ssh -T git@renkulab.io
git@renkulab.io: Permission denied (publickey) working on this template: https://renkulab.io/gitlab/aaron.spring/s2s-ai-challenge-template/-/blob/master/README.md
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Hi, since this storage setting of 16GB max was introduced (and I updated to renku=0.16 today), I cannot run this notebook anymore on renkulab.io: https://renkulab.io/gitlab/aaron.spring/s2s-ai-challenge-template/-/blob/master/notebooks/ML_train_and_predict.ipynb
Traceback:
...
Error updating the git index:
Error cleaning LFS object: write /work/s2s-ai-challenge-template/.git/lfs/tmp/210917465: no space left on device
error: packet write failed
error: external filter 'git-lfs filter-process --skip' failed
fatal: data/ecmwf_forecast-input_2020_biweekly_deterministic.zarr/t2m/0.0.0.0.0: clean filter 'lfs’ failed
exit status 128
…
The files I am pulling are less than 16 GB.
2 replies
we want to call to your attention to the maintenance that renkulab.io will be undergoing later today (at 10:30AM CEST for 2 hours).
During this time all services will be unavailable and all user sessions will be killed without the possibility of recovery.
We take the opportunity to remind you to subscribe to our status page if you wish to receive notifications about future maintenance.
Thank you for using renku!
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`ls -l /var/run/rstudio-server/revocation-list` that gives
`-rw------- 1 rstudio users 0 Aug 26 19:03 /var/run/rstudio-server/revocation-list`
All docker images I compiled after that have broken RStudio. So, I revert back to same `Dockerfile`, same `install.R`, same everything than the previous working one... and I still got a broken RStudio with the message
"500: Internal Error, could not start rstudio in time"
(this is registry.renkulab.io/sciviews/svbox-renku:d59816e). On a terminal from Jupyterlab, I have:
`/usr/lib/rstudio-server/bin/rserver --www-port=8787
27 Aug 2021 14:06:27 [rserver] ERROR system error 1 (Operation not permitted) [path: /var/run/rstudio-server/revocation-list, description: Could not set revocation file permissions to 600 for file: /var/run/rstudio-server/revocation-list]; ...`
and
`ls -l /var/run/rstudio-server/revocation-list
-rw------- 1 rstudio-server rstudio-server 0 Aug 26 17:01 /var/run/rstudio-server/revocation-list`
Obviously, RStudio is started with the wrong (default) "rstudio-server" user, but it should be "rstudio". How two compilations of Docker images with same data could give two different results?
25 replies
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make-values.sh providing my gitlab url & application credentials. Then I installed renku using helm providing the generated values. Every pod runs fine except for the renku-gateway-auth one which fails with "Obtaining public key from https://<redacted>/auth/realms/Renku" which leads me to believe that something is wrong with the keycloak configuration (note that I have not done any specific configuration except for the make-values.sh). Browsing https://<redacted>/auth/realms/Renku gets me a keycloak page with "We are sorry...Page not found".
Any tips on what to configure for keycloak ?
11 replies
%run -m rpy2.situation
rpy2 version:
3.4.5
Python version:
3.9.5 | packaged by conda-forge | (default, Jun 19 2021, 00:32:32)
[GCC 9.3.0]
Looking for R's HOME:
Environment variable R_HOME: /usr/local/lib/R
Calling R RHOME: /opt/conda/lib/R
Environment variable R_LIBS_USER: None
Warning: The environment variable R_HOME differs from the default R in the PATH.
R's additions to LD_LIBRARY_PATH:
/usr/local/lib/R/lib
R version:
In the PATH: R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Loading R library from rpy2: OK
Additional directories to load R packages from:
None
C extension compilation:
include:
['/usr/local/lib/R/include']
libraries:
['R', 'pcre2-8', 'lzma', 'bz2', 'z', 'rt', 'dl', 'm', 'icuuc', 'icui18n']
library_dirs:
['/usr/local/lib', '/usr/local/lib/R/lib']
extra_compile_args:
[]
extra_link_args:
['-Wl,--export-dynamic', '-fopenmp']
I believe this shows that there are two separate installations. I can run the rpy2 one by changing the R_HOME variable (os.environ['R_HOME'] = '/opt/conda/lib/R') but I then do not have access to the packages installed by R. So my question is, should I just add the R folder to my library folder to use the packages installed by install.R, or is there a more direct way to use the exact same R from the start? I have tried to set the home to the conda folder inside install.R, but it tells me that the folder is not writable.
Thank
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I seem to have corrupted a bit my project somehow. It does not prevent it from working (or so that I can notice), but at every commit, I get a lot of errors like these above.
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The problem is now that students who attended the first course cannot properly fork X2. They end up getting X1 even though they choose to fork X2. This is probably a gitter question. Does anyone know what to do so students A (now in group B) can fork X2?
5 replies
Hi there! I have tried to clone a repository from a challenge names "s2s-ai-challenge" and it gives me an authentication error when using the renku clone command:
renku clone https://renkulab.io/gitlab/antonioperezvelasco/s2s-ai-challenge-predictia.git
I have tried to use my e-mail and my username with the corresponden password, but I'm not able to solve the error
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I have two out of 38 students who told me they could not save their work. They would get the attached message when they try to git push the tracked, and committed changes. Any help is appreciated:
Locking support detected on remote "origin". Consider enabling it with: $ git config lfs.https://renku.unifr.ch/gitlab/<student_name>/sp21-sgg-00272.git/info/lfs.locksverify true To https://renku.unifr.ch/gitlab/<student_name>/sp21-sgg-00272.git ! [rejected] HEAD -> master (fetch first) error: failed to push some refs to 'https://renku.unifr.ch/gitlab/<student_name>/sp21-sgg-00272.git' hint: Updates were rejected because the remote contains work that you do hint: not have locally. This is usually caused by another repository pushing hint: to the same ref. You may want to first integrate the remote changes hint: (e.g., 'git pull ...') before pushing again. hint: See the 'Note about fast-forwards' in 'git push --help' for details.
3 replies
Hello everyone, as you may have noticed by the recent notifications, we are planning to release a new version of Renku on renkulab.io tomorrow afternoon at 16:00 CET. This new version of Renku brings significant changes and improvements but it also requires us to shut down all active user sessions before doing the upgrade. Therefore please make sure you shut down any active sessions you may have on renkulab.io by 16:00 CET tomorrow (November 4th). If you leave any sessions running when we start the update process any data or code in them that has not been saved will be lost.
Please let me know if you have any questions or concerns. The update process should be finished within a few hours at most. We do not anticipate that similar interruptions will occur any time in the near future.
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Dear renkulab users,
the Renkulab 0.10.0 rollout went fine and you can now enjoy working with Renku again :tada:
Also, in case you were not aware: there was a small outage this morning on renkulab.io, see the post-mortem, if you had open sessions it's possible that unsaved work was kept in an auto-saved branch on your project. See this post for more details on how to potentially recover unsaved work and how the auto-save feature works.
Hi! I'm rather new to renku, and I'm trying to build an image based on this environment.yml: https://renkulab.io/gitlab/geert.vangeest/ngs-introduction-training/-/blob/master/environment.yml . However, during building it gives the following error:
UnavailableInvalidChannel: The channel is not accessible or is invalid.
channel name: bioconda
channel url: https://conda.anaconda.org/bioconda
error code: 404
You will need to adjust your conda configuration to proceed.
Use `conda config --show channels` to view your configuration's current state,
and use `conda config --show-sources` to view config file locations.e.g. adding conda config --add channels bioconda to the Dockerfile did not help. How should I proceed?
9 replies
