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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.

Policies

Servers

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).

Use of EID accounts

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.

User roles

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 sudo access on the Edu POD, and will 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.

Class/semester groups

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.

  • Each class has an associated class Unix group (e.g. Bio369i)
  • Each class/semester combination also has an associated Unix group (e.g. Bio369i_Fall2018)
  • Users associated with a class/semester are assigned to both the class and class/semester Unix groups
    • the class/semester Unix group will be their primary group by default

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 organization

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:

  • Home directory access is user-only so that students cannot see each others work
    • Home directories do not have quotas so that larger data files can be stored there
  • Work areas for each class ID and course (class/semester)
    • Files (e.g. assignments and data files) can be stored in the shared class/semester Work directory
    • Instructors can use the Work area class directory to store files that will be used multiple semesters.
  • A single Scratch area for each class ID

File system structure details:

  • /stor/home
    • contains user home directories (as ZFS file systems)
    • directory permission only allow access by the owning account
      • instructors & TAs can view via sudo
    • directory group is the user's default Unix group (usually a class/semester group)
    • there are no quotas applied to home directories
    • snapshots are enabled for home directories
  • /stor/work
    • has a class directory ZFS for each class ID (e.g. /stor/work/Bio369i)
      • intended for resources common to many course offering semesters
      • owned by the class Unix group
      • permissions allow read/write by the class Unix group.
    • each class also has a semester directory ZFS for each course offering (e.g. /stor/work/Bio369i_Fall2018)
      • intended for resources specific to a particular class/semester, as well as multi-user projects at the instructor's discretion
      • owned by the class/semester Unix group
      • permissions allow read/write by the class/semester Unix group.
  • /stor/scratch
    • has a class directory ZFS for each class (e.g. /stor/scratch/Bio369i)
      • intended for temporary/externally downloaded resources
      • owned by the class Unix group
      • permissions allow read/write by the class Unix group.

SSH access

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:

  • educcomp01.ccbb.utexas.edu
  • educcomp02.ccbb.utexas.edu
  • educcomp04.ccbb.utexas.edu

Desktop file system access via Samba

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. 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 the EDU pod is:

  • smb://educstor01.ccbb.utexas.edu/users – Samba share for an individual Home directory on the EDU POD.

For Windows users, the Samba URL for the EDU pod is:

  • \\educstor01.ccbb.utexas.edu\users – Samba share for an individual Home directory on the EDU POD.

Direct Samba access to the class Work area is not available, but symbolic links in home directories can provide access.

Data/account retention

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.

Software

The EDU pod has standard POD utilities and bioinformatics software installed as well as web-based application servers: JupyterHub server and R Studio server.

The web-based applications are accessed from a menu at https://edupod.cns.utexas.edu.

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.

Maintenance

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 (generally once day per month on the last Thursday), during which time POD resources will not be available. Dates for maintenance are posted in advance on the BRCF Users wiki home page. 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.

Course management UI

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.

Course management roles

There are 3 roles in the class management UI: Admin (maint), Instructor, and TA.

  • the Admin can perform all functions
    • including authorizing Instructor users
  • Instructor users can
    • add classes and semesters
    • manage enrollment
    • specify TA users
    • submit help requests
      • e.g. software installation, data retention, etc.
  • TA users can
    • manage enrollment
    • submit help requests

Course management

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:

  • CNBR (required) - the class number identifier (e.g. Bio369i)
  • Year (required) - calendar year for the course (e.g. 2021)
  • Semester (required) - semester for the course (e.g. Fall, Spring,  Summer)
  • Unique ID (required) - unique number for one of the course sections
    • any 5-digit number is ok
  • Instructor (optional) - a single instructor account
    • if there is more than one instructor, additional instructors can be listed as TAs
  • TAs (optional) - TA account(s)
  • Students (optional) - active student accounts
  • Dropped students (optional) - students who were once active but are no longer in the class

In response the system will:

  • Create a Unix group for the class ID (e.g. Bio369i) and the course offering (e.g. Bio369i_Fall2018)
  • Create work and scratch ZFSs for the class as described above
  • Ensure Instructor and are TAs members of the sudo group
  • Deploy EID-named account information for the Instructor, TAs and Students to the POD, with the appropriate group associations.

Course enrollment management

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.

Bulk roster upload

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.

Individual account management

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).

The Edu Accounts page (https://rctf-account-request.icmb.utexas.edu/edu-pod/wp-admin/edit.php?post_type=edupod_user) lists all known accounts, and 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:

  • UT EID (required)
  • First and Last Name
  • Role (Instructor, TA, Student) (required)

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.

File Management

File system/storage overview

To review (see File System Organization and Data/Account Retention)

  1. Home directories under /stor/home:
    • Are only accessible by the account owner (and by the root superuser account)
    • Are the current directory when a user logs in via SSH or accesses the RStudio or JupyterHub server web applications
    • Are meant for student-specific work
    • Do not have quotas
    • Do have snapshots enabled (copy-on-write when files change)
    • Are also fully backed up weekly
    • Are archived to tape at TACC once a semester is over and the course is administratively closed
      • and are removed from the file system (along with associated student accounts)
  2. Course/Semester and Course directories under /stor/work:
    • Are accessible to all accounts in the specified Course and Course/Semester
    • Are meant for course-specific files (e.g. homework assignments and associated data)
    • Do not have quotas or snapshots
    • Are fully backed up weekly
    • Are archived to tape at TACC once a semester is over and the course is administratively closed
      • but are not removed from the file system
  3. Course/Semester and Course directories under /stor/scratch:
    • Similar to Work area directories in #2 above, but are not backed up
    • Are meant for storing large data files that do not need to be backed up

Managing assignment files

There are a number of options for managing homework assignment files, for example:

  1. Post assignments in the shared /stor/work/<Course_Semester> directory. 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/
  2. Post assignments to Canvas. Have students download to their personal computers, then Upload to their Home directory in RStudio Server. When complete, have students copy the files from their EDU pod Home directory to their personal computer using scp, then upload to Canvas.
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