GIS tools

GIS tools#

  • Puhti has the widest GIS software portfolio of the CSC supercomputers, and possibly of all supercomputers in the world.

  • Pre-installed software makes it easy to start working on Puhti.

  • GIS tools are originally not planned for supercomputers -> limited ability to utilize the computing power.

  • GIS installations at CSC have been done partly with GeoPortti funding.

GIS tools available in Puhti#

  • Ames Stereo Pipeline for processing stereo images

  • ArcGIS Python API

  • CloudCompare for visualizing, editing and processing point clouds

  • FORCE for mass-processing of medium-resolution satellite images

  • GDAL for geospatial data formats

  • Geoconda - Python spatial analysis libraries

  • GRASS GIS - General purpose GIS software family for viewing, editing and analysing geospatial data

  • LAStools for LiDAR datasets

  • MATLAB

  • OpenDroneMap for processing aerial drone imagery

  • Orfeo ToolBox for remote sensing applications

  • PCL for 2D/3D image and point cloud processing

  • PDAL for point cloud translations and processing

  • QGIS - General purpose GIS software family for viewing, editing and analysing geospatial data

  • R for GIS - R spatial analysis libraries

  • SAGA GIS - General purpose GIS software family for viewing, editing and analysing geospatial data

  • Sen2Cor for atmospheric, terrain and cirrus correction of the Sentinel-2 products

  • Sen2mosaic for downloading, preprocessing and mosaicing of Sentinel-2 products

  • SNAP for remote sensing applications

  • WhiteboxTools - An advanced geospatial data analysis platform

  • Zonation - Spatial conservation prioritization framework

  • pytorch for deep learning

  • tensorflow for deep learning

GIS tools available in Mahti#

GIS tools available in LUMI#

  • GDAL for geospatial data formats

  • Geoconda - Python spatial analysis libraries

  • GRASS GIS - General purpose GIS software family for viewing, editing and analysing geospatial data

  • PDAL for point cloud translations and processing

  • QGIS - General purpose GIS software family for viewing, editing and analysing geospatial data

  • SAGA GIS - General purpose GIS software family for viewing, editing and analysing geospatial data

  • pytorch for deep learning

  • tensorflow for deep learning

  • Additional, easy to install yourself EasyBuild recepies for CGAL, GDAL, GEOS, ncview, PROJ, R.

GIS tools NOT available on supercomputers

Commercial tools

  • MATLAB:

    • Users from universities: license from university + CSC license -> OK

    • Users from research institutes: need own licence, because MathWorks considers research institute users as commercial

  • LasTools:

    • Some tools available for “free”

    • No license from CSC

    • Easy to use your own license

  • ArcGIS Python API:

    • For many tools, a connection to ArcGIS Online is required.

  • In general, only tools with floating licenses can be used

    • Tools with node-locked licenses -> cPouta

GIS tools with R, Python or CLI support#

Software

R

Python

CLI

CloudCompare

-

CloudComPy*

Yes

GRASS

rgrass*

GRASS GIS Python libraries

Yes

OrfeoToolBox

-

OTB Python API*

Yes

PDAL

-

pdal

Yes

QGIS

qgisprocess*

PyQGIS

qgis_process

SagaGIS

Rsagacmd

PySAGA*

saga_cmd

SNAP

-

snappy, snapista

GPT

WhiteboxTools

whiteboxR*

WhiteboxTools

Yes

Additionally Ames Stereo Pipeline, FORCE, LasTools, OpenDroneMap, PCL and Zonation have a command-line interface.

* are not available in Puhti currently, but should be possible to install, ask if you need any of them.

See also, GIS tools supporting computing in parallel.

Modules

  • Supercomputers are a shared computing environment with many mutually incompatible tools installed

  • By default only basic Linux tools are available

  • Pre-installed tools are available via modules

  • One module: single program or group of similar programs

  • Usage:

    • Check documentation for available module names and versions.

    • Load on or more modules -> the system can find the provided tools

    • Use tools from the loaded module(s)

Example: loading the module for GDAL

module load gdal
gdalinfo /xx/data.tif

Documentation#