jupyter hub login issue

[rjs360]

Hi there, Can you tell me what the login credentials are for the jupyter hub docker? I believe I have successfully installed the ethoscope-lab/ethoscopy docker image on my node, but I am stuck at the jupyter hub login page. I tried "default" login credentials posted online (jovyan/jupyter) and my node login credentials, but they do not work.

thanks for any info on this. -Ruud

[rjs360]

Ok never mind that question, I found the login credentials here: https://hub.docker.com/r/ggilestro/ethoscope-lab

But currently it seems it is not working: after login in with said credentials I get this error at http://localhost/hub/spawn-pending/ethoscopelab:

"Spawn failed: Server at http://127.0.0.1:44341/user/ethoscopelab/ didn't respond in 30 seconds"

Does that error look familiar? I may not have setup the ethoscope-lab docker properly (no experience with docker as of today).

Thanks for any help. -Ruud

[ggilestro]

Did you mount the docker to use an external home folder? If yes, you just need to make sure that the ethoscopelab user has rw access to that folder.

[rjs360]

I followed the instructions here: https://bookstack.lab.gilest.ro/books/ethoscopy/page/getting-started

The only thing I had to add was: ":0.91" after "ggilestro/ethoscope-lab" to access the latest image/container and allow it to be downloaded.

Should I do more than that, prior to trying to access port 8080 in a browser?
E.g., I am seeing different instructions at your github (https://github.com/gilestrolab/ethoscopy/tree/main/docker)

I just tried the same installation procedure on another machine running node software (but without any ethoscope wifi connection) at home, and while it seems to install the docker container just fine, I cannot even access localhost:8080 (this may have something to do with network properties from what I can read online), with a "connection was reset" error being thrown.

As an alternative, since I am not looking to necessarily have many users access ethoscopy, would the "basic" installation in a python environment be equally functional as the docker version?

-Ruud

[ggilestro]

The second set of instructions on github is there just to explain how the image was created. You can disregard that. The bookstack instructions are the way to go.

If you get this error:

"Spawn failed: Server at http://127.0.0.1:44341/user/ethoscopelab/ didn't respond in 30 seconds"

It means the docker container starts fine but cannot access the home folder of the user you're logging in with. Usually an issue of credentials or perhaps you did not create an ethoscopelab folder in your home?

[ggilestro]

Hi @rjs360 - I have updated the instruction set on the bookstack. Would you be so kind to have a look there and see if now makes sense? I think some important information regarding home folders was given for granted.

[rjs360]

Thanks @ggilestro; this is helpful for me, and looks like it may solve my earlier issue with my attempt on my node. I will give this a try later (today I hope). One thing that I ran into (as stated above) is that I had to specify the tag for the latest ethoscopy image that had to be installed. Is that still the case?

I.e. when I used ".... ggilestro/ethoscope-lab" in the command, I ran into an error stating that it could find the latest image (or something similar). This seemed to be an issue that other dockerhub users (for other softwares) run into sometimes, as there was a solution online (i.e., specify the latest image version tag; in this case adding ":0.91"). This seemed to work (i.e., installation moved forward), other than the "spawn failed" error later...

I will report back.

[ggilestro]

yes, this was also an overlook on my side. I had the image uploaded as 0.91 but not latest which is the default tag. Now this is fixed thanks to you.

[rjs360]

Ok, apologies for this lengthy comment; I am still having an issue. I am going to dump the complete output of the various installation commands, hope that is ok. I figure it may help diagnose. I ran the following on my freshly created node:

"sudo pacman -S docker"

This actually threw an error, stating that I should use the -Sy flag to install a few database file for 'core', 'extra', 'community', 'multilib', 'ethoscope'. I figured this may be due to the fact that I hadn't run any ethoscopes on this node, or updated the node software via localhost:8888 (I am using a secondary node machine on which I am troubleshooting this docker issue). So I used the -Sy flag instead.

output:

:: Synchronizing package databases... core 143.6 KiB 116 KiB/s 00:01 [######################] 100% extra 1636.8 KiB 667 KiB/s 00:02 [######################] 100% community 7.0 MiB 2.02 MiB/s 00:03 [######################] 100% multilib 145.5 KiB 713 KiB/s 00:00 [######################] 100% ethoscope 1044.0 B 2.14 KiB/s 00:00 [######################] 100% error: failed retrieving file 'core.db' from manjaro.barata.pt : Could not resolve host: manjaro.barata.pt warning: too many errors from manjaro.barata.pt, skipping for the remainder of this transaction error: failed retrieving file 'core.db' from mirror.ragenetwork.de : Could not resolve host: mirror.ragenetwork.de warning: too many errors from mirror.ragenetwork.de, skipping for the remainder of this transaction :: Some packages should be upgraded first... resolving dependencies... looking for conflicting packages...

Packages (3) archlinux-keyring-20230504-1 manjaro-keyring-20230615-1 manjaro-system-20230401-1

Total Download Size: 1.72 MiB Total Installed Size: 2.34 MiB Net Upgrade Size: 0.04 MiB

:: Proceed with installation? [Y/n] y :: Retrieving packages... archlinux-keyrin... 1164.5 KiB 254 KiB/s 00:05 [######################] 100% manjaro-keyring-... 563.0 KiB 840 KiB/s 00:01 [######################] 100% manjaro-system-2... 29.0 KiB 211 KiB/s 00:00 [######################] 100% Total (3/3) 1756.5 KiB 291 KiB/s 00:06 [######################] 100% (3/3) checking keys in keyring [######################] 100% (3/3) checking package integrity [######################] 100% (3/3) loading package files [######################] 100% (3/3) checking for file conflicts [######################] 100% (3/3) checking available disk space [######################] 100% :: Processing package changes... (1/3) upgrading archlinux-keyring [######################] 100% ==> Appending keys from archlinux.gpg... ==> Disabling revoked keys in keyring... -> Disabled 2 keys. ==> Updating trust database... gpg: marginals needed: 3 completes needed: 1 trust model: pgp gpg: depth: 0 valid: 1 signed: 21 trust: 0-, 0q, 0n, 0m, 0f, 1u gpg: depth: 1 valid: 21 signed: 96 trust: 0-, 0q, 0n, 21m, 0f, 0u gpg: depth: 2 valid: 73 signed: 27 trust: 73-, 0q, 0n, 0m, 0f, 0u gpg: next trustdb check due at 2023-07-07 ==> Updating trust database... gpg: next trustdb check due at 2023-07-07 ==> Delete expired Key by Jonas Strassel ==> Updating trust database... gpg: marginals needed: 3 completes needed: 1 trust model: pgp gpg: depth: 0 valid: 1 signed: 20 trust: 0-, 0q, 0n, 0m, 0f, 1u gpg: depth: 1 valid: 20 signed: 96 trust: 0-, 0q, 0n, 20m, 0f, 0u gpg: depth: 2 valid: 73 signed: 27 trust: 73-, 0q, 0n, 0m, 0f, 0u gpg: next trustdb check due at 2023-07-12 (2/3) upgrading manjaro-keyring [######################] 100% ==> Appending keys from manjaro.gpg... gpg: error reading key: No public key gpg: error reading key: No public key gpg: error reading key: No public key gpg: error reading key: No public key gpg: error reading key: No public key gpg: error reading key: No public key gpg: error reading key: No public key gpg: error reading key: No public key ==> Locally signing trusted keys in keyring... -> Locally signed 3 keys. ==> Importing owner trust values... gpg: setting ownertrust to 4 ==> Disabling revoked keys in keyring... -> Disabled 8 keys. ==> Updating trust database... gpg: marginals needed: 3 completes needed: 1 trust model: pgp gpg: depth: 0 valid: 1 signed: 21 trust: 0-, 0q, 0n, 0m, 0f, 1u gpg: depth: 1 valid: 21 signed: 96 trust: 0-, 0q, 0n, 21m, 0f, 0u gpg: depth: 2 valid: 73 signed: 27 trust: 73-, 0q, 0n, 0m, 0f, 0u gpg: next trustdb check due at 2023-07-07 (3/3) upgrading manjaro-system [######################] 100% ==> Checking for 'os-prober' setup ... 'os-prober' was already enabled by the user. ==> Checking if graphic drivers need an update ... :: Running post-transaction hooks... (1/2) Reloading system manager configuration... (2/2) Arming ConditionNeedsUpdate...

resolving dependencies... looking for conflicting packages...

Packages (1) docker-1:24.0.0-1

Total Download Size: 26.90 MiB Total Installed Size: 107.25 MiB Net Upgrade Size: -6.30 MiB

:: Proceed with installation? [Y/n] y :: Retrieving packages... docker-1:24.0.0-... 26.9 MiB 2.44 MiB/s 00:11 [######################] 100% error: failed retrieving file 'docker-1:24.0.0-1-x86_64.pkg.tar.zst' from manjaro.barata.pt : Could not resolve host: manjaro.barata.pt warning: too many errors from manjaro.barata.pt, skipping for the remainder of this transaction error: failed retrieving file 'docker-1:24.0.0-1-x86_64.pkg.tar.zst' from mirror.ragenetwork.de : Could not resolve host: mirror.ragenetwork.de warning: too many errors from mirror.ragenetwork.de, skipping for the remainder of this transaction (1/1) checking keys in keyring [######################] 100% (1/1) checking package integrity [######################] 100% (1/1) loading package files [######################] 100% (1/1) checking for file conflicts [######################] 100% (1/1) checking available disk space [######################] 100% :: Processing package changes... (1/1) upgrading docker [######################] 100% :: Running post-transaction hooks... (1/4) Creating system user accounts... (2/4) Reloading system manager configuration... (3/4) Reloading device manager configuration... (4/4) Arming ConditionNeedsUpdate...

After this I ran:

"sudo systemctl enable --now docker"

output: Created symlink /etc/systemd/system/multi-user.target.wants/docker.service → /usr/lib/systemd/system/docker.service.

Then I created the folder "mnt/ethoscopelab" inside of my "home/rs" folder, and after that finally ran:

"sudo docker run -d -p 8080:8080 \ --name ethoscope-lab \ --volume /ethoscope_data/results:/mnt/ethoscope_results:ro \ --volume /home/rs:/mnt/ethoscopelab \ --restart=unless-stopped \ ggilestro/ethoscope-lab"

output:

Unable to find image 'ggilestro/ethoscope-lab:latest' locally latest: Pulling from ggilestro/ethoscope-lab 6e3729cf69e0: Pull complete ade329ff1403: Pull complete db3b5a805d84: Pull complete 208cd0f39b71: Pull complete 2f5b8bde0770: Pull complete fc7dfbacb6a0: Pull complete d8af36bc5c2f: Pull complete a4091873ae51: Pull complete 4f4fb700ef54: Pull complete dbaa6eb48730: Pull complete 0f93cb5fb545: Pull complete e531ba29484c: Pull complete 2b94541afb63: Pull complete 603f046b4b69: Pull complete 035b4fb2f684: Pull complete 6014db82c829: Pull complete c83c39cf81be: Pull complete bdaaee586218: Pull complete 0bbbede71baf: Pull complete c4d6e925f196: Pull complete 97f149329ee7: Pull complete 30edd0484956: Pull complete 39242e5c00be: Pull complete Digest: sha256:6659ef047fe18a68dc73065890fd2433e0fc0adf73a5315c5bcae82e85c4abaf Status: Downloaded newer image for ggilestro/ethoscope-lab:latest 04a361d6c07e6d72d1fc367901d63cf1234e9894b7a8005eafe934b35dc8ec8d

I checked if docker is running:

"sudo docker ps"

output: CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES 04a361d6c07e ggilestro/ethoscope-lab "sh -c jupyterhub" 28 minutes ago Up 28 minutes 8000/tcp, 0.0.0.0:8080->8080/tcp, :::8080->8080/tcp ethoscope-lab

So the docker image/container seems to be running, but when I point Firefox to "localhost:8080", it tells me that the connection was reset, and no jupyterlab login page (as before) is loaded...

Any thoughts?

Thanks for the continued support on this. -Ruud

On Thu, Jun 15, 2023 at 9:41 AM Giorgio Gilestro @.***> wrote:

yes, this was also an overlook on my side. I had the image uploaded as 0.91 but not latest which is the default tag. Now this is fixed thanks to you.

— Reply to this email directly, view it on GitHub https://github.com/Lblackhurst29/ethoscopy/issues/2#issuecomment-1593088208, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABSQSRR47FAO257DYHHXRK3XLMGH7ANCNFSM6AAAAAAZA5XLAA . You are receiving this because you were mentioned.Message ID: @.***>