diff options
Diffstat (limited to 'benchmarks/Dockerfile')
| -rw-r--r-- | benchmarks/Dockerfile | 167 |
1 files changed, 103 insertions, 64 deletions
diff --git a/benchmarks/Dockerfile b/benchmarks/Dockerfile index 3d6e952..cead00d 100644 --- a/benchmarks/Dockerfile +++ b/benchmarks/Dockerfile @@ -12,6 +12,7 @@ RUN apt-get update && \ curl \ g++ \ git \ + gudhi-utils \ hdf5-tools \ libcgal-dev \ libboost-dev \ @@ -53,6 +54,15 @@ RUN curl -LO https://raw.githubusercontent.com/Ripser/ripser/dev/benchmarks/sphe && 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 . +COPY o3_4096.txt . +COPY clifford_torus_50000.points.csv . + +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 o3_1024.txt) >o3_1024.off \ +&& (echo "OFF\n4096 0 0" && cat o3_4096.txt) >o3_4096.off \ +&& (echo "nOFF\n4 50000 1 0" && cat clifford_torus_50000.points.csv) >clifford_torus_50000.points.off + FROM benchmark-setup as benchmark-ripser @@ -65,31 +75,40 @@ ENV PATH="${PATH}:/ripser/ripser" WORKDIR /benchmark RUN time -v -o sphere_3_192.ripser.txt ripser sphere_3_192.distance_matrix --dim 2 +RUN time -v -o o3_1024.ripser.txt ripser o3_1024.txt --format point-cloud --dim 3 --threshold 1.8 --ratio 2 +RUN time -v -o o3_4096.ripser.txt ripser o3_4096.txt --format point-cloud --dim 3 --threshold 1.4 --ratio 2 +RUN time -v -o clifford_torus_50000.ripser.txt ripser clifford_torus_50000.points.csv --format point-cloud --dim 2 --threshold .11 --ratio 2 + RUN time -v -o random.ripser.txt ripser random_point_cloud_50_16_.txt --format point-cloud --dim 7 RUN time -v -o fractal-r.ripser.txt ripser fractal_9_5_2_random_edge_list.txt_0.19795_distmat.txt --dim 2 RUN time -v -o dragon-2.ripser.txt ripser dragon_vrip.ply.txt_2000_.txt --format point-cloud --dim 1 # RUN time -v -o genome.ripser.txt ripser human_gene_distmat.txt --dim 1 -RUN time -v -o o3_1024.ripser.txt ripser o3_1024.txt --format point-cloud --dim 3 --threshold 1.8 --ratio 2 FROM benchmark-setup as benchmark-gudhi -WORKDIR /gudhi - -RUN curl -LO "https://gforge.inria.fr/frs/download.php/file/37696/2018-09-04-14-25-00_GUDHI_2.3.0.tar.gz" \ -&& tar xf 2018-09-04-14-25-00_GUDHI_2.3.0.tar.gz \ -&& cd 2018-09-04-14-25-00_GUDHI_2.3.0 \ -&& mkdir build \ -&& cd build \ -&& cmake -DCMAKE_BUILD_TYPE="Release" .. \ -&& make rips_distance_matrix_persistence - -ENV PATH="${PATH}:/gudhi/2018-09-04-14-25-00_GUDHI_2.3.0/build/utilities/Rips_complex" +# WORKDIR /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="${PATH}:/gudhi/2018-09-04-14-25-00_GUDHI_2.3.0/build/utilities/Rips_complex" +# +# WORKDIR /benchmark +# RUN time -v -o sphere_3_192.gudhi.txt rips_distance_matrix_persistence -d3 -p2 sphere_3_192.distance_matrix WORKDIR /benchmark -RUN time -v -o sphere_3_192.gudhi.txt rips_distance_matrix_persistence -d3 -p2 sphere_3_192.distance_matrix - +RUN time -v -o sphere_3_192.gudhi.txt gudhi-rips-distance-matrix-persistence -d3 -p2 sphere_3_192.distance_matrix +# RUN time -v -o fractal-r.gudhi.txt gudhi-rips-distance-matrix-persistence -d3 -p2 fractal_9_5_2_random_edge_list.txt_0.19795_distmat.txt +RUN time -v -o o3_1024.gudhi.txt gudhi-rips-persistence -d4 -p2 -r 1.8 o3_1024.off +RUN time -v -o o3_4096.gudhi.txt gudhi-rips-persistence -d4 -p2 -r 1.4 o3_4096.off +RUN time -v -o clifford_torus_50000.gudhi.txt gudhi-rips-persistence -d3 -p2 -r 0.11 clifford_torus_50000.off FROM benchmark-setup as benchmark-dipha @@ -117,43 +136,44 @@ dipha --dual --benchmark --upper_dim 3 sphere_3_192.complex sphere_3_192.dipha-m -FROM benchmark-setup as benchmark-eirene037 - -WORKDIR /eirene - -RUN curl -LO https://julialang-s3.julialang.org/bin/linux/x64/0.6/julia-0.6.4-linux-x86_64.tar.gz \ -&& tar xf julia-0.6.4-linux-x86_64.tar.gz - -RUN curl -LO "http://gregoryhenselman.org/eirene/ewExternalFiles/Eirene0_3_7.zip" \ -&& unzip Eirene0_3_7.zip \ -&& cd Eirene0_3_7 - -# ENV PATH="${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-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 @@ -168,16 +188,22 @@ WORKDIR /eirene #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 + julia --eval 'maxdim = 2; using Eirene; using DelimitedFiles; eirene([0 1; 1 0]); println(@elapsed (d = readdlm("sphere_3_192.distance_matrix"); 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' >sphere_3_192.eirene.out.txt + +RUN time -v -o o3_1024.eirene.txt \ + julia --eval 'maxdim = 2; 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 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 + 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 '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 + 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)) @@ -202,11 +228,24 @@ RUN pip install numpy scipy dionysus 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 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 -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));' +COPY --from=benchmark-ripser /benchmark /benchmark +COPY --from=benchmark-gudhi /benchmark /benchmark +COPY --from=benchmark-dipha /benchmark /benchmark +COPY --from=benchmark-dipha-multicore /benchmark /benchmark +COPY --from=benchmark-eirene /benchmark /benchmark +# COPY --from=benchmark-eirene037 /benchmark /benchmark +COPY --from=benchmark-dionysus2 /benchmark /benchmark -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));' +RUN ls -l /benchmark |