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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="${PATH}:/external/julia-1.1.0/bin"
RUN julia --eval 'using Pkg; Pkg.add("Plotly"); Pkg.add("Eirene"); using Eirene;'
WORKDIR /benchmark
RUN curl -LO https://raw.githubusercontent.com/Ripser/ripser/dev/benchmarks/sphere_3_192/sphere_3_192_points.dat \
&& curl -LO https://raw.githubusercontent.com/Ripser/ripser/dev/benchmarks/sphere_3_192/sphere_3_192.distance_matrix \
&& curl -LO https://raw.githubusercontent.com/Ripser/ripser/dev/benchmarks/sphere_3_192/sphere_3_192.complex \
\
&& curl -LO https://github.com/n-otter/PH-roadmap/raw/master/data_sets/roadmap_datasets_distmat/fractal_9_5_2_random_edge_list.txt_0.19795_distmat.txt \
&& curl -LO https://github.com/n-otter/PH-roadmap/raw/master/data_sets/roadmap_datasets_distmat/dipha/fractal_9_5_2_random.bin \
\
&& curl -LO https://github.com/n-otter/PH-roadmap/raw/master/data_sets/roadmap_datasets_point_cloud/dragon_vrip.ply.txt_2000_.txt \
\
# && curl -LO https://github.com/n-otter/PH-roadmap/raw/master/data_sets/roadmap_datasets_distmat/human_gene_distmat.txt \
\
&& curl -LO https://github.com/n-otter/PH-roadmap/raw/master/data_sets/roadmap_datasets_point_cloud/random_point_cloud_50_16_.txt \
&& curl -LO https://github.com/n-otter/PH-roadmap/raw/master/data_sets/roadmap_datasets_distmat/dipha/random_50_16.bin
COPY o3_1024.txt .
FROM benchmark-setup as benchmark-ripser
WORKDIR /ripser
RUN git clone https://github.com/Ripser/ripser.git \
&& cd ripser \
&& make
ENV PATH="${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 --format point-cloud --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 --format point-cloud --dim 1
# RUN time -v -o genome.ripser.txt ripser human_gene_distmat.txt --dim 1
RUN time -v -o o3_1024.ripser.txt ripser o3_1024.txt --format point-cloud --dim 3 --threshold 1.8 --ratio 2
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
RUN time -v -o o3_1024.eirene.txt \
julia --eval 'using Eirene; using DelimitedFiles; eirene([0 1; 1 0]); println(@elapsed eirene(transpose(readdlm("o3_1024.txt")), model="pc", record="none", maxdim=3, maxrad=1.8))' > o3_1024.eirene.out.txt
#
# using Eirene; using DelimitedFiles; eirene([0 1; 1 0]); println(@elapsed result=eirene(transpose(readdlm("/Users/uli/Bitbucket/ripser/examples/o3_1024.txt")), model="pc", record="none", maxdim=3, maxrad=1.8))
# using Eirene; using DelimitedFiles; eirene([0 1; 1 0]); println(@elapsed result=eirene(transpose(readdlm("/Users/uli/Bitbucket/ripser/examples/o3_2048.txt")), model="pc", record="none", maxdim=3, maxrad=1.6))
# using Eirene; using DelimitedFiles; eirene([0 1; 1 0]); println(@elapsed result=eirene(transpose(readdlm("/Users/uli/Bitbucket/ripser/examples/o3_4096.txt")), model="pc", record="none", maxdim=3, maxrad=1.4))
#
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));'
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