During the last two weeks I ran some tests to answer a few questions that had been accumulating:

  1. Should I disable hyper-threading (ht)?
  2. How much does doubling the available memory improve performance?
  3. Mirror, mirror on the wall, who has the fastest JVM of them all?


The machine in question has a single 2.8GHz Intel Xeon processor with 2GB RAM and is running Linux (2.6.9-42.0.3.ELsmp).

The application is a web application with a large (several gigabytes) Lucene index and Berkeley DB for storing data. The main interest was the performance of the data import procedure, though I also had a brief look at the search and retrieval performance.

The following (Java 6) VMs were tested:

Note that even though the machine has a 64-bit processor, I used the 32-bit versions of the JVMs as these are faster than (or the same speed as) the corresponding 64-bit versions (depending on whether the JVM is smart enough to always use 32-bit pointers whenever the heap size is small enough).

Some of the tests were repeated with some of the JVM parameters described by Henrik Stahl. But I never managed to beat the default configuration! So I ended up using only -Xms and -Xmx for all tests.


Median response time (s) for running 1’000 queries sequentially:

Median response time (s) for running 1’000 queries from 10 parallel clients each:

Total time (h) for loading and indexing (in a single thread) all data (UniProt release 12.2):


Hyper-threading can slow down single-threaded applications a bit (perhaps depending on whether the bottleneck is garbage collection, which can be done in a separate thread, or IO). But as soon as there are lots of threads there appears to be a clear benefit in keeping hyper-threading enabled.

More memory is better (surprise)… Doubling the memory in the system from 2 to 4gb (and increasing the heap size from 1 to 2gb) improved performance by about a third for some configurations. Doubling again however may not be worth the expense (diminishing returns).

The latest version of Sun’s JVM appears to be a bit ahead of the others… for now!