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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.

The account management interface for the EDU POD is at this URL:  https://rctf-account-request.icmb.utexas.edu/edu-pod/ (accessible only from the UT campus network or with the  UT VPN service active).

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 now 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 tied to TACC 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 will be UT EIDs.

The Admin, Instructors and TAs will 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

Bioinformatics-related courses will have a class designation (e.g. Bio369i) and a semester (e.g. Fall 2018). POD administration policies will revolve around these class and class/semester concepts.

  • Each class will have an associated class Unix group (e.g. Bio369i)
  • Each class/semester combination will also have an associated Unix group (e.g. Bio369i_Fall2018)
  • Users associated with a class/semester will be 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 will also revolve around 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 here
  • Work areas for each class ID and course (class/semester)
    • Collaborative multi-user projects can be located here
  • A single Scratch area for each class ID

File system structure details:

  • /stor/home
    • will contain user home directories (as ZFS file systems)
    • directory permission 700 (instructors & TAs can view via sudo)
      • set and enforced by Puppet even if changed by user
    • directory group will be the user's default Unix group (usually a course offering group)
    • there are no quotas applied to home directories
    • snapshots are not enabled for home directories
  • /stor/work
    • will have 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 instructor and class group
      • permission 2750 (writable only by owner; readable by class)
        • set but not enforced by Puppet
    • each class will have a nested 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 instructor and course offering group
      • permission 2770 (writable by anyone in the group)
  • /stor/scratch
    • will have a class directory ZFS for each class (e.g. /stor/scratch/Bio369i)
      • intended for temporary/externally downloaded resources
      • owned by the instructor and class group
      • permission 2770 (writable by anyone in the group)
        • set but not enforced by Puppet

SSH access

Instructors, TAs and active students can use SSH to access command-line computation resources, either 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.

Desktop file system access via Samba

The Samba remote file system protocol allows you 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 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, the instructor may request that student Home directories and Work class/semester directories be archived to tape at ranch and removed from Edu POD storage. Before removal occurs, instructors may request that specified directories be retained on the POD. Additionally, Home directories for students that are still enrolled in other classes will not be affected.

Software

The Edu POD will have all standard POD utilities and bioinformatics software installed. In addition, instructors wish to make use of both web-based application servers: JupyterHub server with Python3 and R Studio server, so those will be installed on all EDU Edu compute servers.

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.

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
  • Semester (required) - semester for the course
  • Unique ID (required) - unique number for the course
  • 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. The Class Roster uploaded should be in CSV format, with a column named EID or UTEID that lists the student UT EIDs.

Re-uploading will be allowed, 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. The Edu Accounts page (https://rctf-account-request.icmb.utexas.edu/edu-pod/wp-admin/edit.php?post_type=edupod_user) lists all existing 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 create new accounts.

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.

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