Updated gtsam readme and example configure scripts

INSTALL

@@ -235,8 +235,3 @@ an Autoconf bug.  Until the bug is fixed you can use this workaround:
 `configure' also accepts some other, not widely useful, options.  Run
 `configure --help' for more details.
 
-`--enable-gsl=yes(no)'
-     Whether to enable the GSL library
-
-`--enable-atlas=yes(no)'
-     Whether to enable the ATLAS library

README

@@ -13,6 +13,7 @@ Please see USAGE for an example on how to use GTSAM.
 
 The code is organized according to the following directory structure:
  
+  3rdparty    local copies of third party libraries - currently the headers for Eigen3
   base        provides some base Math and data structures, as well as test-related utilities
   geometry    points, poses, tensors, etc
   inference   core graphical model inference such as factor graphs, junction trees, Bayes nets, Bayes trees 
@@ -26,16 +27,8 @@ the more involved tests, which test the entire library:
   
   tests       more involved tests that depend on slam
 
-Furthermore the MATLAB wrapper generator code is run as well
-
-  wrap        MATLAB wrapper generation code
-  gtsam.h     interface file for which wrappers will be generated
-  toolbox     MATLAB proxy classes and wrappers generated
-  matlab      examples and tests of the above  		
-
 Finally, there are some local libraries built needed in the rest of the code:
 
-  colamd      COLAMD and CCOLAMD by Tim Davis needed for re-ordering
   CppUnitLite unit test library
   doc         documentation
   m4          local M4 macros
@@ -46,9 +39,6 @@ Important Installation Notes Specific to GTSAM
 1)
 GTSAM requires the following libraries to be installed on your system:
  - BOOST version 1.40 or greater (install through Linux repositories or MacPorts)
- - BLAS, ATLAS, and LAPACK (libblas, libatlas, and liblapack in Debian/Ubuntu
-                            repositories, on Mac these should already installed
-                            with the OS)
 
 2)
 GTSAM uses CCOLAMD to find good variable elimination orders.  You can download
@@ -78,11 +68,11 @@ compiling gtsam:
 
 For Debugging (native Snow Leopard g++ compiler):
 ./configure CXXFLAGS="-fno-inline -g -Wall" \
-    LDFLAGS="-fno-inline -g -Wall" --with-toolbox=$HOME/toolbox/
+    LDFLAGS="-fno-inline -g -Wall" 
 
 For Debugging (Linux or MacPorts g++ compilers):
 ./configure CXXFLAGS="-fno-inline -g -Wall -D_GLIBCXX_DEBUG" \
-    LDFLAGS="-fno-inline -g -Wall" --with-toolbox=$HOME/toolbox/
+    LDFLAGS="-fno-inline -g -Wall" 
 
 For Performance:
 ./configure CXXFLAGS="-DNDEBUG -O3" LDFLAGS="-O3" --with-toolbox=$HOME/toolbox/
@@ -114,17 +104,3 @@ By verifying all the test results are positive, you can make sure that the funct
 libraries are correct.
 
 
-Compile Matlab Toolbox:
------------------------
-1) Start Matlab
-2) Go to File->Set Path and add the toolbox directory where you installed the
-   GTSAM Matlab Toolbox
-3) Change your current directory to the GTSAM Matlab Toolbox
-4) Type 'make_gtsam' at the Command Window
-
-
-Run Matlab Unit Tests:
------------------------
-In the matlab command window, change directory to $gtsam/matlab and then type 'run_tests', which will 
-invoke the matlab unit tests.
-

myconfigure

@@ -1 +1 @@
-../configure --prefix=$HOME CFLAGS="-fno-inline -g -Wall" CXXFLAGS="-fno-inline -g -Wall" LDFLAGS="-fno-inline -g -Wall" --disable-static --enable-blas --enable-lapack --disable-fast-install
+../configure --prefix=$HOME CFLAGS="-fno-inline -g -Wall" CXXFLAGS="-fno-inline -g -Wall" LDFLAGS="-fno-inline -g -Wall" --disable-static  --disable-fast-install

myconfigure.profiling

@@ -1,3 +1,4 @@
 #../configure --prefix=$HOME/borg-simplelinear --with-toolbox=$HOME/toolbox/ --with-boost=/opt/local/include/ CXXFLAGS="-fno-inline -g -DNDEBUG -O3" CFLAGS="-fno-inline -g -DNDEBUG -O3" LDFLAGS="-fno-inline -g -DNDEBUG -O3" --disable-static --enable-blas --enable-lapack
 #../configure --disable-fast-install --prefix=$HOME/borg-simplelinear --with-toolbox=$HOME/toolbox/ --with-boost=/opt/local/include/ CXXFLAGS="-fno-inline -g -D_GLIBCXX_DEBUG -DNDEBUG" CFLAGS="-fno-inline -g -D_GLIBCXX_DEBUG -DNDEBUG" LDFLAGS="-fno-inline -g " --disable-static --enable-blas --enable-lapack
-../configure --prefix=$HOME/borg --with-boost=/opt/local/include/ CPPFLAGS="-g -DNDEBUG -O3" LDFLAGS="-g -DNDEBUG -O3" --disable-static --enable-blas --enable-lapack
+#../configure --prefix=$HOME/borg --with-boost=/opt/local/include/ CPPFLAGS="-g -DNDEBUG -O3" LDFLAGS="-g -DNDEBUG -O3" --disable-static --enable-blas --enable-lapack
+../configure --prefix=$HOME/borg --with-boost=/opt/local/include/ CPPFLAGS="-g -DNDEBUG -O3" LDFLAGS="-g -DNDEBUG -O3" --disable-static

myconfigure.timing

@@ -1,2 +1,3 @@
-../configure --prefix=$HOME --with-toolbox=$HOME/toolbox/ CPP="/opt/local/bin/cpp-mp-4.5" CC="/opt/local/bin/gcc-mp-4.5" CXX="/opt/local/bin/g++-mp-4.5" CPPFLAGS="-DENABLE_TIMING -DNDEBUG -O3" LDFLAGS="-DNDEBUG -O3" --disable-static --enable-blas --enable-lapack
+../configure --prefix=$HOME --with-toolbox=$HOME/toolbox/ CPP="/opt/local/bin/cpp-mp-4.5" CC="/opt/local/bin/gcc-mp-4.5" CXX="/opt/local/bin/g++-mp-4.5" CPPFLAGS="-DENABLE_TIMING -DNDEBUG -O3" LDFLAGS="-DNDEBUG -O3" --disable-static
+#../configure --prefix=$HOME --with-toolbox=$HOME/toolbox/ CPP="/opt/local/bin/cpp-mp-4.5" CC="/opt/local/bin/gcc-mp-4.5" CXX="/opt/local/bin/g++-mp-4.5" CPPFLAGS="-DENABLE_TIMING -DNDEBUG -O3" LDFLAGS="-DNDEBUG -O3" --disable-static --enable-blas --enable-lapack
 #../configure --prefix=$HOME/borg-simplelinear --with-boost=/opt/local/include/ CPP="/opt/local/bin/cpp-mp-4.5" CC="/opt/local/bin/gcc-mp-4.5" CXX="/opt/local/bin/g++-mp-4.5" CXXFLAGS="-DNDEBUG -g" CFLAGS="-DNDEBUG -g" LDFLAGS="-DNDEBUG -g" --disable-static --enable-blas --enable-lapack