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GIS tools

GIS tools#

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

  • Pre-installed software makes it easy to start working with 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 poing 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 spataial 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 download, 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

  • 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 in 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 own license

  • ArcGIS Python API:

    • For many tools connection to ArcGIS Online required.

  • In general only tools with floating licenses possible

    • 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 commandline interface.

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

Modules

  • Supercomputers are 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 a module(s) -> the system can find the tools provided by the module

    • Use tools from the loaded module

Example. Loading module for GDAL

module load gdal
gdalinfo /xx/data.tif

Documentation#

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