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I am not able to understand that after module system is introduced in our java language. Is java9 and above still platform independent or not ? I am asking this question because I have read that now every application will have its own jre inside it. So, how will this single jre run on all OS, like windows, Linux, or Mac OS.
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You are conflating two different changes recently made to the Java platform:
Recently Oracle announced the phasing out of the Java Web Start technologies, in addition to the already-deprecated Applet technology. See item JDK-8184998 in Java 9 Release Notes:
Java Deployment Technologies are deprecated and will be removed in a future release
Java Applet and WebStart functionality, including the Applet API, The Java plug-in, the Java Applet Viewer, JNLP and Java Web Start including the javaws tool are all deprecated in JDK 9 and will be removed in a future release.
End-users will no longer be encouraged to install a JDK or JRE on their computer.
For more details, see the eight-page 2018-03 white paper from Oracle, Java Client Roadmap Update.
So then, how are developers of Swing or JavaFX apps to deliver their software to the end-user?
Oracle suggests packaging up your app along with a JVM & JRE for delivery as a single launch-ready applications on that appears on the client to be just another app alongside the native apps. Such “double-clickable” app-packaging has been commonly done on the Mac since the beginning of Java. But what was once an obscure art on other host environments (Linux, BSD, Windows, etc.) will now be the norm, as it is on macOS.
In yesteryear, bundling a Java runtime with your app required jumping over some licensing hurdles. The legalities have eased with arrival of the open-source OpenJDK project, and possibly with other implementations†.
You will need to prepare different releases of your app for each hosting environment. While your Java code runs independently of the host OS, the JVM is built of native code to interact with one specific kind of host. So you will need to build a Linux release with a Linux JVM, a macOS release with a macOS JVM, and so on. While that may seem like a downer, the upside is that you no longer need to worry about users having the wrong JVM version installed, or no JVM at all. Now the JVM’s presence and version are under your control. Your end-users and customers will no longer need to be aware that your app is Java-based.
That need for app-packaging has nothing to do with the modularization of Java. As I said, it has been done for decades on the Mac.
What modularization brings to the party is that the JVM/JRE you bundle into your delivered app can be customized to contain only the Java Modules actually utilized by your particular app. This results in a smaller size, so your finished app is smaller, downloads are faster, less storage is used, and your app may load faster.
The open-source jlink “Java Linker” tool helps with the packaging work, so you can assemble and optimize a set of modules and their dependencies (only the ones actually called by your app) into a custom run-time image. This modular run-time image format is defined in JEP 220.
† On a related note, you may want to read the white paper Java Is Still Free to understand how and where to obtain a Java implementation for your app, and what support may or may not be offered in either free-of-cost or paid releases.
By the way, you may find helpful this Answer on a related Question, with a flowchart of choosing various sources of a Java implementation.
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