Configuring RStudio Server for Oracle R Enterprise

In this blog post I will show you the configurations that are necessary for RStudio Server to work with Oracle R Enterprise on your Oracle Database server. In theory if you have just installed ORE and then RStudio Server, everything should work, but if you encounter any issues then check out the following.

Before I get started make sure to check out my previous blog posts on installing R Studio Server. The first blog post was installing and configuring RStudio Server on the Oracle BigDataLite VM. This is an automated install. The second blog post was a step by step guide to installing RStudio Server on your (Oracle) Linux Database Server and how to open the port on the VM using VirtualBox.

Right. Let's get back to configuring to work with Oracle R Enterprise. The following assumes you have complete the second blog post mentioned above.

1. Edit the rserver.conf files

Add in the values and locations for RHOME and ORACLE_HOME

sudo vi /etc/rstudio/rserver.conf
    rsession-ld-library-path=RHOME/lib:ORACLE_HOME/lib

2. Edit the .Renviron file.

Add in the values for ORACLE_HOME, ORACLE_HOSTNAME and ORACLE_SID

cd /home/oracle
sudo vi .Renviron
    ORACLE_HOME=ORACLE_HOME
    ORACLE_HOSTNAME=ORACLE_HOSTNAME
    ORACLE_SID=ORACLE_SID
 
export ORACLE_HOME
export ORACLE_HOSTNAME
export ORACLE_SID

3. To access the Oracle R Distribution

Add the following to the usr/lib/rstudio-server/R/modules/SessionHelp.R file for the version of Oracle R Distribution you installed prior to installing Oracle R Enterprise.

.rs.addFunction( "httpdPortIsFunction", function() {
   getRversion() >= "3.2"
})

You are all done now with all the installations and configurations.

Installing RStudio Server on an (Oracle) Linux server

In a previous blog post I showed how you can install and get started with using RStudio on a server by using RStudio Server. My previous post showed how you could do that on the Oracle BigDataLite VM. On this VM everything was nicely scripted and set up for you. But when it comes to installing it on a different server, well things can be a bit different.

The purpose of this blog post is to go through the install steps you need to follow on your own server or Oracle Database server. The following is based on a server that is setup with Oracle Linux. (I'm actually using the Oracle DB Developer VM).

1. Download the latest version of RStudio Server.

Use the following link to download RStudio Server. But do a quick check on the RStudio server to get the current version number.

wget https://download2.rstudio.org/rstudio-server-rhel-0.99.892-x86_64.rpm

The following shows you what you will see when you run this command.

--2016-03-16 06:22:30--  https://download2.rstudio.org/rstudio-server-rhel-0.99.892-x86_64.rpm
Resolving download2.rstudio.org (download2.rstudio.org)... 54.192.28.107, 54.192.28.54, 54.192.28.12, ...
Connecting to download2.rstudio.org (download2.rstudio.org)|54.192.28.107|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 38814908 (37M) [application/x-redhat-package-manager]
Saving to: ‘rstudio-server-rhel-0.99.892-x86_64.rpm’

100%[============================================================>] 38,814,908  6.54MB/s   in 6.0s  

2016-03-16 06:22:37 (6.17 MB/s) - ‘rstudio-server-rhel-0.99.892-x86_64.rpm’ saved [38814908/38814908]

2. Install RStudio Server

sudo yum install --nogpgcheck rstudio-server-rhel-0.99.892-x86_64.rpm

when prompted if it is OK to install, enter y (highlighted in bold below)

Loaded plugins: langpacks
Examining rstudio-server-rhel-0.99.892-x86_64.rpm: rstudio-server-0.99.892-1.x86_64
Marking rstudio-server-rhel-0.99.892-x86_64.rpm to be installed
Resolving Dependencies
--> Running transaction check
---> Package rstudio-server.x86_64 0:0.99.892-1 will be installed
--> Finished Dependency Resolution
ol7_UEKR3/x86_64                                                                    | 1.2 kB  00:00:00    
ol7_addons/x86_64                                                                   | 1.2 kB  00:00:00    
ol7_latest/x86_64                                                                   | 1.4 kB  00:00:00    
ol7_optional_latest/x86_64                                                          | 1.2 kB  00:00:00    

Dependencies Resolved

===========================================================================================================
 Package               Arch          Version             Repository                                   Size
===========================================================================================================
Installing:
 rstudio-server        x86_64        0.99.892-1          /rstudio-server-rhel-0.99.892-x86_64        280 M

Transaction Summary
===========================================================================================================
Install  1 Package

Total size: 280 M
Installed size: 280 M

Is this ok [y/d/N]: y

Downloading packages:
Running transaction check
Running transaction test
Transaction test succeeded
Running transaction
  Installing : rstudio-server-0.99.892-1.x86_64                                                        1/1
groupadd: group 'rstudio-server' already exists
rsession: no process found
ln -s '/etc/systemd/system/rstudio-server.service' '/etc/systemd/system/multi-user.target.wants/rstudio-server.service'
rstudio-server.service - RStudio Server
   Loaded: loaded (/etc/systemd/system/rstudio-server.service; enabled)
   Active: active (running) since Wed 2016-03-16 10:46:00 PDT; 1s ago
  Process: 3191 ExecStart=/usr/lib/rstudio-server/bin/rserver (code=exited, status=0/SUCCESS)
 Main PID: 3192 (rserver)
   CGroup: /system.slice/rstudio-server.service
           ├─3192 /usr/lib/rstudio-server/bin/rserver
           └─3205 /usr/lib64/R/bin/exec/R --slave --vanilla -e cat(R.Version()$major,R.Version()$minor,~+~sep=".")

Mar 16 10:46:00 localhost.localdomain systemd[1]: Started RStudio Server.
  Verifying  : rstudio-server-0.99.892-1.x86_64                                                        1/1

Installed:
  rstudio-server.x86_64 0:0.99.892-1                                                                      

Complete!

3. Open RStudio using a web browser.

Open your favourite web browser and put in the host name or the IP address of your server. In my example I'm using the Oracle DB Developer VM to demonstrate the install, so I can use localhost, followed by the port number for RStudio Server.

Log in using your Server username and password. This is oracle/oracle on the VM.

4. Use and Enjoy

If you get logged into RStudio Server then you will see a screen something like the following!

Job Done and Enjoy!

5. An Extra Step is using the Oracle DB Developer VM

If you want to use RStudio on the Oracle DB Developer VM from your local OS, then you will need to open the port 8787 on the VM. To do this power down the VM, if you have it open. The open the Network section of the VM settings. I'm using VirtualBox. And then click on the Port Forwarding.

Click on OK to save your Port Forwarding setting and then click on the OK button again to close the Network settings for the VM.

Now start up the VM. When it has loaded and you have the desktop displayed in the VM window, you should now be able to connect to RStudio in the VM, from your local machine.

To do this open your web browser on your local machine and type in

http://localhost:8787

You should now get the RStudio login in screen that is shown in point 3 above. Go ahead, login and enjoy.

6. A little warning

Make sure to log out of RStudio when you are finished using it. If you don't then your R environment may not have been saved and you will get a message when you log in next. Now we don't want that happenings, so just log out of RStudio. You can do that by looking at the top right hand corner of the RStudio Server application.

I will have one more blog post on how you can configure RStudion Server to work with an Oracle Database server that has Oracle R Enterprise installed.

Installing RStudio Server on Oracle BigDataLite VM

A very popular tool for data scientists is RStudio. This tool allows you to interactively work with your R code, view the R console, the graphs and charts you create, manage the various objects and data frames you create, as well shaving easy access to the R help documentation. Basically it is a core everyday tool.

The typical approach is to have RStudio installed on your desktop or laptop. What this really means is that the data is pulled to your desktop or laptop and all analytics is performed there. In most cases this is fine but as your data volumes goes does does the limitations of using R on your local machine.

An alternative is to install a version called RStudio Server on an analytics server or on the database server. You can now use the computing capabilities of this server to overcome some of the limitations of using R or RStudio locally. Now you will use your web browser to access RStudio Server on your database server.

In this blog post I will walk you through how to install and get connected to RStudio Server on the Oracle BigDataLite VM.

After starting up the Oracle BigDataLite VM and logging into the Oracle user (password=welcome1) you will see the Start Here icon on the desktop. You will need to double click on this.

This will open a webpage on the VM that contains details of all the various tools that are installed on the VM or are ready for you to install and configure. This information contains all the http addresses and ports you need to access each of these tools via a web browser or some other way, along with the usernames and passwords you need to use them.

One of the tools lists is for RStudio Server. This product is not installed on the VM but Oracle has provided a script that you can run to perform the install in an automated way. This script is located in:

[oracle@bigdatalite ~]$ cd  /home/oracle/scripts/

Use the following command to run the RStudio Server install script.

[oracle@bigdatalite scripts]$ ./install_rstudio.sh

The following is the output from running this script and it will be displayed in your terminal window. You can use this to monitor the progress of the installation.

Retrieving RStudio
--2016-03-12 02:06:15--  https://download2.rstudio.org/rstudio-server-rhel-0.99.489-x86_64.rpm
Resolving download2.rstudio.org... 54.192.28.12, 54.192.28.54, 54.192.28.98, ...
Connecting to download2.rstudio.org|54.192.28.12|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 34993428 (33M) [application/x-redhat-package-manager]
Saving to: `rstudio-server-rhel-0.99.489-x86_64.rpm'

100%[======================================>] 34,993,428  5.24M/s   in 10s     

2016-03-12 02:06:26 (3.35 MB/s) - `rstudio-server-rhel-0.99.489-x86_64.rpm' saved [34993428/34993428]

Installing RStudio
Loaded plugins: refresh-packagekit, security, ulninfo
Setting up Install Process
Examining rstudio-server-rhel-0.99.489-x86_64.rpm: rstudio-server-0.99.489-1.x86_64
Marking rstudio-server-rhel-0.99.489-x86_64.rpm to be installed
public_ol6_UEKR3_latest                                  | 1.2 kB     00:00     
public_ol6_UEKR3_latest/primary                          |  22 MB     00:03     
public_ol6_UEKR3_latest                                                 568/568
public_ol6_latest                                        | 1.4 kB     00:00     
public_ol6_latest/primary                                |  55 MB     00:12     
public_ol6_latest                                                   33328/33328
Resolving Dependencies
--> Running transaction check
---> Package rstudio-server.x86_64 0:0.99.489-1 will be installed
--> Finished Dependency Resolution

Dependencies Resolved

================================================================================
 Package        Arch   Version       Repository                            Size
================================================================================
Installing:
 rstudio-server x86_64 0.99.489-1    /rstudio-server-rhel-0.99.489-x86_64 251 M

Transaction Summary
================================================================================
Install       1 Package(s)

Total size: 251 M
Installed size: 251 M
Downloading Packages:
Running rpm_check_debug
Running Transaction Test
Transaction Test Succeeded
Running Transaction
  Installing : rstudio-server-0.99.489-1.x86_64                             1/1 
useradd: user 'rstudio-server' already exists
groupadd: group 'rstudio-server' already exists
rsession: no process killed
rstudio-server start/running, process 5037
  Verifying  : rstudio-server-0.99.489-1.x86_64                             1/1 

Installed:
  rstudio-server.x86_64 0:0.99.489-1                                            

Complete!
Restarting RStudio
rstudio-server stop/waiting
rsession: no process killed
rstudio-server start/running, process 5066

When the installation is finished you are now ready to connect to the RStudio Server. So open your web browser and enter the following into the address bar.

http://localhost:8787/

The initial screen you are presented with is a login screen. Enter your Linux username and password. In the case of the BigDataLite VM this will be oracle/welcome1.

Then you will be presented with the RStudio Server application in your web browser, as shown below. As you can see it is very similar to using RStudio on your desktop. Happy Days! You are now setup and able to run RStudio on the database server.

Make sure to log out of RStudio Server before closing down the window.

If you don't log out of RStudio Server then the next time you open RStudio Server your session will automatically open. Perhaps this is not the best for security, so try to remember to log out each time.

By now using RStudio Server on the Oracle Database server I can not get some of the benefits of computing capabilities of this server. Although there are still the typical limitations with of using R. But now I access RStudio on the database server and process the data on the database server, all from my local PC or laptop.

Everything is nicely setup and ready for you to install on the BigDataLite VM (thank you Oracle). But what about when we want to install RStudion Server on a different server. What are the steps necessary to install, configure and log in. Yes they should be similar but I will give a complete list of steps in my next blog post.

OUG Ireland 2016: a roaring success

Last week we had out OUG Ireland annual conference. Traditionally it has been a 1 day conference and in the past few years we have had an extra day where we had the likes of Tom Kyte (we miss you), Maria Colgan, etc give a full day seminar.

But over the past few years a few of the committee have been constantly asked about when we would have a second day of presentations (just like we have for the one day event).

After lots of discussions and looking at budgets and relooking at budgets, then looking at possible alternative venues we worked out a way to have a 2 day conference.

So last week we had our new 2 day conference in the Gresham hotel in the centre of Dublin. Check out the agenda here.

The day before the conference (on the Wednesday) I had arranged for a speakers drinks meet-up. There was lots of people travelling in from all across Europe to present, so this was a good way to get everyone together over a few beers. We met in a micro brewery in Dublin. It was a fun evening with people coming and going throughout the evening and some people stayed for the entire evening. (Oh my poor credit card!)

On Thursday we all got together with all the 275+ attendees at in the Gresham Hotel.

We had 4 tracks that covered DBA, Developer, Business Analytics and Apps. The rooms were just the right size for these tracks, with most of the rooms being full for each of the presentations. With some presentations there was people standing around the sides and down the back. All of this helped to add to the atmosphere. The exhibitors were only there for the first day. This is something we need to look at for next year to get them to attend the 2 days.

On the Wednesday evening we had an Oracle ACE Dinner that was sponsored by OTN (THANK YOU) and they also provided the ACEs with conference ribbons. Also thank you to the OTN ACE programme for providing some travel support to the various ACE Directors.

On the second day (Friday) we kind of got of a slow start for the first sessions of the day, but this must have been due to the snow we had in Dublin that morning. But from the second sessions onwards we were back to packed rooms. Because of this great turn out on the second day, helps us justify having a 2 day conference next years.

I got a chance to talk to lots and lots of people over the course of the 2 days and every single person was talking about the conference being 2 days and Please doing this next year and the year after and the year after, etc.

One of the highlights from the end of the second day was the Q&A panel discussion on the Oracle Optimiser. On this panel we had Jonathan Lewis, Joze Senegacnik and Martin Widlake. I managed to rope in a friend Alan Kelly to be the quiz master for the session. The Q&A Panel session was scheduled for 45minutes. But despite the best efforts to encourage the attendees to finished up, they kept on asking questions and the panel kept on answering. This session ran for an additional 45 minutes. Yes that was a 90 minute session.

All in all the 2 day OUG Conference was a roaring success and I would like to thank all the speakers, the attendees and the various sponsors for making this event happen.

Check out Debra's blog post about the conference.

Check out Martin Widlake's blog post about the conference.

Oh and there was a Yeast and Sourdough Bread Making symposium during OUG Ireland where a number of the peoples got to talk about and share their experiences on making bread.