2 Server Management

2.1 Core Administrative Tasks

2.1.1 Configuration Files

RStudio Server uses several configuration files all located within the /etc/rstudio directory. Configuration files and folders include:

rserver.conf Core server settings
rsession.conf Settings related to individual R sessions
notifications.conf Notifications to be delivered to user sessions Pro
logging.conf Configuration of the logging system including logger type, location, and level
crash-handler.conf Configuration of the crash handling system (see Automated Crash Reporting)
profiles User and group resource limits Pro
r-versions Manual specification of additional versions of R Pro
ip-rules IP access rules (allow or deny groups of IP addresses) Pro
load-balancer Load balancing configuration Pro
health-check Template for content to return for server health checks Pro
google-accounts Mappings from Google accounts to local accounts Pro
file-locks Configuration for file locking
login.html Custom HTML for login page
themes/ Custom editor color schemes
keybindings/ Custom IDE keybindings
snippets/ Editor snippet files
templates/ Default templates for new files created in the IDE
dictionaries/ Custom spelling languages and dictionaries

The rserver.conf and rsession.conf files are created by default during installation however the other config files are optional so need to be created explicitly. It should be noted that the rsession.conf file must be readable by each RStudio user, so it should be given appropriate permissions (e.g. 644).

The notifications.conf and r-versions files are created, but their entries are commented out as an example.

Whenever making changes to configuration files you need to restart the server for them to take effect. You can do this using the restart command of the server management utility:

$ sudo rstudio-server restart

2.1.2 Configuring the run-time data directory

RStudio Server Pro needs to write several temporary files while running to function properly. The directory at which these files is written can be set by the server-data-dir configuration option by modifying /etc/rstudio/rserver.conf like so:

server-data-dir=/var/run/rstudio-server

The data directory defaults to /var/run/rstudio-server but you can change it to any directory. The specified location must be readable by any users of RStudio Server.

2.1.3 Stopping and Starting

During installation RStudio Server is automatically registered as a daemon which starts along with the rest of the system. The exact nature of this will depend on the init system in use on your system: - On systems using systemd (such as Debian 7, Ubuntu 15, and RedHat/CentOS 7), this registration is performed as a systemd script at /etc/systemd/system/rstudio-server.service. - On systems using Upstart (such as older versions of Debian and Ubuntu, and RedHat/CentOS 6), this registration is performed using an Upstart script at /etc/init/rstudio-server.conf. - On systems using init.d, including RedHat/CentOS 5, an init.d script is installed at /etc/init.d/rstudio-server.

To manually stop, start, and restart the server you use the following commands:

$ sudo rstudio-server stop
$ sudo rstudio-server start
$ sudo rstudio-server restart

To check the current stopped/started status of the server:

$ sudo rstudio-server status

2.1.4 Managing Active Sessions

There are a number of administrative commands which allow you to see what sessions are active and request suspension of running sessions.

To list all currently active sessions:

$ sudo rstudio-server active-sessions

2.1.4.1 Suspending Sessions

When R sessions have been idle (no processing or user interaction) for a specified period of time (2 hours by default) RStudio Server suspends them to disk to free up server resources. When the user next interacts with their session it is restored from disk and the user resumes right back where they left off. This is all done seamlessly such that users aren’t typically aware that a suspend and resume has occurred.

To manually suspend an individual session:

$ sudo rstudio-server suspend-session <pid>

To manually suspend all running sessions:

$ sudo rstudio-server suspend-all

The suspend commands also have a “force” variation which will send an interrupt to the session to request the termination of any running R command:

$ sudo rstudio-server force-suspend-session <pid>
$ sudo rstudio-server force-suspend-all

The force-suspend-all command should be issued immediately prior to any reboot so as to preserve the data and state of active R sessions across the restart.

2.1.4.2 Killing Sessions

If you are for any reason unable to cooperatively suspend an R session using the commands described above you may need to force kill the session. Force killing a session results in SIGKILL being sent to the process, causing an immediate termination.

To force kill an individual session:

$ sudo rstudio-server kill-session <pid>

To force kill all running sessions:

$ sudo rstudio-server kill-all

Note that these commands should be exclusively reserved for situations where suspending doesn’t work as force killing a session can cause user data loss (e.g. unsaved source files or R workspace content).

2.1.5 Taking the Server Offline

If you need to perform system maintenance and want users to receive a friendly message indicating the server is offline you can issue the following command:

$ sudo rstudio-server offline

When the server is once again available you should issue this command:

$ sudo rstudio-server online

2.1.6 Upgrading to a New Version

If you perform an upgrade of RStudio Server and an existing version of the server is currently running, then the upgrade process will also ensure that active sessions are immediately migrated to the new version. This includes the following behavior:

  • Running R sessions are suspended so that future interactions with the server automatically launch the updated R session binary
  • Currently connected browser clients are notified that a new version is available and automatically refresh themselves.
  • The core server binary is restarted

To upgrade to a new version of RStudio Server you simply install the new version. For example on Debian/Ubuntu:

$ sudo gdebi <rstudio-server-package.deb>

For RedHat/CentOS:

$ sudo yum install <rstudio-server-package.rpm>

For openSUSE / SLES:

$ sudo zypper install <rstudio-server-package.rpm>

2.2 Logging

RStudio Server provides the ability to change various facets of its logging functionality, such as changing the logger type (syslog vs file) on a per-binary or per-section basis. In most configurations, it is recommended that you do not change the logging configuration, but in some circumstances it is desirable to turn on debug logging to help troubleshoot issues.

2.2.1 Configuration File

The logging configuration file is located at /etc/rstudio/logging.conf. It allows you to specify logging options in a hierarchy of three different types:

  1. Global ([*])
  2. Per-binary ([@binary name])
  3. Per log section ([log section name])

For example:

/etc/rstudio/logging.conf

[*]
log-level=info
logger-type=syslog

[@rserver]
log-level=debug
logger-type=file
max-size-mb=10

[file-locking]
log-dir=/var/log/file-locking
log-file-mode=600

This configuration specifies that by default, all logging should be sent to syslog at info level or higher. Debug logging is enabled for the rserver binary specifically, where logs are written to file with a maximum log file size of 10MB, in the default /var/log/rstudio-server directory. File locking logging is also specifically redirected to a different logging directory, /var/log/file-locking, with a specific file creation mode of 600. All logging sections named file-locking which occur in the rserver process will be logged to file, whereas the same logging sections in other binaries will continue to be logged to syslog.

The following settings may be specified:

/etc/rstudio/logging.conf

Config Option Description Default Value
log-level The minimum log level to capture. Can be one of debug, info, warn, or error. warn
logger-type The type of logger to use. Can be one of stderr, syslog, or file. syslog

When using the file logger, the following can also be specified:

Config Option Description Default Value
log-dir The log directory to store log files in. The resulting log file name is based on the binary name (and optionally the process ID). /var/log/rstudio-server
log-file-mode The filemode to use when creating the log file. Must be a valid POSIX octal file mode. 666 (All read/write)
log-file-include-pid Whether to include the process id in the filename. Useful for differentiating between multiple processes of the same name. Can be 0 (false) or 1 (true) 0 (false)
rotate Whether or not to rotate the log file as it reaches maximum size. Can be 0 (false) or 1 (true) 1 (true)
max-size-mb Maximum allowable size of the file before it is rotated. Only applicable if rotate is enabled. 2 (MB)

2.2.1.1 List of Logging Sections

The following is a list of logging sections that may be used within the logging configuration file.

Section Name Description
file-locking Logging of file locking operations, such as processes acquiring and releasing locks.

2.2.1.2 Reloading Configuration

In order to reload the logging settings during run-time of a process, simply send the SIGHUP signal to the desired process, and the logging configuration will be reloaded for that binary.

For example, to send the SIGHUP signal to the rserver process after changing the configuration file:

pidof rserver | sudo xargs kill -s SIGHUP

2.3 Administrative Dashboard

RStudio Server includes an administrative dashboard with the following features:

  1. Monitoring of active sessions and their CPU and memory utilization;
  2. The ability to suspend, forcibly terminate, or assume control of any active session;
  3. Historical usage data for individual server users (session time, memory, CPU, logs);
  4. Historical server statistics (CPU, memory, active sessions, system load); and
  5. Searchable server log (view all messages or just those for individual users)

The dashboard can be an invaluable tool in understanding server usage and capacity as well as to diagnose and resolve problems.

Note that at this time, historical monitoring is not available for sessions spawned via the Job Launcher.

2.3.1 Enabling the Dashboard

The administrative dashboard is accessed at the following URL:

http://<server-address>/admin

The administrative dashboard is disabled by default. To enable it you set the admin-enabled option. You can also specify that only users of certain group have access to the dashboard using the admin-group option. For example:

/etc/rstudio/rserver.conf

admin-enabled=1
admin-group=rstudio-admins

You can specify a single group as the above example does or a comma-delimited list of groups. For example:

/etc/rstudio/rserver.conf

admin-group=server-admins,rstudio-admins,domain-admins

Note that changes to the configuration will not take effect until the server is restarted.

2.3.2 Administrator Superusers

You can further designate a certain user or group of users as administrative “superusers”. Superusers have the following additional privileges:

  1. Suspend or terminate active sessions
  2. Assume control of active sessions (e.g. for troubleshooting)
  3. Login to RStudio as any other server user

Administrative superusers do not have root privilege on the system, but rather have a narrow set of delegated privileges that are useful in managing and supporting the server. You can define the users with this privilege using the admin-superuser-group setting. For example:

/etc/rstudio/rserver.conf

admin-superuser-group=rstudio-superuser-admins

Note that as with the admin groups above, you can specify a single group as the above example does or a comma-delimited list of groups. For example:

/etc/rstudio/rserver.conf

admin-superuser-group=rstudio-superuser-admins,domain-admins

Changes to the configuration will not take effect until the server is restarted.

2.3.2.1 User Impersonation Restrictions

Note that the ability to login as other users and assume control of existing sessions is not available if you are authenticating with Google Accounts or proxied authentication. This is because these authentication mechanisms use a different user-identity mechanism which isn’t compatible with the way that user session impersonation is implemented.

2.3.3 Server Log Time Zone

You can control the time zone in which the server logs are displayed in the admin dashboard by the use of the admin-monitor-log-use-server-time-zone option. For example:

/etc/rstudio/rserver.conf

admin-monitor-log-use-server-time-zone=1

Setting this option to 1 will display the server logs in the server’s time zone. The default value of 0 will display the log times in UTC.

2.4 Automated Crash Reporting

RStudio Server allows you to automatically capture crash dumps for all RStudio processes and upload them to our crash database for easy reporting, allowing us to more easily determine the exact cause of crashes without adding administrative overhead to your team by requiring you to manually collect crash dumps. As user privacy is of utmost concern, these crash dumps only contain stack information, such as the names of the functions that were on the callstack at the time of the crash. No heap information is stored within the dumps, so no sensitive user data is captured in the crash dumps. The IP address of the machine uploading the reports is captured and used only to determine the unique amount of users experiencing a crash.

2.4.1 Crash Handler Configuration

A separate RStudio process is responsible for handling crashes, and may be configured similar to other RStudio processes by modifying the config file /etc/rstudio/crash-handler.conf. In RStudio Server, automated crash handling is disabled by default, though we recommend that you enable it. The following shows a table of available configuration options.

/etc/rstudio/crash-handler.conf

Config Option Description Required (Y/N) Default Value
crash-handling-enabled Enables/disables automatic capturing of crash dumps for all RStudio processes. N 0 (disabled) for RStudio Server Pro, 1 (enabled) for RStudio Server Open Source
crash-db-path Location of the path where crash dumps should be stored on disk. This path must be readable and writeable by all RStudio users. N /tmp/crashpad_database
uploads-enabled Enables/disables automatic uploading of crash dumps to our crash reporting service. If this is disabled, you will have to manually upload crash dumps. N 1 (enabled)
upload-url Web URL where crash reports are uploaded. You should likely not change this setting unless RStudio Support instructs you to do so. N
upload-proxy Proxy server to connect to when submitting the minidump. Only applicable on Linux - uses the default system-wide setting on OSX. If left blank, any system-wide setting specified will be used. This should be in the form of [scheme]://[host]:[port], where scheme may be one of the following: http https socks4 socks4a socks5 or socks5h. For more information, see https://curl.haxx.se/libcurl/c/CURLOPT_PROXY.html N

For most RStudio Server installations, it is sufficient to merely set crash-handling-enabled=1 in the config file, like so:

/etc/rstudio/crash-handler.conf

crash-handling-enabled=1

2.4.2 Manually Uploading Crash Dumps

In some cases, you may be unable to automatically upload crash dumps to the crash reporting service because of lack of internet connectivity or simply because you want to manually upload crash dumps. RStudio allows you to manually upload crash dumps at any time by invoking the following command:

rstudio-server upload-minidump /path/to/minidump