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Christopher Creswell

Christopher Creswell

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Motivation and intended usage:

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To get an RStudio Server in the kubernetes cluster, the user goes to https://hpcportal.cc.lehigh.edu, then clicks on the "Lehigh CoursesClass Apps" dropdown menu along the top of the page and selects "RStudio server (kubernetes)" for the generic RStudio instance in kubernetes, or the particular application for their course if applicable (a course can get its own entry here if it maps a network shared drive that is specific to the course).  They are brought to a form where they can select the version of R that they want, and then they can click the "Launch" button.  It takes a minute or so for the instance to start, and then a "Connect to RStudio Server" button appears that takes the user to their RStudio instance.

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The user's home directory is limited in size to 5 gigabytesthe same home directory that they see on HPC nodes in the sol and hawk clusters to make getting data into and out of RStudio easier.

Session management:

For as long as it is still running, the user's RStudio Server is available at https://rstudio.cc.lehigh.edu/<username>/.  The user can also get to it by going back to https://hpcportal.cc.lehigh.edu/ and clicking on the "My Interactive Sessions" link along the top menu bar.

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In order to use the RStudio Server in the kubernetes cluster, users must exist in the OOD application.  If you want to use this system with your course, please create a help request for the Systems Engineering Team (SET) here:
https://jira.cc.lehigh.edu/servicedesk/customer/portal/1
Please include a list of all users of the system including all instructors, TAs, and students.  SET will make sure the proper accounts are provisioned for everyone.

Known issues:

A harmless error that shows up on starting an RStudio session that we have not yet found a way to prevent is this one:

2022-01-26T20:04:48.938685Z [rsession-<username>] WARNING No memory control group found in /proc/self/cgroup; LOGGED FROM: std::__cxx11::string rstudio::core::system::{anonymous}::getMemoryCgroup() src/cpp/core/system/LinuxResources.cpp:335

This error is related to a version mismatch between the kubernetes, the container engine it's using to run RStudio, and the OS running both.  It should eventually go away when we are able to upgrade everything to use the same version of cgroups, which are used to control the resources granted to containers.  Everything will still work fine in spite of this error.


Upon using the "plot" function in RStudio, this error may appear:

Warning message:
In grSoftVersion() :
  unable to load shared object '/usr/local/lib/R/modules//R_X11.so':
  libXt.so.6: cannot open shared object file: No such file or directory


This is also harmless - the plot function still works.  The error is caused by the way the container was built - the RStudio images are based on the Rocker project (https://www.rocker-project.org/ ) and this is related to the way they built the image.  An update to the image would fix it - we'll raise an issue in the Rocker project's github to make sure they are aware of it.