[Biojava-l] Multiple Sequence Alignment - Limits?

[John Kern]

Hello Hannes,

When programs run out of memory it can be insightful to look at them
via the operating system. It helps to determine if the program
consumes all the memory or is hitting another limit. These comments
are specific to Lunix. All versions of UNIX have similar shells. If
you are running Windows, this is not relevant.

Process size can be limited by a shell on unix systems.

$ man sh
$ ulimit -a
core file size          (blocks, -c) 0
data seg size           (kbytes, -d) unlimited
scheduling priority             (-e) 20
file size               (blocks, -f) unlimited
pending signals                 (-i) 16382
max locked memory       (kbytes, -l) 64
max memory size         (kbytes, -m) unlimited
open files                      (-n) 1024
pipe size            (512 bytes, -p) 8
POSIX message queues     (bytes, -q) 819200
real-time priority              (-r) 0
stack size              (kbytes, -s) 8192
cpu time               (seconds, -t) unlimited
max user processes              (-u) unlimited
virtual memory          (kbytes, -v) unlimited
file locks                      (-x) unlimited

On my system, there are now limits. What are the results on your system?

If the shell is not limiting your process and as other have pointed
out the JVM isn't limited, the program top can be very insightful.
http://www.kernelhardware.org/linux-top-command/

When the program is running out of memory, does top confirm you have
no more memory?

Regards,
John