N-Body fun

Posted by Moser on 14 Dec 2010

Update: Replaced the GIF by a video.

We currently have to do a simple two-dimensional n-body simulation of gravitation for a university course in practical parallel programming. It uses MPI and OpenMP for parallelism. For benchmarks we were supplied with a model of a spiral galaxy which (in the original example) was passed by by an massive object. I tweaked the system so that this object now rather goes through the galaxy:

Some numbers: The model consists of 402 objects, a step of simulation is 1000 years long, the loop consists of 1.4M steps, a frame was generated every 2500 steps. This took about 25 minutes using 14 MPI processes (no OpenMP).

Find GnuPG revocation certificate on unmountable partition

Posted by Moser on 06 Jul 2010

When you encounter a hard disk crash like I did recently (my fault - dropped my laptop), one of the most important files to restore is your GnuPG private key ring or at least a revocation certificate for your public key(s). I did not have any backup :-(. But at least I had created a revocation certificate, which was now hidden somewhere on my unmountable partition. Scalpel, a file carving tool, helped me out. There is a Ubuntu package (and I believe there should be packages for most distributions):

sudo apt-get install scalpel

It’s configuration is in /etc/scalpel/scalpel.conf. It offers some GPG related rules, but none for a revocation certificate. I used these rules:

revoc	y	100000	-----BEGIN\040PGP\040PUBLIC\040KEY\040BLOCK-----\x0aVersion:\040GnuPG\040v1.4.10\040(GNU/Linux)\x0aComment:\040A\040revocation\040certificate\040should\040follow
revoc	y	100000	-----BEGIN\040PGP\040PUBLIC\040KEY\040BLOCK-----\x0aVersion:\040GnuPG\040v1.4.9\040(GNU/Linux)\x0aComment:\040A\040revocation\040certificate\040should\040follow
revoc	y	100000	-----BEGIN\040PGP\040PUBLIC\040KEY\040BLOCK-----\x0aVersion:\040GnuPG\040v1.4.8\040(GNU/Linux)\x0aComment:\040A\040revocation\040certificate\040should\040follow

I wasn’t quite sure which version of GPG I had installed at the time I created the keys, so I created rules for all possible versions. (See manpage for syntax explanation.)

It took about 2 hours to scan the image of my 250 GB hard drive and scalpel successfully restored my revocation certificate.

I also tried some of the supplied rules but I think they are not suitable for restoring files from an image of a whole hard drive. (Most of them just look for two bytes that mark the beginning of the file.)

slow, slower, activerecord-jdbcsqlite3-adapter

Posted by Moser on 09 Feb 2010

I did a little performance test to find out which database to use in a JRuby desktop application. To have a comparison value I also ran the test (insert, find+update, destroy each 500 times) with MRI and the native sqlite3 driver. It revealed that the jdbcsqlite3 adapter is really sloooooooooow:

$ ruby test.rb sqlite3

                 user     system   total     real
insert           0.4500   0.0900   0.5400 (  7.303116)
find and update  0.4900   0.1400   0.6300 (  6.984390)
destroy          0.3300   0.1100   0.4400 (  7.261199)

$ jruby test.rb jdbcsqlite3

                 user     system   total     real
insert          17.2500   0.0000  17.2500 ( 17.250000)
find and update 16.3270   0.0000  16.3270 ( 16.327000)
destroy         15.0900   0.0000  15.0900 ( 15.089000)

$ jruby test.rb h2

                 user     system   total     real
insert           1.9320   0.0000   1.9320 (  1.932000)
find and update  0.7800   0.0000   0.7800 (  0.780000)
destroy          0.3180   0.0000   0.3180 (  0.318000)

That’s what I call an easy decision. My setup can be downloaded here.

Difference between do-end and {} blocks

Posted by Moser on 07 Feb 2010

There is a important difference between the two block syntaxes in Ruby: Their precedence. Consider following code:

def method1(*args)
  puts "method1 got a block" if block_given?

def method2(*args)
  puts "method2 got a block" if block_given?

method1 method2 do

method1 method2 {

You would expect both method calls to produce the same result, wouldn’t you? Output:

method1 got a block
method2 got a block

Obviously the do-end block is passed to the first method in the expression while the {} block is passed to the method called directly before it. Another example shows that the assignment does not count as a method call here:

class Foo
  def bar=(o)
    puts "Foo#bar= got a block" if block_given?
foo = Foo.new

foo.bar = method1 method2 do
#method1 got a block

foo.bar = method1 method2 {
#method2 got a block

Accessing DeviceKit with DBus and Python

Posted by Moser on 08 Jan 2010

Under the impression of loosing some really important data because of a damaged partition table on a USB flash drive I am developing a backup strategy for my system. I know myself and so I decided that I need to automate this. While trying to figure out how one can run a script as soon as a specific drive is mounted, I came across DeviceKit. It’s the planned replacement of HAL and is used in Ubuntu Karmic. Udev is not an option for me, because I don’t want to mess around with mounting myself (and I hate running stuff as root…). So here is what I found out about using DBus and DeviceKit in Python:

import dbus

bus = dbus.SystemBus()

proxy = bus.get_object("org.freedesktop.DeviceKit.Disks", 
iface = dbus.Interface(proxy, "org.freedesktop.DeviceKit.Disks")
#enumerates all devices
print iface.EnumerateDevices()

#gets the device kit path of a specific device
path = iface.FindDeviceByDeviceFile("/dev/sdc1") 
#= "/org/freedesktop/DeviceKit/Disks/devices/sdc"

#gets an object representing the device specified by the path
device = bus.get_object("org.freedesktop.DeviceKit.Disks", path) 

#prints some XML that shows you the available methods, signals and properties
print device.Introspect()

#gets a proxy for getting properties
device_prop = dbus.Interface(device, "org.freedesktop.DBus.Properties")

#you need to specify an interface (properties could be ambiguous)
print device_prop.Get("org.freedesktop.DeviceKit.Disks.Device", "device-mount-paths")

#gets a proxy you can call methods on
device_iface = dbus.Interface(device, "org.freedesktop.DeviceKit.Disks.Device")

#unmounts the partition
device_iface.FilesystemUnmount(dbus.Array([], 's'))

The DBus API of DeviceKit is documented here. Now we want to be notified when a drive is mounted:

import dbus
import gobject
from dbus.mainloop.glib import DBusGMainLoop

def device_added_callback(device):
    print 'Device %s was added' % (device)

def device_changed_callback(device):
    print 'Device %s was changed' % (device)

#must be done before connecting to DBus

bus = dbus.SystemBus()

proxy = bus.get_object("org.freedesktop.DeviceKit.Disks", 
iface = dbus.Interface(proxy, "org.freedesktop.DeviceKit.Disks")

#addes two signal listeners
iface.connect_to_signal('DeviceAdded', device_added_callback)
iface.connect_to_signal('DeviceChanged', device_changed_callback)

#start the main loop
mainloop = gobject.MainLoop()

A typical output when a flash drive is plugged in looks like this:

Device /org/freedesktop/DeviceKit/Disks/devices/sdc was added
Device /org/freedesktop/DeviceKit/Disks/devices/sdc1 was added
Device /org/freedesktop/DeviceKit/Disks/devices/sdc1 was changed

With this knowledge I’m currently working on a little python script that runs in background and executes a shell script when a file system is mounted. I’ll post it, when it’s finished :-)

Sequel single table inheritance

Posted by Moser on 20 Oct 2009

Sequel’s STI is not so well documented as ActiveRecord’s is. Because it cost me about 20 minutes to find out about it’s syntax, I post a little example.

class A < Sequel::Model
  plugin :single_table_inheritance, :object_type

class B < A

The second argument is the name of the column to be used to store the class name in DB. Don’t use ‘type’ here, it collides with Ruby’s Object#type. This works with version 3.5.0 and should work with any version >= 2.12.0.