Free Software Explorations

Using LPSOLVE for linear programming problems.

2014-11-04T08:39:00.001-08:00

Although Gnumeric and LibreOffice CALC spreadsheet softwares can solve linear programming problems, these do not include postoptimality or sensitivity reports. But not to worry.

The free standing LP program LPSOLVE can be used to solve linear programming problems and is capable of producting sensitity reports.
Let us illustrate how to use this software on a simple program.

Create a file, simple.py with the following contents:

max: 5000 X+ 3000 Y;


C1: X + Y   <=  8;
C2: 2 X + Y <= 10;

Note that LPSOLVE will do the automatic conversion of the above problem to a standard from internally, the user need not explicity rewrite the model to include slack, surplus or artificial variables. From the command line, issue lp_solve -S7 simple.py . This will tell the program to solve the lp problem specification and solve for the optimum values of the variables and to produce a complete report :

Model name: 
                 X        Y 
Maximize      5000     3000 
C1               1        1 <=        8
C2               2        1 <=       10
Type          Real     Real 
upbo           Inf      Inf 
lowbo            0        0 

Scale factors:
R0                   scaled at 0.000237841
C1                   scaled at 0.840896
C2                   scaled at 0.594604
X                    scaled at 0.840896
Y                    scaled at 1.18921

Value of objective function: 28000

Actual values of the variables:
X                               2
Y                               6

Actual values of the constraints:
C1                              8
C2                             10

Objective function limits:
                                 From            Till       FromValue
X                                3000            6000          -1e+30
Y                                2500            5000          -1e+30

Dual values with from - till limits:
                           Dual value            From            Till
C1                               1000               5              10
C2                               2000               8              16
X                                   0          -1e+30           1e+30
Y                                   0          -1e+30           1e+30

Tableau at iter 2:
             -3             -4
  2      2.0000000     -1.4142136      5.0453785
  1     -1.4142136      2.0000000      2.3784142
        -0.2828427     -0.8000000      6.6595598

The output contains the model formulation, scaling factors used, value of objective function(28000), value of the variables,X=2 ad Y=6 constraint values (value of slacks), and the final final tableu at termination If there were errors in the specification file, the software may not output the reusults. Thee flag -S7 gives the most detailed output. Here are other flag setttings:

-S0: Print nothing
         -S1: Only objective value
         -S2: Obj value+variables (default)
         -S3: Obj value+variables+constraints
         -S4: Obj value+variables+constraints+duals
         -S5: Obj value+variables+constraints+duals+lp model
         -S6: Obj value+variables+constraints+duals+lp model+scales
         -S7: Obj value+variables+constraints+duals+lp model+scales+lp tableau

It is beyond the scope of this article to explain or interpret the output values retuned by LPSOLVE. That might be explained in another artcle in our other blogs.

The Ceres nonlinear least squares solver from Google. Part 1. Installation.

2012-05-11T05:11:00.000-07:00

Introduction

Ceres is a new C++ library and optimization software for nonlinear least squares problems. It is aimed for fitting models in statistics and finds use in computer vision at Google. It was released as an open source software with BSD license by Google and was developed by Sameer Aggarwal and Keir Mierle. The home page is at
http://code.google.com/p/ceres-solver/. The following are features of Ceres:

A friendly API: build your cost function one residual at a time
Automatic differentiation
Robust loss functions
Local parameterizations
Threaded Jacobian evaluators and linear solvers
Dense QR factorization (using Eigen) for small problems
Sparse Cholesky factorization (using SuiteSparse) for large sparse problems
Specialized solvers for bundle adjustment problems in computer vision.
Scales from servers to cell phones.
Supports Linux and MacOS with future support for Windows and iOS and Android.

We are surprised that the instructions for installing Ceres software is in a pdf file in documentation of the installer. So we read the documentation and publish the instructions which we followed and seen to work.

Installing Ceres using a terminal

1. Create a subdirectory ceres-1.0 and cd to that created directory. 2. Download using wget.

$mkdir ceres-1.0   
$ cd ceres-1.0   
$ wget -ct 0 http://ceres-solver.googlecode.com/files/ceres-solver-1.0.0.tar.gz   
wget -ct 0 http://ceres-solver.googlecode.com/files/ceres-solver-1.0.0.tar.gz --2012-05-11 15:09:52--  http://ceres-solver.googlecode.com/files/ceres-solver-1.0.0.tar.gz 
Resolving ceres-solver.googlecode.com... 209.85.175.82 Connecting to ceres-solver.googlecode.com|209.85.175.82|:80... connected. HTTP request sent, awaiting response... 200 OK 
Length: 3461260 (3.3M) [application/x-gzip] Saving to: `ceres-solver-1.0.0.tar.gz'  100%[====================================================================================>] 
3,461,260   65.1K/s   in 54s       2012-05-11 15:10:47 (62.2 KB/s) - `ceres-solver-1.0.0.tar.gz' saved [3461260/3461260]

3. Untar the gzipped file by typing tar xzvvf ceres-solver-1.0.0.tar.gz. Change the current directory to ceres-solver-1.0.0.

Software Dependencies

4. Install various dependency files. You need to install the following softwares in order for Ceres to do its thing: cmake, gflags, glog, eigen , suitesparse and protobuf:

sudo apt-get install cmake
wget -ct 0 http://gflags.googlecode.com/files/gflags-2.0.tar.gz   
tar xzvvf gflags-2.0.tar.gz   cd gflags-2.0    
./configure --prefix=/usr/local    
make    
cd ..    
wget http://google-glog.googlecode.com/files/glog-0.3.2.tar.gz    
tar xzvvf glog-0.3.2.tar.gz     
cd glog-0.3.2/    
./configure --with-gflags=/usr/local/   
make    
sudo make install       
sudo apt-get install libeigen3-dev    
sudo apt-get install libsuitesparse-dev    
sudo apt-get install libprotobuf-dev

5. Now it is time to install the Ceres software.

mkdir ceres-bin   
cd ceres-bin   
cmake ../ceres-solver-1.0.0   
cmake ../ceres-solver-1.0.0 -DEIGEN_INCLUDE=/usr/include/eigen3   
make -j3

Example

6. Running the example:

examples/simple_bundle_adjuster ../ceres-solver-1.0.0/data/problem-16-22106-pre.txt
   0: f: 1.598216e+06 d: 0.00e+00 g: 5.67e+18 h: 0.00e+00 rho: 0.00e+00 mu: 1.00e-04 li:  0
   1: f: 1.116401e+05 d: 1.49e+06 g: 1.42e+18 h: 5.48e+02 rho: 9.50e-01 mu: 3.33e-05 li:  1
   2: f: 4.923547e+04 d: 6.24e+04 g: 8.57e+17 h: 3.21e+02 rho: 6.79e-01 mu: 3.18e-05 li:  1
   3: f: 1.884538e+04 d: 3.04e+04 g: 1.45e+17 h: 1.25e+02 rho: 9.81e-01 mu: 1.06e-05 li:  1
   4: f: 1.807384e+04 d: 7.72e+02 g: 3.88e+16 h: 6.23e+01 rho: 9.57e-01 mu: 3.53e-06 li:  1
   5: f: 1.803397e+04 d: 3.99e+01 g: 1.35e+15 h: 1.16e+01 rho: 9.99e-01 mu: 1.18e-06 li:  1
   6: f: 1.803390e+04 d: 6.16e-02 g: 6.69e+12 h: 7.31e-01 rho: 1.00e+00 mu: 3.93e-07 li:  1

Ceres Solver Report
-------------------
                                     Original                  Reduced
Parameter blocks                        22122                    22122
Parameters                              66462                    66462
Residual blocks                         83718                    83718
Residual                               167436                   167436

                                        Given                     Used
Linear solver                     DENSE_SCHUR              DENSE_SCHUR
Preconditioner                            N/A                      N/A
Ordering                                SCHUR                    SCHUR
num_eliminate_blocks                      N/A                    22106
Threads:                                    1                        1
Linear Solver Threads:                      1                        1

Cost:
Initial                          1.598216e+06
Final                            1.803390e+04
Change                           1.580182e+06

Number of iterations:
Successful                                  6
Unsuccessful                                0
Total                                       6

Time (in seconds):
Preprocessor                     1.000000e+00
Minimizer                        5.000000e+00
Total                            6.000000e+00
Termination:               FUNCTION_TOLERANCE

4520:~/Downloads/ceres-1.0/ceres-bin$

In the next part, we explain the example and try to understand the API for using the Ceres Software.

Create bootable "live" LInux or BSD usb drives with unetbootin

2012-04-05T07:44:00.001-07:00

Unetbootin is a powerful system utility to create bootable usb drives with your favorite distribution(although may not be the latest version). You need at least a usb flash drive with 2Gbytes capacity, but it is better to use 4 Gbytes, the price difference is small enough.

You also need gparted utility to format and partition your drive. If these are not available in your LInux OS, install them using your software package installer system or if you have moderate skills, download, compile and install from sources. You can install apt-get and synaptic, we wonder why Ubuntu removed this from their newest distribution.

Insert your usb drive, saving important files to your hard disk. Then use gparted to format using "ext2" if you want to try Puppy LInux. Otherwise you can also format using MS FAT32 so you can even save files readable in Windows!

Issue df in the command line after using gparted. Your usb should be detected, usually the drive is accessible using the name /media. For example, my pqi branded usb is readble/writable as /media/d32b6e24-c9dd-4073-8f24-63981d635de1.

Next issue sudo unetbootin. You will be presented with subwindow giving you choices of Operating Systems, including BSDs!(freebsd and netbsd.). Yes you can use the internet to download the operating system ISO images, but it would be masochism as realtime downloading is a pain! Instead copy the iso link using the mouse and use wget instead. In fact it tooke me more than two hours to download a live Linux Mint iso image!

I have downloaded linux mint using wget -ct 0 http://ftp.heanet.ie/pub/linuxmint.com/stable/10/linuxmint-10-gnome-cd-i386.iso

Here is my wget for free bsd. Mercifully it is a small size,
wget -ct 0 http://nchc.dl.sourceforge.net/project/lubi/Zipped%20Disk%20Images/1/freebsd-8.0.img.gz

For puppy, use

wget -ct 0 http://distro.ibiblio.org/pub/linux/distributions/puppylinux/puppy-5.3.1/slacko-5.3.1-SCSI-MAIN.iso

Here is a screenshot of unetbootin:

Note that your usb must be mounted when you use unetbootin. Click on the small button with .... Then hightlight the location of your downloaded iso. Then click on ok button. Wait a while and unetbootin will tell you when it is safe to reboot!

I have done this puppy and linuxmint and freebsd. I find the bsd distribution difficult to install, it needs more information! Here are some screenshots of opening screen for puppy:

And here is for LinuxMint.

Pupppy linux is fast to boot, but it is so slow shutting down! It incorporates the seamonkey browser.
As for LInuxmint,it uses a very old version of Firefox, 3.5.0, the newest version is already at 12.0! Oh well, we cannot have everything.

Itis surprising that Knoppix, the pioneering live-CD Linux distribution is not in the list of unetbootin!

Will Spyder be our new Python IDE?

2012-04-04T20:15:00.000-07:00

Your author has tried Emacs, Vi, eric4, drpython, spe, gedit, jedit, anjuta,idle, geany
kate, kedit, when writing Python programs, or modules

Among the editors/IDE mentioned eric4 comes close to be the most ideal for me, except that
is somewhat slow. Spe on the otherhand, has that unusual cursor-editor missynchronization.What
character you type sometimes does not appear immediately! It is disconcerting to say the least.

Here is a short list of features I demand to have in an editor:

Quick zooming, unzooming. I wonder why editors do not implement or have removed
the standard browser Ctrl-plus or Ctrl-minus for easy viewing of source codes?
Interactive debugging support.
Indent/unindent highlighted code blocks.
Folding and unfolding code blocks. Not an absolute requirement.

Spyder aims to be the standard scientific python editor/ide. It is available in Ubuntu apt-get but it refused to run due to some versioning errors. One day last week, I got an email announcement from the scipy mailing list that there is a new version of spyder. So we tried installing it from the sources.Here are the steps:

wget -ct 0 http://spyderlib.googlecode.com/files/spyder-2.1.9.zip
unzip spyder-2.1.9.zip 
cd spyder-2.1.9/
sudo python2.7 setup.py install
spyder

That works! and that is the latest version of spyder. Spyder on default mode opens the following windows in one screen: console,editor and a tabbed inspector explorer/window for objects, variables, and files. Typing scientific on the console window gave the following information:

>>> scientific
This is a standard Python interpreter with preloaded tools for scientific 
computing and visualization:

>>> import numpy as np  # NumPy (multidimensional arrays, linear algebra, ...)
>>> import scipy as sp  # SciPy (signal and image processing library)

>>> import matplotlib as mpl         # Matplotlib (2D/3D plotting library)
>>> import matplotlib.pyplot as plt  # Matplotlib's pyplot: MATLAB-like syntax
>>> from pylab import *              # Matplotlib's pylab interface
>>> ion()                            # Turned on Matplotlib's interactive mode

Within Spyder, this intepreter also provides:
    * special commands (e.g. %ls, %pwd, %clear)
    * system commands, i.e. all commands starting with '!' are subprocessed
      (e.g. !dir on Windows or !ls on Linux, and so on)

>>>

We will spend more time with our newest editor/ide, but spyder looks very, very promising.

AlgoPy-automatic differentiation for Python programs

2012-03-25T05:36:00.001-07:00

Note: There was failure in running the example in my system consisting of Python 2.7 and the 0.3.1 version of AlgoPy.

Introduction

I had a problem determining the gradient of the ordinal logistic model and I could not find online references on the formula for the gradient. You see it takes around 6 seconds to compute the parameters of model using the BFGS (Broyden, Fletcher, Goldfarb, Shanno) optimizer.

I have heard of ADOL-C before for automatic differentiation, in fact I was browsing the second hand Book Sale and I found a reference book with Java-Forte programs on a CD. That turned me off, since Forte is relative old IDE and I decided NOT to buy it. So lets try an automatic differentiation package for Python.

The home page is at http://packages.python.org/algopy/ homepage.

The documentation at the homepage states the purpose of AlgoPy nicely:

The purpose of AlgoPy is the evaluation of higher-order derivatives in the forward and reverse mode of Algorithmic Differentiation (AD) of functions that are implemented as Python programs. Particular focus are functions that contain numerical linear algebra functions as they often appear in statistically motivated functions. The intended use of AlgoPy is for easy prototyping at reasonable execution speeds. More precisely, for a typical program a directional derivative takes order 10 times as much time as time as the function evaluation. This is approximately also true for the gradient.

Capabilities of AlgoPy

AlgoPy promises to compute the following if possible the following:

evaluation of derivatives useful for nonlinear continuous optimization
gradient
Jacobian
Hessian
Jacobian vector product
vector Jacobian product
Hessian vector product
vector Hessian vector product
higher-order tensors
Taylor series evaluation

Installation

I am using the latest Ubuntu OS ( march 24, 2012
Oneiric Ocelot) on my laptop which serves as my main computer. Try to see the version of your installed default Python by issuing python --version. I see that I have 2.7.2+ Now try this:

sudo easy_install-2.7 algopy

That's all! Here are the terminal output messages

sudo easy_install-2.7 algopy
Searching for algopy
Reading http://pypi.python.org/simple/algopy/
Reading http://packages.python.org/algopy
Reading http://www.github.com/b45ch1/algopy
Best match: algopy 0.3.1
Downloading http://pypi.python.org/packages/source/a/algopy/algopy-0.3.1.zip#md5=84edf4722e0f67ae254d663906893ff5
Processing algopy-0.3.1.zip
Running algopy-0.3.1/setup.py -q bdist_egg --dist-dir /tmp/easy_install-SvuPun/algopy-0.3.1/egg-dist-tmp-8pSEhA
.dev
warning: manifest_maker: MANIFEST.in, line 1: 'recursive-include' expects    ...

zip_safe flag not set; analyzing archive contents...
algopy.__init__: module references __file__
algopy.tracer.tests.environment: module references __file__
Adding algopy 0.3.1 to easy-install.pth file

Installed /usr/local/lib/python2.7/dist-packages/algopy-0.3.1-py2.7.egg
Processing dependencies for algopy
Finished processing dependencies for algopy

Actually easy_install has three versions in my machine, namely easy_install easy_install-2.6 easy_install-2.7 I got the following error for instance by typing easy_install only:

sudo easy_install algopy
[sudo] password for toto: 
Traceback (most recent call last):
  File "/usr/local/bin/easy_install", line 5, in 
    from pkg_resources import load_entry_point
  File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 2676, in 
    parse_requirements(__requires__), Environment()
  File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 552, in resolve
    raise DistributionNotFound(req)

It is much better to install easy_install to your system than downloading the tarred package from the homepage and unpacking and installing it via python setup.py install

Trying out an example

import numpy, algopy
from algopy import UTPM, exp

def eval_f(x):
    """ some function """
    return x[0]*x[1]*x[2] + exp(x[0])*x[1]

# forward mode without building the computational graph
# -----------------------------------------------------
x = UTPM.init_jacobian([3,5,7])
y = eval_f(x)
algopy_jacobian = UTPM.extract_jacobian(y)
print 'jacobian = ',algopy_jacobian

# reverse mode using a computational graph
# ----------------------------------------

# STEP 1: trace the function evaluation
cg = algopy.CGraph()
x = algopy.Function([1,2,3])
y = eval_f(x)
cg.trace_off()
cg.independentFunctionList = [x]
cg.dependentFunctionList = [y]

# STEP 2: use the computational graph to evaluate derivatives
print 'gradient =', cg.gradient([[3.,5,7]])
print 'Jacobian =', cg.jacobian([[3.,5,7]])
print 'Hessian =', cg.hessian([[3.,5.,7.]])
print 'Hessian vector product =', cg.hess_vec([[3.,5.,7.]],[[4,5,6]])

When the above is executed in my laptop, it prints to the console or terminal the following:

.
>>> import numpy, algopy
>>> from algopy import UTPM, exp
>>> 
>>> def eval_f(x):
...     """ some function """
...     return x[0]*x[1]*x[2] + exp(x[0])*x[1]
... 
>>> # forward mode without building the computational graph
... # -----------------------------------------------------
... x = UTPM.init_jacobian([3,5,7])
>>> y = eval_f(x)
>>> algopy_jacobian = UTPM.extract_jacobian(y)
>>> print 'jacobian = ',algopy_jacobian
jacobian =  [ 135.42768462   41.08553692   15.        ]
>>> 
>>> # reverse mode using a computational graph
... # ----------------------------------------
... 
>>> # STEP 1: trace the function evaluation
... cg = algopy.CGraph()
>>> x = algopy.Function([1,2,3])
>>> y = eval_f(x)
>>> cg.trace_off()

>>> cg.independentFunctionList = [x]
>>> cg.dependentFunctionList = [y]
>>> 
>>> # STEP 2: use the computational graph to evaluate derivatives
... print 'gradient =', cg.gradient([[3.,5,7]])
gradient = [array([ 135.42768462,   41.08553692,   15.        ])]
>>> print 'Jacobian =', cg.jacobian([[3.,5,7]])
Jacobian =
Traceback (most recent call last):
  File "", line 1, in 
  File "/usr/local/lib/python2.7/dist-packages/algopy-0.3.1-py2.7.egg/algopy/tracer/tracer.py", line 262, in jacobian
    self.pushforward(utpm_x_list)
  File "/usr/local/lib/python2.7/dist-packages/algopy-0.3.1-py2.7.egg/algopy/tracer/tracer.py", line 103, in pushforward
    f.__class__.pushforward(f.func, f.args, Fout = f)
  File "/usr/local/lib/python2.7/dist-packages/algopy-0.3.1-py2.7.egg/algopy/tracer/tracer.py", line 637, in pushforward
    out  = func(*args)
  File "/usr/local/lib/python2.7/dist-packages/algopy-0.3.1-py2.7.egg/algopy/utpm/utpm.py", line 73, in __getitem__
    tmp = self.data.__getitem__((slice(None),slice(None)) + tuple(sl))
IndexError: invalid index
>>> print 'Hessian =', cg.hessian([[3.,5.,7.]])
Hessian =
Traceback (most recent call last):
  File "", line 1, in 
  File "/usr/local/lib/python2.7/dist-packages/algopy-0.3.1-py2.7.egg/algopy/tracer/tracer.py", line 349, in hessian
    self.pushforward(utpm_x_list)
  File "/usr/local/lib/python2.7/dist-packages/algopy-0.3.1-py2.7.egg/algopy/tracer/tracer.py", line 103, in pushforward
    f.__class__.pushforward(f.func, f.args, Fout = f)
  File "/usr/local/lib/python2.7/dist-packages/algopy-0.3.1-py2.7.egg/algopy/tracer/tracer.py", line 637, in pushforward
    out  = func(*args)
  File "/usr/local/lib/python2.7/dist-packages/algopy-0.3.1-py2.7.egg/algopy/utpm/utpm.py", line 73, in __getitem__
    tmp = self.data.__getitem__((slice(None),slice(None)) + tuple(sl))
IndexError: invalid index
>>> print 'Hessian vector product =', cg.hess_vec([[3.,5.,7.]],[

Ouch, we have fatal errors! We do have the latest version of AlgoPy (0.3.1). But you may be luckier than me.

We are a little sorry for this post. But we will come back soon, we need to visit the mailing list or the algopy group (if there is). We will come back soon!

Its about time Python get serious with Statistics! Introducing Scikits.statsmodels (Linux Ubuntu)), Part 1

2012-03-07T01:54:00.000-08:00

You can of course perform powerful statistical routines using Python, Rpy module and R. But greater joy is now coming to pure Python users with the Scikits.statsmodels package.

Install the scikits.statsmodels module

Python >= 2.5
NumPy >= 1.4.0 
SciPy >= 0.7

sudo apt-get install python python-setuptools python-numpy python-scipy

Download the software scikits.statsmodels module

wget -ct 0 http://pypi.python.org/packages/source/s/scikits.statsmodels/scikits.statsmodels-0.3.1.tar.gz#md5=1f55b53d161544b95ca2709c9731c00c

tar -xvvf scikits.statsmodels-0.3.1.tar.gz
sudo python setup.py install

Test the installed module

sudo apt-get install ipython

import scikits.statsmodels.api as sm
help(sm)

Help on module scikits.statsmodels.api in scikits.statsmodels:  NAME     scikits.statsmodels.api - Statistical models  FILE     /home/toto/testsoftware/scikits.statsmodels-0.3.1/scikits/statsmodels/api.py  DESCRIPTION      - standard `regression` models            - `GLS` (generalized least squares regression)       - `OLS` (ordinary least square regression)       - `WLS` (weighted least square regression)       - `GLASAR` (GLS with autoregressive errors model)            - `GLM` (generalized linear models)       - robust statistical models            - `RLM` (robust linear models using M estimators)       - `robust.norms` estimates       - `robust.scale` estimates (MAD, Huber's proposal 2).       - sandbox models       - `mixed` effects models       - `gam` (generalized additive model

In [17]: dir(sm)
Out[17]: 
['GLM',
 'GLS',
 'GLSAR',
 'Logit',
 'MNLogit',
 'OLS',
 'Poisson',
 'Probit',
 'RLM',
 'WLS',
 '__builtins__',
 '__doc__',
 '__file__',
 '__name__',
 '__package__',
 'add_constant',
 'categorical',
 'datasets',
 'families',
 'iolib',
 'nonparametric',
 'regression',
 'robust',
 'test',
 'tools',
 'tsa',
 'version']

Additional resources

http://statsmodels.sourceforge.net/

http://groups.google.com/group/pystatsmodels

The regression example from the homepage

import numpy as np
import scikits.statsmodels.api as sm


# get data
nsample = 100
x = np.linspace(0,10, 100)
X = sm.add_constant(np.column_stack((x, x**2)))
beta = np.array([1, 0.1, 10])
y = np.dot(X, beta) + np.random.normal(size=nsample)


# run the regression
results = sm.OLS(y, X).fit()

# look at the results
print results.summary()

     Summary of Regression Results     
=======================================
| Dependent Variable:            ['y']|
| Model:                           OLS|
| Method:                Least Squares|
| Date:               Wed, 07 Mar 2012|
| Time:                       17:58:02|
| # obs:                         100.0|
| Df residuals:                   97.0|
| Df model:                        2.0|
==============================================================================
|                   coefficient     std. error    t-statistic          prob. |
------------------------------------------------------------------------------
| x1                      1.060         0.1353         7.8344         0.0000 |
| x2                    0.09398        0.01309         7.1802         0.0000 |
| const                   9.848         0.2927        33.6490         0.0000 |
==============================================================================
|                          Models stats                      Residual stats  |
------------------------------------------------------------------------------
| R-squared:                     0.9729   Durbin-Watson:              1.803  |
| Adjusted R-squared:            0.9724   Omnibus:                    3.108  |
| F-statistic:                    1742.   Prob(Omnibus):             0.2114  |
| Prob (F-statistic):         9.776e-77   JB:                         2.791  |
| Log likelihood:                -139.9   Prob(JB):                  0.2477  |
| AIC criterion:                  285.8   Skew:                     -0.4176  |
| BIC criterion:                  293.6   Kurtosis:                   2.927  |
------------------------------------------------------------------------------

Installing the latest free 3.5rc3 libreoffice productivity tools

2012-02-18T20:06:00.000-08:00

The problem with the built-in package system in Ubuntu is that the softwares in the repositories may be one or two or even three versions behind! My old version of libreoffice was at 3.4. It is now at Version 3.5. But the disadvantage of manually installing the latest version is that there will be NO automatic updates!

Download the compressed installer

http://download.documentfoundation.org/libreoffice/stable/3.5.0/deb/x86_64/LibO_3.5.0_Linux_x86-64_install-deb_en-US.tar.gz

http://download.documentfoundation.org/libreoffice/stable/3.5.0/deb/x86/LibO_3.5.0_Linux_x86_install-deb_en-US.tar.gz

Uncompressed the downloaded file
Remove old traces of LibreOffice

sudo apt-get remove libreoffice

sudo apt-get purge

Install the downloaded file

sudo dpkg -i *.deb

Install the desktop integration.

cd desktop-intergration
sudo dpkg -i *.deb

Your new LibreOffice installation should now be able to run from the Destkop GUI Applications.

Congratulations on having a free alternative to Microsoft Windows Office Applications in Linux Operating sytem.

Why University of California at Berkeley chose Google over Microsoft for email/calendaring services

2011-12-23T16:43:00.000-08:00

As a public univerity supported by people's taxes, the transparency of UC Berkeley in selecting Google over Microsoft to provide online email and calendaring services is very welcome. Here is a decision table showing the strengths and weaknesses of the two opposite solutions (one free, the other commercial).

Productivity Suite Comparison Matrix

Install Sympy: A symbolic math software package in pure Python!

2011-10-29T21:02:00.001-07:00

What is nice about Sympy?

It aims to be a simple but full-featured, extensible computer algebra system and it is written in pure Python. There is no need for external libraries!

Here are some information extracted from the home page of sympy.
What are the available features in Sympy?

The current core of Sympy have the following capabilities:

basic arithmetics *,/,+,-,**
basic simplification (like a*b*b + 2*b*a*b -> 3*a*b**2)
expansion (like (a+b)**2 -> a**2 + 2*a*b + b**2)
functions (exp, ln, ...)
complex numbers (like exp(I*x).expand(complex=True) -> cos(x)+I*sin(x))
differentiation
taylor (laurent) series
substitution (like x -> ln(x), or sin -> cos)
arbitrary precision integers, rationals and floats
noncommutative symbols
pattern matching

What are the avaialable modules aside from the core?

more functions (sin, cos, tan, atan, asin, acos, factorial, zeta, legendre)
limits (like limit(x*log(x), x, 0) -> 0)
integration using extended Risch-Norman heuristic
polynomials (division, gcd, square free decomposition, groebner bases, factorization)
solvers (algebraic, difference and differential equations, and systems of equations)
symbolic matrices (determinants, LU decomposition...)
mpmath (multiprecision floating-point arithmetic)
geometric algebra (GA)
Pauli and Dirac algebra
quantum physics
geometry module
plotting (2D and 3D)
code generation (C, Fortran, LaTeX)

We wish that Sympy will become standard and integrate with the other package called Symbolic. It is a long time coming. This will not supplant the need for Maxima and will enable Python loving scientists and applied and research mathematicians. But I got the following error on installing Sympy in Oneiric:

sudo apt-get install sympy 
[sudo] password for toto:   
Reading package lists... Done 
Building dependency tree         Reading state information... Done 
E: Unable to locate package sympy 
toto@toto-Aspire-4520:~$ sudo apt-get install python-sympy 
Reading package lists... Done 
Building dependency tree        
Reading state information... Done 
The following NEW packages will be installed:   
python-sympy 0 upgraded, 1 newly installed, 0 to remove and 2 not upgraded. 
Need to get 1,694 kB of archives. After this operation, 9,490 kB of additional disk space will be used. 
Get:1 http://ph.archive.ubuntu.com/ubuntu/ oneiric/universe python-sympy all 0.6.7-1.1 [1,694 kB] Fetched 1,694 kB in 19s (84.8 kB/s)                                                                                           
Selecting previously deselected package python-sympy. (Reading database ... 552034 files and directories currently installed.) 
Unpacking python-sympy (from .../python-sympy_0.6.7-1.1_all.deb) ... Processing triggers for man-db ... 
Processing triggers for menu ... Setting up python-sympy (0.6.7-1.1) ... Processing triggers for menu ... 
Processing triggers for python-support ... Compiling /usr/lib/pymodules/python2.6/mpmath/libmp/exec_py3.py ... SyntaxError: ('invalid syntax', ('/usr/lib/pymodules/python2.6/mpmath/libmp/exec_py3.py', 1, 12, 'exec_ = exec\n'))  Compiling /usr/lib/pymodules/python2.7/mpmath/libmp/exec_py3.py ... SyntaxError: ('invalid syntax', ('/usr/lib/pymodules/python2.7/mpmath/libmp/exec_py3.py', 1, 12, 'exec_ = exec\n'))  Compiling /usr/lib/pymodules/python2.7/mpmath/tests/extratest_gamma.py ... SyntaxError: ('invalid syntax', ('/usr/lib/pymodules/python2.7/mpmath/tests/extratest_gamma.py', 50, 35, '        print("%s ok;" % name, end=\' \')\n'))  Compiling /usr/lib/pymodules/python2.7/mpmath/tests/torture.py ... SyntaxError: ('invalid syntax', ('/usr/lib/pymodules/python2.7/mpmath/tests/torture.py', 80, 27, '            print(".", end=\' \')\n'))

Yet when I fired up ipython and imported Sympy, there were no errors. But lets spend more time with this package on our blog. Oh, I removed sympy and reinstalled the package using sudo easy_install-2.7 sympy Here are some simple examples.

>>> sympy.factor("(x^2 + 2*a*x + a^2)")
(a + x)**2

>>> sympy.diff("x^2*y", "x")
2*x*y

>>> sympy.diff("log(y)")
1/y

>>> sympy.simplify("(x-a)/(x-a)")
1

Of course we just cannot trust the results blindly. Integration is somewhat convoluted. Here is the help documentation for integrate:

integrate(expr, *args, **kwargs)
    integrate(f, var, ...)
    
    Compute definite or indefinite integral of one or more variables
    using Risch-Norman algorithm and table lookup. This procedure is
    able to handle elementary algebraic and transcendental functions
    and also a huge class of special functions, including Airy,
    Bessel, Whittaker and Lambert.
    
    var can be:
    
    - a symbol                   -- indefinite integration
    - a tuple (symbol, a, b)     -- definite integration
    
    Several variables can be specified, in which case the result is multiple
    integration.
    
    Also, if no var is specified at all, then the full anti-derivative of f is
    returned. This is equivalent to integrating f over all its variables.
    
    **Examples**
    
    >>> from sympy import integrate, log
    >>> from sympy.abc import a, x, y
    
    >>> integrate(x*y, x)
    x**2*y/2
    
    >>> integrate(log(x), x)
    x*log(x) - x

This is module worth having in your system. We hope that this will be more robust as time goes by.

Kile works in KDE window manager in Ubuntu! and the video cam, wireless, and microphone divices all work!

2011-10-23T19:38:00.000-07:00

I got a surprise when I tried KIle in the kdm (KDE window manager or desktop). Kile latex IDE works fine in it and there are no more annoying messages about creating a default factory method. I can now insert math symbols selected from the left panel.
Its still the same 2.1.0 version of Kile. So I suspect that there were wrong settings for GNOME when I was still in Ubuntu 11.04.

This may now be my default window manager in my laptop while my ACER ONE still uses unity desktop. The system response is perceptibly fast!!

I went back to GNOME and I pleasantly discovered that I got my video and microphones and wireless working! Of course I updated my packages after upgrading to the Ocelot Ubuntu distribution. This may have fixed any issues with the softwares in the first upgrade.

Scite 2.03 is immovable on the desktop!

2011-09-28T05:59:00.000-07:00

After trying out drpython, I installed scite and run it. But bad luck struck under Ubuntu. The editor screen cannot be moved! It was immobile on the left side of the screen and I cannot strangely zoom it. So another editor bit the dust in our Ubuntu natty narwhal OS powered desktop!

Note: Feb. 19, 2012. I looked at scite and since I have upgraded to Ubuntu oneiric ocelot OS version, Scite is working properly.

Dr Python is a nice lightweight Python editor but there is something wrong with screen rendering.

2011-09-28T05:51:00.000-07:00

The following image shows that the screen rendering of drpython leaves much to be desired.

You have to scroll down and up so that the screen will be properly rendered.

Octobet 30, 2011: The funny and erroneous black bars have disappeared! after a few updates!

Alternative sites for information on free-software.

2011-09-11T16:07:00.000-07:00

I will start collecting some urls which are good sources for free-software. The first esteemed entry is

As usual, most posts I have written are works in progress.

Installing Gretl in Ubuntu Natty

2011-09-09T07:48:00.000-07:00

I get segmentation fault on startup of gretl. Here are some steps I took to make it run again
on my 64 bit ACER laptop. Download the 1.9.5 source code by clicking on

sourceforge: gretl

The actual download site link I got was

http://nchc.dl.sourceforge.net/project/gretl/gretl/1.9.5/gretl-1.9.5.tar.bz2

and if you prefer the command line(with a network connection!)

wget -ct0 http://nchc.dl.sourceforge.net/project/gretl/gretl/1.9.5/gretl-1.9.5.tar.bz2,

but that is not recommeded as the actual download site may be too busy!

Now go to the directory where the bzip file is, and unpack it with

tar xjvvf gretl-1.9.5.tar.bz2

then, goto the gretl-1.9.5 directory, and perform the standard

./configure; make; make install

incantation to compile and install from source files.

Here are some errors I got when compiling the sources:

../lib/src/gretl_fft.c:22:19: fatal error: fftw3.h: No such file or directory

Fix: install libfftw3 development files.(libfftw3-dev)

../lib/src/monte_carlo.c:40:17: fatal error: gmp.h: No such file or directory

Fix: install gmp development files. (libgmp3-dev)

Typing gretl on the command line does not do anything! So we type gretl again and the TAB key:
gretl
gretl gretlcli gretl_x11

Trying out gretlcli,

toto@toto-Aspire-4520:~/Downloads/gretl-1.9.5$ gretlcli
gretlcli: symbol lookup error: /usr/lib/libgretl-1.0.so.0: undefined symbol: omp_get_wtime

So back to installing omp (open MP). Fix: install libgomp-1-dbg

Darn, I still get the error!

gretlcli: symbol lookup error: /usr/lib/libgretl-1.0.so.0: undefined symbol: omp_get_wtime

So I thought that that we remove some remaining packages which are not in use anymore.

sudo apt-get autoremove.

Now we get a sweet response from grelcli:

gretlcli
gretl version 1.9.5
Copyright Ramu Ramanathan, Allin Cottrell and Riccardo "Jack" Lucchetti
This is free software with ABSOLUTELY NO WARRANTY
Current session: 2011-09-09 09:45
gretl is process 20218, '/usr/local/bin/gretlcli'
gretldir is maybe '/usr/local/share/gretl/'?

"help" gives a list of commands
Type "open filename" to open a data set
? ^C

and typing gretl now give us a more familiar qui (from our experience with previous versions).

I ahve upgraded to the newest Ubuntu distribution Oneiric Ocelot and gretl seems to work ("seemst to") because I have to spend more time with this econometrics software.

Links to Online Documentation

2011-07-24T00:33:00.000-07:00

I am starting to gather links to manuals, tutorials of free software.

Maxima Computer Algebra System.
Manual: http://maxima.sourceforge.net/docs/manual/en/maxima.html
Python Programming Language.
Main Documentation Page: www.python.org/doc/
Reference: docs.python.org/reference/
R statistical software.
Index to manuals: http://cran.r-project.org/manuals.html
Gretl Econometrics Software.
Gretl-Guide: http://ricardo.ecn.wfu.edu/pub/gretl/manual/en/gretl-guide.pdf
Scipy and Numpy.
http://docs.scipy.org/doc/

Plotting Small Samples with R.

2011-07-08T09:36:00.000-07:00

R has a comprehensive set of routines for visualization of data. Here we show some of its capabilities on a small sample Y containing positive values.

library("vioplot") X <- c(rnorm(50, 10, 3),rnorm(50, 15, 5)) Y <- c(runif(10, 5, 20)) par(mfrow=c(3,3)) pie(Y, main="Small sample", sub="A Pie Chart") dotchart(Y, main="Small sample", sub="A Dot Chart") stripchart(Y, main="Small Sample", sub="A Strip chat") barplot(Y, main="Small sample", sub="A vertical Bar Chart") barplot(Y, horiz=T, main="Small sample", sub="A Horizontal Bar Chart") boxplot(Y, main="Small sample", sub="A box plot") vioplot(Y) # package vioplot title <- "A vio plot" plot(Y, type="p", main="Small Sample", sub="A Scatterplot") plot(Y, type="l", main="Small Sample", sub="A Line plot")

First a few observations:

1.The vioplot function does not allow seting the main title or sub title. Instead you should call title("title of graph") after the call to vioplot.

2. Pie charts are not well loved by statisticians, they cannot represent negative values and its difficult to judge magnitudes.

Here is a screenshot of the small sample plots.

Next time we will present plots which can handle a larger number of data points.

Updating Opera to Version 11.5! (Again to Version 11.61.1250)

2011-06-28T18:10:00.000-07:00

I am currently updating the Opera software to Version 11.5 codenamed Swordfish. Opera is a standards compliant software with a history of introducing innovations liked tabbed browsing and speed dial.

Further reading: Inquirer.net

And click here for an impressive list of the changes in 11.50 Swordfish edition.

Feb 19, 2012: I will be upgrading to version 11.61today! How time flies!
The default software manager spents a long time to install the downloaded file. So I have to do a manual install:

sudo dpkg -i opera_11.61.1250_amd64.deb 
(Reading database ... 677957 files and directories currently installed.)
Preparing to replace opera 11.52.1100 (using opera_11.61.1250_amd64.deb) ...
Unpacking replacement opera ...
Setting up opera (11.61.1250) ...
Error in file "/usr/share/applications/gnumeric.desktop": "zz-application/zz-winassoc-xls" is an invalid MIME type ("zz-application" is an unregistered media type)
Updating software catalog...this may take a moment.
Software catalog update was successful.

How to move and resize Windows in Ubuntu 11.04

2011-06-19T16:08:00.000-07:00

Funny, I was not paying attention to my 11.04 Natty Narwhal Ubuntu Desktop. I dont like surprises and
the new Ubuntu surprised me when I noticed there are no more window Maximize, Minimize, buttons on the top corners.

Anyway, to move windows, Press Alt-F7 with the mouse on the window you want to move. Move the mouse to the final location of the window.

To resize windows, Press Alt-F8, and move the mouse up or down to resize vertically or left-right to resize horizontally.

We will revise our just recent posts on Latexila and Texmaker.In time, we might love this strange behavior of Ubuntu. Right now, we dont. Please bring back the traditional window controls!

latexila, an Integrated Gnome Latex editor

2011-06-19T15:33:00.000-07:00

Latexila, is currently at version 2.06 in my new Ubuntu 11.04 Linux desktop at my ACER 4520 laptop computer.

I can only two things and I am surprised both Latexila and Texmaker suffers from the same major problems, namely Windows cannot be resized, and Windows cannot be moved. Here is a snapshot of Latexila in my ACER:

June 20, 2011. This just in! I discovered that Ubuntu 11.04 windows do not contain Windows minimize and maximize buttons or controls. Press F7 while mouse is on the window and move the windows to the desired location. Press Al-F8 to to resize the windows. This is unnerving for new users of 11.04 Ubuntu.

October 30, 2011. The spate of package updates after updating Ubuntu to the latest and greatest version oneiric ocelot has fixed the above issues!

Texmaker, current version not functioning well

2011-06-19T15:22:00.000-07:00

I encourage developers to produce more softwares and we will focus on describing how well they are designed and testing them for ease of use.

I have installed texmaker and it is a far cry from the old versions. It sports a new version of
the graphical interface and is more integrated with other latex utilities like Kile. However, I am shocked that

windows cannot be resized! windows cannot be moved!

These are negatives for the current version (2.2.1) of this Latex editor.

This just in! I discovered that Ubuntu 11.04 windows do not contain Windows minimize and maximize buttons or controls. Press F7 while mouse is on the window and move the windows to the desired location. Press Al-F8 to to resize the windows. This is unnerving for new users of 11.04 Ubuntu.

Ubuntu 11.04 Natty Narwhal: Kile Latex IDE is broken

2011-06-19T14:16:00.001-07:00

When I first tried using Kile in my new OS Ubuntu 11.04, it refused to insert math symbol selected from the left panel. So I removed the application and reinstalled again only now the program does not even run!

For published bug reports, see https://bugs.launchpad.net/ubuntu/+source/kile/+bug/772631. I am now
trying to downgrade the version of KIle now back to 2.0.

Tried first to install a beta 5 version (kile_2.1.0~svn2010122beta5-1ubuntu1~natty1~ppa1_amd64.deb) but it still does not execute??!).

Even the downgrade does not work even!
Will watch for developments on Kile.

In the meantime I have installed texmaker and trying out its capabilities. The important thing in Linux is the freedom to choose from various softwares. Now a dedicated Latex editor is not only for beginners of Latex, it can also be used as a productivity enhancement for intermediate and advanced users of Latex, when time is important. Of course we allow other people the freedom to say that real Latex users dont use dedicated Latex editors, Emacs or Vi will do!

February 19, 2012. Kile works now in my upgraded Ubuntu Oneiric Ocelot. But Kile is still in version 1.2.

Ubuntu 11.04 breaks a lot of third party software

2011-06-15T06:41:00.000-07:00

Ubuntu 11.04 does not package anymore some of the computational programs. The result is that
the software installation may not give hints of trouble, but running them give segmentation fault!

Here is one about Euler:

toto@toto-Aspire-4520:~$ euler

(euler:4939): Gdk-CRITICAL **: IA__gdk_char_width: assertion `font != NULL' failed
Segmentation fault

Gretl, an econmetrics package also gives a segmentation fault error. From gretl.sourceforge.net,
there is this message:

The default gretl package for Ubuntu 11.04 (natty) is broken; it should be replaced with gretl version 1.9.5, which is available via packages.debian.org.

We will add more after we install and run them in the latest version of Ubuntu.

An amazing open letter from the Free Software Foundation about Gmail.

2011-05-09T19:03:00.001-07:00

Did you know that, like you, nearly 50% of the 40,000 subscribers to the FSF's supporter mailing list have an @gmail.com email address?

JavaScript, once lauded for adding simple visual effects to web pages, is now used by web sites like Gmail to run powerful programs on your computer. These programs, like any other program running on your computer, should be free software. But right now, the vast majority of JavaScript programs do not respect your essential freedoms to run, study, modify and share them. They take control of your computer away from you; the same control we have been working for over 25 years to protect.

Because of the incredibly high percentage of Gmail-using free software supporters, we're taking action to raise awareness about how to use Gmail without using proprietary software. We'll also be working on longer term solutions, but the most immediate positive step to take is to stop running the proprietary programs.

Many people suggest that you shouldn't use Gmail at all, because it means losing control over your data and privacy. We agree that this is a very important factor for you to consider when choosing how you will handle your email.

But since you are already using Gmail, please help us build momentum for change by not using the proprietary JavaScript on your system -- and helping others to do the same.

Yours sincerely,
Matt Lee
Campaigns Manager
Free Software Foundation

--

Sent from the Free Software Foundation,
51 Franklin Street
Fifth Floor
Boston, MA 02110-1335
United States

Maxima released!

2011-04-18T02:09:00.000-07:00

From the mailing list of Maxima software:

Announcing Maxima 5.24

Maxima is a GPL'd branch of Macsyma, the venerable symbolic
computation system. Maxima 5.24 is a bug fix and feature
enhancement release. The current version is 5.24.0.

Maxima has functions to work with polynomials, matrices, finite sets,
integrals, derivatives and differential equations, linear algebra,
plotting, floating point and arbitrary-precision arithmetic, etc.

Maxima can run on MS Windows and various flavors of Unix,
including MacOS X.
There is a precompiled executable installer for Windows,
RPM's for Linux, and source code tar.gz.

Maxima is implemented in Common Lisp; several Lisps can compile
and run Maxima, including CMUCL, SBCL, Clisp, GCL, and ECL.
The default Windows installer (maxima-5.24.0.exe) was compiled
with GCL, while maxima-5.24.0-ccl.exe was compiled with Clozure CL.

The Maxima project welcomes new participants. You can contribute
in several ways: reporting bugs, fixing bugs, writing new add-on
packages, revising core functions, user interfaces, documentation, ....
Why not see what's happening on the mailing list and consider how
you might contribute to the project.

Thanks to everyone who contributed to the 5.24 release.

Regards,
Robert Dodier
Maxima developer and 5.24 release manager

Project page:
http://sourceforge.net/projects/maxima

Documentation:
http://maxima.sourceforge.net/documentation.html

Bug reports. You must create a Sourceforge login
before filing a bug report (anonymous reports no longer allowed).
http://sourceforge.net/tracker/?group_id=4933&atid=104933

Mailing list. Please sign up before posting a message.
http://maxima.sourceforge.net/maximalist.html

Download page:
http://sourceforge.net/project/showfiles.php?group_id=4933

Ports page:
http://apps.sourceforge.net/mediawiki/maxima/index.php?title=Maxima_ports

Project home page:
http://maxima.sourceforge.net

Change log:
http://maxima.cvs.sourceforge.net/*checkout*/maxima/maxima/ChangeLog-5.24

The current stable version at maxima.sourceforge is 5.18.1, which is older than my Ubuntu 10.04 package version Maxima 5.21.1!

Installing the latest version over the Ubuntu version may result in aggravations. You are on your own.

Our main blog is suffering from WP supercache bug.

2011-04-09T02:12:00.000-07:00

When I put the url http://adorio-research.org in the address bar of the browser, I only get a blank page! Here is the contents of the blank page with the comment delimeters removed:

Page not cached by WP Super Cache. Blank Page. Check output buffer usage by plugins.

Page not cached by WP Super Cache. No closing HTML tag. Check your theme.

Yet when I go to a specific post like http://adorio-research.org/?p=3470,that post jus shows up fine! Going to settings of the plugins, I get this one for WP Super Cache:

Permlink Structure Error

A custom url or permalink structure is required for this plugin to work correctly. Please go to the Permalinks Options Page to configure your permalinks.

I wanted to remove the WP Super Cache plugin but it does not appear in the list of installed plugins! We have an unhappy future days trying to fix this WP Super Cache problem.