Using the clusters

Below are a variety of notes for getting the most out of the parallel systems and research compute assets.

These include:

Connecting & Running Jobs

  • For Windows machines, MobaXterm has proven to be an effective free client; Putty is another free option.
  • The screen and TMUX utilities are installed to facilitate running GUI-powered and other jobs requiring stable SSH connections.  MEH 138 has console access for euler/noether/fermat/mandelbrot; this is another way to leave something running easily.
    • For TMUX directions see here.
    • For Screen directions try this link, or here.


The mathematicians and penguins are equipped with computational environments (note – loads vary by machine):

  • Maple
    • /opt/maple2022/bin/xmaple (GUI)
    • /opt/maple2022/bin/maple  (Command line)
  • Matlab (see: toolboxes list) – /usr/local/MATLAB/R2018a/bin/matlab and/or /usr/local/MATLAB/R2020a/bin/matlab
  • NetLogo – /usr/local/NetLogo_6.1.0/NetLogo
  • The NVIDIA CUDA tools (see /usr/local/CUDA)
  • R Studio
    • on mandelbrot use: QMLSCENE_DEVICE=softwarecontext rstudio
    • on all other systems use: rstudio

Operating Systems

  • Ubuntu Linux is the usual OS (currently 22 LTS); exceptions include the BCCD, which runs LittleFe.


  • Network storage (NFS), available from most hosts
    • /mnt/sharedFiles – hosted on Noether
    • /mnt/diskBox (Synology DS410Play; mirrored, striped RAID 8 terabytes)
    • /mnt/disk2Box (a second Synology device) is available from select hosts
    • An additional mount point at /export/nethome is being deployed for individual user storage; this is also hosted on Noether.
  • Most machines have a /mnt/localstorage directory; this is a large, machine-local disk. Pascal has multiple partitions available (see /media) including several 3 TB drives and a smaller SSD.

General Tips

  • The Unix/Linux OS family allows the “:” character in filenames.  Windows does not… (bulk rename utilities are available, however)
  • Spaces in filenames on Unix/Linux are good to avoid.  (Permitted, but not recommended…!