2023/06/26 20:21:35 [notice] 242217#242217: getrlimit(RLIMIT_NOFILE): 1024:524288
2023/06/26 20:21:35 [notice] 242217#242217: start worker processes
2023/06/26 20:21:35 [notice] 242217#242217: start worker process 242218
sirepo/job_driver/__init__.py:408:init_module modules=['local']
sirepo/pkcli/job_supervisor.py:82:default_command ip=127.0.0.1 port=8001
sirepo/pkcli/service.py:241:tornado ip=0.0.0.0 port=8000
error: jupyterlab-server: not installed run `pip install jupyterlab-server==2.8.2`
etc/run-jupyterhub.sh: line 1: kill: (242027) - No such process
2023/06/26 20:21:36 [notice] 242217#242217: signal 15 (SIGTERM) received from 242025, exiting
2023/06/26 20:21:36 [notice] 242218#242218: exiting
2023/06/26 20:21:36 [notice] 242218#242218: exit
2023/06/26 20:21:36 [notice] 242217#242217: signal 17 (SIGCHLD) received from 242218
2023/06/26 20:21:36 [notice] 242217#242217: worker process 242218 exited with code 0
2023/06/26 20:21:36 [notice] 242217#242217: exit

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Sorry, I had a fix but forgot to push. Try now.

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rorour commented Jun 27, 2023

Thanks. I'm now running into this- should i run npm install -g configurable-http-proxy?

[D 2023-06-26 20:30:05.501 JupyterHub proxy:704] Proxy cmd: ['configurable-http-proxy', '--ip', '127.0.0.1', '--port', '8002', '--api-ip', '127.0.0.1', '--api-port', '8111', '--error-target', 'http://127.0.0.1:8081/jupyter/hub/error', '--log-level', 'debug']
[E 2023-06-26 20:30:05.505 JupyterHub proxy:711] Failed to find proxy ['configurable-http-proxy']
    The proxy can be installed with `npm install -g configurable-http-proxy`.To install `npm`, install nodejs which includes `npm`.If you see an `EACCES` error or permissions error, refer to the `npm` documentation on How To Prevent Permissions Errors.

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Yes but realizing how this works now I think it is goofy to make the user install all deps. I'm going to move the install into etc/run-jupyterhub.sh. I'll report back when done.

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c34fddf Deps are now installed for you. Please try again.

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Works now and I think it's much better with the installations in the script.

@rorour rorour enabled auto-merge (squash) June 27, 2023 18:00
@rorour rorour merged commit 9362b5e into master Jun 27, 2023
@rorour rorour deleted the 5994-run-jupyterhub branch June 27, 2023 18:18
Benbenbenin0 added a commit that referenced this pull request Jul 13, 2023
* Fix #5879 radia cylindrical divisions (#5923)

* Fix #5947: move pump_type and rename laser gain tab (#5952)

* Fix #5945: add description for thermal lensing (#5957)

* fix #5937 omega beam centering and error handling (#5959)

* Fix #5944: silas plot units (#5963)

Also fixes new drift and lens module names. Replace chirp with tau_0

* fix #5965 omega fixes (#5966)

- added default values for simWorkflow
- improved layouts
- improved genesis error handling

* Fix #5931: show error if no epics server on start monitor (#5956)

* Fix #5974 radia local cut plane (#5975)

* Fix #5974 - adds center to cut point when specified

---------

Co-authored-by: mkeilman <mkeilman@radiasoft.net>

* fix #3932 include rpnVariables for twissReport cache (#5968)

* fix #5414 added more precision and removed quotes from elegant csv output (#5967)

* fix #5942 match silas results with notebook (#5964)

* Fix #5954: improve silas panel layout (#5960)

* Fix #5596 Add file_lock concurrency protection (#5848)

* Fix #5596 Add file_lock concurrency protection
- Fix #5740 ensure serial greater than incoming and on disk
- Fix #5742 restricted critical sections and removed most
- Fix #5743 migrate_guest_to_persistent_user locks new and guest uid
- Fix #5744 simulation_dir uses lock_user
- Fix #5745 validate version in save_simulation_json
- Fix #5746 removed lock on auth.unchecked_get_user
- Fix #5747 complete_registration passed display_name
- Fix #5749 removed auth_db locking, verified all critical sections
- Fix #5750 thread locking only in flask
- Fix #5751 add auth.create_and_login_user for testing

* fix radiasoft/raydata#62: remove unused options (Simulation Documentation URL, Export as Zip, Python Source) in raydata settings submenu (#5891)

* Fix #5642 pkuinit.restart_or_fail if `_ping_supervisor` fails (#5643)

* fix #5979 fix missing case in plot axis tick formatting (#5987)

* Fix #5978: fixed scale bug in hellweg (#5992)

* fix #5982 use new hellweg binary output format, gamma vs beta (#5997)

* Fix #5983 copy reacts build files into /static (#5984)

* fix #5998 improve hellweg source generation, fixed energy scaling (#5999)

* Fix #5991 - omit one-time eval (#6006)

* Fix #5996: add particles keyword to hellweg (#6001)

* Fix #6018 static_files.gen correctly copies react bundle files (#6019)

* Fix #5943: error message non premium (#5971)

* Fix #5994: make etc/run-jupyterhub.sh work again (#5995)

* Fix #5994: make etc/run-jupyterhub.sh work again

- notebook must now be installed explicitly
- serverextension call is no longer needed with the version of notebook we install
- jupyterhub_debug was removed in favor of feature_config.debug but this
needed to be cascaded in the jupyterhub conf jinja

* fix list

* importable package is with an underscore

* install deps so users dont have to

---------

Co-authored-by: Raven <ravenmarieorourke@gmail.com>

* fix #6029 omega qcall work-around (#6030)

* fix #5734 fixes for email login on react (#5973)

* Fix #5819 radia lock objects (#5969)

* fix #6013 work-around hellweg rf fields bug (#6014)

* Fix #5948 always calculate n0 and n2 using fenics (#6015)

* Fix #6004: change laser pulse units (#6016)

* Fix #6032 - try small instead of subscript (#6035)

* Fix #6044 - replaced segmentationCylRadius field in view (#6045)

Co-authored-by: mkeilman <mkeilman@radiasoft.net>

* fix #5588 omega improvements (#6054)

* Fix #6055 default to tornado api_server in dev mode (#6072)

* Fix #6055 default to tornado api_server in dev mode

* Fix #6074 remove google_tag_manager

---------

Co-authored-by: Raven <ravenmarieorourke@gmail.com>

* Fix #6083: auth.login creates the uid (#6084)

In 791364f the api_authEmailAuthorized
code was changed from passing the user model we acquired based on
searching by the email token to one acquired by searching for the uid
into auth.login.

Previous behavior: 791364f#diff-109de77eab3047455095be7e4c1f5f1d918083adaa02b87d5c862a8e513e8436L61
Behavior introduced in 791364f: 791364f#diff-109de77eab3047455095be7e4c1f5f1d918083adaa02b87d5c862a8e513e8436R89

But, the uid isn't present on the model. auth.login
creates the user and populates the uid. In the case where we have
multiple records in auth_email_user_t without a uid the query would
return all of the records even though we are looking for just one.

This reverts the behavior to what it was previously.

* fix #6077 fix to omega for new opal release (#6090)

* Fix #5936: beamline named amplifier for silas (#6043)

* Fix #6037: replace experimental comparison with new example (#6080)

* Fix #6046: "completed reports" instead of "animation" (#6051)

* fix #6093 silas crystal UI improvements (#6094)

* Fix #6017 improve cloudmc 3d toolbar (#6027)

* fix #5829 implement parallel geometry extraction (#6048)

* Fix #6049 - all object edges now black (#6050)

* Fix #6047 - added axis ratio parameter (#6052)

* fix 6095 increase server_test timeout (#6096)

* fix #6058: raydata start and stop search times pre-populated (#6082)

* Fix #6095 added TestClient.DEFAULT_TIMEOUT_SECS (#6098)

* Fix #6101 increase timeouts in file_lock_test (#6102)

---------

Co-authored-by: Michael Keilman <30352290+mkeilman@users.noreply.github.com>
Co-authored-by: Gurhar Khalsa <49498231+gurhar1133@users.noreply.github.com>
Co-authored-by: Paul Moeller <moeller@radiasoft.net>
Co-authored-by: mkeilman <mkeilman@radiasoft.net>
Co-authored-by: Rob Nagler <github@q33.us>
Co-authored-by: Raven <ravenmarieorourke@gmail.com>
Co-authored-by: Evan Carlin <evan@carlin.com>
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2 participants