Opening a Rstudio session on UKB RAP
Hi,
I'm trying to use the RAP platform for the first time, I created my project (our application is ongoing since few months), successfully obtain the data, but when I ask for a R session, it never open, I get the following message:
“job-gpbgfbjjbkyzzq1gp6bzvq1g.dnanexus.cloud took too long to respond.”
I tried at different time point but never succeed to connect even after 1h of reloading the page (and even without accessing the cost is taken).
Did I missed some steps or there's too many people connected at the same time?
Thanks
Karine Alcala
Comments
19 comments
Hi Karine,
I'm not sure whether the problem is the RStudio tool or your whole RAP session. Please could you check whether you are able to access the tabular data via the cohort browser, as described here: https://dnanexus.gitbook.io/uk-biobank-rap/getting-started/working-with-ukb-data .
Also, when you say “never succeed to connect”, do you mean that the monitor page continually says “Initializing”, or does it get to “Ready” but then won't open?
Hi,
I have the message “Ready” I can click on “open”, it opens a new window, but this new one remain blank with the the message mentioned above in the middle.
Yes I can visualize the data when I'm going to explore (I just tested with age and I can see the barplot).
Thanks for the extra detail, we are investigating and will get back to you later today. In the meantime, you could try using R without the RStudio GUI by opening a JupyterLab (Single Node, Python_R) and starting a R notebook.
Thanks, I will try with Jupiter.
Hi Karine, another thing to try:
after starting an RStudio job, after it says ready, instead of clicking “Open”, please click “i” (info)
and then select “Open JupyterLab” from the side info panel
Do you get the same problem? , or do you get
If so, click “New Session”. Does that fail?
(see https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research-analysis-platform/using-rstudio-on-the-research-analysis-platform)
By the way, if you use RStudio, it is important to Terminate each session when you have finished, as it doesn't have a timeout like the normal jupyterlab and will continue to cost money if you leave it un-terminated when you log off.
Hi,
If I choose “Open with JupyterLab” instead of open, I got the same problem:
Yes I'm clicking each time on terminate.
Please contact the dnanexus support team, which can be done by clicking SUPPORT from the RAP landing page, or by emailing ukbiobank-support@dnanexus.com .
(If any other researchers have experienced this problem, please add a comment, especially if you know the fix).
Thanks, I will do it
Hi,
To add another information, my colleague cannot access R as well, she got the same message than me “too long to response”.
Hi Karine, that is probably relevant, so I suggest your colleague should also contact the dnanexus support team, and tell them that it relates to your issue. Is there anyone at your institute for whom it does work?
One other possibility is some kind of network problem, so it might be worth asking your local IT network experts for advice. Maybe you have a non-standard default port set up or something.
Hi Karine, did you find a fix yet? If so, please could you add some details to this thread, for future reference.
Hi Rachel,
I will meet tomorrow with our IT team to see if we can fix it on our side, I keep you updated. Thanks!
Hi,
We just solved the issue, it was probably on our organisation side. Sorry for the inconvenience.
Karine
Thanks for letting us know (it is nice to get good news).
Hi,
I am running into the same problem (already emailed access about it). Are there any quick work-arounds?
Thank you!
Best,
Josefina
Hi Josefina, please ask your local IT Network experts for advice. It might be a firewall problem, possibly related to the default port.
I'm very curious about this. I've had this issue a few times in the last 24 hours using standard JupyterLab notebook sessions. Sometimes, when I open JupyterLab, I see the same error message as others have reported. Other times, it runs fine. Just now, the job opened fine, and so I navigated to my notebook to open it, but then I got an error on opening the .ipynb file that the connection to the server was lost. When I closed out the tab of JupyterLab and re-opened it, I got the message reported by others above. I'm on my home wifi network and don't tend to experience wifi-related issues.
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