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If I'm deploying to servers with WebSphere 6.1 (Java 1.5), should I use IBM's JDK on my build box? Or will Sun's JDK compile to the same binary?
If I should use IBM's, where can I get the Windows x64 version?
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They should compile to the same bytecode specification, although they may compile different bytecode (much as in the same way different C compilers generate different machine code). I don't think there would be any problems in running the resulting code - I've compiled Java 1.4 on a Mac and then deployed to IBM's J9 running on a PocketPC before with no problems (this was before J9 could handle Java 5 bytecode).
Regardless, I'd definitely make your compilation platform a bullet point on your readme file so that your client can see if it is a problem.
Alternatively, you could build and deploy with ANT, and use Sun's JDK with ANT.
The IBM JDK ships with J9 VM and SUN JDK runs on Hotspot VM which have different algorithms to function. You application may not perform the same if you deploy and tune in SUN JDK and your production uses IBM JDK for WAS. Check with the vendors and open a ticket,let us know how it goes.