added cc to heinz

Author: Eline van Mantgem

CMakeLists.txt

@@ -0,0 +1,243 @@
+cmake_minimum_required( VERSION 2.8 )
+
+project( Heinz )
+
+set( BK_MaxFlow_Hdr
+  src/externlib/maxflow-v3.01/graph.h
+  src/externlib/maxflow-v3.01/block.h
+)
+
+set( Heinz_Hdr
+  src/parser/parser.h
+  src/parser/mwcsparser.h
+  src/parser/stpparser.h
+  src/parser/stppcstparser.h
+  src/parser/identityparser.h
+  src/parser/dimacsparser.h
+  src/preprocessing/rule.h
+  src/preprocessing/negdeg01.h
+  src/preprocessing/negedge.h
+  src/preprocessing/posedge.h
+  src/preprocessing/negcircuit.h
+  src/preprocessing/negdiamond.h
+  src/preprocessing/negmirroredhubs.h
+  src/preprocessing/negdominatedhubs.h
+  src/preprocessing/posdeg01.h
+  src/preprocessing/posdiamond.h
+  src/preprocessing/shortestpath.h
+  src/solver/spqrtree.h
+  src/solver/blockcuttree.h
+  src/mwcs.h
+  src/analysis.h
+  src/solver/enumsolverunrooted.h
+  src/solver/impl/solverimpl.h
+  src/solver/impl/solverunrootedimpl.h
+  src/solver/impl/solverrootedimpl.h
+  src/solver/solver.h
+  src/solver/solverunrooted.h
+  src/solver/solverrooted.h
+  src/solver/impl/treesolverimpl.h
+  src/solver/impl/treesolverunrootedimpl.h
+  src/solver/impl/treesolverrootedimpl.h
+  src/solver/impl/cplex_incumbent/incumbent.h
+  src/solver/impl/cplex_incumbent/pcstincumbent.h
+  src/solver/impl/cplex_cut/backoff.h
+  src/solver/impl/cplex_cut/nodecut.h
+  src/solver/impl/cplex_cut/nodecutuser.h
+  src/solver/impl/cplex_cut/nodecutlazy.h
+  src/solver/impl/cplex_cut/nodecutrooted.h
+  src/solver/impl/cplex_cut/nodecutunrooted.h
+  src/solver/impl/cplex_cut/bk_alg.h
+  src/solver/impl/cplexsolverimpl.h
+  src/solver/impl/cutsolverrootedimpl.h
+  src/solver/impl/cutsolverunrootedimpl.h
+  src/solver/impl/cplex_heuristic/heuristicrooted.h
+  src/solver/impl/cplex_heuristic/heuristicunrooted.h
+  src/solver/impl/cplex_branch/branch.h
+  src/mwcsgraph.h
+  src/mwcspreprocessedgraph.h
+  src/utils.h
+  src/mwcsgraphparser.h
+)
+
+set( Heinz_Src
+  src/utils.cpp
+)
+
+set( Heinz_Monte_Carlo_Hdr
+  src/solver/impl/treeheuristicsolverimpl.h
+  src/solver/impl/treeheuristicsolverrootedimpl.h
+  src/solver/impl/treeheuristicsolverunrootedimpl.h
+)
+
+set( Heinz_Monte_Carlo_Src 
+  src/utils.cpp
+)
+
+set( Heinz_Print_Graph_Src
+  src/printgraph.cpp
+  src/utils.cpp
+		src/colorcoding/ColorCoding.cpp src/colorcoding/ColorCoding.h src/colorcoding/Vertex.cpp src/colorcoding/Vertex.h src/colorcoding/ColorSet.cpp src/colorcoding/ColorSet.h src/colorcoding/Vertices.cpp src/colorcoding/Vertices.h src/colorcoding/ColorCodingUnrooted.cpp src/colorcoding/ColorCodingUnrooted.h src/colorcoding/ColorCodingRooted.h src/colorcoding/ColorCodingRooted.cpp src/colorcoding/ColorCodingBlockCut.cpp src/colorcoding/ColorCodingBlockCut.h src/colorcoding/CcUnrooted.h src/colorcoding/CcAdapter.h src/colorcoding/CcRooted.h src/colorcoding/CcBlockcut.cpp src/colorcoding/CcBlockcut.h)
+
+set( GitCommand1 "symbolic-ref HEAD 2> /dev/null | cut -b 12-" )
+execute_process( COMMAND git symbolic-ref HEAD  WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
+                 COMMAND tail -c -7 COMMAND tr -d "\\n" OUTPUT_VARIABLE GitBranch )
+set( GitCommand2 "log --pretty=format:\\\"%h\\\" -1" )
+execute_process( COMMAND git log --pretty=format:%h WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
+                 COMMAND head -n 1  COMMAND tr -d "\\n" OUTPUT_VARIABLE GitHashtag )
+set( HEINZ_VERSION \"${GitBranch}-${GitHashtag}\" )
+
+set( LIBOGDF_ROOT "$ENV{HOME}/ogdf" CACHE PATH "Additional search directory for OGDF library" )
+set( LIBLEMON_ROOT "$ENV{HOME}/lemon/" CACHE PATH "Additional search directory for lemon library" )
+
+set( MEMORY_LIMIT 10240 CACHE STRING "Memory limit in MB" )
+
+if( NOT CPLEX_INC_DIR OR NOT CPLEX_LIB_DIR OR NOT CONCERT_INC_DIR OR NOT CONCERT_LIB_DIR )
+	set( CPLEX_AUTODETECTION_PREFIXES "$ENV{HOME}/ILOG;/opt/ibm/ILOG;$ENV{HOME}/Applications/IBM/ILOG" CACHE STRING "CPLEX automatic lookup directories" )
+	foreach( CplexInstallPrefix ${CPLEX_AUTODETECTION_PREFIXES} )
+		file( GLOB_RECURSE CplexLibraryPaths ${CplexInstallPrefix}/*/cplex/lib/*/libcplex.a )
+		if( CplexLibraryPaths )
+			list( LENGTH CplexLibraryPaths NumPath )
+			if( NumPath GREATER 1 )
+				message( WARNING "Found multiple CPLEX installations in ${CplexInstallPrefix}, automatically selecting the first one, please set {CPLEX|CONCERT}_{INC|LIB}_DIR manually if this is not the right selection" )
+			else()
+				message( "Found CPLEX's installation in ${CPlexInstallPrefix}" )
+			endif()
+			list( GET CplexLibraryPaths 0 CplexLibraryPath )
+
+			set( MyRegex "${CplexInstallPrefix}/(.*)/cplex/?/lib/(.*)/libcplex.a" )
+			string( REGEX MATCH "${MyRegex}" ValidatedCplexLibPath ${CplexLibraryPath} )
+			if( NOT ValidatedCplexLibPath )
+				message( WARNING "Unable to recognize ${CplexLibraryPath} as a valid CPLEX path" )
+			else()
+				string( REGEX REPLACE "${MyRegex}" "\\1" CplexHome ${ValidatedCplexLibPath} )
+				string( REGEX REPLACE "${MyRegex}" "\\2" CplexArch ${ValidatedCplexLibPath} )
+
+				set( CPLEX_INC_DIR   "${CplexInstallPrefix}/${CplexHome}/cplex/include"            CACHE PATH "CPLEX's include dir" )
+				set( CPLEX_LIB_DIR   "${CplexInstallPrefix}/${CplexHome}/cplex/lib/${CplexArch}"   CACHE PATH "CPLEX's library dir" )
+				set( CONCERT_INC_DIR "${CplexInstallPrefix}/${CplexHome}/concert/include"          CACHE PATH "Concert's include dir" )
+        set( CONCERT_LIB_DIR "${CplexInstallPrefix}/${CplexHome}/concert/lib/${CplexArch}" CACHE PATH "Concert's library dir" )
+
+				break()
+			endif()
+		else()
+			message( "Unable to find CPLEX and Concert installation in ${CplexInstallPrefix}" )
+		endif()
+	endforeach()
+
+	if( NOT CPLEX_INC_DIR OR NOT CPLEX_LIB_DIR OR NOT CONCERT_INC_DIR OR NOT CONCERT_LIB_DIR )
+		message( "Unable to autodeted CPLEX's and Concert's installation directories, please set {CPLEX|CONCERT}_{INC|LIB}_DIR manually" )
+	else()
+		message( "Autodetected CPLEX's include dir   : ${CPLEX_INC_DIR}" )
+		message( "Autodetected CPLEX's library dir   : ${CPLEX_LIB_DIR}" )
+		message( "Autodetected Concert's include dir : ${CONCERT_INC_DIR}" )
+		message( "Autodetected Concert's library dir : ${CONCERT_LIB_DIR}" )
+	endif()
+endif()
+
+if(NOT CMAKE_BUILD_TYPE)
+  set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build, options are: Debug Release Profile" FORCE)
+endif(NOT CMAKE_BUILD_TYPE)
+
+SET(CMAKE_XCODE_ATTRIBUTE_CLANG_CXX_LIBRARY "libstdc++")
+set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS} -Wall -Wextra -Wno-long-long -Wno-unused-parameter -Wno-unknown-pragmas -g -ggdb -O0 -DDEBUG -DVERBOSE")
+set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS} -Wno-long-long -Wno-unused-parameter -Wno-unknown-pragmas -O3 -DNDEBUG")
+set(CMAKE_CXX_FLAGS_PROFILE "${CMAKE_CXX_FLAGS} -Wall -Wextra -Wno-long-long -Wno-unused-parameter -Wno-unknown-pragmas -O3 -g -ggdb -DNDEBUG")
+
+set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -Wno-write-strings -Wno-unused-variable" )
+add_definitions( -DIL_STD )
+configure_file( src/config.h.in ${PROJECT_SOURCE_DIR}/src/config.h )
+
+if( ${CMAKE_SYSTEM_NAME} MATCHES "Darwin" )
+  set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libstdc++ " )
+endif()
+
+
+include_directories( ${CPLEX_INC_DIR} ${CONCERT_INC_DIR} "${LIBLEMON_ROOT}/include" "${LIBOGDF_ROOT}/include" "src" "src/externlib" )
+link_directories( ${CPLEX_LIB_DIR} ${CONCERT_LIB_DIR} "${LIBLEMON_ROOT}/lib" "${LIBOGDF_ROOT}/lib" )
+
+set( CommonLibs
+	m
+	ilocplex
+	cplex
+	concert
+	pthread
+	emon
+	OGDF
+)
+
+add_executable( heinz-mc EXCLUDE_FROM_ALL src/mwcs-mc.cpp ${Heinz_Monte_Carlo_Src} ${Heinz_Monte_Carlo_Hdr} ${Heinz_Hdr} )
+target_link_libraries( heinz-mc emon OGDF pthread )
+
+add_executable( heinz src/mwcs.cpp ${Heinz_Src} ${Heinz_Hdr} )
+target_link_libraries( heinz ${CommonLibs} )
+
+add_executable( heinz_mwcs_mc src/dimacs/heinz_mwcs_mc.cpp ${Heinz_Monte_Carlo_Src} ${Heinz_Monte_Carlo_Hdr} ${Heinz_Hdr} )
+target_link_libraries( heinz_mwcs_mc emon OGDF pthread )
+
+add_executable( heinz_mwcs_dc src/dimacs/heinz_mwcs_dc.cpp ${Heinz_Src} ${Heinz_Hdr} )
+target_link_libraries( heinz_mwcs_dc ${CommonLibs} )
+
+add_executable( heinz_mwcs_no_dc src/dimacs/heinz_mwcs_no_dc.cpp ${Heinz_Src} ${Heinz_Hdr} )
+target_link_libraries( heinz_mwcs_no_dc ${CommonLibs} )
+
+add_executable( heinz_mwcs_no_pre src/dimacs/heinz_mwcs_no_pre.cpp ${Heinz_Src} ${Heinz_Hdr} )
+target_link_libraries( heinz_mwcs_no_pre ${CommonLibs} )
+
+add_executable( heinz_pcst_mc src/dimacs/heinz_pcst_mc.cpp ${Heinz_Monte_Carlo_Src} ${Heinz_Monte_Carlo_Hdr} ${Heinz_Hdr} )
+target_link_libraries( heinz_pcst_mc emon OGDF pthread )
+
+add_executable( heinz_pcst_dc src/dimacs/heinz_pcst_dc.cpp ${Heinz_Src} ${Heinz_Hdr} )
+target_link_libraries( heinz_pcst_dc ${CommonLibs} )
+
+add_executable( heinz_pcst_no_dc src/dimacs/heinz_pcst_no_dc.cpp ${Heinz_Src} ${Heinz_Hdr} )
+target_link_libraries( heinz_pcst_no_dc ${CommonLibs} )
+
+add_executable( heinz_pcst_no_pre src/dimacs/heinz_pcst_no_pre.cpp ${Heinz_Src} ${Heinz_Hdr} )
+target_link_libraries( heinz_pcst_no_pre ${CommonLibs} )
+
+add_executable( heinz_rpcst_mc src/dimacs/heinz_rpcst_mc.cpp ${Heinz_Monte_Carlo_Src} ${Heinz_Monte_Carlo_Hdr} ${Heinz_Hdr} )
+target_link_libraries( heinz_rpcst_mc emon OGDF pthread )
+
+add_executable( heinz_rpcst_no_dc src/dimacs/heinz_rpcst_no_dc.cpp ${Heinz_Src} ${Heinz_Hdr} )
+target_link_libraries( heinz_rpcst_no_dc ${CommonLibs} )
+
+add_executable( heinz_rpcst_no_pre src/dimacs/heinz_rpcst_no_pre.cpp ${Heinz_Src} ${Heinz_Hdr} )
+target_link_libraries( heinz_rpcst_no_pre ${CommonLibs} )
+
+add_executable( print EXCLUDE_FROM_ALL ${Heinz_Print_Graph_Src} ${Heinz_Hdr} ${CommonObjs} )
+target_link_libraries( print emon OGDF pthread )
+
+add_executable( check_mwcs_solution EXCLUDE_FROM_ALL src/dimacs/check_mwcs_solution.cpp src/utils.cpp )
+target_link_libraries( check_mwcs_solution emon OGDF pthread )
+
+add_executable( check_pcst_solution EXCLUDE_FROM_ALL src/dimacs/check_pcst_solution.cpp src/utils.cpp )
+target_link_libraries( check_pcst_solution emon OGDF pthread )
+
+enable_testing()
+add_test( heinz_mwcs_no_dc ${PROJECT_SOURCE_DIR}/test/run.py ./heinz_mwcs_no_dc ./check_mwcs_solution ${PROJECT_SOURCE_DIR}/test/lymphoma.stp lymphoma.dimacs )
+add_test( heinz_mwcs_dc ${PROJECT_SOURCE_DIR}/test/run.py ./heinz_mwcs_dc ./check_mwcs_solution ${PROJECT_SOURCE_DIR}/test/lymphoma.stp lymphoma.dimacs )
+add_test( heinz_mwcs_no_pre ${PROJECT_SOURCE_DIR}/test/run.py ./heinz_mwcs_no_pre ./check_mwcs_solution ${PROJECT_SOURCE_DIR}/test/lymphoma.stp lymphoma.dimacs )
+add_test( heinz_mwcs_mc ${PROJECT_SOURCE_DIR}/test/run.py ./heinz_mwcs_mc ./check_mwcs_solution ${PROJECT_SOURCE_DIR}/test/lymphoma.stp lymphoma.dimacs )
+add_test( heinz_pcst_no_dc ${PROJECT_SOURCE_DIR}/test/run.py ./heinz_pcst_no_dc ./check_pcst_solution ${PROJECT_SOURCE_DIR}/test/i640-003.stp i640-003.dimacs )
+add_test( heinz_pcst_dc ${PROJECT_SOURCE_DIR}/test/run.py ./heinz_pcst_dc ./check_pcst_solution ${PROJECT_SOURCE_DIR}/test/i640-003.stp i640-003.dimacs )
+add_test( heinz_pcst_no_pre ${PROJECT_SOURCE_DIR}/test/run.py ./heinz_pcst_no_pre ./check_pcst_solution ${PROJECT_SOURCE_DIR}/test/i640-003.stp i640-003.dimacs )
+add_test( heinz_pcst_mc ${PROJECT_SOURCE_DIR}/test/run.py ./heinz_pcst_mc ./check_pcst_solution ${PROJECT_SOURCE_DIR}/test/i640-003.stp i640-003.dimacs )
+add_test( heinz_rpcst_no_dc ${PROJECT_SOURCE_DIR}/test/run.py ./heinz_rpcst_no_dc ./check_pcst_solution ${PROJECT_SOURCE_DIR}/test/i101M2.stp i101M2.dimacs )
+add_test( heinz_rpcst_no_pre ${PROJECT_SOURCE_DIR}/test/run.py ./heinz_rpcst_no_pre ./check_pcst_solution ${PROJECT_SOURCE_DIR}/test/i101M2.stp i101M2.dimacs )
+add_test( heinz_rpcst_mc ${PROJECT_SOURCE_DIR}/test/run.py ./heinz_rpcst_mc ./check_pcst_solution ${PROJECT_SOURCE_DIR}/test/i101M2.stp i101M2.dimacs )
+add_custom_target( check COMMAND ${CMAKE_CTEST_COMMAND} DEPENDS 
+  check_mwcs_solution 
+  check_pcst_solution 
+  heinz_pcst_dc 
+  heinz_pcst_mc 
+  heinz_pcst_no_dc 
+  heinz_pcst_no_pre 
+  heinz_rpcst_mc 
+  heinz_rpcst_no_dc 
+  heinz_rpcst_no_pre 
+  heinz_mwcs_dc 
+  heinz_mwcs_mc 
+  heinz_mwcs_no_dc 
+  heinz_mwcs_no_pre 
+)

LICENSE

@@ -0,0 +1,20 @@
+The MIT License (MIT)
+
+Copyright (c) 2014 Mohammed El-Kebir, Gunnar W. Klau
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+the Software, and to permit persons to whom the Software is furnished to do so,
+subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

README.md

@@ -0,0 +1,95 @@
+#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
+
+
+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

TODO.md

@@ -0,0 +1,33 @@
+High priority:
+
+* Get rid of distinction between run and construct
+* Put bi/tri information in base class preprocessing rules
+* Rooted formulation: identify S... and exploit
+* Bug in multi-threading: cutCount = 0
+* If there is only one root node => use rooted separation...
+* Encapsulate connected components separation in NodeCut class (argument x_values not needed)
+* Unit test: solution is an entire connected component in the input graph
+* If #separated cuts drops below threshold stop separating in the root node!
+
+New preprocessing rules:
+
+* Look at biconnected components
+* Diamond with two pos nodes at center and one corner with deg 2
+* Positive deg 1 nodes, merge those (if they have a score below LB!)
+
+Low priority:
+
+* More sophisticated branching rules (favor y-vars)
+* Use rooted formulation in unrooted call backs (addLocal)
+* Handle components inside callbacks (get rid of enumeration functionality)
+
+Done:
+
+* Only do min cut separation on nodes i that are not part of non-zero component containing the root
+* Remove NodeCut::_root
+
+Not done:
+
+* Construct local h at every call! Slower...
+* Branch on stars... cplex does a better job
+* Break ties: smallest deg[i] - posDeg[i]