Initial commit of tool

.gitattributes

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+solvers/* linguist-vendored
+src/tensorcsp/* linguist-vendored

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# CUSTOM Exclusions
+# IPython notebooks
+*.ipynb
+/.idea/*
+
+# Compressed Benchmarks
+*.zip
+
+# Local experiment data
+/experiments/*
+# Local figure data
+/figures/*
+
+# C++ object files
+/cpp/*.o
+/cpp/*/*.o
+/cpp/*/*/*.o
+/cpp/*/*/*/*.o
+
+# VSCode files
+/cpp/.vscode/*
+/cpp/*.code-workspace
+
+# Singularity container
+tensororder

LICENSE

@@ -1,21 +1,21 @@
-MIT License
-
-Copyright (c) 2019 Vardi's Group
-
-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.
+MIT License
+
+Copyright (c) 2019 Vardi's Group
+
+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.

Makefile

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+export TENSORORDER_DIR=$(dir $(abspath $(lastword $(MAKEFILE_LIST))))
+
+tensororder: Singularity
+	singularity build tensororder Singularity
+
+clean:
+	rm tensororder

README.md

@@ -1,2 +1,37 @@
-# TensorOrder
-A tool for weighted model counting through tensor network contraction
+# TensorOrder
+A Python 3 tool for automatically contracting tensor networks for weighted model counting.
+
+## Running with Singularity
+Because of the variety of dependencies used in the various tree decomposition tools, it is recommended to use the [Singularity](https://www.sylabs.io/) container to run TensorOrder.
+
+### Building the container
+The container can be built with the following commands (make requires root to build the Singularity container):
+```
+git clone https://github.com/vardigroup/TensorOrder.git
+cd TensorOrder
+sudo make
+```
+
+### Usage
+Once built, example usage is:
+```
+./tensororder --method="line-Flow" < "benchmarks/cubic_vertex_cover/cubic_vc_50_0.cnf"
+```
+
+
+## Running without Singularity
+TensorOrder can also be used directly as a Python 3 tool. The primary script is located in `src/tensororder.py`. Example usage is
+```python src/tensororder.py --method="line-Flow" < "benchmarks/cubic_vertex_cover/cubic_vc_50_0.cnf" ```
+
+TensorOrder requires the following python packages (see [requirements.txt](requirements.txt) for a working set of exact version information if needed):
+1. `click`
+2. `numpy`
+3. `python-igraph`
+4. `networkx`
+5. `cached_property`
+
+Moreover, the various tensor methods each require additional setup.
+* For KCMR-metis and KCMR-gn, METIS must be installed using the instructions [here](src/tensorcsp).
+* For line-Tamaki and factor-Tamaki, the tree-decomposition solver Tamaki must be compiled using the `heuristic` instructions [here](solvers/TCS-Meiji).
+* For line-Flow and factor-Flow, the tree-decomposition solver FlowCutter must be compiled using the instructions [here](solvers/flow-cutter-pace17).
+* For line-htd and factor-htd, the tree-decomposition solver htd must be compiled using the instructions [here](solvers/htd-master).

Singularity

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+Bootstrap: docker
+From: python:3.7-slim
+
+%setup
+    cp -R ${TENSORORDER_DIR-$PWD}/solvers ${SINGULARITY_ROOTFS}/solvers
+    cp -R ${TENSORORDER_DIR-$PWD}/src ${SINGULARITY_ROOTFS}/src
+    wget http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz -P ${SINGULARITY_ROOTFS}/solvers/
+
+%post
+    apt-get update
+
+    # TensorOrder
+    apt-get -y install g++ make libxml2-dev zlib1g-dev
+    pip install click numpy python-igraph networkx cached_property
+
+    # METIS
+    apt-get -y install g++ make cmake
+    cd /solvers/
+    tar -xvf metis-5.1.0.tar.gz
+    rm metis-5.1.0.tar.gz
+    cd /solvers/metis-5.1.0
+    make config shared=1
+    make
+    make install
+    pip install metis
+
+    # TCS-Meiji
+    # deal with slim variants not having man page directories (which causes "update-alternatives" to fail)
+    mkdir -p /usr/share/man/man1
+    apt-get install -y make openjdk-11-jdk
+    cd /solvers/TCS-Meiji
+    make heuristic
+
+    # FlowCutter
+    apt-get -y install g++
+    cd /solvers/flow-cutter-pace17
+    chmod +x ./build.sh
+    ./build.sh
+
+    # Htd
+    apt-get -y install g++ cmake
+    cd /solvers/htd-master
+    cmake .
+    make
+
+%environment
+    export METIS_DLL=/solvers/metis-5.1.0/build/Linux-x86_64/libmetis/libmetis.so
+
+%help
+    This is a Singularity container for the TensorOrder tool.
+    See "$SINGULARITY_NAME --help" for usage.
+
+%runscript
+    export TENSORORDER_CALLER="$SINGULARITY_NAME"
+    exec python /src/tensororder.py "$@"
+
+

benchmarks/cubic_vertex_cover/cubic_vc_50_0.cnf

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+p cnf 50 75
+1 26 0
+1 2 0
+1 11 0
+2 4 0
+2 48 0
+3 32 0
+3 19 0
+3 23 0
+4 13 0
+4 41 0
+5 13 0
+5 34 0
+5 17 0
+6 32 0
+6 7 0
+6 42 0
+7 46 0
+7 10 0
+8 38 0
+8 37 0
+8 30 0
+9 21 0
+9 38 0
+9 10 0
+10 27 0
+11 21 0
+11 20 0
+12 23 0
+12 15 0
+12 36 0
+13 44 0
+14 45 0
+14 24 0
+14 40 0
+15 35 0
+15 20 0
+16 36 0
+16 48 0
+16 27 0
+17 45 0
+17 39 0
+18 26 0
+18 39 0
+18 50 0
+19 50 0
+19 22 0
+20 22 0
+21 36 0
+22 47 0
+23 46 0
+24 43 0
+24 31 0
+25 28 0
+25 43 0
+25 30 0
+26 42 0
+27 29 0
+28 31 0
+28 47 0
+29 49 0
+29 48 0
+30 34 0
+31 47 0
+32 35 0
+33 35 0
+33 49 0
+33 37 0
+34 44 0
+37 50 0
+38 46 0
+39 43 0
+40 44 0
+40 41 0
+41 42 0
+45 49 0

requirements.txt

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+cached-property==1.5.1
+certifi==2018.4.16
+Click==7.0
+decorator==4.3.0
+llvmlite==0.26.0
+metis==0.2a4
+networkx==2.1
+numba==0.41.0
+numpy==1.15.0
+python-igraph==0.7.1.post6
+scipy==1.1.0
+sparse==0.5.0+16.ge80efc7.dirty

solvers/TCS-Meiji/LICENSE

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+MIT License
+
+Copyright (c) 2017 Hisao Tamaki, Hiromu Ohtsuka, Takuto Sato, Keitaro Makii
+
+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.