From 5f6a9c1c7bf860d3e4baf29b625f71bdb30507a0 Mon Sep 17 00:00:00 2001 From: Ulrich Bauer Date: Sun, 1 Sep 2019 11:31:29 +0200 Subject: removed benchmark files --- benchmarks/Dockerfile | 321 -------------------------------------------------- 1 file changed, 321 deletions(-) delete mode 100644 benchmarks/Dockerfile (limited to 'benchmarks/Dockerfile') diff --git a/benchmarks/Dockerfile b/benchmarks/Dockerfile deleted file mode 100644 index e349648..0000000 --- a/benchmarks/Dockerfile +++ /dev/null @@ -1,321 +0,0 @@ -# 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 - -- cgit v1.2.3