The Educational POD (Edu POD) is a special BRCF POD dedicated to educational support; that is, to be used in bioinformatics classroom instruction. As such its operations and management differs somewhat from standard BRCF PODs. This page, intended for instructors and their TAs, details the operational policies and procedures for the Edu POD.
The Edu POD currently consists of a storage server (educstor01) with 24 4TB disks, three Dell PowerEdge R640 compute servers (educcomp01, educcomp02, educcomp04) with 52 cores/104 hyper-threads and 1TB of RAM. All server hostnames are in the ccbb.utexas.edu domain (e.g. educcomp01.ccbb.utexas.edu).
There is also a virtual host name, edupod.cns.utexas.edu, that acts as a front-end, redirecting requests to specific back-end compute server based on server load. This virtual hostname can be used to access SSH, R Studio and JupyterHub servers unless a specific host is required (e.g. if a tmux or screen session is desired).
Since the Edu POD will be used to support official UT courses, UT EIDs are used for student accounts rather than the standard BRCF accounts. Likewise, authentication is performed using UT EID authentication protocols rather than central password storage and deployment.
All account EIDs must be entered in lowercase when logging in, either by SSH or to the RStudio/JupyterHub web applications. Please let your students know to enter their EIDs using all lowercase letters! |
There are 4 roles: Admin, Instructor, TA, and Student.
The single Admin account is maint. Instructor, TA, and Student accounts are UT EIDs.
The Admin, Instructors and TAs have access to the Class Management web application (https://rctf-account-request.icmb.utexas.edu/edu-pod/ accessible only from the UT campus network or with the UT VPN service active). Students will not have access to the Class management application.
In addition to the Admin, Instructors and TAs also have sudo access on the Edu POD, but should use it sparingly; for example, to look into student Home directories which have 700 permissions (user access only).
sudo should not be used for any of the following, as these are functions performed by the BRCF automated deployment system:
Courses have a class designation (e.g. Bio369i) and a semester (e.g. Fall 2018). POD administration policies revolve around these class and class/semester concepts.
The goal is to allow access to both general class materials that should be available to any semester (via the class Unix group) as well as specific materials for a particular class semester (via the class/semester Unix group).
Note that some users (e.g. instructors and TAs, and some students) may be associated with multiple classes (hence multiple class/semesters).
File system structures also follows the class and class/semester concepts. Edu POD Home/Work/Scratch areas are slightly different from standard BRCF PODs, with the following goals:
File system structure details:
Instructors, TAs and active students can use SSH to access command-line computation resources, using the edupod.cns.utexas.edu virtual hostname or by specifying a specific EDU POD compute server (e.g. educcomp01.ccbb.utexas.edu).
SSH access from outside the UT campus network requires either the use of UT VPN service, or public key encryption as described at Passwordless Access via SSH.
If students encounter issues accessing the edupod.cns.utexas.edu virtual host, have them try accessing a specific server instead. For example:
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The Samba remote file system protocol allows users to mount POD storage from desktop or laptop computers as if it were a local file system. This allows users to drag/drop files to/from their Home directories using their computer's file system browser.
Samba access is available from UT campus network addresses or from outside of UT using the UT VPN service.
For Mac users, the Samba URL for mounting EDU pod storage is:
For Windows users, the Samba URL for mounting EDU pod storage is:
Direct Samba access to the class Work area is not available, but symbolic links in home directories can provide access.
Following standard BRCF processes, Home and Work areas will be backed up weekly (non-incremental). Scratch is never backed up.
Once a class is over, it is marked as "No longer active" in the EDU pod account management interface. Once a class is inactive, associated accounts are deleted and their Home directories directories archived to TACC's ranch tape archive system and removed from EDU pod storage. Home directories for students that are still enrolled in other classes are not affected. Work area class and class/semester directories are also archived to ranch at the same time, but are not removed.
Edu POD application software should, to the extent feasible, remain stable while the class is in progress. This means that general software upgrades will not be performed during the semester unless needed due to a security update.
Maintenance windows will still be scheduled during which time POD resources will not be available. Dates for maintenance are posted in advance on the BRCF Users wiki home page. We generally schedule maintenance one day per month, the day and time designed to interfere with the fewest classes/labs. Instructors may request variances from the posted dates/times, and these will be honored to the extent possible.
Security updates (required by UT's Institutional Security Office (ISO)), will be applied during maintenance windows using the unattended-upgrades package, configured in manual mode, then using sudo unattended-upgrade -d to apply. Note that if the security updates modify the kernel, updating all dependent software via sudo apt-get dist-upgrade may be required. It is known that such updates can break Python and R packages. If this occurs, the BRCF support team will address these issues in a timely manner.
The EDU pod has a large variety of bioinformatics utilities and tools installed that can be invoked from a Linux command line. Users can install additional software that does not require administrative (sudo) access, or instructors can request that additional programs be installed via the rctf-support@utexas.edu support email.
Web-based application servers for R Studio and JupyterHub are available from a menu after directing a browser to the https://edupod.cns.utexas.edu. This URL is a front-end virtual host that load balances requests, directing them to one of the back-end physical compute servers.
If students encounter issues accessing the https://edupod.cns.utexas.edu virtual host, have them try accessing a specific server instead. For example: |
Instructors may also request that additional software be installed. Such requests should be made at least two weeks before the start of a class. However, since users cannot install Python packages in the JupyterHub server environment, requests to install of Python packages into the JupyterHub environment will generally be handled within one or two business days.
Note that the system and JupyterHub server Python3 installations are separate. All add-on JupyterHub server Python3 packages and many add-on system Python3 packages are installed explicitly, but there are a number of pre-installed system Python3 packages. As a result, there may be a few differences between the available system and JupyterHub server Python3 packages. Instructors should be aware that such difference can exist, and request package installations where needed.
See About R and R Studio Server for information about R Studio Server and how to troubleshoot common problems.
There is a web-based UI for managing courses and enrollment, accessible by the Admin, by Instructors and by TAs:
This is a separate account management from the standard BRCF account management UI. Like the standard BRCF web application, the EUD POD course management application is accessible only from the UT campus network or with the UT VPN service active.
See https://rctf-account-request.icmb.utexas.edu/edu-pod/operational-information/ for usage information.
There are 3 roles in the class management UI: Admin (maint), Instructor, and TA.
A course offering is a combination of a class identifier (e.g. Bio369i) and a semester (e.g. Fall 2018).
Existing courses can be managed here: https://rctf-account-request.icmb.utexas.edu/edu-pod/wp-admin/edit.php?post_type=edupod_course, and new courses can be added here: https://rctf-account-request.icmb.utexas.edu/edu-pod/wp-admin/post-new.php?post_type=edupod_course.
Edu POD courses have the following properties:
In response the system will:
Managing the students enrolled in a course can be done either through bulk upload of a Class Roster in the Edit Edu Course interface, or one at a time through the Edit Edu Accounts interface.
The UI provides bulk upload of student information for a course in the Edit Edu Course interface.
Initially, instructors will browse their local computers to upload a Roster file using the "Class Roster" field. Once this is done that roster can be selected from the Rosters listed on the "Class Roster" page.
The Class Roster uploaded should be in CSV format, with a column named EID or UTEID that lists the student UT EIDs. Other columns may be present but will be ignored. The CSV file lines must be terminated with a linefeed character (e.g. CR+LF, as on Windows, or just LF as in Unix). Note that some Mac applications use a single CR to terminate lines – this will not work.
Re-uploading is supported, adding any new entries but not deleting any missing ones.
To add students to a course, the account first needs to be created if it is not already in the system (e.g., if the account does not appear in the TAs or Students lists).
If the user account is not in the list of known users (https://rctf-account-request.icmb.utexas.edu/edu-pod/wp-admin/edit.php?post_type=edupod_user), the Add New Account page (https://rctf-account-request.icmb.utexas.edu/edu-pod/wp-admin/post-new.php?post_type=edupod_user) can be used to add EID accounts to the system, just by typing in the EID then Publishing the information.
Account information maintained for Edu POD accounts includes:
Once the account is in the system, either the Edit Edu Account page or the Edit Edu Course interface can be used to add student(s) to a course.
To review (see File System Organization and Data/Account Retention)
There are a number of options for managing homework assignment files, for example:
Instructors can post assignments to their shared /stor/work/<Course_Semester> directory in a number of ways, as describe in the next Posting assignments to the shared course directory section below. After posting an assignment, instructors can have students copy it to their Home directory using a Terminal pane in RStudio Server, renaming it. When finished, use an RStudio Server Terminal pane to copy back to the shared /stor/work/<Course_Semester> directory.
# Copy/rename homework assignment to user home directory, # which is the default current directory in an RStudio Terminal window. cp /stor/work/MOL290C_Fall2021/homework1.R homework1.amb599.R # When complete, copy the finished assignment back to the shared course/semester directory # Note the -p option ensures the file's date/time stamp is preserved cp -p homework1.amb599.R /stor/work/MOL290C_Fall2021/ |
Upload assignment files can be done in several ways:
Using one of these methods, instructors can stage files in the shared /stor/work/<Course_Semester> directory in either one or two steps.
The two-step process involves first transferring the files to your Home directory using one of the methods described below, then copying the files from there to the shared /stor/work/<Course_Semester> directory using an RStudio Server Terminal pane. For example, in a Terminal pane. For example, if your course is MOL290C_Fall2021:
cp -p ~/homework1.R /stor/work/MOL290C_Fall2021/ |
In the one-step process, you first create a symbolic link to your shared /stor/work/<Course_Semester> directory in your Home directory, then use that as part of the destination path when uploading files to your Home directory. Such a symbolic link can be created, for example, in a Terminal pane:
# Change to your Home directory, then create a symbolic link called "MOL290C_Fall2021" cd ln -s -f /stor/work/MOL290C_Fall2021 |