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If a program (or R package or Python package) you regularly used under Ubuntu 14.04 is missing in the new Ubuntu 18.04 environment, please Contact Us.
We are working to update our POD Software Information to reflect globally-installed software available under Ubuntu 18.04, but it currently reflects only the 14.04 environment.
Incompatible user-installed programs
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The Ubuntu O/S 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 The exception is for large 3rd party programs or tool suites, which are build built in /stor/system/opt, which is a directory on the shared storage server.). Many
If you installed 3rd party programs, however, the installation binaries are usually written to your home directory, /stor/home/<user_name>, which is on the shared storage server. These programs may refer to system libraries (or R or Python packages) that are incompatible with the Ubuntu 18.04 environment.
The steps needed to address such incompatibilities depends on the type of program and installation:
- For programs downloaded as pre-built binaries, check the maintainer's website for a version compatible with Ubuntu 18.04.
- For programs downloaded as source and built by you, move the previous binaries (often in ~/bin or ~/.local/bin), then perform a clean build from existing (or updated) source code.
- For R packages, your local installations are in your ~/R directory. Rename that directory (e.g. to ~/R.previous) so you can refer to it to see which packages you installed, then re-install those packages.
- For Python packages, your local installations are in your ~/.local/lib/python2.7 or ~/.local/lib/python3 directories. Rename those directories (e.g. to ~/.local/lib/python2.7.previous) so you can refer to it to see which packages you installed, then re-install those packages.
Notes on R Studio Server and JupyterHub Server
In our new Ubuntu 18.04 environment, all compute servers have both web-based R Studio 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/
- R Studio Server can be accessed directly by appending rstudio to the server URL
- for example: https://gsafcomp01.ccbb.utexas.edu/rstudio
- JupyterHub Server can be accessed directly by appending jupyterhub to the server URL
- for example: https://gsafcomp01.ccbb.utexas.edu/jupyterhub
The default version of R under Ubuntu 18.04 is 3.4.4, 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 R versions 3.5 and later, and will be installing a 3.5.x version of R soon. It will be available from the command line via a command like R-3.5.x, but will not be used by R Studio Server.
The JupyterHub Server's Python environment is maintained in a Python3-based virtual environment separate from the system (command-line) Python.