Installing UQTkV3.0 on MAC OS x 10

Version 3 of UQ Toolkit is out.

The UQ Toolkit (UQTk) is a collection of libraries and tools for the quantification of uncertainty in numerical model predictions. Just like version 2, version 3.0 offers intrusive and non-intrusive methods for propagating input uncertainties through computational models, tools for sensitivity analysis, methods for sparse surrogate construction, and Bayesian inference tools for inferring parameters from experimental data.

Installing UQTk version 2 on a Mac was easy. Use gcc or clang and fire up the make file, but for version 3, the team has now shifted to cmake and if you want python interface you also need SWIG.

Just like in life, additional dependencies bring additional complexity and chances of things going wrong. Well this was my experience while installing UQtk version 3 on my mac.

Here are my running notes while installing the library on OS X 10.

Cmake doesn’t come preinstalled on a Mac. So get it from here. Installation is easy.


I didn’t have swig so had to download swig from here

Installing is 4 steps

  • Go to the untarred directory,
  • ./configure
  • make
  • sudo make install

I forgot the 4th step and got the following error while installing uqtk

CMake Error at /Applications/CMake.app/Contents/share/cmake-3.6/Modules/FindPackageHandleStandardArgs.cmake:148(message):

Could NOT find SWIG (missing: SWIG_EXECUTABLE SWIG_DIR)

Call Stack (most recent call first): /Applications/CMake.app/Contents/share/cmake-3.6/Modules/

— Configuring incomplete, errors occurred!

See also “/Users/sukhbindersingh/PROJECTS/UQTk_v3.0/builddir/CMakeFiles/CMakeOutput.log”.

 

So make sure, you do all the four steps…

 

SWIG needs PCRE-Perl compatible Regular expression library, which was not available on my mac, so download that too from here

Download PCRE not PCRE2. I wasted time installing PCRE2 to find that swig doesn’t recognise it.

 

Make CMAKE work in command line

 

Now cmake opens up as GUI in Mac OS by defauly, but we need command line version, so we have following 3 options

One may add CMake to the PATH:

PATH=”/Applications/CMake.app/Contents/bin”:”$PATH”

Or, to install symlinks to ‘/usr/local/bin’, run:

sudo “/Applications/CMake.app/Contents/bin/cmake-gui” –install

Or, to install symlinks to another directory, run:

sudo “/Applications/CMake.app/Contents/bin/cmake-gui” –install=/path/to/bin

 

I opted for the second option, mostly because it was simplest and I want cmake to available everywhere and every time I need it

sudo “/Applications/CMake.app/Contents/bin/cmake-gui” –install

 

Where are your gcc, gfortran, and clang?

 

Once we have all these and before you start, we have to check few things. In this installation, I wanted to use gcc, gfortran, and clang for my setup, so get to know where they are located in your system by using the ‘which’ command

The Installations

 

In the terminal, go to the UQTk_v3.0 directory

  • mkdir builddir
  • cd builddir/
  • cmake -DCMAKE_Fortran_COMPILER=/usr/local/bin/gfortran -DCMAKE_C_COMPILER=/usr/bin/gcc -DCMAKE_CXX_COMPILER=/usr/bin/clang ../../UQTk_v3.0

 

Replace green text with your own path.

Once the cmake configuration is complete successfully, type make

All will go ok, until you hit this error.

In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__config:23:

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/

MacOSX10.11.sdk/usr/include/unistd.h:510:14:error:declaration of ‘optarg’ has a different language linkage

extern char *optarg; /*

getopt(3) external variables */

^

/Users/sukhbindersingh/PROJECTS/UQTk_v3.0/cpp/lib/include/gen_defs.h:49:14: note:

previous declaration is here

extern char *optarg;

^

1 error generated.

make[2]: *** [cpp/lib/CMakeFiles/uqtk.dir/tools/multiindex.cpp.o] Error 1

 

Well this is easy to solve and I think it’s an error in the file. Open gen_defs.h file from cpp/lib/include and comment the following line as shown.

extern char *optarg

 

 

Another error that I faced was the missing gfortran library because of no LIBRARY_PATH.

ld: library not found for -lgfortran

clang: error: linker command failed with exit code 1 (use -v to see invocation)

make[2]: *** [cpp/app/gen_mi/gen_mi] Error 1

make[1]: *** [cpp/app/gen_mi/CMakeFiles/

gen_mi.dir/all] Error 2

make: *** [all] Error 2

 

This meant my libgfortran.a was not in the LIBRARY_PATH, so let’s find where the library is and then set the LIBRARY_PATH environment variable pointing it to that folder.

Locate libgfortran*.a

sudo find /usr -iname ‘libgfortran*.a’

 

Found them here.

/usr/local/gfortran/lib/i386/libgfortran.a

/usr/local/gfortran/lib/libgfortran.a

Set the environment variable to that folder.

export LIBRARY_PATH=/usr/local/gfortran/lib/

 

Compilation should continue smoothly and at last type make install and you should have everything installed.


Type ctest to check your installation


Recap

 

So here’s recap of the steps.

  1. mkdir builddir
  2. cd builddir
  3. cmake -DCMAKE_Fortran_COMPILER=/usr/local/bin/gfortran -DCMAKE_C_COMPILER=/usr/bin/gcc -DCMAKE_CXX_COMPILER=/usr/bin/clang ../../UQTk_v3.0 [Without python]

    or cmake -DPyUQTk=ON -P-DCMAKE_Fortran_COMPILER=/usr/local/bin/gfortran -DCMAKE_C_COMPILER=/usr/bin/gcc -DCMAKE_CXX_COMPILER=/usr/bin/clang ../../UQTk_v3.0 [With python]

  4. make
  5. make install

I faced two problems,

  1. error:declaration of ‘optarg’ has a different language linkage Solution: comment the offending line.
  2. ld: library not found for –lgfortran clang: error: linker command failed with exit code 1 Solution: export LIBRARY_PATH=/usr/local/gfortran/lib/

Using PyUQTk option gave me lot of problem, have delayed installing python binding for now due to lack of time.

Well now this is done, will spend couple of weekends looking at the library, you can fork the entire library from my github page. It has all the libs, so if the compliers are similar, they can be used as is without going through all this steps.

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Using Aliases In windows CMD

If you are like me and use mac and Linux at home and use windows at work. Then the following will be regular errors.

‘ls’ is not recognized as an internal or external command, operable program or batch file.

I always use ls, clear, cat etc. in my CMD shell and eventually get the following errors. This has happened a lot of time for me to do something about it. Fortunately, there’s an easy way to setup alias in the cmd windows and never see this nasty ‘not recognised’ error. First create a text file like this.

You can use any other commands that you use regularly. Next, open the cmd windows and type the following command

Doskey /macrofile=path/to/alias/file/filename

As shown in the next figure. That’s it.

Here’s how it works, no more nag error messages

Don’t want to type this message every time, create a windows shortcut like this  

That’s it!!

Exploring Matplotlib Styles

Last week got some free time. Used it to upgrade my python installation on Mac, a long awaited task.

Looking at the upgrade log, was most excited to finally see the new version of matplotlib.

So launched it and went straight to the new style package.

Matplotlib is great at graphs but the default style before 1.4.3 left many things wanting.

The style package adds support for easy-to-switch plotting “styles” with the same parameters as a matplotlibrc file.

import matplotlib.pyplot as plt

What are different styles available in matplotlib?

print(plt.style.available)

[u'dark_background', u'bmh', u'grayscale', u'ggplot', u'fivethirtyeight']

Here’s how to use this.

But first let’s generate some data

import numpy as np
data = np.sin(np.linspace(0, 2*np.pi))

The default plot

plt.plot(data, 'r-o')

default_matplotlib_1.4.3_styles

Let’s use ggplot

plt.style.use('ggplot') 
plt.plot(data, 'r-o')

ggplot_matplotlib_style

Dark Background like excel 2007

plt.style.use('dark_background')
plt.plot(data, 'r-o')

dark_background_matplotlib

BMH style

plt.style.use(‘bmh’)
plt.plot(data, 'r-o')

bmh_matplotlib_style

Graystyle

plt.style.use(‘grayscale’)
plt.plot(data, 'r-o')

grayscale_matplotlib_style

fivethirtyeight Style

plt.style.use(‘fivethirtyeight’)
plt.plot(data, 'r-o')

fivethirtyeight_matplotlib

We can even add our own custom .mplstyle files to ~/.matplotlib/stylelib or call use with a URL pointing to a file with matplotlibrc settings. Follow the following link to define your own style.

A Gentle Introduction to the Finite Element Method

FEM Introduction numerical

Almost every engineer today have some knowledge of theoretical and practical aspects of FEM. And many have played with various software packages at some point of time.

Well that is enough if you just want to perform analysis but if you want to truly understand the mathematical aspects of FEM and want to get a feel of the numerical methods under the hood of FEM then this short lecture is for you.

Here’s the introduction, plucked straight from the course. IF you like it, you will enjoy the lecture.

The course is divided into five lessons and all this in 100 pages. Happy Learning!!

If you haven’t been hiding under a stone during your studies of engineering, mathematics or physics, it is very likely that you have already heard about the Finite Element Method. Maybe you even know some theoretical and practical aspects and have played a bit with some FEM software package. What you are going to find here is a detailed and mathematically biased introduction to several aspects of the Finite Element Method.

This is not however a course on the Analysis of the method. It is just a demonstration of how it works, written as applied mathematicians usually write it. There is going to be mathematics involved, but not lists of theorems and proofs. We are also going from the most particular cases towards useful generalizations, from example to theory.

It is going to be one hundred pages with many figures and many ideas repeated over and over, so that you can read it with ease. These notes have evolved during the decade I have been teaching finite elements to mixed audiences of mathematicians, physicists and engineers. The tone is definitely colloquial. I could just claim that these are my classnotes and that’s what I’m like.

There’s much more than that. First, I believe in doing your best at being entertaining when teaching. At least that’s what I try. Behind that there is
a deeper philosophical point: take your work (and your life) seriously but, please, don’t take yourself too seriously.

I also believe that people should be duly introduced when they meet. All this naming
old time mathematicians and scientists only by their last names looks to me too much
like the Army. Or worse, high school!

I think you have already been properly introduced to the great Leonhard Euler, David Hilbert, Carl Friedrich Gauss, Pierre Simon Laplace and George Green. If you haven’t so far, consider it done here. This is not about history.

It’s just good manners. Do you see what I mean by being colloquial?

Anyway, this is not about having fun, but since we are at it, let us try to have a good time while learning. If you take your time to read these notes with care and try the exercises at the end of each lesson, I can assure that you will have made a significant step in your scientific persona. Enjoy!

Click the below link to access the excellent PDF. Don’t forget to thanks to Francisco Jaview Sayas !

A gentle introduction to the Finite Element Method by Francisco–Javier Sayas

Quick Intro to 2D and 3D Visualization in Python

contour_visualization_with_python
Posted a quick tutorial introducing visualization in python.

This tutorial offers a quick look at some common 2d and 3d Visualization available in python. This tutorial is meant to give anyone a quick start in matplotlib and mayavi.mlab.

The tutorial was written as part of CSRP program of AeSIAA which I am volunteering as a mentor to few aeronautical students.

View the tutorial by clicking this Quick Intro to 2D and 3D Visualization in Python