Java command-line tool to edit a directed graph with n vertices, vertices named 0 to n-1, into a di-cograph. This is the version that was included in my bachelor thesis. I will not continue development here, but I intend to separate the Modular Decomposition and rebuild it to be Java or C++ only.
Changes to all files that were not created by myself are denoted by comments starting with: "//F.L.".
Changed were: ModDecomp.cpp /.h in MD, also Commons.h in FP_to_DMD; all files except SplitDirection, RecSubProblem and FactPermElement in src/java/dicograph/modDecomp.
Supported input: .dot, .txt as matrix with 0/1 entries, .jtxt for JGraphT-toString() format. For .dot and .jtxt, the vertices must be labeled from 0 to n-1.
Copyright (C) 2019 Fynn Leitow
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
Comilation of the C++ sources (necessary)
- boost 1.55 or higher
- cmake
- gcc
Compilation of the Java sources:
- Java Development Kit 8
- maven
- Cplex v.12.7 (older versions might work, too)
command to install all requirements on ubuntu:
sudo apt-get install openjdk-8-jdk cmake maven libboost-all-dev
Clone this project together with its submodules
git clone --recurse-submodules https://github.com/LyteFM/di-cograph-java.git
(If you've already cloned it, you can get the submodules via:
git submodule update --init --recursive)
Compile the necessary C++/C sources. Use $ make -j x with x cores and 2GB RAM per core.
mkdir FP_to_DMD/build MD/build logs
cd FP_to_DMD/build/
cmake ..
make -j 2
cd ../../MD/build/
cmake ..
make -j 2
cd ../../OverlapComponentProg/
make -j 2
cd ..
Add CPlex-jar to your local maven repository and compile. (change the path; for a different Cplex version you can either keep -Dversion or also change the POM.xml)
mvn install:install-file -Dfile=/opt/ibm/ILOG/CPLEX_Studio1271/cplex/lib/cplex.jar -DgroupId=ilog -DartifactId=cplex -Dversion=12.7 -Dpackaging=jar
mvn package
mv target/DCEdit-1.0.jar .
(The working directory for the .jar must me this folder. The 'target' folder can be deleted)
Run some examples. Specify the path to your Cplex-binaries-folder if using ILP
java -Xmx2048m -jar DCEdit-1.0.jar -test 5 50 10 -MD
java -Xmx2048m -jar DCEdit-1.0.jar -test 5 50 10 -lazy -gforce
java -Xmx2048m -Djava.library.path=/opt/ibm/ILOG/CPLEX_Studio1271/cplex/bin/x86-64_linux -jar DCEdit-1.0.jar -test 5 50 10 -lazy -ilp -v
Important note on memory management:
For larger n, the JVM will require more memory. Increase it e.g. to 2GB by adding -Xmx2048m as first java-option.
When running CPlex for larger n, the RAM will fill up quickly and a large enough swap file will be required. While OSX manages the Swap dynamically, on Linux a large-enough file must be allocated, else the kernel will kill the process. For n=50, limiting the number of threads to 4 on an 8-core system by adding -threads 4 resulted in full 16 GB memory + 8-10 GB Swap usage. According to the documentation, IloCplex.Param.WorkMem should limit the memory usage; It can be changed with e.g. with -mem 64 but did not help much.