Visualisation software

NeSI provides a variety of visualisation software solutions via modules. Available software and software versions vary between the Mahuika and Māui Ancil systems. Additional software can be provided upon request, see section Supported Applications.

Most software only requires a CPU node to run, but some software, in particular high-performance 3D visualisation software, can utilise a GPU node for better performance. Where possible, both CPU and GPU variants of the same software are provided for maximum flexibility; please make sure to select the correct module version as described below.

Apart from interactive operation, many visualisation solutions also support batch mode ("headless") operation, allowing users to submit large visualisation jobs to the HPC.

In the following installed packages are listed for:

  • Scripting Languages with Visualisation Capabilities

  • 2D Visualisation Software

  • 3D Visualisation Software

Scripting Languages with Visualisation Capabilities

Python

The Python language comes with packages such as "matplotlib" for general-purpose 2D visualisation, or "vtk" (see VTK section on this page) for 3D visualisation.

Available Modules

Module Name Mahuika Māui Ancil Comment
Anaconda2/5.2.0-GCC-7.1.0   Anaconda distribution of Python 2
Anaconda2/2019.10-GCC-7.1.0   Anaconda distribution of Python 2
Anaconda3/5.2.0-GCC-7.1.0   Anaconda distribution of Python 3
Anaconda3/2019.03   Anaconda distribution of Python 3
Anaconda3/2019.07-gimkl-2018b   Anaconda distribution of Python 3
Anaconda3/2020.02-GCC-7.1.0   Anaconda distribution of Python 3
Miniconda3/4.4.10   Minimal Anaconda distribution of Python 3
Miniconda3/4.5.12   Minimal Anaconda distribution of Python 3
Miniconda3/4.7.10   Minimal Anaconda distribution of Python 3
Miniconda3/4.8.2   Minimal Anaconda distribution of Python 3
Miniconda3/4.8.3   Minimal Anaconda distribution of Python 3
Python-GPU/3.6.3-gimkl-2017a   GPU-enabled Python 2
Python-Geo/2.7.14-gimkl-2017a   Python 2 for geospatial applications
Python-Geo/2.7.16-gimkl-2018b   Python 2 for geospatial applications
Python-Geo/3.6.3-gimkl-2017a   Python 3 for geospatial applications
Python-Geo/3.7.3-gimkl-2018b   Python 3 for geospatial applications
Python-Geo/3.8.2-gimkl-2020a   Python 3 for geospatial applications
Python/2.7.14-gimkl-2017a   Python 2 base packages
Python/2.7.16-gimkl-2018b   Python 2 base packages
Python/2.7.16-intel-2018b   Python 2 base packages
Python/2.7.18-gimkl-2020a   Python 2 base packages
Python/3.6.3-gimkl-2017a   Python 3 base packages
Python/3.7.3-gimkl-2018b   Python 3 base packages
Python/3.8.1-gimkl-2018b   Python 3 base packages
Python/3.8.2-gimkl-2020a   Python 3 base packages

 

R

The R language comes with built-in 2D plotting capabilities that can be extended with additional packages.

Available Modules

Module Name Mahuika Māui Ancil Comment
R/3.4.2-gimkl-2017a  ✔   R base package
R/3.5.0-gimkl-2017a  ✔   R base package
R/3.5.1-gimkl-2017a   R base package
R/3.5.3-gimkl-2018b   R base package
R/3.6.1-gimkl-2018b   R base package
R/3.6.2-gimkl-2020a   R base package
R/4.0.1-gimkl-2020a   R base package
R/3.5.1-gimkl-2018b   R base package
R/3.6.1-gimkl-2018b   R base package
R-Geo/3.6.1-gimkl-2018b   R for geospatial applications
R-Geo/3.6.2-gimkl-2020a   R for geospatial applications
R-Geo/4.0.1-gimkl-2020a   R for geospatial applications
Rstudio/1.1.456   Rstudio IDE

 

NCL

The NCAR Command Language provides visualisation capabilities which are mostly used in the weather and climate fields.

Available Modules

Module Name Mahuika Māui Ancil Comment
NCL/6.2.0-GCC-7.1.0    ✔ NCL base package
NCL/6.4.0-GCC-7.1.0    ✔ NCL base package
NCL/6.6.2-intel-2018b  ✔   NCL base package

 

MATLAB

The MATLAB programming language comes with built-in visualisation capabilities.

Available Modules

Module Name Mahuika Māui Ancil Comment
MATLAB/2016b  
MATLAB/2017b  
MATLAB/2018b  
MATLAB/2019b  
MATLAB/2020a    

 

2D Visualisation Software

IRIS

IRIS is a Python-based visualisation tool that is mainly used in the weather and climate fields.

Available Modules

Module Name Mahuika Māui Ancil Comment
Anaconda2/5.2.0-GCC-7.1.0    ✔ IRIS v1.13.0
Anaconda2/2019.10-GCC-7.1.0   IRIS v2.2.1.dev0
Anaconda3/5.2.0-GCC-7.1.0    ✔ IRIS v1.13.0 
Anaconda3/2019.03   IRIS v1.13.0
Anaconda3/2020.02-GCC-7.1.0   IRIS v2.4.0

 

Ncview

Ncview is a visual browser for netCDF files.

Available Modules

Module Name Mahuika Māui Ancil Comment
ncview/2.1.7-gimkl-2018b    
NCVIEW/2.1.8-GCC-7.1.0    ✔  

 

XCONV

XCONV is a visual browser for netCDF and Unified Model format files.

Available Modules

Module Name Mahuika Māui Ancil Comment
XCONV/1.93    ✔  

 

3D Visualisation Software

ParaView

ParaView is a high-performance 3D visualisation tool. The headless versions only provide ParaView Server, which can operate in batch mode, as well as in client-server operation.

For interactive sessions, it is highly recommended to use ParaView with the NICE DCV cloud visualisation software for best performance. Client-server mode, where a ParaView GUI runs on a local machine and connects to a ParaView server on the HPC, is also an option but requires much more network bandwidth than NICE DCV and thus may be slower.

Parallelisation

The CPU based versions of ParaView use the OpenSWR rasteriser as well as the OSPRay ray tracer for rendering graphics. These support parallel operation for better performance, but are configured to only use a single core by default. Run the following commands before launching ParaView GUI or ParaView Server if you want to use more cores (depending on the number of cores available in your session):

export KNOB_MAX_WORKER_THREADS=<number of cores>
export OSPRAY_THREADS=<number of cores>

ParaView Server also supports parallel execution using MPI, see "Setting up Client-Server Mode" below.

Available Modules

Module Name Mahuika Māui Ancil Comment
ParaView/5.3.0-gimkl-2017a    
ParaView/5.4.1-gimkl-2017a-Python-2.7.14    
ParaView/5.4.1-gimkl-2018b-Python-2.7.16    
ParaView/5.4.1-gimpi-2018b    
ParaView/5.5.2-gimpi-2018a-Server-EGL   Headless version for GPUs, no GUI operation
ParaView/5.5.2-gimpi-2018b-GUI-Mesa   GUI version for CPUs, no headless operation
ParaView/5.5.2-gimpi-2018b-Server-OSMesa   Headless version for CPUs, no GUI operation
ParaView/5.6.0-gimkl-2018b-Python-3.7.3      
ParaView/5.6.0-gimpi-2017a-Server-OSMesa   Headless version for CPUs, no GUI operation
ParaView/5.6.0-gimpi-2018b    
ParaView/5.6.0-gimkl-2018b-Python-3.7.3    

 

Setting up Client-Server Mode

If you want to use ParaView in client-server mode, use the following setup:

  • Load one of the ParaView Server modules listed above and launch the server in your interactive visualisation session on the HPC:
mpiexec -np <number of MPI ranks> pvserver
  • Create an SSH tunnel for port "11111" from the HPC to your local machine using, e.g., the ssh program (Linux and MacOS) or MobaXterm (Windows)
  • Launch the ParaView GUI on your local machine and go to "File > Connect"
  • Click on "Add Server", choose server type "Client / Server", host "localhost" (as we will be using the SSH tunnel), and port "11111", then click on "Configure"
  • Select the new server and click on "Connect"

VisIt

VisIt is a high-performance 3D visualisation tool. At this point, only GUI-based interactive sessions on CPUs via NICE DCV are supported, GPU support and client-server operation will be added later.

Available Modules

Module Name Mahuika Māui Ancil Comment
VisIt/2.13.3-gimpi-2018b-GUI-Mesa   GUI version for CPUs

 

VTK

The Visualization ToolKit (VTK) can be used for 3D visualisation in various programming languages, in particular with the Python scripting language.

Available Modules

Module Name Mahuika Māui Ancil Comment
VTK/6.3.0-gimkl-2017a-Python-2.7.14   VTK6 with Python bindings
VTK/7.1.1-gimkl-2018b-Python-2.7.16   VTK7 with Python bindings
VTK/8.1.1-GCC-7.1.0-Anaconda2-5.2.0   VTK8 with Python bindings

 

Labels: support application visualisation
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