What does OpenJDK JMH “score error” exactly mean?

This is the margin of error for the score. In most cases, that is a half of confidence interval. Think about it as if there is a “±” sign between “Score” and “Score error”. In fact, the human-readable log will show that:

Result: 1.986 ±(99.9%) 0.009 ops/ns [Average]
  Statistics: (min, avg, max) = (1.984, 1.986, 1.990), stdev = 0.002
  Confidence interval (99.9%): [1.977, 1.995]


# Run complete. Total time: 00:00:12

Benchmark                  Mode  Samples   Score  Score error   Units
o.o.j.s.HelloWorld.hello  thrpt        5   1.986        0.009  ops/ns