Building (hackishly) rubygems from CMake-based tarballs

Here is my attempt was making a user-space bundle install of the SimGrid’s Ruby bindings. I created a gemspec for the source tarball in a hackish way. Basically I just made a system “cmake .” call in the extconf.rb file when building the gem extensions. Here’s the result:

$ cat Gemfile
source :rubygems

gem “simgrid-ruby”
$ SIMGRID_ROOT=/opt/simgrid-3.6.2 bundle install –path vendor
…
…
make install
[ 66%] Built target SG_ruby
[100%] Built target SG_rubydag
Install the project…
– Install configuration: “”
CMake Error at cmake_install.cmake:47 (FILE):
file cannot create directory: /usr/local/ruby/1.9.1/x86_64-linux. Maybe
need administrative privileges.

make: *** [install] Error 1

-edit Gemfile
$ cat Gemfile
source :rubygems

gem “simgrid-ruby”, :path => “~/tmp/simgrid-ruby” # where I have
simgrid-ruby.git cloned
$ SIMGRID_ROOT=/opt/simgrid-3.6.2 bundle install
/home/aespinosa/LocalDisk/opt/ruby/lib/ruby/1.9.1/yaml.rb:56:in `’:
Using simgrid-ruby (0.0.4890e3f) from source at ~/tmp/simgrid-ruby
Using bundler (1.0.21)
Updating .gem files in vendor/cache
* simgrid-ruby at `~/tmp/simgrid-ruby` will not be cached.
Your bundle is complete! It was installed into ./vendor
$ cd vendor/ruby/1.9.1/gems/simgrid-ruby-0.0.4890e3f/examples/
$ bundle exec ruby MasterSlave.rb
Tremblay:Master:(1) 0.000000] [ruby/INFO] args[0]=20
[Tremblay:Master:(1) 0.000000] [ruby/INFO] args[1]=50000000
[Tremblay:Master:(1) 0.000000] [ruby/INFO] args[2]=1000000
[Tremblay:Master:(1) 0.000000] [ruby/INFO] args[3]=4
[Tremblay:Master:(1) 0.000000] [ruby/INFO] Master Sending Task_0 to
slave 0 with Compute Size 50000000.0
[Tremblay:Master:(1) 0.215872] [ruby/INFO] Master Sending Task_1 to
slave 1 with Compute Size 50000000.0
[Tremblay:Master:(1) 0.381834] [ruby/INFO] Master Sending Task_2 to
slave 2 with Compute Size 50000000.0
…
…
[Bourassa:Slave:(2) 6.234851] [ruby/INFO] Slave ‘slave 0′ done
executing task Task_16.
[Fafard:Slave:(4) 6.243210] [ruby/INFO] Slave ‘slave 2′ done executing
task Task_18.
[Ginette:Slave:(5) 6.759426] [ruby/INFO] Slave ‘slave 3′ done
executing task Task_19.
[Tremblay:Master:(1) 6.772657] [ruby/INFO] Master : Everything’s Done
Simulation time : 6.77266
$

Sort of works! Basically since rubygems installed the entire manifest (I placed
everything in the tarball) on the gem directory, the lib/*.so and lib/*.rb files
somehow fall in place.
Problems arise in the build when the gem installer cannot replace the
RUBYARCHDIR string in the Makefile to install it in isolation
(https://github.com/rubygems/rubygems/blob/master/lib/rubygems/ext/builder.rb)

I made a fork of a repository with the gemspec package in
https://github.com/aespinosa/simgrid-ruby . For now this
hackish-setup satisfies my needs of a user-space installation of
simgrid-ruby bindings.

ADEM on github

For my first Ruby project, I reimplemented ADEM from scratch. ADEM is tool for automatically installing applications on the Open Science Grid via pacman. Here is a glimpse of the interface.

ADEM is a tool for deploying and managing software on the Open Science Grid.

  Usage:
    adem command [options]

  Examples:
    adem config --display
    adem sites --update
    adem app --avail

  Further help:
    adem config -h/--help        Configure ADEM
    adem sites -h/--help         Manipulate the site list
    adem app -h/--help           Application installation
    adem help                    This help message

The original subversion repository is found in https://svn.ci.uchicago.edu/svn/vdl2/SwiftApps/adem-osg. A Github repository is also mirrored in git://github.com/aespinosa/adem.git

Happy grid computing!

Correspondence on presidentiable’s science agenda

A few days ago, I sent facebook messages to all of the presidential candidates. It was hard to distinguish between fan-generated accounts and the real ones. Amazed by my own facebook stalking skills, I got replies from Dick Gordon and Eddie Villanueva. Here was my message to all of them:

hi,

I’m deciding on my ballot as an absentee voter. as a scientist, please point me to pages/documents about your science & innovation agenda. I sent this message to all the candidates’ facebook pages.

also, please make a response aside from “increase the R & D” budget. it’s like saying ‘world peace’ in a beauty pageant.

thank you

Response from Richard Gordon. Most of the initiatives he mentioned are highly googlable press articles. This guy know his technology stuff:

Allan, kindly look up track record on the net. My Subic cybercity program as well as GIS and GPS mapping implemented in the 90′s. Check also Project 143 and the geo-hazard mapping initiatives with the Red Cross to address disasters and calamities. V-12 program for Filipinos abroad to help promote tourism with telcos using sms is another initiative. Also go to www. senate.gov.ph for transcript of debates re my position on agricultural modernization, and ST and IT development. Thanks.

Response from Eddie Villanueva. I think the reply was referring to a section his platform page. Some of the party’s stand reitarated the current government’s policy such as mother tongue-based education. Also, I’m still waiting for a reply on the email address he gave in the response:

hello! please email your concern to bagongpilipinas@gmail.com
you may also want to visit http://broeddie.ph for the information that you might need.

Bangon Pilipinas!

I will update this page as soon as I get a response from the other candidates, provided that it is their real facebook account that I corresponded to.

SwiftScript Vim syntax file

One weekend I was reading an article howto made a Vim syntax file. In application I decided to make one for the Swift workflow system. Most of the script contains simple word matches for some Swift keywords. Then I copied the matching rules for comments from the C syntax files in the standard Vim distribution. For a preview, checkout the screenshot below which uses the desert256.vim colorscheme in a gnome-terminal:

Fig. a Swift workflow syntax highlighted

The syntax file can be downloaded from my graduate student code-shanty page.

memcache-ing everything in an ActiveRecord model.

I was writing a script that was interactive with a database. The script was being invoked 400 times by a java program. It wasn’t too happy forking too many processes at a time. First I thought that mysql can only handle so many remote connections. Here is my attempt to reduce database load to almost 0 percent.

cache_fu was too dependent on being installed in Rails environment. Commenting out the code which referred to Rails variables made the ruby interpreter not complain. But according to the memcached server logs, nothing was being cached at all! I ended up using the low-level access API fauna.

Wrapping all the ActiveRecord::Base.find…() operations in the fauna-documented recipe, all of the SELECT * statements are now being cached. But the problem that remains is that the models still make ‘SHOW FIELDS..’ queries to the database whenever the object is first invoked. And since the script is being invoked 400 times, only bandwidth and round trip times were saved by the caching effort.

I poked through the metaprogramming examples in the pick-axe book and resulted to overriding my models like this:

require 'memcached'
require 'digest/md5'
require 'active_record'

class Variation < ActiveRecord::Base
  def self.digest
    Digest::MD5.hexdigest(self.to_s).to_s
  end

  def self.columns=(cached_columns)
    @cached_columns= cached_columns
    def self.columns
      @cached_columns
    end
    @cached_columns
  end
end

cache = Memcached.new
begin
  Variation.columns = cache.get(Variation.digest)
rescue Memcached::NotFound
  Variation.columns
  cache.set(Variation.digest, Variation.columns)
end
cache = nil

Now everything is cached!