Hello,
I am using RStudio workbench. I am doing a task that takes quite long time. I get an error message and my session ends even though I am in Rstudio.
Is there anyway to extend active session in RStudio?
Thanks.
What might happen, in case it is a more computationally intensive job, it might consume all resources and got killed due to lack of memory. What did the error message say?
Thanks for your answer. I am re-running my analysis with larger instance type. I have been running RStudio using High priority mode (as per suggestion in the tutorials).
As per your suggestion, I booked the higher instance type but still got the same error. I checked the log file for the recent job. Few lines from the log is pasted below:
==> /var/log/rstudio-server.log <==
09 Mar 2023 14:43:31 [rserver] INFO Reading rserver configuration from /etc/rstudio/rserver.conf
09 Mar 2023 14:43:31 [rserver] INFO Connecting to sqlite3 database at /var/lib/rstudio-server/rstudio.sqlite
09 Mar 2023 14:43:31 [rserver] INFO Creating database connection pool of size 20 (source: default maximum with 20 CPUs)
09 Mar 2023 14:43:31 [rserver] INFO Starting floating license manager license-manager
Please report this to ukbiobank-support@dnanexus.com since they could get access to your log file and project. Would be nice to hear from you then what was the root cause :).
I had a meeting with the support group. The main issue was technical in my case. I used to get the error mentioned above. Even though there was the error, my function was running which I was not aware of. The support group made me aware of this. I was able to complete my task.
I also received links for the tutorials about working in cloud environment (I am totally new) and how it relates to SLURM environment.
I am currently having the same issue as above but after I get the error “Unable to establish connection with RStudio Server when executing 'get_active_sessions” my whole posit session crashes. On the RAP monitor page my posit session changes from running to pending, and when I try to open my session I get this page (attached). Eventually when the session changes from pending to running, I still get the page below when I try to open the session. My wifi connection is working and the rest of the RAP appears to be working.
After a while the session does open however my previous work is lost and it starts a new session rather than continuing my previous one.
Comments
12 comments
What might happen, in case it is a more computationally intensive job, it might consume all resources and got killed due to lack of memory. What did the error message say?
You can try to change the instance type, full list of all available is here: https://20779781.fs1.hubspotusercontent-na1.net/hubfs/20779781/Product%20Team%20Folder/Rate%20Cards/BiobankResearchAnalysisPlatform_Rate%20Card_Current.pdf
The error message that I received is:
"Unable to establish connection with RStudio Server when executing 'get_active_sessions'".
OK, so then I would try to rerun with a larger instance type. Plus, Rstudio should be used in High priority mode.
https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research-analysis-platform/managing-job-priority
https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research-analysis-platform/managing-job-priority#spot-vm-interruptions
Hello,
Thanks for your answer. I am re-running my analysis with larger instance type. I have been running RStudio using High priority mode (as per suggestion in the tutorials).
thank you for the link.
Hello again,
As per your suggestion, I booked the higher instance type but still got the same error. I checked the log file for the recent job. Few lines from the log is pasted below:
Close
I am not sure if it is the memory issue. Can you suggest me anything else, please?
Thanks a lot.
Please report this to ukbiobank-support@dnanexus.com since they could get access to your log file and project. Would be nice to hear from you then what was the root cause :).
I reported my issue to the support group. Waiting to hear from them.
I will update you and thanks for your time :)
Hello,
I would like to update you regarding my issue.
I had a meeting with the support group. The main issue was technical in my case. I used to get the error mentioned above. Even though there was the error, my function was running which I was not aware of. The support group made me aware of this. I was able to complete my task.
I also received links for the tutorials about working in cloud environment (I am totally new) and how it relates to SLURM environment.
Thanks.
Thanks for the update!
Hello,
I am currently having the same issue as above but after I get the error “Unable to establish connection with RStudio Server when executing 'get_active_sessions” my whole posit session crashes. On the RAP monitor page my posit session changes from running to pending, and when I try to open my session I get this page (attached). Eventually when the session changes from pending to running, I still get the page below when I try to open the session. My wifi connection is working and the rest of the RAP appears to be working.
After a while the session does open however my previous work is lost and it starts a new session rather than continuing my previous one.
Any help would be hugely appreciated.
Thanks!
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