From 2def213ae4222a61baf40dc00e80142a4165ba82 Mon Sep 17 00:00:00 2001 From: Ulrich Bauer Date: Fri, 19 Jul 2019 21:39:49 +0200 Subject: updated docker file --- benchmarks/Dockerfile | 41 ++++++++++++++++++++--------------------- 1 file changed, 20 insertions(+), 21 deletions(-) diff --git a/benchmarks/Dockerfile b/benchmarks/Dockerfile index c67db52..e349648 100644 --- a/benchmarks/Dockerfile +++ b/benchmarks/Dockerfile @@ -39,11 +39,18 @@ 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 \ +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 \ @@ -53,12 +60,9 @@ 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_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 . -COPY o3_4096.txt . -COPY clifford_torus_50000.points.txt . - 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 @@ -69,12 +73,13 @@ 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.distance_matrix --dim 2 +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 @@ -92,7 +97,7 @@ 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.distance_matrix --dim 2 +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 @@ -109,7 +114,7 @@ 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.distance_matrix --dim 2 +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 @@ -126,7 +131,7 @@ 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.distance_matrix --dim 2 +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 @@ -154,7 +159,7 @@ FROM benchmark-setup as benchmark-gudhi # 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-distance-matrix-persistence -d3 -p2 sphere_3_192.distance_matrix >sphere_3_192.gudhi.out.txt +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 @@ -176,14 +181,8 @@ 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 - -COPY o3_1024_1.8.dipha . 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 - -# COPY o3_4096_1.4.dipha . # 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 - -# COPY dragon_2000.dipha . # RUN time -v -o dragon-2.dipha.txt dipha --dual --benchmark --upper_dim 2 dragon_2000.dipha dragon_2000.dipha.diagram @@ -251,7 +250,7 @@ WORKDIR /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 = 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 + 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 -- cgit v1.2.3