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

After connecting to Stanage (see Establishing a SSH connection), start an interactive session with the following command:

srun --pty bash -i

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

module load GEOS/3.11.1-GCC-12.2.0
module load GEOS/3.10.3-GCC-11.3.0
module load GEOS/3.9.1-GCC-11.2.0
module load GEOS/3.9.1-GCC-10.2.0

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 Stanage (see Establishing a SSH connection), start an interactive session (e.g. using the srun --pty bash -i command). Run the following module commands

module load R/4.0.5-foss-2020b
module load GEOS/3.9.1-GCC-10.2.0

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. GEOS has been installed using the default Easybuild config files.

Build logs and test reports can be found in $EBROOTGEOS/easybuild with a given module loaded.

Testing

Create a file called geos_hello_world.c with the following content (source):

#include <stdio.h>  /* for printf */
#include <stdarg.h> /* for va_list */

/* Only the CAPI header is required */
#include <geos_c.h>

static void
geos_msg_handler(const char* fmt, ...)
{
    va_list ap;
    va_start(ap, fmt);
    vprintf (fmt, ap);
    va_end(ap);
}

int main()
{
    /* Send notice and error messages to the terminal */
    initGEOS(geos_msg_handler, geos_msg_handler);

    /* Read WKT into geometry object */
    GEOSWKTReader* reader = GEOSWKTReader_create();
    GEOSGeometry* geom_a = GEOSWKTReader_read(reader, "POINT(1 1)");

    /* Convert result to WKT */
    GEOSWKTWriter* writer = GEOSWKTWriter_create();
    char* wkt = GEOSWKTWriter_write(writer, geom_a);
    printf("Geometry: %s\n", wkt);

    /* Clean up allocated objects */
    GEOSWKTReader_destroy(reader);
    GEOSWKTWriter_destroy(writer);
    GEOSGeom_destroy(geom_a);
    GEOSFree(wkt);

    /* Clean up the global context */
    finishGEOS();
    return 0;
}

Next compile the geos_hello_world.c file:

$ cc geos_hello_world.c -o geos_hello_world -l geos_c
$ ./geos_hello_world

Output should look like this:

Geometry: POINT (1.0000000000000000 1.0000000000000000)