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Question: "rstudio initialization error: unable to connect to service" after logging in to the Master node's Rstudio Server's login page
1
2.8 years ago by
hao.lin20
hao.lin20 wrote:

Hi Team,

After I installed starcluster to bring up a cluster using ami-a3d126c8. I can't successfully start the rstudio session on the master node, but I can on the worker nodes.

Using the web browser to connect to the Rstudio Server's login page on the master node,  after log in with username 'ubuntu' and password 'bioc', i get the rstudio initialization error:  unable to connect to service. I ssh into the master node, and do some checking. I ran command 'su rstudio-server verify-installation', and I got ERROR system error 13 (Permission denied).  After I google the error, only a little bit useful information returned and all pointed to potential missing home directory of the user.  But I have checked my home directory for username 'ubuntu' exists with proper permission.

On the other hand however, if i connect to any of the worker nodes, i can successfully log in to R-studio server. I also try just bringing up one-node cluster which has only the master node, i can log in successfully too.

Can anyone help? This will be much appreciated.

thank you so much

Hao

modified 2.8 years ago • written 2.8 years ago by hao.lin20
3
2.8 years ago by
Dan Tenenbaum ♦♦ 8.2k
United States
Dan Tenenbaum ♦♦ 8.2k wrote:

In order to use MPI with a cluster, Rstudio needs to be started in a special way. That way seems to be having issues.

If you don't need to use MPI, you don't need to start RStudio Server in that special way. So you can disable it by ssh'ing to the master node and editing the file /etc/rstudio/rserver.conf and adding a '#' at the beginning of the second line. Then run

sudo rstudio-server restart

And RStudio Server should work.

I will look into the MPI issue.

Dan

1

Hello,

I had the same issue just now - being able to connect with RStudio on the worker nodes but not the master node of a cluster. I am using a customized Bioconductor AMI and Starcluster.

Dans instructions have solved my problem.

Thank you very much for the help,

Nikolai

1

Dan,

A quick question, i observed that when the cluster was brought up originally, the second line in /etc/rstudio/rserver.conf wasn't there in the beginning but was added sometime later in the cluster starting process. do you know when and how was the second line added to the rserver.conf?

thanks

Hao

2

Ah yes, looking at this again I see that there is a script called /usr/local/bin/restart-rss.sh and it runs every minute via crontab. To disable it, type

crontab -e

And comment out (with a # character) the line that runs this script.

If you don't do it, it will overwrite the change you made to rserver.conf.

0
2.8 years ago by
hao.lin20
hao.lin20 wrote:

Dan,

Thank you so much for looking into this. The proposed solution certainly works for non-MPI schemes. I look forward to your further update on the MPI running issue.

Hao