ls-cwi/heinz

Name: heinz

Owner: CWI - Life Sciences group

Description: Single species module discovery

Created: 2014-01-24 08:35:54.0

Updated: 2017-07-26 04:15:59.0

Pushed: 2017-02-13 11:14:59.0

Homepage: null

Size: 104341

Language: C++

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README

Compilation instructions

Dependencies

• LEMON 1.3
• ILOG CPLEX (>= 12.0)
• OGDF (v. 2012.07)

Compiling

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/ ..

Running heinz

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