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Diffstat (limited to 'benchmarks/Dockerfile')
| -rw-r--r-- | benchmarks/Dockerfile | 321 |
1 files changed, 321 insertions, 0 deletions
diff --git a/benchmarks/Dockerfile b/benchmarks/Dockerfile new file mode 100644 index 0000000..e349648 --- /dev/null +++ b/benchmarks/Dockerfile @@ -0,0 +1,321 @@ +# 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 \ + gudhi-utils \ + 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="${PATH}:/external/julia-1.1.0/bin" + +RUN julia --eval 'using Pkg; Pkg.add("Plotly"); Pkg.add("Eirene"); using Eirene;' + + +WORKDIR /benchmark +COPY sphere_3_192_points.dat . +COPY sphere_3_192.complex . +COPY o3_1024.txt . +COPY o3_1024_1.8.dipha . +COPY o3_4096.txt . +# COPY o3_4096_1.4.dipha . +COPY clifford_torus_50000.points.txt . +# COPY dragon_2000.dipha . + + + +RUN curl -LO https://github.com/n-otter/PH-roadmap/raw/master/data_sets/roadmap_datasets_distmat/fractal_9_5_2_random_edge_list.txt_0.19795_distmat.txt \ +&& curl -LO https://github.com/n-otter/PH-roadmap/raw/master/data_sets/roadmap_datasets_distmat/dipha/fractal_9_5_2_random.bin \ +\ +&& curl -LO https://github.com/n-otter/PH-roadmap/raw/master/data_sets/roadmap_datasets_point_cloud/dragon_vrip.ply.txt_2000_.txt \ +\ +# && curl -LO https://github.com/n-otter/PH-roadmap/raw/master/data_sets/roadmap_datasets_distmat/human_gene_distmat.txt \ +\ +&& curl -LO https://github.com/n-otter/PH-roadmap/raw/master/data_sets/roadmap_datasets_point_cloud/random_point_cloud_50_16_.txt \ +&& curl -LO https://github.com/n-otter/PH-roadmap/raw/master/data_sets/roadmap_datasets_distmat/dipha/random_50_16.bin + +RUN (echo "OFF\n2000 0 0" && cat dragon_vrip.ply.txt_2000_.txt) >dragon_vrip.ply.txt_2000_.off \ +&& (echo "OFF\n50 0 0" && cat random_point_cloud_50_16_.txt) >random_point_cloud_50_16_.off \ +&& (echo "OFF\n1024 0 0" && cat sphere_3_192_points.dat) > sphere_3_192.off \ +&& (echo "OFF\n1024 0 0" && cat o3_1024.txt) >o3_1024.off \ +&& (echo "OFF\n4096 0 0" && cat o3_4096.txt) >o3_4096.off \ +&& (echo "nOFF\n4 50000 0 0" && cat clifford_torus_50000.points.txt) >clifford_torus_50000.points.off + + +FROM benchmark-setup as benchmark-ripser + +WORKDIR /ripser +RUN git clone https://github.com/Ripser/ripser.git \ +&& cd ripser \ +&& git checkout dev \ +&& make + +ENV PATH="${PATH}:/ripser/ripser" + +WORKDIR /benchmark +RUN time -v -o sphere_3_192.ripser.txt ripser sphere_3_192_points.dat --format point-cloud --dim 2 +RUN time -v -o o3_1024.ripser.txt ripser o3_1024.txt --format point-cloud --dim 3 --threshold 1.8 --ratio 2 +RUN time -v -o o3_4096.ripser.txt ripser o3_4096.txt --format point-cloud --dim 3 --threshold 1.4 --ratio 2 +RUN time -v -o clifford_torus_50000.ripser.txt ripser clifford_torus_50000.points.txt --format point-cloud --dim 2 --threshold .15 --ratio 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 + + +FROM benchmark-ripser as benchmark-ripser-no-emergent + +WORKDIR /ripser/ripser +RUN git pull && git checkout benchmarks/disable-emergent-pairs \ +&& make + +WORKDIR /benchmark +RUN time -v -o sphere_3_192.ripser-no-emergent.txt ripser sphere_3_192_points.dat --format point-cloud --dim 2 +RUN time -v -o random.ripser-no-emergent.txt ripser random_point_cloud_50_16_.txt --format point-cloud --dim 7 +RUN time -v -o fractal-r.ripser-no-emergent.txt ripser fractal_9_5_2_random_edge_list.txt_0.19795_distmat.txt --dim 2 +RUN time -v -o dragon-2.ripser-no-emergent.txt ripser dragon_vrip.ply.txt_2000_.txt --format point-cloud --dim 1 +# RUN time -v -o genome.ripser-no-emergent.txt ripser human_gene_distmat.txt --dim 1 +RUN time -v -o o3_1024.ripser-no-emergent.txt ripser o3_1024.txt --format point-cloud --dim 3 --threshold 1.8 --ratio 2 +RUN time -v -o o3_4096.ripser-no-emergent.txt ripser o3_4096.txt --format point-cloud --dim 3 --threshold 1.4 --ratio 2 +RUN time -v -o clifford_torus_50000.ripser-no-emergent.txt ripser clifford_torus_50000.points.txt --format point-cloud --dim 2 --threshold .15 --ratio 2 + + +FROM benchmark-ripser as benchmark-ripser-store-reduced + +WORKDIR /ripser/ripser +RUN git pull && git checkout benchmarks/store-reduced-matrix \ +&& make + +WORKDIR /benchmark +RUN time -v -o sphere_3_192.ripser-store-reduced.txt ripser sphere_3_192_points.dat --format point-cloud --dim 2 +RUN time -v -o random.ripser-store-reduced.txt ripser random_point_cloud_50_16_.txt --format point-cloud --dim 7 +# RUN time -v -o fractal-r.ripser-store-reduced.txt ripser fractal_9_5_2_random_edge_list.txt_0.19795_distmat.txt --dim 2 +# RUN time -v -o dragon-2.ripser-store-reduced.txt ripser dragon_vrip.ply.txt_2000_.txt --format point-cloud --dim 1 +# RUN time -v -o genome.ripser-store-reduced.txt ripser human_gene_distmat.txt --dim 1 +RUN time -v -o o3_1024.ripser-store-reduced.txt ripser o3_1024.txt --format point-cloud --dim 3 --threshold 1.8 --ratio 2 +# RUN time -v -o o3_4096.ripser-store-reduced.txt ripser o3_4096.txt --format point-cloud --dim 3 --threshold 1.4 --ratio 2 +# RUN time -v -o clifford_torus_50000.ripser-store-reduced.txt ripser clifford_torus_50000.points.txt --format point-cloud --dim 2 --threshold .15 --ratio 2 + + +FROM benchmark-ripser as benchmark-ripser-use-reduced + +WORKDIR /ripser/ripser +RUN git pull && git checkout benchmarks/use-reduced-matrix \ +&& make + +WORKDIR /benchmark +RUN time -v -o sphere_3_192.ripser-use-reduced.txt ripser sphere_3_192_points.dat --format point-cloud --dim 2 +RUN time -v -o random.ripser-use-reduced.txt ripser random_point_cloud_50_16_.txt --format point-cloud --dim 7 +# RUN time -v -o fractal-r.ripser-use-reduced.txt ripser fractal_9_5_2_random_edge_list.txt_0.19795_distmat.txt --dim 2 +# RUN time -v -o dragon-2.ripser-use-reduced.txt ripser dragon_vrip.ply.txt_2000_.txt --format point-cloud --dim 1 +# RUN time -v -o genome.ripser-use-reduced.txt ripser human_gene_distmat.txt --dim 1 +RUN time -v -o o3_1024.ripser-use-reduced.txt ripser o3_1024.txt --format point-cloud --dim 3 --threshold 1.8 --ratio 2 +# RUN time -v -o o3_4096.ripser-use-reduced.txt ripser o3_4096.txt --format point-cloud --dim 3 --threshold 1.4 --ratio 2 +# RUN time -v -o clifford_torus_50000.ripser-use-reduced.txt ripser clifford_torus_50000.points.txt --format point-cloud --dim 2 --threshold .15 --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="${PATH}:/gudhi/2018-09-04-14-25-00_GUDHI_2.3.0/build/utilities/Rips_complex" +# +# WORKDIR /benchmark +# RUN time -v -o sphere_3_192.gudhi.txt rips_distance_matrix_persistence -d3 -p2 sphere_3_192.distance_matrix + +WORKDIR /benchmark +RUN time -v -o sphere_3_192.gudhi.txt gudhi-rips-persistence -d3 -p2 sphere_3_192.off >sphere_3_192.gudhi.out.txt +# RUN time -v -o fractal-r.gudhi.txt gudhi-rips-distance-matrix-persistence -d3 -p2 fractal_9_5_2_random_edge_list.txt_0.19795_distmat.txt >fractal-r.gudhi.out.txt +RUN time -v -o o3_1024.gudhi.txt gudhi-rips-persistence -d4 -p2 -r 1.8 o3_1024.off >o3_1024.gudhi.out.txt +RUN time -v -o o3_4096.gudhi.txt gudhi-rips-persistence -d4 -p2 -r 1.4 o3_4096.off >o3_4096.gudhi.out.txt +RUN time -v -o clifford_torus_50000.gudhi.txt gudhi-rips-persistence -d3 -p2 -r 0.15 clifford_torus_50000.points.off >clifford_torus_50000.gudhi.out.txt + + +FROM benchmark-setup as benchmark-dipha + +WORKDIR /dipha + +RUN git clone https://github.com/DIPHA/dipha.git \ +&& cd dipha \ +&& mkdir build \ +&& cd build \ +&& cmake .. \ +&& make + +ENV PATH="${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 +RUN time -v -o o3_1024.dipha.txt dipha --dual --benchmark --upper_dim 4 o3_1024_1.8.dipha o3_1024_1.8.dipha.diagram +# RUN time -v -o o3_4096.dipha.txt dipha --dual --benchmark --upper_dim 4 o3_4096_1.4.dipha o3_4096_1.4.dipha.diagram +# RUN time -v -o dragon-2.dipha.txt dipha --dual --benchmark --upper_dim 2 dragon_2000.dipha dragon_2000.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 + +RUN time -v -o o3_1024.dipha-multicore.txt mpiexec --allow-run-as-root --mca btl_vader_single_copy_mechanism none \ +dipha --dual --benchmark --upper_dim 4 o3_1024_1.8.dipha o3_1024_1.8.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.eirene037.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.eirene037.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.eirene037.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.eirene037.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 'maxdim = 2; using Eirene; using DelimitedFiles; eirene([0 1; 1 0]); println(@elapsed (d = transpose(readdlm("sphere_3_192_points.dat")); result = eirene(d, model="pc", record="none", maxdim=maxdim))); for i in 0:maxdim print("dim $(i): "); show(stdout, "text/plain", (barcode(result , dim = i))); println(); end' >sphere_3_192.eirene.out.txt + +RUN time -v -o o3_1024.eirene.txt \ + julia --eval 'maxdim = 3; maxrad = 1.8; using Eirene; using DelimitedFiles; eirene([0 1; 1 0]); println(@elapsed (d = transpose(readdlm("o3_1024.txt")); result = eirene(d, model="pc", record="none", maxdim=maxdim, maxrad=maxrad))); for i in 0:maxdim print("dim $(i): "); show(stdout, "text/plain", (barcode(result , dim = i))); println(); end' > o3_1024.eirene.out.txt + +RUN time -v -o o3_4096.eirene.txt \ + julia --eval 'maxdim = 3; maxrad = 1.4; using Eirene; using DelimitedFiles; eirene([0 1; 1 0]); println(@elapsed (d = transpose(readdlm("o3_4096.txt")); result = eirene(d, model="pc", record="none", maxdim=maxdim, maxrad=maxrad))); for i in 0:maxdim print("dim $(i): "); show(stdout, "text/plain", (barcode(result , dim = i))); println(); end' > o3_4096.eirene.out.txt + +# RUN time -v -o clifford_torus_50000.points.eirene.txt \ +# julia --eval 'maxdim = 2; maxrad = .15; using Eirene; using DelimitedFiles; eirene([0 1; 1 0]); println(@elapsed (d = transpose(readdlm("clifford_torus_50000.points.txt")); result = eirene(d, model="pc", record="none", maxdim=maxdim, maxrad=maxrad))); for i in 0:maxdim print("dim $(i): "); show(stdout, "text/plain", (barcode(result , dim = i))); println(); end' > clifford_torus_50000.eirene.out.txt + +RUN time -v -o dragon-2.eirene.txt \ + julia --eval 'maxdim = 1; using Eirene; using DelimitedFiles; eirene([0 1; 1 0]); println(@elapsed (d = transpose(readdlm("dragon_vrip.ply.txt_2000_.txt")); result = eirene(d, model="pc", record="none", maxdim=maxdim))); for i in 0:maxdim print("dim $(i): "); show(stdout, "text/plain", (barcode(result , dim = i))); println(); end' >dragon-2.eirene.out.txt + +RUN time -v -o fractal-r.eirene.txt \ + julia --eval 'maxdim = 2; using Eirene; using DelimitedFiles; eirene([0 1; 1 0]); println(@elapsed (d = (m->(m+transpose(m))/2)(readdlm("fractal_9_5_2_random_edge_list.txt_0.19795_distmat.txt")); result = eirene(d, record="none", maxdim=maxdim))); for i in 0:maxdim print("dim $(i): "); show(stdout, "text/plain", (barcode(result , dim = i))); println(); end' >fractal-r.eirene.out.txt + +RUN time -v -o random.eirene.txt \ + julia --eval 'maxdim = 7; maxrad = 1.7753855751520569; using Eirene; using DelimitedFiles; eirene([0 1; 1 0]); println(@elapsed (d = transpose(readdlm("random_point_cloud_50_16_.txt")); result = eirene(d, model="pc", record="none", maxdim=maxdim, maxrad=maxrad))); for i in 0:maxdim print("dim $(i): "); show(stdout, "text/plain", (barcode(result , dim = i))); println(); end' >random.eirene.out.txt + +# +# using Eirene; using DelimitedFiles; eirene([0 1; 1 0]); println(@elapsed result=eirene(transpose(readdlm("/Users/uli/Bitbucket/ripser/examples/o3_1024.txt")), model="pc", record="none", maxdim=3, maxrad=1.8)) +# using Eirene; using DelimitedFiles; eirene([0 1; 1 0]); println(@elapsed result=eirene(transpose(readdlm("/Users/uli/Bitbucket/ripser/examples/o3_2048.txt")), model="pc", record="none", maxdim=3, maxrad=1.6)) +# using Eirene; using DelimitedFiles; eirene([0 1; 1 0]); println(@elapsed result=eirene(transpose(readdlm("/Users/uli/Bitbucket/ripser/examples/o3_4096.txt")), model="pc", record="none", maxdim=3, maxrad=1.4)) +# + +FROM benchmark-setup as benchmark-dionysus2 + +WORKDIR /dionysus2 + +RUN pip install numpy scipy dionysus + +# RUN git clone https://github.com/mrzv/dionysus.git \ +# && cd dionysus \ +# && mkdir build \ +# && cd build \ +# && cmake .. \ +# && make rips-pairwise +# +# ENV PATH="${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 fractal.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));' + + +FROM benchmark-setup as benchmark-output + +COPY --from=benchmark-ripser /benchmark /benchmark +COPY --from=benchmark-gudhi /benchmark /benchmark +COPY --from=benchmark-dipha /benchmark /benchmark +COPY --from=benchmark-eirene /benchmark /benchmark +# COPY --from=benchmark-eirene037 /benchmark /benchmark +COPY --from=benchmark-dionysus2 /benchmark /benchmark + +COPY --from=benchmark-ripser-no-emergent /benchmark /benchmark +COPY --from=benchmark-ripser-store-reduced /benchmark /benchmark +COPY --from=benchmark-ripser-use-reduced /benchmark /benchmark + +RUN ls -l /benchmark + |