Versions Compared

Old Version 6

changes.mady.by.user Anna Battenhouse

Saved on

compared with

New Version 7

changes.mady.by.user Anna Battenhouse

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

  • JupyterHub Server
    • Clicking "Logout" in JupyterHub server does not work – it displays a "404 page not found" error.
  • Command-line programs
    • The following programs may not be working currently, but we are working to correct them asapASAP.
      • bcl2fastq
      • gossamer
      • glimmer2
    • On the EDU pod, the 3rd party programs used by Josh Beckham's FRI stream (e.g. Gold) are not yet working.
    • A few R packages may not be working correctly on some upgraded machines. These may include:
      • Seurat
      • Signac
      • ChIPseeker
  • Storage server access
    • The rssh program that allows direct access to the shared storage server via SSH (e.g. scp, rsync, sftp) is not available in Ubuntu 20.04. We are actively working to implement a suitable replacement. Meanwhile, files can be transferred to/from the storage server through any of a POD's compute server via scp, rsync, sftp.

...

All compute servers have both web-based R Studio RStudio Server and JupyterHub Server installed. A menu allowing you to select from the installed web-based applications is available by specifying any POD compute server name in a web browser; for example: https://gsafcomp01.ccbb.utexas.edu/

Also see below for R and Python versions for a summary of changes to command-line versions of R and Python.

RStudio differences

The version of R in RStudio under Ubuntu 18.04 was either R 3.6.1 or R 4.0.3, as documented at Web-based RStudio and JupyterHub software. Servers with RStudio using R 4.0.3 will still use that version, although we plan to upgrade the R version to R 4.2 going forward. However the servers using R 3.6.1 will now run R 3.6.3. We do not anticipate that this will affect user-installed packages, but if you run into issues, move your ~/R directory out of the way as described at Global package installation conflicts, then re-install your package(s). If the problem persists please Contact Us.

The default version of R under Ubuntu 20.04 is 3.6.3, and this is the version used by the R Studio Server web application. We are aware that many new R packages are only available for later R versions, and will be installing a R 4.2 version of R soon later in 2023.

As part of the upgrade to the base R program, some R packages have also been upgraded.  While we don't anticipate any problems arising from these updates, if you do notice a problem or have any questions, please Contact Us.

JupyterHub differences

The default system Python under Ubuntu 18.04 was Python 3.6.9, and the web-based JupyterHub Server used that version. The default system Python under 20.04 is Python 3.8.10. The differences between the Python 3.6 and 3.8 environments may affect your Python Notebook programs.

As for the set of available JupyterHub Server packages, the JupyterHub Server's Python environment is maintained in a Python3-based virtual environment separate from the system (command-line) Python, so all those packages are centrally managed by us. If you run into issues trying to use a Python package in the new JupyterHub environment, please Contact Us.
As part of the upgrade to the base Python program, some python packages have also been upgraded.  While we don't anticipate any problems arising from these updates, if you do notice a problem or have any questions, please Contact Us.

...

These can be binaries built from source, or in the case of Python /Pyton3 and R/R Studio serverRStudio Server, add-on packages.

Globally-installed programs

If a program or R package or Python package you regularly used under Ubuntu 18.04 is missing or doesn't work in the new Ubuntu 20.04 environment, please Contact Us after trying the troubleshooting tips described below.

We are working to update our POD Software Information to reflect globally-installed software available under Ubuntu 20.04, but it currently reflects only the 18.04 environment.

...

Programs you installed under Ubuntu 18.04 may no longer work.

The Ubuntu O/S OS is installed on local hard disks on each POD compute server, so that's where system programs, system libraries, most add-on programs and add-on libraries are installed. (The exception is for large 3rd party programs or tool suites, which are built in /stor/system/opt, a directory on the shared storage server.)

...