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Pebl is known to run on Linux and Mac OSX and should also run on Windows andany platform that supports Python 2.5 and numpy. Pebl depends on the followingpackages:
Numpy: tested with version 1.0.4 but should work with other recent versions
Pydot: tested with version 1.0.2
Matplotlib (optional): tested with version 0.91.2 but should work with otherrecent versions
Graphviz (optional): any recent version of dot and neato
IPython1 (optional): curently, require r2815 from svn trunk
boto (optional): any recent version
Install Python 2.5¶
Check what version of Python you have with:
You can download Python 2.5 from http://python.org/download
Note
Pebl requires Python 2.5 or greater and will not run under earlier versions.
Install easy_install¶
easy_install lets you install python packages and their requirements in oneeasy step. Unfortunately, easy_install is not distributed with python and needsto be installed separately.
Download ez_setup.py from http://peak.telecommunity.com/dist/ez_setup.py
Run python ez_setup.py to install easy_install
Run easy_install –help to make sure that it is in your path. Onunix-type systems, it is usually installed in /usr/bin/ and on Windows inC:Python2.5Scripts
Install Numpy¶
Numpy can be tricky to install because it require C and Fortran compilers andseveral libraries. You can try installing it from source using easy_install:
If that doesn’t work or if you’d rather install using a binary package, consulthttp://www.scipy.org/Download.
Install Pebl¶
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You can now install (or upgrade) pebl and it’s required dependencies usingeasy_install:
Note
The current version of Pebl is 1.0.2
If you have downloaded the source code for Pebl (or installing pebl from svn),you can run sudo python setup.py install from pebl’s root directoryinstead.
Testing Pebl Installation¶
To test pebl installation, you can run the automated unit tests by first install nose:
and then running nose from the command line, in any directory:
If you haven’t installed all the optional dependencies, certain tests will failbut the name of the tests should make it clear whether it’s a normal feature oran optional one.
Installing optional dependencies¶
Certain features of pebl require additional dependencies. You only need toinstall these if you need the optional features. Without the optional features,you can load data, learn networks and output networks in dot format, althoughnot as an image. If installing pebl on a cluster, the optional features areonly necessary on the controller or the machine used interactively by theuser.
For creating HTML reports of Pebl results¶
Pebl uses Graphviz to visualize networks and matplotlib for plotting. If usingPebl on a cluster, these don’t need to be installed on the worker nodes.
Install Graphviz from http://www.graphviz.org/Download.php
Install matplotlib from http://matplotlib.sourceforge.net/installing.html
Finally, install simplejson using easy_install:
simplejson sometimes fails to install on Windows. In that case, you can use abinary package:
To test the html-report feature, run:
For the XGrid Task Controller¶
Apple XGrid is a grid solution for Apple computers that lets desktops anddedicated servers be used in a computational grid.
The Xgrid task controller only runs on platforms where XGrid is available(currently, only Mac OSX). Pebl uses the PyXG package to access the XGridcontroller:
To test the XGrid feature, find the location where pebl was installed byeasy_install and navigate to the src/pebl/test.manual directory. There, createa file called xgridconfig.txt and include the relevant configurationparameters. The file should look like:
Then, execute the test_xgrid.py test:
Pebl will create and run 10 short learners over the XGrid. It will print someinformation about submitting and retrieving data from the Xgrid controller andfinally print a list of machines where the tasks ran.
For the IPython1 Task Controller¶
IPython1 is the next version of the popular IPython shell that also includes aninteractive, clustering solution. Pebl can use IPython1 to execute learners inparallel.
You will need to install both IPython and IPython1. IPython1 is in activedevelopment and pebl requires a specific version. Once, IPython1 is oficiallyreleased, we will use that package:
To test the IPython1 feature, make sure that IPython1’s ipcluster is in thepath and run:
The test will create three local IPython1 engines and run tasks on them. Thetest cannot, unfortunately, terminate the engines and that needs to be donemanually. Simply run ‘ps’ and terminate the appropriate processes.
For the EC2 Task Controller¶
Amazon EC2 is an on-demand cloud computing solution from Amazon. It allowsusers to rent computing power on an as-needed basis. Pebl can reserve, create,use and terminate EC2 instances automatically. More information available athttp://aws.amazon.com/ec2/
Before you can use Amazon’s EC2 platform, you need to register with Amazon andcreate the required authentication credentials. Consult the Getting StartedGuide atAmazon for further information.
Pebl uses the boto package to interact with EC2:
Also see the instructions above for installing dependencies for the IPython1Task Controller (which is required by the EC2 Task Controller).
To test the EC2 feature, find the location where pebl was installed byeasy_install and navigate to the src/pebl/test.manual directory. There, createa file called ec2config.txt and include the relevant configurationparameters. The file should look like:
Then, execute the test_ec2.py test:
Pebl will reserve and use 3 EC2 instances, upgrade the version of peblinstalled, run 10 shorts tasks on them and terminate the instances whenfinished. If all works sucessfully, Pebl will print the hostnames of themachines used.
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For developing Pebl¶
Pebl developers will also need nose for testing and sphinx for generating htmldocumentation: