Attention

The ShARC HPC cluster was decommissioned on the 30th of November 2023 at 17:00. It is no longer possible for users to access that cluster.

geos

GEOS (Geometry Engine, Open Source) is a C/C++ port of a subset of the Java Topology Suite (JTS), which in turn is a library that:

  • Provides an object model for planar geometry together with a set of fundamental geometric functions.

  • JTS conforms to the Simple Features Specification for SQL published by the Open GIS Consortium.

  • JTS is designed to be used as a core component of vector-based geomatics software such as geographical information systems.

  • It can also be used as a general-purpose library providing algorithms in computational geometry.

Caution

GEOS is typically loaded as an external dependency for R. Please ensure you select the matching GCC compiler versions of your version of R and the GEOS libraries.

Usage

To make this library available, run one of the following:

module load libs/geos/3.6.1/gcc-4.9.4
module load libs/geos/3.6.1/gcc-8.2

This also activates the matching version of the GCC compiler suite (as its C++ standard library is required by GEOS.)

The rgeos interface in R

rgeos is a CRAN package that provides an R interface to geos. It is not installed in R by default so you need to install a version in your home directory.

After connecting to ShARC (see Establishing a SSH connection), start an interactive session (e.g. using the qrshx command). Run the following module commands

module load apps/R/3.2.0
module load compilers/gcc/4.8.2
module load libs/gcc/4.8.2/geos/3.6.1

Launch R and run the command

install.packages('rgeos')

If you’ve never installed an R package before on the system, it will ask you if you want to install to a personal library. Answer y to any questions you are asked.

The library will be installed to a sub-directory called R in your home directory and you should only need to perform the above procedure once.

Once you have performed the installation, you will only need to run the module commands above to make the geos library available to the system. Then, you use rgeos as you would any other library in R

library('rgeos')

Installation notes

This section is primarily for administrators of the system.

Version 3.6.1

GEOS 3.6.1 was compiled with 4.9.4 and 8.2.0 versions of the GCC compiler suite.

GCC version 8.2.0

  1. Download, configure, build, test and install Qsub submitting this script.

  2. The installer script automatically creates a module file and logs.

GCC version 4.9.4

  1. Download, configure, build, test and install using this script, ensuring that all stderr and stdout is redirected to a log file.

  2. Install this modulefile as /usr/local/modulefiles/libs/geos/3.6.1/gcc-4.9.4

Potentially useful output at the end of the configure run

Swig: false
Python bindings: false
Ruby bindings: false

The build was tested by running make check from the build directory:

# TOTAL: 1
# PASS:  1
# SKIP:  0
# XFAIL: 0
# FAIL:  0
# XPASS: 0