1.1. Setup of the Osmose environment

1.1.1. Download Java

Since Osmose numerical JAVA core is coded in JAVA, Java need to be installed. Beforehand, let us clarify some of the acronyms regarding the Java technologies.

JVM: Java Virtual Machine. It is a set of software programs that interprets the Java byte code.

JRE: Java Runtime Environment. It is a kit distributed by Sun to execute Java programs. A JRE provides a JVM and some basic Java libraries. A JRE is needed to run Osmose. It can be downloaded from https://www.java.com/fr/download/.

JDK or SDK: Java (or Software) Development Kit bound to the programmer. It provides a JRE, a compiler, useful programs, examples and the source of the API (Application Programming Interface: some standard libraries). A JDK is needed in order to modify the Osmose Java code.

1.1.2. Download R

The Osmose-Java core is embedded in an Osmose-R package, which allows to pre-process, run and post-process Osmose outputs. Therefore, it is strongly advised that R be installed. Download instructions are available for Windows, Linux and Mac Os X.

It is also recommended to install the RStudio GUI (https://rstudio.com/).

1.1.3. Defining the Osmose target directory

Since Osmose version 3.3.4, Java executables and demo configuration files have been moved out of the R build to meet CRAN requirements on size package. These files are now downloaded from the Internet and moved to a local directory.

By default, a temporary directory is used; but in this case, the Java code will be downloaded at each new session. To define a directory where to put these downloads, the user need to edit or create a ~/.Renviron file and to define the OSMOSE_DIR environment variable. More defined can be found on the Osmose-R CRAN page