#Heinz with Color Coding included Heinz is an existing ILP progam to identify functional modules. Here, a different approach using a dynamic programming solution called Color Coding is added
- LEMON 1.3
- ILOG CPLEX (>= 12.0)
- OGDF (v. 2012.07)
Get heinz from github:
git clone <HTTPS clone URL (see on the right side of this page)>
First, LEMON 1.3 needs to be installed:
wget http://lemon.cs.elte.hu/pub/sources/lemon-1.3.tar.gz
tar xvzf lemon-1.3.tar.gz
cd lemon-1.3
cmake -DCMAKE_INSTALL_PREFIX=~/lemon
make install
Note: On Mac OS 10.9, comment out the following two lines and add the code below at line 159 in CMakeLists.txt before doing make install.
#ADD_SUBDIRECTORY(demo)
#ADD_SUBDIRECTORY(tools)
if( ${CMAKE_SYSTEM_NAME} MATCHES "Darwin" )
set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libstdc++ " )
endif()
You can remove the LEMON sources now, i.e., rm -rf lemon-1.3.
Next, OGDF needs to be installed:
wget http://www.ogdf.net/lib/exe/fetch.php/tech:ogdf.v2012.07.zip
unzip tech\:ogdf.v2012.07.zip
cd OGDF
./makeMakefile.sh
mkdir ~/ogdf
mkdir ~/ogdf/lib
mkdir ~/ogdf/include
make
cp _release/libOGDF.a ~/ogdf/lib/
cp -R ogdf ~/ogdf/include/
Note: On Mac OS 10.9, before doing ./makeMakefile.sh edit line 40 in makeMakefile.config as follows.
release = -stdlib=libstdc++ -O2
You can remove the OGDF sources now, i.e., rm -rf OGDF.
Next, Heinz can be compiled:
mkdir build
cd build
cmake ..
make
In case auto-detection of LEMON, OGDF or CPLEX fails, do
cmake \
-DLIBLEMON_ROOT=~/lemon \
-DLIBOGDF_ROOT=~/root \
-DCPLEX_INC_DIR=~/ILOG/cplex/include/ \
-DCPLEX_LIB_DIR=~/ILOG/cplex/lib/x86-64_osx/static_pic \
-DCONCERT_LIB_DIR=~/ILOG/concert/lib/x86-64_osx/static_pic \
-DCONCERT_INC_DIR=~/ILOG/concert/include/ ..
To run heinz on the test instances:
./heinz -n ../data/test/NodesPCST.txt -e ../data/test/EdgesPCST.txt
Or do:
make check
To run heinz on the DIMACS MWCS instances, do:
./heinz -stp ../data/DIMACS/mwcs/ACTMOD/HCMV.stp
For the PCST DIMACS instances use:
./heinz -stp-pcst ../data/DIMACS/pcst/PCSPG-JMP/K100.2.stp