docker file for benchmark

2 files changed, 211 insertions, 0 deletions

diff --git a/benchmarks/Dockerfile b/benchmarks/Dockerfile
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+++ b/benchmarks/Dockerfile
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+# FROM ubuntu:latest
+
+#FROM ubuntu:18.10 as benchmark-setup
+# RUN echo "deb http://archive.ubuntu.com/ubuntu/ cosmic main restricted universe" > /etc/apt/sources.list
+
+FROM ubuntu:19.04 as benchmark-setup
+
+RUN apt-get update && \
+    apt-get install -y \
+    apt-utils \
+    cmake \
+    curl \
+    g++ \
+    git \
+    hdf5-tools \
+    libcgal-dev \
+    libboost-dev \
+    libboost-filesystem-dev \
+    libboost-test-dev \
+    libgmp3-dev \
+    libmpfr-dev \
+    libtbb-dev \
+    libopenmpi-dev \
+    make \
+    python-minimal \
+    python-pip \
+    time \
+    unzip \
+ && rm -rf /var/lib/apt/lists/*
+
+WORKDIR /external
+
+RUN curl -LO https://julialang-s3.julialang.org/bin/linux/x64/1.1/julia-1.1.0-linux-x86_64.tar.gz \
+	&& tar xf julia-1.1.0-linux-x86_64.tar.gz
+ENV PATH="${PATH}:/external/julia-1.1.0/bin"
+
+RUN julia --eval 'using Pkg; Pkg.add("Plotly"); Pkg.add("Eirene");  using Eirene;'
+
+
+WORKDIR /benchmark
+RUN curl -LO https://raw.githubusercontent.com/Ripser/ripser/dev/benchmarks/sphere_3_192/sphere_3_192_points.dat  \ 
+&& curl -LO https://raw.githubusercontent.com/Ripser/ripser/dev/benchmarks/sphere_3_192/sphere_3_192.distance_matrix \
+&& curl -LO https://raw.githubusercontent.com/Ripser/ripser/dev/benchmarks/sphere_3_192/sphere_3_192.complex \
+\
+&& curl -LO https://github.com/n-otter/PH-roadmap/raw/master/data_sets/roadmap_datasets_distmat/fractal_9_5_2_random_edge_list.txt_0.19795_distmat.txt \
+&& curl -LO https://github.com/n-otter/PH-roadmap/raw/master/data_sets/roadmap_datasets_distmat/dipha/fractal_9_5_2_random.bin \
+\
+&& curl -LO https://github.com/n-otter/PH-roadmap/raw/master/data_sets/roadmap_datasets_point_cloud/dragon_vrip.ply.txt_2000_.txt \
+\
+# && curl -LO https://github.com/n-otter/PH-roadmap/raw/master/data_sets/roadmap_datasets_distmat/human_gene_distmat.txt \
+\
+&& curl -LO https://github.com/n-otter/PH-roadmap/raw/master/data_sets/roadmap_datasets_point_cloud/random_point_cloud_50_16_.txt \
+&& curl -LO https://github.com/n-otter/PH-roadmap/raw/master/data_sets/roadmap_datasets_distmat/dipha/random_50_16.bin
+
+
+
+FROM benchmark-setup as benchmark-ripser
+
+WORKDIR /ripser
+RUN git clone https://github.com/Ripser/ripser.git \
+&& cd ripser \
+&& make
+
+ENV PATH="${PATH}:/ripser/ripser"
+
+WORKDIR /benchmark
+RUN time -v -o sphere_3_192.ripser.txt    ripser sphere_3_192.distance_matrix --dim 2
+RUN time -v -o random.ripser.txt    ripser random_point_cloud_50_16_.txt --dim 7
+RUN time -v -o fractal-r.ripser.txt    ripser fractal_9_5_2_random_edge_list.txt_0.19795_distmat.txt --dim 2
+RUN time -v -o dragon-2.ripser.txt    ripser dragon_vrip.ply.txt_2000_.txt --dim 1
+# RUN time -v -o genome.ripser.txt    ripser human_gene_distmat.txt --dim 1
+
+
+
+FROM benchmark-setup as benchmark-gudhi
+
+WORKDIR /gudhi
+
+RUN curl -LO "https://gforge.inria.fr/frs/download.php/file/37696/2018-09-04-14-25-00_GUDHI_2.3.0.tar.gz" \
+&& tar xf 2018-09-04-14-25-00_GUDHI_2.3.0.tar.gz \
+&& cd 2018-09-04-14-25-00_GUDHI_2.3.0 \
+&& mkdir build \
+&& cd build \
+&& cmake -DCMAKE_BUILD_TYPE="Release" .. \
+&& make rips_distance_matrix_persistence 
+
+ENV PATH="${PATH}:/gudhi/2018-09-04-14-25-00_GUDHI_2.3.0/build/utilities/Rips_complex"
+
+WORKDIR /benchmark
+RUN time -v -o sphere_3_192.gudhi.txt     rips_distance_matrix_persistence -d3 -p2 sphere_3_192.distance_matrix
+
+
+
+FROM benchmark-setup as benchmark-dipha
+
+WORKDIR /dipha
+
+RUN git clone https://github.com/DIPHA/dipha.git \
+&& cd dipha \
+&& mkdir build \
+&& cd build \
+&& cmake .. \
+&& make
+
+ENV PATH="${PATH}:/dipha/dipha/build"
+
+WORKDIR /benchmark
+RUN time -v -o sphere_3_192.dipha.txt     dipha --dual --benchmark --upper_dim 3 sphere_3_192.complex sphere_3_192.dipha.diagram
+
+
+
+FROM benchmark-dipha as benchmark-dipha-multicore
+
+RUN time -v -o sphere_3_192.dipha-multicore.txt     mpiexec --allow-run-as-root --mca btl_vader_single_copy_mechanism none \
+dipha --dual --benchmark --upper_dim 3 sphere_3_192.complex sphere_3_192.dipha-multicore.diagram
+
+
+
+FROM benchmark-setup as benchmark-eirene037
+
+WORKDIR /eirene
+
+RUN curl -LO https://julialang-s3.julialang.org/bin/linux/x64/0.6/julia-0.6.4-linux-x86_64.tar.gz \
+&& tar xf julia-0.6.4-linux-x86_64.tar.gz
+
+RUN curl -LO "http://gregoryhenselman.org/eirene/ewExternalFiles/Eirene0_3_7.zip" \
+&& unzip Eirene0_3_7.zip \
+&& cd Eirene0_3_7
+
+# ENV PATH="${PATH}:/eirene/julia-9d11f62bcb/bin"
+
+# RUN julia --eval 'Pkg.clone("https://github.com/Eetion/Eirene.jl.git"); using Eirene'
+# RUN julia --eval ' \
+#	Pkg.clone("https://github.com/bnels/PlotlyJS.jl.git"); \
+#	Pkg.checkout("PlotlyJS","fix-jsstring"); \
+#	Pkg.add("Eirene");'
+RUN /eirene/julia-9d11f62bcb/bin/julia --eval ' \
+	Pkg.clone("https://github.com/bnels/PlotlyJS.jl.git"); \
+	Pkg.checkout("PlotlyJS","fix-jsstring");'
+RUN /eirene/julia-9d11f62bcb/bin/julia --eval 'Pkg.add("Distances"); Pkg.add("JLD"); Pkg.add("Blink"); Pkg.add("Plotly"); Pkg.add("MultivariateStats");'
+RUN /eirene/julia-9d11f62bcb/bin/julia --load /eirene/Eirene0_3_7/Eirene0_3_7_mutable.jl --eval 'eirene([0 1; 1 0]);'
+
+WORKDIR /benchmark
+RUN time -v -o sphere_3_192.eirene.txt \
+    /eirene/julia-9d11f62bcb/bin/julia --load /eirene/Eirene0_3_7/Eirene0_3_7_mutable.jl --eval 'eirene([0 1; 1 0]); p = readdlm("sphere_3_192.distance_matrix"); \
+    tic(); eirene(p, record="none", bettimax=2); toc();' >sphere_3_192.eirene037.out.txt
+RUN time -v -o dragon-2.eirene.txt \
+    /eirene/julia-9d11f62bcb/bin/julia --load /eirene/Eirene0_3_7/Eirene0_3_7_mutable.jl --eval 'eirene([0 1; 1 0]); p = readdlm("dragon_vrip.ply.txt_2000_.txt"); \
+    tic(); eirene(p, rowsare="points", record="none", bettimax=1); toc();' >dragon-2.eirene037.out.txt
+RUN time -v -o fractal-r.eirene.txt \
+    /eirene/julia-9d11f62bcb/bin/julia --load /eirene/Eirene0_3_7/Eirene0_3_7_mutable.jl --eval 'eirene([0 1; 1 0]); p = readdlm("fractal_9_5_2_random_edge_list.txt_0.19795_distmat.txt"); \
+    tic(); eirene(p, record="none", bettimax=2); toc();' >fractal-r.eirene037.out.txt
+RUN time -v -o random.eirene.txt  \
+    /eirene/julia-9d11f62bcb/bin/julia --load /eirene/Eirene0_3_7/Eirene0_3_7_mutable.jl --eval 'eirene([0 1; 1 0]); p = readdlm("random_point_cloud_50_16_.txt"); \
+    tic(); eirene(p, rowsare="points", record="none", bettimax=7); toc();' >random.eirene037.out.txt
+
+
+
+FROM benchmark-setup as benchmark-eirene
+
+WORKDIR /eirene
+
+#RUN curl -LO https://julialang-s3.julialang.org/bin/linux/x64/1.1/julia-1.1.0-linux-x86_64.tar.gz \
+#&& tar xf julia-1.1.0-linux-x86_64.tar.gz
+#ENV PATH="${PATH}:/eirene/julia-1.1.0/bin"
+
+#RUN julia --eval 'using Pkg; Pkg.add("Plotly"); Pkg.add("Eirene"); using Eirene'
+
+WORKDIR /benchmark
+RUN time -v -o sphere_3_192.eirene.txt \
+	julia --eval 'using Eirene; using DelimitedFiles; eirene([0 1; 1 0]); println(@elapsed eirene(transpose(readdlm("sphere_3_192.distance_matrix")), record="none", maxdim=2))' >sphere_3_192.eirene.out.txt
+RUN time -v -o dragon-2.eirene.txt \
+	julia --eval 'using Eirene; using DelimitedFiles; eirene([0 1; 1 0]); println(@elapsed eirene(transpose(readdlm("dragon_vrip.ply.txt_2000_.txt")), model="pc", record="none", maxdim=1))' >dragon-2.eirene.out.txt
+RUN time -v -o fractal-r.eirene.txt \
+	julia --eval 'using Eirene; using DelimitedFiles; eirene([0 1; 1 0]); println(@elapsed eirene(transpose(readdlm("fractal_9_5_2_random_edge_list.txt_0.19795_distmat.txt")), record="none", maxdim=2))' >fractal-r.eirene.out.txt
+#RUN time -v -o random.eirene.txt  \
+#	julia --eval 'using Eirene; using DelimitedFiles; eirene([0 1; 1 0]); println(@elapsed eirene(transpose(readdlm("random_point_cloud_50_16_.txt")), model="pc", record="none", maxdim=7))' >random.eirene.out.txt
+
+
+
+FROM benchmark-setup as benchmark-dionysus2
+
+WORKDIR /dionysus2
+
+RUN pip install numpy scipy dionysus
+
+# RUN git clone https://github.com/mrzv/dionysus.git \
+# && cd dionysus \
+# && mkdir build \
+# && cd build \
+# && cmake .. \
+# && make rips-pairwise
+# 
+# ENV PATH="${PATH}:/dionysus2/dionysus/build/examples/rips"
+
+WORKDIR /benchmark
+# RUN time -v -o sphere_3_192.dionysus-cpp.txt  rips-pairwise sphere_3_192_points.dat -s3
+
+RUN time -v -o sphere.dionysus-py.txt python -c 'import dionysus as d; from numpy import loadtxt, inf; import math; from scipy.spatial.distance import squareform; \
+	d.cohomology_persistence(d.fill_rips(squareform(loadtxt("sphere_3_192.distance_matrix")), 3, inf));'
+
+RUN time -v -o dragon-2.dionysus-py.txt python -c 'import dionysus as d; from numpy import loadtxt, inf; import math; from scipy.spatial.distance import squareform; \
+	d.cohomology_persistence(d.fill_rips(loadtxt("dragon_vrip.ply.txt_2000_.txt"), 2, inf));'
+
+RUN time -v -o sphere.dionysus-py.txt python -c 'import dionysus as d; from numpy import loadtxt, inf; import math; from scipy.spatial.distance import squareform; \
+	d.cohomology_persistence(d.fill_rips(squareform(loadtxt("fractal_9_5_2_random_edge_list.txt_0.19795_distmat.txt")), 3, inf));'
diff --git a/benchmarks/readme.txt b/benchmarks/readme.txt
new file mode 100644
index 0000000..ddf0c8a
--- /dev/null
+++ b/benchmarks/readme.txt
@@ -0,0 +1,5 @@
+building: docker build .
+
+running interactive: docker run -ti <name of image>
+
+