2. Installation

There are two methods to install Japsa in your computer. The first method (using pre-compiled package in JDK 1.8) is straight-forward and can be used for any operating systems, including Windows. The second method (compile from source code) requires some extra tools (make and JDK) but may yield better runtime performance as the package will be compiled with the same version of the Java Virtual Machine used to run.

2.1. Install from the pre-compiled package

Pre-compiled package of Japsa is made available under each release. Installation from this will not require extra build tools such as javac, git, and make.

Just download a JapsaRelease (e.g., from https://github.com/mdcao/japsa/releases), unpack the tarball and run the install.sh script (install.bat for Windows) in the release directory:

tar zxvf JapsaRelease.tar.gz
cd JapsaRelease

The installation will ask for specific details to install the package. If you agree with its suggestion, just type Enter. The questions are:

  • Directory to install japsa: Enter a directory to install japsa
  • Default memory allocated to jvm: Enter a default amount of memory allocated to the Java Virtual Machine. This value should be smaller than the size of your computer. This value, however, can be changed for each specific invocation of a program.
  • Enforce your jvm to run on server mode: Type y if your java support running in server mode.
  • Path to HDF library: Enter path to HDF library. Generally, you need to have HDFViewer (https://www.hdfgroup.org/products/java/release/download.html) installed, and enter the path to file libjhdf5.so (on Linux/Unix/Mac) or to jhdf5.dll (Windows). This is only required if you intend to use npReader( jsa.np.f5reader). Note that we tested with hdfj version 2.10.1, which you can download from https://support.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdf-java-2.10.1/bin/

2.2. Obtain source code and compile

This installation method is recommended as japsa will be compiled with the same Java version used to run it. This method however requires Java Development Kit and Make to be installed. This method has not been tested with Windows.

First, download the latest source code:

git clone https://github.com/mdcao/japsa
cd japsa

or download from a release (Check out https://github.com/mdcao/japsa/releases for the latest releases):

wget https://github.com/mdcao/japsa/releases/download/v1.7-08a/JapsaRelease.tar.gz
tar zxvf JapsaRelease.tar.gz
cd JapsaRelease

and run `make’ to compile and install japsa:

make install \
  [INSTALL_DIR=~/.usr/local \]
  [MXMEM=7000m \]
  [SERVER=true \]

This will install japsa according the directives:

  • INSTALL_DIR: specifies the directory to install japsa
  • MXMEM: specifies the default memory allocated to the java virtual machine
  • SERVER: specifies whether to launch the java virtual machine in server mode
  • JLP: specifies paths to libjhdf5 (needed for npReader)

If any of the above directives are not specified, the installation will ask during the installation.

To uninstall Japsa, run the following in the japsa directory:

make uninstall INSTALL_DIR=~/.usr/local

where INSTALL_DIR points the directory Japsa was installed.