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 | |
| Miniconda3/4.9.2 | ✔ | Minimal Anaconda distribution of Python 3 | |
| Python-GPU/3.6.3-gimkl-2017a | ✔ | GPU-enabled Python 3 | |
| 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 | |
| Python/3.9.5-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 | ✔ | ||
| MATLAB/2020b | ✔ | ||
| MATLAB/2021a | ✔ |
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 | ✔ | ||
| ParaView/5.9.0-gimkl-2020a-Python-3.8.2 | ✔ |
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 |