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Rok Roškar
@rokroskar
done!
Philip Durbin
@pdurbin
🎉
meschultheiss
@meschultheiss
Hello, I think I lost some work this morning : I tried to commit a file which was too large and then the jupyterlab env started to freeze. I managed to remove the large file from the commit and then push but I had conflicts to solve. Then the jupyterlab was so slow I closed the environment, hoping that renku would have autosaved my work. But after launching a new env, I was back to my work status from yesterday, and no trace of this morning work. What did I miss ? Any chance there is a copy of my notebook I cannot see ?
Also, what are the good practices to push a work with too large files ? e.g. an .html viz that was created for preview
7 replies
Waldo Rivier
@waldorivier_gitlab
Hello Renku's Team
is it possible to keep JupyterLab 's user setting between logoff / logon ?
2 replies
Waldo Rivier
@waldorivier_gitlab
Thanks for your help and have a nice day
waldorivier
@waldorivier
image.png
2 replies
Chandrasekhar Ramakrishnan
@ciyer
Hi @waldorivier. It took a little longer than had planned, but I have an example of a project that restores the JupyterLab settings. https://renkulab.io/projects/cramakri/jupyter-preferences
9 replies
meschultheiss
@meschultheiss

Hello renku team! I have an issue when building the docker image and therefore cannot start my environment. I have a warning "the docker image build failed".
I think the problem comes from the geopandas package installation. The same issue appears independently of pip or conda.

The logs are the following:

Running with gitlab-runner 13.3.1 (738bbe5a)
on renkulab-runner-2-1TB S25j9XrP
Preparing the "docker" executor
00:05
Using Docker executor with image docker:stable ...
Using locally found image version due to if-not-present pull policy
Using docker image sha256:6972c414f322dfa40324df3c503d4b217ccdec6d576e408ed10437f508f4181b for docker:stable ...
Preparing environment
00:02
Running on runner-s25XXX58-concurrent-0 via 6fabf7a874d3...
Getting source from Git repository
02:03
Fetching changes with git depth set to 50...
Reinitialized existing Git repository in /builds/gitlab/marc-edouard.schultheiss/mobis2019_activityspace/.git/
error: RPC failed; curl 52 Empty reply from server
fatal: the remote end hung up unexpectedly
ERROR: Job failed: exit code 1

5 replies
Rok Roškar
@rokroskar
Hi all: tomorrow we will have another "renku tea-time talk" - this time by @pameladelgado on the topic of deploying renku on your own infrastructure. Details on discourse: https://renku.discourse.group/t/renku-talks-ii-2020/175/2
Melvin Wong
@mwong009
hi, i have a question regarding renku dataset add command

renku dataset add command automatically sets the name of the data to the last part of the url.

how do I add data to the dataset while also having the option to rename the file?

lets say the url to the data is: drive.switch.ch/index.php/s/abcdefg/download,
i run the command renku dataset add -eo my_dataset drive.switch.ch/index.php/s/abcdefg/download
the name of the link on the repo will be displayed as: data/my_dataset/download

how can i set the label of my data in the dataset to a specific name that i want?
do we have an option like renku dataset add --label custom_data_label my_dataset url://of_my/data?
Chandrasekhar Ramakrishnan
@ciyer
Hi @mwong009! I think the --destination/-d flag is what you want in this case. See https://renku.readthedocs.io/projects/renku-python/en/latest/commands.html#working-with-data
Melvin Wong
@mwong009

Hi @mwong009! I think the --destination/-d flag is what you want in this case. See https://renku.readthedocs.io/projects/renku-python/en/latest/commands.html#working-with-data

I think that creates a sub-directory. I've tried that and it doesnt rename the file, it only sets the location of the file

Chandrasekhar Ramakrishnan
@ciyer
Ah, now I think understand what you want.
Chandrasekhar Ramakrishnan
@ciyer
I just checked with the developers. This isn't possible at the moment (it used to be, but this feature was removed because it was exposed in a confusing way).
The way to handle this is to do a renku dataset add and then a renku mv to rename the file.
Melvin Wong
@mwong009
ok thanks
Rok Roškar
@rokroskar
@mwong009 do you use another command-line utility that downloads files from these links with the correct filename? I'm trying to find a link from switch drive that would work with wget and can't seem to do so.
Melvin Wong
@mwong009
@rokroskar so What i did was creating a link with my .csv file in Switchdrive and it gives me a drive.switch.ch/index.php/s/abcdefg/download link when i can then use the renku command renku dataset add -eo my_dataset drive.switch.ch/index.php/s/abcdefg/download to import it into the dataset
I can view the data using pandas.read_csv('data/my_dataset/download')
if you click on sharing in switch drive and copy the 'public link' into the url box, itopens up a new page that will show you a .../.../download link
Rok Roškar
@rokroskar
Thanks @mwong009, I can generate the link now - we should be able to process the metadata in the header that we get from that link to set the filename correctly, I'll open an issue for that. Thanks for pointing it out!
Ludger
@LudgerGoeminne_twitter
Hi All I'm not sure if this is the right place to post this, but when I create a basic R project in Renku, I can't add datasets in the "Datasets" tab and I get the following message: "Knowledge Graph integration must be activated to view the lineage and the datasets, but there is a problem with the knowledge graph integration for this project. To resolve this problem, you should contact the development team on Gitter or GitHub."
I followed that link and that's how I ended up here :)
Does anyone of you know how to solve this problem? I tried creating a public, private and internal basic R project, but all three give the same problem...
Rok Roškar
@rokroskar
Hi @LudgerGoeminne_twitter sorry you're having trouble - can you let me know which project this is?
Ludger
@LudgerGoeminne_twitter
I already removed it, but I made a new one to demonstrate it: it's called "testproject2"
Rok Roškar
@rokroskar
Aha I see - I don't have access to that instance of renku - could you contact your support? It may be that one of the services needs to be restarted if this is a persistent problem
amirrezaie1415
@amirrezaie1415
image.png
Hello, by mistake I draged and droped two times my 300 files in the data folder. And for each file, the message in the image is shown. Is it possible to apply "Overwrite" once for all files? The same is also happening when I have large number of files (each of which are around 20 MB ) and for each file a message is popping up saying that "are you sure you want to upload your file :) "
Thanks!
amirrezaie1415
@amirrezaie1415

I have also another question. I am uploading one large file (1 GB) by just dragging and dropping in the data folder. Previous times that I had tried, there was a green progress bar showing how much of the data has been uploaded, but this time there is nothing! (The word "Complete" in the image below is because of the previous small file that I uploaded successfully!)

image.png

2 replies
Rok Roškar
@rokroskar
Hi @amirrezaie1415 I'm not really sure about using the JupyterLab interface for uploading a lot of files (or large files) - we recommend that you make a dataset either with the renku CLI or in the renku UI and use that to handle adding files to the project. The former requires you to have the renku CLI installed on whatever machine you want to data to your project from. If you go through the web UI, you can just drag and drop.
Melvin Wong
@mwong009
Hello, I tried importing a project that I have from Github, and everything seems ok. I have one small problem, my prject in Github has an existing requirements.txt file, when i do a renku init --force, it somehow overwrites the requirements.txt file and deleted everything in it.
Melvin Wong
@mwong009
to add on, the top-level .gitignore file was also replaced by a default one after renku init --force.
Rok Roškar
@rokroskar
hi @mwong009 - yes this needs some better docs - but the original files were put into a branch that you can restore them from. It should be called something like pre_renku_init_123456where the number at the end is the sha of the commit that was at the HEAD before you ran renku init --force
amirrezaie1415
@amirrezaie1415
Hello, I was wondering, by any chance, if it is possible to install and use python IDE's such as Pycharm within RENKU?
4 replies
Rok Roškar
@rokroskar
Tomorrow is another "Renku tea-time talks" session - we'll have a presentation about a really exciting new effort to automatically add ML-specific metadata to the knowledge graph automatically via a plug-in. It currently supports scikit-learn, keras and pytorch and requires very minimal changes to existing code, but allows the user to view information about model performance, data and parameters used, etc. via a few simple CLI commands. Please join us! The details can be found here: https://renku.discourse.group/t/renku-talks-ii-2020/175/3
waldorivier
@waldorivier
Hallo Team, is it possible to have an external access to a server running on a renku projekt instance ? thanks for your help! Waldo
7 replies
Damian Roqueiro
@droqueiro_gitlab

Dear Renku Team,
Thank you for all the work you put into the platform!
I posted a question a few days ago in the forum:
https://renku.discourse.group/t/renku-on-a-slurm-cluster/236

In summary, have you had experience setting up Renku on a Slurm cluster? Feel free to reply my post or contact me with a direct message.

Thanks in advance for your help. Damian.

Eric Pohl
@pohleric
Hello,
I would like to use Renku R Jupyter Notebooks for a course in geography. For this, I require the GDAL (https://gdal.org/) bindings from the "rgdal" package. I can install the rgdal package but cannot load it, which suggests to me that GDAL is not installed. I cannot locate gdal using the terminal. My question is thus: Is GDAL installed, and if so, where? And if it is not installed, would there be the possibility to install it?
14 replies
Mattias de Hollander
@mdehollander
Hi, I really like the Renku platform and how it combines data management with interactive analysis. Where can I find more information on resources you can use with it? I see the maximum size per dataset is 1 GB. Are there any limitations for the total amount of data (in different projects) you can store? And is there a maximum run time for an interactive environment? It would be nice to know this kind of things before using it at larger scale and advising it to other people. Thanks!
5 replies
Marc-Edouard Schultheiss
@marced_gitlab
Hello, I can't start a new environment on my project and can't understand why. The Docker image build failed. I tried to remove packages from the requirements but it does not change anything. Any idea how I can solve the issue ?
12 replies
meschultheiss
@meschultheiss
Hello ! My jupyterlab is freezing and I cannot interact with the CLI or save my notebook, or shut down a kernel. This is actually a recurrent problem but usually it unfreezes quicker.
Probable cause of the problem: I unsuccessfully tried to launch a voila visualisation of my notebook, which is maybe still running in the background but that I cannot stop. What can I do if I don't want to loose my work by simply closing the environment from renkulab ? (project MAPS, userid: marc-edouard.schultheiss). I tried to connect to my environment from another window but keeps loading and loading.
1 reply
James Runnalls
@jamesrunnalls_gitlab
Hi! I am trying to publish some HTML documentation using GitLab pages, but the "pages" functionality seems to be missing from the renku gitlab instance. Is this something that could be activated?
4 replies
Eric Pohl
@pohleric
I was wondering with another teacher if renku could host other applications like QGIS. Is that something that in theory would be possible?
16 replies
Erol Orel
@triphon:matrix.org
[m]
Hi there, the image is failing to build on my topic-modelling project. Two different error messages:
1) error: RPC failed; curl 52 Empty reply from server