We might miss this for rc2 but I can confirm this has not been fixed since rc1.

If I modify your script to just read from the IO objects popen3 returns, MRI also blocks until 10 seconds have elapsed.

[] ~/projects/jruby $ time rvm ruby-2.2 do ruby test.rb
"123456789\n"

real    0m10.509s
user    0m0.300s
sys 0m0.242s

Based on that, it seems like this is not necessarily something we're doing wrong. A read against the InputStream you acquire will attempt to read to 1024 bytes or EOF. Since the process is still running, there's no EOF, so it blocks waiting for more data.

JRuby 1.7 blocks until process end with normal IO read, but returns quickly for the InputStream read, so there is a behavior change here. However the behavior change may be more correct.

I'm open to input here. JRuby 9k's InputStream here is just doing a call to IO read.

According to the Java API document, I think InputStream#read blocks until one byte read, but doesn't block until buffer filled.

https://docs.oracle.com/javase/8/docs/api/java/io/InputStream.html#read-byte:A-

This method blocks until input data is available, end of file is detected, or an exception is thrown.
there is an attempt to read at least one byte. 

Ruby IO has readpartial. So you can read partially. But InputStream doesn't have such a method. So you can't read partially from InputStream.

I want to process some part of my application in Java code for performance reason.
And I need to read partially from InputStream.