Refined Buneman Trees

of the size of the heap during the execution time. Hopefully the data extacted
in this way would present a clear image of the heap size trend.
15.2.1 The Linux ps command
The first option considered was the Linux command ps - report process status
- which reports various information about a process or group of processes, including
allocated memory. However, since we are measuring the size of a Java
program running on a Java Virtual Machine, any information obtained from
beyond the JVM would only reflect the characteristics of the JVM, and would
therefore be very unreliable. We only know that the program we wish to profile
is contained inside the space of the JVM, but we have no clue how big the
program actually is. We would only have an upper limit.
An example of the uselessness of the ps command when dealing with the
JVM is the fact that we might set initial heap sizes differently, for example a
high value and a low value, observe that the memory consumption is different in
the two cases, but also that the memory consumption reported by ps grows in
both cases! Clearly, if we set the initial heap size low to begin with, and measure
the maximum heap size reported by ps, and then set the initial heap size in a
new experiment higher than the previous reported maximum - we would not
expect that the reported heap size would ever exceed the new minimum. But it
does!
The experiment is a bit tricky; we need to start fork a process with the JVM
running on some sample data. Then quickly, before the process terminates, we
must run ps -vg a few times to get snapshots of the process running. But it is
possible to do, and here are the results: firstly, runs with small heap size, where
the reported start and end process size are around 10 and 14 MB. (Note: the
output has been edited to provide clarity)
$ java -Xms1000000 -Xmx1000000000 RBT test.phylip &
[1] 29376
$ ps -v
PID TIME RSS %MEM
29376 0:03 10868 2.1
29376 0:12 11452 2.2
29376 0:22 13472 2.6
Secondly, a large initial heap size, reporting a memory usage between 16 and
26 MB. (Note: the output has been edited to provide clarity)
$ java -Xms100000000 -Xmx1000000000 RBT test.phylip &
[1] 29420
$ ps -v
PID TIME RSS %MEM
29420 0:02 16044 3.1
29420 0:08 22264 4.3
29420 0:17 25840 5.0
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