diff options
Diffstat (limited to 'benchmarks/Dockerfile')
| -rw-r--r-- | benchmarks/Dockerfile | 39 |
1 files changed, 28 insertions, 11 deletions
diff --git a/benchmarks/Dockerfile b/benchmarks/Dockerfile index cead00d..92bbb2c 100644 --- a/benchmarks/Dockerfile +++ b/benchmarks/Dockerfile @@ -55,13 +55,13 @@ RUN curl -LO https://raw.githubusercontent.com/Ripser/ripser/dev/benchmarks/sphe COPY o3_1024.txt . COPY o3_4096.txt . -COPY clifford_torus_50000.points.csv . +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 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 +&& (echo "nOFF\n4 50000 0 0" && cat clifford_torus_50000.points.txt) >clifford_torus_50000.points.off FROM benchmark-setup as benchmark-ripser @@ -77,7 +77,7 @@ 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 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 @@ -104,11 +104,11 @@ 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 -# 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 +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 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 @@ -127,13 +127,24 @@ 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 -FROM benchmark-dipha as benchmark-dipha-multicore +# 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 + + + +# 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 @@ -193,7 +204,13 @@ 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 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 + 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 @@ -243,9 +260,9 @@ 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-dipha-multicore /benchmark /benchmark COPY --from=benchmark-eirene /benchmark /benchmark # COPY --from=benchmark-eirene037 /benchmark /benchmark COPY --from=benchmark-dionysus2 /benchmark /benchmark RUN ls -l /benchmark + |