Download the required software

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Best practices for using the HPC-VCL

The HPC-VCL may be used to:

  • Visualize complex graphics or interactively use software in GUI mode, such as MATLAB, Fluent and VMD.
  • Run a web browser client to access the iRODS file system to click to upload or download files between the iRODS file system and the HPC file system.
  • Run a web browser client on the HPC to click and download files from web servers that do not support wget.
  • The HPC-VCL is not meant to be a substitute for learning Linux or the command line. Program execution and file manipulation should still be done from the command line to the extent possible, and the use of the web browser should be limited to necessary operations. Actions like using a web browser or drag and drop to the Trash can create unexpected consequences, such as creating small hidden files that quickly fill a user's home directory.

    Run applications from the scratch directory. Before opening an application, cd to the scratch directory on /share. By default, applications will usually generate output files and log files in the current working directory.


    To reserve an HPC-VCL image, go to

    Blank or distorted GUIs for Mac users, especially MATLAB

    This is assuming you have already set the VCL Preferences to have Color Depth.

    The "Color Depth" needs to be set less than 32 in the VCL settings, and that is the default; however, it seems there is a problem in Microsoft RDP where it does not read in that information from the RDP file.

    So instead of just clicking on the RDP file to let the application open it automatically, with apologies, you will have to do:

    For MATLAB: you might and probably will get the following error messages, but these should not affect the appearance or functionality of MATLAB.

    Gtk-Message: 12:13:58.315: Failed to load module "pk-gtk-module"
    Gtk-Message: 12:13:58.323: Failed to load module "canberra-gtk-module"

    Interactive visualization and graphical interfaces

    The HPC-VCL is used for interactive visualization because RDP renders a remote desktop faster than SSH with X11. For the majority of users, there will be no noticeable differences between the VCL and an interactive compute node when setting up the environment or calling a program.

    Note that there are no GPUs on HPC-VCL nodes and the number of available cores is limited to those allocated to the VCL image.

    module load matlab
    module load vmd

    Memory or compute intensive applications requiring remote display

    The default HPC-VCL image has limited compute/memory resources compared with most of the compute nodes. While bsub and bsub -Is can be used while on the HPC-VCL, direct display from a compute node to the HPC-VCL is not supported. To run an application requiring a remote display from a compute node, do the following:

  • RDP into the HPC-VCL.
  • From a terminal on the HPC-VCL, log in to a standard login node by doing ssh -X
  • Request an interactive session on a compute node by doing bsub -Is [options] tcsh. (See the general instructions for requesting an interactive session.)
  • Run the application.
  • iRODS

    The HPC-VCL is also an iRODS client, and the iRODS file system can be accessed by the VCL. See the datascience website for instructions.

    Once an iRODS account has been initialized, open the Firefox web browser on the HPC-VCL and go to

    Last modified: March 23 2022 13:46:50.

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