java VM optoins change

[IanSudbery]

Hi All,

Seems that between JDK 8 and JDK 9 the option -XX:+UseParNewGC has been depreciated, and removed in JDK 10. We use this in at least some of our calls to picard, for example, when we call MarkDuplicates in pipeline_bamstats.

What do we think is the best way forward here? We could pin java to JDK 9, or we could change the option to use a different garbage collector. Apparently people recommend -XX:+UseG1GC, which is supported JDK 7 or later. Or we could just leave it out.

Does anyone know why we specify a particular garbage collector, and a view on the best way to move forward. If I don't hear anything, I'll just remove the specification of a particular GC.

[sebastian-luna-valero]

Hi,

Please note that Java has undergone important licensing changes in the recent years:

https://www.oracle.com/uk/java/technologies/java-se-support-roadmap.html

I would therefore stick to JDK 21:

https://www.oracle.com/uk/java/

Regarding garbage collection, see:

https://docs.oracle.com/en/java/javase/21/gctuning/available-collectors.html#GUID-414C9D95-297E-4EE3-B0D9-36F158A83393

and the very first thing I would try is removing the existing config and check how it goes:

Unless your application has rather strict pause-time requirements, first run your application and allow the VM to select a collector.

But go through the docs to double check your preference.