Question

I was testing a Molecular Dynamic algorithm, which have, among others, an class Particle compose by 9 array of doubles to store particles components (velocity, force and position in a 3D environment).

I test the algorithm using 5 inputs sizes:

Size (MB) Time (s)
0.06      0.36     (fits in cache L2)
0.14      1.79     (fits in cache L2)
0.60      36.86    (fits in cache L3)
1.35      182.24   (fits in cache L3)
17.38     566.55   (it only fits in RAM)

Than I change the Particles layout from array to ArrayList. In order to have a continuous memory block, I had created the arrayList with the size that will occupy:

ArrayList <Double> px = new ArrayList <Double>(Input_Size);

I run the version in the same conditions of the testes described above, and the results were:

Size (MB) Time (s)
0.06      0.608
0.14      2.78
0.60      57.15
1.35      299.24
17.38     1436,42

The test environment as:

AMD Opteron Processor 6174, 800 MHz, 12 MB Cache L3, with 24 cores;

I am getting a speed-down of about 2x. Is this normal? should not be expecting almost the same times in both version, since ArrayList is allocated continuous in memory like the array?

EDIT:

Running with the option **-XX:+PrintCompilation**

  WITH ARRAY:

 1       java.util.jar.Manifest$FastInputStream::readLine (167 bytes)
  2       sun.nio.cs.UTF_8$Decoder::decodeArrayLoop (553 bytes)
  3       java.lang.String::hashCode (60 bytes)
  4       java.lang.String::charAt (33 bytes)
  5       sun.security.util.ManifestDigester::findSection (180 bytes)
  6       java.lang.Object::<init> (1 bytes)
  7       moldyn.random::update (104 bytes)
  8       moldyn.random::seed (80 bytes)
---   n   java.lang.StrictMath::log (static)
  9       java.lang.Math::log (5 bytes)
 10       moldyn.md::scalingVelocity (82 bytes)
 11       moldyn.Particles::distance (192 bytes)
  1%      moldyn.Particles::force @ 42 (211 bytes)
 12       moldyn.Particles::force (211 bytes)
 13       moldyn.Particles::domove (163 bytes)
 14       moldyn.Particles::domove_out (160 bytes)
  2%      moldyn.Particles::cicle_domove @ 5 (23 bytes)
 15       moldyn.Particles::update_force (49 bytes)
  3%      moldyn.Particles::cicle_forces @ 6 (27 bytes)
 16       moldyn.Particles::mkekin (141 bytes)
  4%      moldyn.Particles::cicle_mkekin @ 9 (33 bytes)
 17       moldyn.Particles::velavg (70 bytes)
  5%      moldyn.Particles::cicle_velavg @ 9 (37 bytes)
 18       moldyn.Particles::cicle_domove (23 bytes)
 19       moldyn.Particles::cicle_forces (27 bytes)
 20       moldyn.Particles::cicle_mkekin (33 bytes)
 21       moldyn.Particles::cicle_velavg (37 bytes)
36.763

WITH ArrayList <Double>....
----

  1       java.util.jar.Manifest$FastInputStream::readLine (167 bytes)
  2       sun.nio.cs.UTF_8$Decoder::decodeArrayLoop (553 bytes)
  3       java.lang.String::hashCode (60 bytes)
  4       java.lang.String::charAt (33 bytes)
  5       sun.security.util.ManifestDigester::findSection (180 bytes)
  6       java.lang.Object::<init> (1 bytes)
---   n   java.lang.System::arraycopy (static)
  7       java.lang.Number::<init> (5 bytes)
  8       java.util.ArrayList::ensureCapacity (58 bytes)
  9       java.lang.Double::valueOf (9 bytes)
 10       java.lang.Double::<init> (10 bytes)
 11       java.util.ArrayList::add (100 bytes)
 12       java.util.ArrayList::RangeCheck (48 bytes)
 13       java.util.ArrayList::set (21 bytes)
 14       moldyn.random::update (104 bytes)
 15       moldyn.random::seed (80 bytes)
---   n   java.lang.StrictMath::log (static)
 16       java.lang.Math::log (5 bytes)
 17       java.util.ArrayList::get (12 bytes)
 18       java.lang.Double::doubleValue (5 bytes)
 19       moldyn.md::scalingVelocity (120 bytes)
 20       moldyn.Particles::distance (240 bytes)
  1%      moldyn.Particles::force @ 42 (211 bytes)
 21       moldyn.Particles::force (211 bytes)
 22       moldyn.Particles::domove (337 bytes)
 23       moldyn.Particles::domove_out (292 bytes)
  2%      moldyn.Particles::cicle_domove @ 5 (23 bytes)
 24       moldyn.Particles::update_force (91 bytes)
  3%      moldyn.Particles::cicle_forces @ 6 (27 bytes)
 25       moldyn.Particles::mkekin (297 bytes)
  4%      moldyn.Particles::cicle_mkekin @ 9 (33 bytes)
 26       moldyn.Particles::velavg (118 bytes)
  5%      moldyn.Particles::cicle_velavg @ 9 (37 bytes)
 27       moldyn.Particles::cicle_domove (23 bytes)
 28       moldyn.Particles::cicle_forces (27 bytes)
 29       moldyn.Particles::cicle_mkekin (33 bytes)
 30       moldyn.Particles::cicle_velavg (37 bytes)
55.98

Answer 1

I have a few thoughts, but no definitive answer:

1. A java.lang.Double is not the same thing as a double primitive. It may be that the autoboxing overhead and extra machinery that goes along with the Double object make a difference. I’d compare the byte code to see if that’s true.
2. It sounds like the choice of double [] or List<Double> is hidden from clients inside your Particle class. If that’s the case, go with the array since it’s an internal implementation detail.
3. I’d be careful about fooling myself with a benchmark test.
4. I’d wonder if your Particle class was mutable or not. That might make a difference. Do position, velocity, and force change continuously and get updated in your object?