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CERT Documentation for 3.2.1

CERT Documentation.

Make sure to use the versions specified or you will need to modify the Link/include paths for each section below.

These instructions assume you are using MS VisualStudio2005.
I ran in to “Updating IntellSense”. This process caused my computer to become inoperable.
The only way I found to disable intellisense was to rename /Program Files/Microsoft Visual Studio 8/VC/vcpackages/FEACP.DLL


Once you have extracted the CERT source files, you will have a directory called:
So the directory bellow will be refered to as, SOURCEDIR from now on.

There are currently four third-party libraries that are being used by CERT 2.0. They are listed below with links to information and downloads.
Boost (pre-built):
Download the boost exe installer and run it.
General information:
Download page:

When downloading Boost, make sure to click “Run” (as opposed to saving the installer to your local disk) when prompted. If not, the installer may not work.  You may see a warning regarding Windows inability to recognize the developer of the package. Just proceed with the installation.
You only need the following variants:
Multithread, DLL
Multithread, Static Routine
You will have the choice of installing the entire boost package or just selected items.
If you do not want to install the complete package, CERT requires the following:
boost_thread libraries

You can also build custom for your system by compiling the code.
The CERT code uses the boost_filesystem, boost_serialization and boost_thread libraries. If using Visual Studio, install to the default directory or you will need to configure the Visual Studio project files to point to the directory you choose.
FFTW (pre-built):
General information:
Windows information and the download link:
Make sure to read the README-WINDOWS file for exporting the library to work with Visual Studio.


Use Version:

LibXML (pre-built):
General information:
Pre-built Window’s libraries:

Download link:

You will need:(if you download more recent versions you will have to modify the include/Link paths in your VisualStudio2005 project) (NOT SURE IF THIS ONE IS NEEDED)
Now create a directory called “libxml” inside your “SOURCEDIR”:
Extract the 3 packages into the directory above:

Additional libraries may also need to be installed (e.g. iconv and zlib). The web page with the pre-built libraries has more details.

The Atlas project should build optimized Blas libraries with a C interface: Atlas also has downloadable binaries, although they may not be optimum for any given system.


Once on the web page above, click on SOFTWARE at the top.
Next choose “Stable”
Now you must choose which version to download.
Since there is only one package that is not for Linux, select that one (There really are two, but the only difference is the compression type).
Currently the package I chose is called “atlas 3.6.0.tar.gz”.
Download the package mentioned above (atlas3.6.0.tar.bz2) and remember where youplaced it. We will come back to it later.
Installing ATLAS on our Windows system:
The build process for the ATLAS project requires a UNIX environment.
 In order to meet this UNIX environment requirement we need to:
Install Cygwin.

It is best to install as complete a Cygwin system as possible in order to avoid having to come back later and manually installing individual packages that are missing and are required for the building process of ATLAS.
This requires at least one hour over a broadband internet connection.
Now that Cygwin is installed and working we can go back to the package we downloaded earlier. It will be easier to move the package in to your cygwin environment (C:\cygwin\home\\) so that you can use linux tools to extract it.
Open a cygwin terminal (Start–>All Programs–>Cygwin–>Cygwin Bash Shell):
The next step assumes you installed a complete version of Cygwin.
cd in to the ATLAS/ directory and simply type: make
You will be asked a number of questions regarding your system. Most of them are listed below:
–>Enter number at top left of screen [0]: I entered 048.
–> have you read the errata file: yes
–>are you ready?:yes
–>ENter your machine type: PentiumIII (This answer varies with each system)
–>Enable Posix threads support? yes—-> Ask Andrew if this is necessary???
–>Enter the number of processors in your system: 1
(leave 0 if not sure, ATLAS will figure it out later)
–>USe express setup? Yes
–>Enter an Architechture name: WinNT_P4SSE2 (!!!MUST USE THIS NAME!!!)
NOTE: When you are done building ATLAS, the “WinNT_P4SSE2″ directory will be located at:
It must be copied to your SOURCEDIRECTORY.
–> Enter Maximum cache size [512]: Your system may display a different value. Don’t change it.
–>Enter file creation Delay in seconds [0]:Not important to us. Leave the default.
–>Use default values for the install? Yes

You will see the message “Configuration COmpleted Succesfully” if all went well.
You will also see the next command you need to enter to begin the install process.
In your Cygwin terminal type:
make install arch=WinNT_P4SSE2
 This may take up to 45 minutes.
When finished you will see the message:
“ATLAS Install Complete”
Now we have to verify our installation was succesfull.
Run the command:
make sanity_test arch=WinNT_P4SSE2
You will again see lots of text scrolling by, but the last couple of lines are important.They should be similar to :
[Sanity_test] Error 1 (ignored)

Alternatively, the Intel Math Kernel Library also provides a cBlas interface.
The Visual studio projects are configured for the intel math kernel library. In order to use Atlas instead of the MKL, in the project configurations: (1) remove the INTELMKL symbol from the preprocessor symbols, (2) replace the mkl_c.lib library with the appropriate Atlas .lib files, and (3) replace the intel include paths with the Atlas library and include paths.
Folder layout:
$ ls
ATLAS Documentation WinNT_P4SSE2 featuredetector mp_auCoder
CERT2_VS2005 MLR aligneyes fftw-3.1.1-dll mptslidingwindow
CERTWrapper Misc eyefinder libxml
$ ls CERT2_VS2005
CERT2_VS2005 CERT2_VS2005.sln CERTDemo TestImages
CERT2_VS2005.ncb CERT2_VS2005.suo ReadMe.txt debug
$ ls CERT2_VS2005/debug
CERT2_VS2005.dll CERT2_VS2005.lib CERTDemo.exp CERTDemo.pdb libfftw3-3.dll
CERT2_VS2005.exp CERT2_VS2005.pdb CERTDemo.ilk NewTestImages libxml2.dll
CERT2_VS2005.ilk CERTDemo.exe CERTDemo.lib iconv.dll zlib1.dll
In addition the Boost library (headers and libraries) is installed at either C:\Program Files\boost or C:\Boost

First you might need to copy:
C:\SOURCEDIR\fftw-3.1.1-dll\libfftw3-3.dllto:C:\SOURCEDIR\CERT2_VS2005\debug\HERE In order to run the CERTDemo.exe Double click on:


wait until it loads the data files, then type in the path to the directory with the images.

—> ..\TestImages

This worked:

For My Builds only:

Change both project’s Include/Link paths to reflect the fact that I use the new version of libxml. Change 24 to 28.

Change both project’s Include/Link paths to reflect the fact that I called my ATLAS build “WinP3″. The C++ code looks for “WinNT_P4SSE2″.