Warning

Iceberg reaches end-of-life on 30th November 2020. If you are running jobs on Iceberg then you need to take urgent action to ensure that your jobs/scripts will run on ShARC or Bessemer. If you have never used ShARC or Bessemer then now is the time to test your scripts. Not all software on Iceberg is available on ShARC/Bessemer.

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.

Usage¶

To make this library available, run the following module commands

module load compilers/gcc/4.8.2
module load libs/gcc/4.8.2/geos/3.4.2

We load version 4.8.2 of gcc since gcc 4.8.2 was used to build this version of 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 iceberg (see Establishing a SSH connection), start an interactive session with the qrsh or qsh 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/3.4.2

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.

qrsh
tar -xvjf ./geos-3.4.2.tar.bz2
cd geos-3.4.2
mkdir -p /usr/local/packages6/libs/gcc/4.8.2/geos/3.4.2
module load compilers/gcc/4.8.2
./configure prefix=/usr/local/packages6/libs/gcc/4.8.2/geos/3.4.2

Potentially useful output at the end of the configure run

Swig: false
Python bindings: false
Ruby bindings: false
PHP bindings: false

Once the configuration was complete, I did

make
make install

Testing¶

Compile and run the test-suite with

make check

All tests passed.

Module File¶

Module File Location: /usr/local/modulefiles/libs/gcc/4.8.2/geos/3.4.2

more /usr/local/modulefiles/libs/gcc/4.8.2/geos/3.4.2
#%Module1.0#####################################################################
##
## geos 3.4.2 module file
##

## Module file logging
source /usr/local/etc/module_logging.tcl
##

proc ModulesHelp { } {
        puts stderr "Makes the geos 3.4.2 library available"
}

set GEOS_DIR /usr/local/packages6/libs/gcc/4.8.2/geos/3.4.2

module-whatis   "Makes the geos 3.4.2 library available"

prepend-path LD_LIBRARY_PATH $GEOS_DIR/lib
prepend-path PATH $GEOS_DIR/bin