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The HPC cluster is built upon a RedHat Enterprise Linux operating system.  The following list mentions some of the more frequent problems JCU researchers have face challenges with:

Windows to Linux transition

  1. Linux is case sensitive, Windows isn't.
  2. Most Linux software is command-line only (no GUI).  I dare say that most Windows software is GUI based.
  3. Windows software will often work with formatted (e.g., RTF) files.  Most Linux software will not understand such files.  When creating file on Windows for use on Linux, you must save files as "plain text".
  4. Windows uses carriage return and new-line characters, similar to typewriters, for what most people think of a "new line".  In Linux, a new-line is all that is required.  Not all software written for linux will be able to ignore the carriage return character - leading to errors or unexpected results.   There is a command (dos2unix) that can convert files created on a Windows platform for use on Linux.
  5. Using spaces, punctuation, and similar in filenames can be problematic.  Unless you have years of experience using Linux, I recommend limiting file/directory names to only use alpha-numeric characters and/or underscores.

PBSPro scripts

  1. The most common mistake in PBS scripts is blank lines.  As a general rule, avoid blank lines in your PBSPro scripts (especially before the last line that starts with #PBS).
  2. Requesting less resource than your job(s) use.  Worst case scenario is that your (or even all users') jobs will be killed.
  3. Requesting significantly more resource than your job(s) use.  Many new HPC users think that requesting 10 CPU cores will mean the job will completes 10 times faster (rarely true).  Unless the software version installed has been written to use multiple cores and you have used the correct syntax to run the job on multiple cores, your job will only use 1 CPU core.
  4. Failure to test the content of PBS script(s) on a HPC login node before submitting jobs.

Software

  1. The HPC cluster is a multi-user environment where not all users choose, or are able, to use the same version of software.  To allow people to access a chosen version of software without altering the software itself, environment modules software has been installed.  Ensure that you have read information available on the HPC wiki in relation to access to installed software.
  2. Many users install software into their home directory.  The location of your home directory will change every time the underlying storage platform is changed.  HPC staff are not required to provide assistance with problems experienced with software you install yourself.  Submitting a service-now job to have HPC staff install software on the system rather than in your home directory. 

Note:  Several pieces of software have very complex/large.  Some examples are: R, perl, python, conda, and matlab.  Environment modules do not exist for sub-components of a software package, the sub-components should be visible though once the correct environment module is loaded.


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