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marine-manche
@marine-manche

Hello,
I have a problem with my Renku project. I'm working with heavy datasets and I don't manage to unzip heavy .bz2 files to pickle them. When I am running my code, the kernel automatically restarts after a few minutes.
I am working with an 8G memory and 64G storage session and the size of the datasets I don't manage to download are about 500MB when they are zipped.
My code works for lighter datasets (below 500MB) so I think it's a size problem. Is there a way to open a session with more resources?

Thanks in advance for your help!

3 replies
Noe Thalheim
@noeleont
Hello everyone
Has someone experience with sync user forks with a upstream repo? I tried using the following approach inside the post-init.sh script, but since the container has no network at this stage this doesn’t work. Currently I’m testing a cron based approach but this doesn’t seem to be the right direction.
4 replies
Waldo Rivier
@waldorivier_gitlab
Hello everyone, could somebody help me for the problem I have submitted below as 22.02.2022 ? thanks a lot for replying and have a nice day. Waldo.
Tasko Olevski
@olevski

Hello everyone, could somebody help me for the problem I have submitted below as 22.02.2022 ? thanks a lot for replying and have a nice day. Waldo.

Hi Waldo you are referring to your image not building in one of your projects? Have you tried simply re-running the CI job? It seems to me like this could be an intermittent problem related to maybe low resources or problems with our Gitlab deployment.

7 replies
ansonrel
@ansonrel
Hello, I think that new Renku projects with R/Bioconductor templates have a problem with the installation of Renku: bash: renku: command not found. I have tested new project with Python/ Minimal Renku and it seems ok. Not sure, but I think it's not only for v1.1.1 but also for prior versions. Does it also happen with other people .. ?
3 replies
Eugenio Naselli
@eunaselli:staffchat.ethz.ch
[m]
hi @rokroskar
I've opened today SwissDataScienceCenter/renku#2523
i think it would be a nice improvement for all kind of deploys
Rok Roškar
@rokroskar
great! Does this mean you'll be submitting a PR :)
Eugenio Naselli
@eunaselli:staffchat.ethz.ch
[m]
It's more of a design choice on your side for this
I wouldn't want to rely on an external container, but i don't know what other tools would you need for that
but if you already use a repository for docker containers...
Rok Roškar
@rokroskar
we don't have to rely on an external container, we can build another one ourselves. But we should definitely not install things in the configmap, I agree with you on that!
Eugenio Naselli
@eunaselli:staffchat.ethz.ch
[m]
do you have any preference on the underlying OS? debian or ubuntu
and/or any specific versions of psql/curl/jq?
Rok Roškar
@rokroskar
lets take this over to the issue so it's easier to identify later - I can point to where I think the implementation/definition should go as well
thanks for bringing this up, it's an important point!
Eugenio Naselli
@eunaselli:staffchat.ethz.ch
[m]
you're welcome
Eric Pohl
@pohleric
Hello, I updated my renku version and now I am getting a message "The session could not start because no image is available. Please select a different commit or start the session with the base image." It seems it doesn't matter which commit I choose - the image is just gone. If I look on the gitlab page, I do not see any container listed there. I made a pinned image when creating the environment for my students. My colleague, who forked my project, gets the same error.
75 replies
Noe Thalheim
@noeleont
Hello everyone, I was wondering if a setting for renku.ini exists to set the maxium session timelimit, i.e. terminating an user session after x minutes with no new input.
4 replies
Javi Rando
@javirandor
Hi, there! My Renku session suddenly stopped and when I went to the Sessions screenn, it appeared as launching again. After a while, it was not starting so I decided to stop it and launch a new one but it will never stop. Any clue about what might be going on and how I can solve it? Thanks a lot.
10 replies
fhuerlimann
@fhuerlimann
Dear Renku team. It would be great if you could assist me with a technical issue: I cannot access a session I started yesterday (sluis/verticalgarden-cvae-florian). For about 3 hours, the status is shown as "starting...". Is this session really starting or is the deployment maybe stuck in a loop? Thanks for your help, Florian.
3 replies
Giulia Ruggeri
@gruggeri

Hello,

I am trying to lunch a session on a forked repository and it says that the docker imagine build failed ( the message from the email is that Pipeline #338770 has failed). In the original repository I am able to start an RStudio session.
I have also started a pipeline under CI/CD in gitlab.
If this helps, it was working last year in the forked repository.
Let me know which other information I can provide for you to be able to help.

Best,
Giulia

22 replies
csulkowskibfs
@csulkowskibfs

Hi everyone,
I am trying to start a session on Renku Health but all of them end up failing before restarting. The session generated after this restart contains none of my files and git appears to be empty.

Specifically, the error message when the session initially fails to start: "There are failures in 1 auxiliary server containers. Please restart your session as this may be an intermittent problem. If issues persist contact your administrator or the Renku team."

Would you know how to solve this?

Sincerely,
Chris

25 replies
Rok Roškar
@rokroskar
image.png
3 replies
@gruggeri here is an example of how to set the pinned image
lappemic
@lappemic

Hi everyone,
Last week i signed up for a renku account through GitHub and did the tutorial. Everything worked fine and i really enjoyed the renku experience. Yesterday i now installed renku CLI (mbp, M1, Monterey), which also worked fine. But since then i get an error when trying to login to the webinterface of renku getting an 422 error. Does anybody know what the issue could be about?

Thanks in advance for any hints.

Best
Michael

10 replies
lappemic
@lappemic
Bildschirmfoto 2022-04-11 um 07.16.36.png
This is the page i get to
Giulia Ruggeri
@gruggeri
Hi Renku dev team. Tomorrow morning and on Thursday afternoon we will be giving a workshop using renku.io with ~20 participants. Just flagging this in case you need to do any maintenance during that time. Thanks! Giulia
1 reply
lappemic
@lappemic
Hi everyone, i just wanted to work on my project. Initializing a new session worked fine for several tried. Now i get the error message '404 Page not found' for several times. First i thought it needs some time to do the commits but after 10 minutes it still does not work. Do you know what the issue is here? -> Project name and error description in the Image
5 replies
Bildschirmfoto 2022-05-09 um 09.00.59.png
lappemic
@lappemic
Bildschirmfoto 2022-05-09 um 13.34.29.png
Rok Roškar
@rokroskar
Hi everyone, we have an RFC (request for comment) open for building better support for external data in Renku - if you're interested and want to use things like S3 and other network attached storage with Renku, please give it a look and feel free to make suggestions! The PR is here: SwissDataScienceCenter/renku-rfc#8
marine-manche
@marine-manche
Hi everyone,
I have forgotten to save my work on renkulab last friday and the autosave that have been restored while opening a session today doesn't contain the work I have done, is there a way I can recover my work?
I can see now on Gitlab that there is a deleted autosave branch but trying to open a new branch from the same commit SHA also doesn't show the work I've done on my last session.
12 replies
Eric Pohl
@pohleric

Hello, when trying to start a session on renku.unifr.ch my students (and me) are stuck with the message:
"Starting session

Checking project data..."
Can someone help?

10 replies
James Runnalls
@JamesRunnalls
Hi All, I am having some trouble deleting repositories. When I try to delete the repo in renkulab.io/gitlab I get the following error: "This project was scheduled for deletion, but failed with the following message: Failed to remove some tags in project container registry. Please try again or contact administrator."
12 replies
Andrei V. Plamada
@aplamada
Hello everyone,
A short question about the JupyterLab . I noticed that File -> Shut Down is not stopping the session. Is this as expected?
4 replies
rihst
@rihst

Hello I am trying to install the epiR package on R on Renkulab. Unfortunately I get the following error message: > install.packages("epiR")
Installing package into ‘/home/rstudio/R/x86_64-pc-linux-gnu-library/4.1’
(as ‘lib’ is unspecified)
trying URL 'https://packagemanager.rstudio.com/cran/__linux__/focal/2022-03-09/src/contrib/epiR_2.0.43.tar.gz'

Content type 'binary/octet-stream' length 1461903 bytes (1.4 MB)

downloaded 1.4 MB

  • installing binary package ‘epiR’ ...
  • DONE (epiR)

The downloaded source packages are in
‘/tmp/RtmpZcs5Qb/downloaded_packages’

library(epiR)
Loading required package: survival
Error: package or namespace load failed for ‘epiR’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/rstudio/R/x86_64-pc-linux-gnu-library/4.1/units/libs/units.so':
libudunits2.so.0: cannot open shared object file: No such file or directory

4 replies
Even though the epiR package appears to be in the indicated directory. Any clues as to what could be the reason for not letting me install this package ? Many Thanks T.
Eugenio Naselli
@eunaselli:staffchat.ethz.ch
[m]
goodmorning
(e.g. a new release coming our way?)
Eugenio Naselli
@eunaselli:staffchat.ethz.ch
[m]
thank you!
Rok Roškar
@rokroskar

@eunaselli:staffchat.ethz.ch note that you can upgrade your gitlab instance whenever you want - you just need to override the image tag in the values file for your deployment. However, do be aware of the upgrade paths of gitlab: https://docs.gitlab.com/ee/update/#upgrade-paths

According to the gitlab docs, the upgrade path should be 14.4.4 -> 14.9.5 -> 14.10.5 so you will need to update your values file and do a helm upgrade two separate times.

Pamela
@pameladelgado
@eunaselli:staffchat.ethz.ch just in case you haven't seen: we made a couple of new renku releases that include GitLab updates to 14.9.5 and 14.10.5, both of which have been rolled out to renkulab.
Eugenio Naselli
@eunaselli:staffchat.ethz.ch
[m]
thank you
i lost the notification, but was following the release notes for that
ruizcrp
@ruizcrp
Hi there, Cyril gave me the link to ask you here directly about our issue. We are having unexplicable issues with one repo. that make working impossible, meaning 504 errors, non-responsiveness and very slow performance. But it seems that only I have this issue. Cyril and another colleague tried to replicate my issue and couldn'tn. To replicate for me I just to have to open an entirely new session in this repo (https://renkulab.io/projects/christian.ruiz/statbot-swiss-db-migration), and rstudio would already give 504 on starting up. Only if lfs is activated. Symtoms (to find the cause) might be that he shows in the logs:
2022-08-10T14:53:26.121761372Z INFO:root:Autosave found remotes/origin/renku/autosave/christian.ruiz@statistik.ji.zh.ch/master/6d901bb/6d901bb
2022-08-10T14:53:26.121815567Z INFO:root:Recovering autosave remotes/origin/renku/autosave/christian.ruiz@statistik.ji.zh.ch/master/6d901bb/6d901bb
But there is no autosave branch. On the renkulabs front-end he also proposes to delete the autosave, which I click on, but apparently he thinks that it is still there. Maybe another symtom: On gitlab he says that the repo is 58GB large. But while browsing through (and Cyril did as well) we can with du and dust not find large files. RIght now, the renku datasets that are loaded have a maximum of 3.7GB. So we could not really figure out, where these 58GB are supposed to be.
If I turn off git lfs, then at least I can reach the repo. It would be really great if you could help us out here.
22 replies
ruizcrp
@ruizcrp
(With jupyterlab he does not crash 504 but is super slow. E.g. opening the terminal took long and the command "renku dataset update --all" took maybe 15-20minutes to give the error: Error: The repository is dirty. Please use the "git" command to clean it. Yes, this after just opening the session and writing it in the jupyterlab terminal)
(We don't have much fancy scripts in that repo. We work very strongly with renku datasets and imported and removed many of them for a long time (trying out many things). We work with duckdb to create a large db-file (3.7GB as mentioned). We do not use renku workflows in this repo. We now use multi-repo CI/CD but I think that these issues happened before we really started with multi-repo CI/CD)
lappemic
@lappemic
Hey there, i am trying to install solaris (https://github.com/CosmiQ/solaris) in a notebook session but i am always failing. Has anyone experience setting up solaris in renku or elsewhere?
Many thanks in advance for any pointers!
Best, Michael
2 replies