diff options
36 files changed, 8 insertions, 1586 deletions
@@ -79,7 +79,7 @@ The input is given either in a file whose name is passed as an argument, or thro - `distance`: full distance matrix; similar to the above, but for all entries of the distance matrix. One line per row of the matrix; only the part below the diagonal is actually read. - `dipha`: DIPHA distance matrix as described on the [DIPHA] website. - `point-cloud`: point cloud; a comma (or whitespace, or other non-numerical character) separated list of coordinates of the points in some Euclidean space, one point per line. - - `binary`: lower distance matrix in binary file format; a sequence of the distance matrix entries below the diagonal in 64 bit double format (IEEE 754, little endian). + - `binary`: lower distance matrix in binary file format; a sequence of the distance matrix entries below the diagonal in 32 bit double format (IEEE 754, little endian). - `sparse`: sparse triplet format; a whitespace separated list of entries of a sparse distance matrix, one entry per line, each of the form *i j d(i,j)* specifying the distance between points *i* and *j*. Each pair of points should appear in the file at most once. - `--dim k`: compute persistent homology up to dimension *k*. - `--threshold t`: compute Rips complexes up to diameter *t*. 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 - diff --git a/benchmarks/output/clifford_torus_50000.ripser.txt b/benchmarks/output/clifford_torus_50000.ripser.txt deleted file mode 100644 index 756f7ae..0000000 --- a/benchmarks/output/clifford_torus_50000.ripser.txt +++ /dev/null @@ -1,23 +0,0 @@ - Command being timed: "ripser clifford_torus_50000.points.txt --format point-cloud --dim 2 --threshold .15 --ratio 2" - User time (seconds): 129.19 - System time (seconds): 12.06 - Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 2:21.35 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 8593448 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 4911670 - Voluntary context switches: 7 - Involuntary context switches: 1506 - Swaps: 0 - File system inputs: 0 - File system outputs: 0 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 0 diff --git a/benchmarks/output/dragon-2.ripser-no-emergent.txt b/benchmarks/output/dragon-2.ripser-no-emergent.txt deleted file mode 100644 index 2693a67..0000000 --- a/benchmarks/output/dragon-2.ripser-no-emergent.txt +++ /dev/null @@ -1,23 +0,0 @@ - Command being timed: "ripser dragon_vrip.ply.txt_2000_.txt --format point-cloud --dim 1" - User time (seconds): 40.30 - System time (seconds): 0.32 - Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:40.66 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 257872 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 150721 - Voluntary context switches: 1 - Involuntary context switches: 462 - Swaps: 0 - File system inputs: 0 - File system outputs: 0 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 0 diff --git a/benchmarks/output/dragon-2.ripser.txt b/benchmarks/output/dragon-2.ripser.txt deleted file mode 100644 index 2319b97..0000000 --- a/benchmarks/output/dragon-2.ripser.txt +++ /dev/null @@ -1,23 +0,0 @@ - Command being timed: "ripser dragon_vrip.ply.txt_2000_.txt --format point-cloud --dim 1" - User time (seconds): 1.78 - System time (seconds): 0.19 - Percent of CPU this job got: 91% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:02.14 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 257864 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 150721 - Voluntary context switches: 2 - Involuntary context switches: 337 - Swaps: 0 - File system inputs: 0 - File system outputs: 0 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 0 diff --git a/benchmarks/output/fractal-r.ripser.txt b/benchmarks/output/fractal-r.ripser.txt deleted file mode 100644 index f245ae3..0000000 --- a/benchmarks/output/fractal-r.ripser.txt +++ /dev/null @@ -1,23 +0,0 @@ - Command being timed: "ripser fractal_9_5_2_random_edge_list.txt_0.19795_distmat.txt --dim 2" - User time (seconds): 13.98 - System time (seconds): 1.01 - Percent of CPU this job got: 98% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:15.16 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 1803484 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 768895 - Voluntary context switches: 1 - Involuntary context switches: 1041 - Swaps: 0 - File system inputs: 0 - File system outputs: 0 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 0 diff --git a/benchmarks/output/o3_1024.dipha-multicore.txt b/benchmarks/output/o3_1024.dipha-multicore.txt deleted file mode 100644 index 9f29568..0000000 --- a/benchmarks/output/o3_1024.dipha-multicore.txt +++ /dev/null @@ -1,23 +0,0 @@ - Command being timed: "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" - User time (seconds): 315.48 - System time (seconds): 2.79 - Percent of CPU this job got: 787% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:40.42 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 288828 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 6 - Minor (reclaiming a frame) page faults: 947004 - Voluntary context switches: 6113 - Involuntary context switches: 7400 - Swaps: 0 - File system inputs: 0 - File system outputs: 16560 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 0 diff --git a/benchmarks/output/o3_1024.dipha.txt b/benchmarks/output/o3_1024.dipha.txt deleted file mode 100644 index 59f810a..0000000 --- a/benchmarks/output/o3_1024.dipha.txt +++ /dev/null @@ -1,23 +0,0 @@ - Command being timed: "dipha --dual --benchmark --upper_dim 4 o3_1024_1.8.dipha o3_1024_1.8.dipha.diagram" - User time (seconds): 45.89 - System time (seconds): 1.32 - Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:47.53 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 1412520 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 1413259 - Voluntary context switches: 742 - Involuntary context switches: 393 - Swaps: 0 - File system inputs: 0 - File system outputs: 128 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 0 diff --git a/benchmarks/output/o3_1024.gudhi.txt b/benchmarks/output/o3_1024.gudhi.txt deleted file mode 100644 index 27f1c3e..0000000 --- a/benchmarks/output/o3_1024.gudhi.txt +++ /dev/null @@ -1,23 +0,0 @@ - Command being timed: "gudhi-rips-persistence -d4 -p2 -r 1.8 o3_1024.off" - User time (seconds): 13.51 - System time (seconds): 0.17 - Percent of CPU this job got: 179% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:07.63 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 624828 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 1 - Minor (reclaiming a frame) page faults: 155463 - Voluntary context switches: 116 - Involuntary context switches: 1252 - Swaps: 0 - File system inputs: 232 - File system outputs: 72 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 0 diff --git a/benchmarks/output/o3_1024.ripser-no-emergent.txt b/benchmarks/output/o3_1024.ripser-no-emergent.txt deleted file mode 100644 index 2c2f69a..0000000 --- a/benchmarks/output/o3_1024.ripser-no-emergent.txt +++ /dev/null @@ -1,23 +0,0 @@ - Command being timed: "ripser o3_1024.txt --format point-cloud --dim 3 --threshold 1.8 --ratio 2" - User time (seconds): 5.24 - System time (seconds): 0.10 - Percent of CPU this job got: 100% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:05.32 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 178804 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 60265 - Voluntary context switches: 1 - Involuntary context switches: 48 - Swaps: 0 - File system inputs: 0 - File system outputs: 0 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 0 diff --git a/benchmarks/output/o3_1024.ripser-store-reduced.txt b/benchmarks/output/o3_1024.ripser-store-reduced.txt deleted file mode 100644 index 4fc65cf..0000000 --- a/benchmarks/output/o3_1024.ripser-store-reduced.txt +++ /dev/null @@ -1,23 +0,0 @@ - Command being timed: "ripser o3_1024.txt --format point-cloud --dim 3 --threshold 1.8 --ratio 2" - User time (seconds): 6.50 - System time (seconds): 0.64 - Percent of CPU this job got: 98% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:07.23 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 1239792 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 514672 - Voluntary context switches: 1 - Involuntary context switches: 100 - Swaps: 0 - File system inputs: 0 - File system outputs: 0 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 0 diff --git a/benchmarks/output/o3_1024.ripser-use-reduced.txt b/benchmarks/output/o3_1024.ripser-use-reduced.txt deleted file mode 100644 index c93a2c0..0000000 --- a/benchmarks/output/o3_1024.ripser-use-reduced.txt +++ /dev/null @@ -1,23 +0,0 @@ - Command being timed: "ripser o3_1024.txt --format point-cloud --dim 3 --threshold 1.8 --ratio 2" - User time (seconds): 6.37 - System time (seconds): 0.56 - Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:06.94 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 1239568 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 514607 - Voluntary context switches: 1 - Involuntary context switches: 111 - Swaps: 0 - File system inputs: 0 - File system outputs: 0 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 0 diff --git a/benchmarks/output/o3_1024.ripser.txt b/benchmarks/output/o3_1024.ripser.txt deleted file mode 100644 index 1d2f195..0000000 --- a/benchmarks/output/o3_1024.ripser.txt +++ /dev/null @@ -1,23 +0,0 @@ - Command being timed: "ripser o3_1024.txt --format point-cloud --dim 3 --threshold 1.8 --ratio 2" - User time (seconds): 2.07 - System time (seconds): 0.11 - Percent of CPU this job got: 96% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:02.26 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 178776 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 60267 - Voluntary context switches: 1 - Involuntary context switches: 81 - Swaps: 0 - File system inputs: 0 - File system outputs: 0 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 0 diff --git a/benchmarks/output/o3_4096.gudhi.txt b/benchmarks/output/o3_4096.gudhi.txt deleted file mode 100644 index 876507a..0000000 --- a/benchmarks/output/o3_4096.gudhi.txt +++ /dev/null @@ -1,23 +0,0 @@ - Command being timed: "gudhi-rips-persistence -d4 -p2 -r 1.4 o3_4096.off" - User time (seconds): 675.55 - System time (seconds): 25.12 - Percent of CPU this job got: 198% - Elapsed (wall clock) time (h:mm:ss or m:ss): 5:52.73 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 18652260 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 4663080 - Voluntary context switches: 42 - Involuntary context switches: 12700 - Swaps: 0 - File system inputs: 0 - File system outputs: 296 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 0 diff --git a/benchmarks/output/o3_4096.ripser-no-emergent.txt b/benchmarks/output/o3_4096.ripser-no-emergent.txt deleted file mode 100644 index 4b1ff37..0000000 --- a/benchmarks/output/o3_4096.ripser-no-emergent.txt +++ /dev/null @@ -1,23 +0,0 @@ - Command being timed: "ripser o3_4096.txt --format point-cloud --dim 3 --threshold 1.4 --ratio 2" - User time (seconds): 174.88 - System time (seconds): 2.05 - Percent of CPU this job got: 100% - Elapsed (wall clock) time (h:mm:ss or m:ss): 2:56.88 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 3861344 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 1672013 - Voluntary context switches: 1 - Involuntary context switches: 594 - Swaps: 0 - File system inputs: 0 - File system outputs: 0 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 0 diff --git a/benchmarks/output/o3_4096.ripser.txt b/benchmarks/output/o3_4096.ripser.txt deleted file mode 100644 index 2a5d61e..0000000 --- a/benchmarks/output/o3_4096.ripser.txt +++ /dev/null @@ -1,23 +0,0 @@ - Command being timed: "ripser o3_4096.txt --format point-cloud --dim 3 --threshold 1.4 --ratio 2" - User time (seconds): 60.51 - System time (seconds): 2.02 - Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 1:02.54 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 3861300 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 1672012 - Voluntary context switches: 2 - Involuntary context switches: 434 - Swaps: 0 - File system inputs: 0 - File system outputs: 0 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 0 diff --git a/benchmarks/output/random.ripser-no-emergent.txt b/benchmarks/output/random.ripser-no-emergent.txt deleted file mode 100644 index cfdb8fc..0000000 --- a/benchmarks/output/random.ripser-no-emergent.txt +++ /dev/null @@ -1,23 +0,0 @@ - Command being timed: "ripser random_point_cloud_50_16_.txt --format point-cloud --dim 7" - User time (seconds): 13.82 - System time (seconds): 0.22 - Percent of CPU this job got: 100% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:14.02 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 339084 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 150128 - Voluntary context switches: 2 - Involuntary context switches: 102 - Swaps: 0 - File system inputs: 0 - File system outputs: 0 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 0 diff --git a/benchmarks/output/random.ripser-store-reduced.txt b/benchmarks/output/random.ripser-store-reduced.txt deleted file mode 100644 index efeb5b5..0000000 --- a/benchmarks/output/random.ripser-store-reduced.txt +++ /dev/null @@ -1,23 +0,0 @@ - Command being timed: "ripser random_point_cloud_50_16_.txt --format point-cloud --dim 7" - User time (seconds): 15.99 - System time (seconds): 0.92 - Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:16.92 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 1366796 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 961778 - Voluntary context switches: 1 - Involuntary context switches: 242 - Swaps: 0 - File system inputs: 0 - File system outputs: 0 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 0 diff --git a/benchmarks/output/random.ripser-use-reduced.txt b/benchmarks/output/random.ripser-use-reduced.txt deleted file mode 100644 index d767db9..0000000 --- a/benchmarks/output/random.ripser-use-reduced.txt +++ /dev/null @@ -1,23 +0,0 @@ - Command being timed: "ripser random_point_cloud_50_16_.txt --format point-cloud --dim 7" - User time (seconds): 16.15 - System time (seconds): 1.03 - Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:17.26 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 1366620 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 964013 - Voluntary context switches: 1 - Involuntary context switches: 118 - Swaps: 0 - File system inputs: 0 - File system outputs: 0 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 0 diff --git a/benchmarks/output/random.ripser.txt b/benchmarks/output/random.ripser.txt deleted file mode 100644 index ac9822c..0000000 --- a/benchmarks/output/random.ripser.txt +++ /dev/null @@ -1,23 +0,0 @@ - Command being timed: "ripser random_point_cloud_50_16_.txt --format point-cloud --dim 7" - User time (seconds): 6.25 - System time (seconds): 0.18 - Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:06.43 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 339084 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 150127 - Voluntary context switches: 1 - Involuntary context switches: 62 - Swaps: 0 - File system inputs: 0 - File system outputs: 0 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 0 diff --git a/benchmarks/output/sphere_3_192.ripser-no-emergent.txt b/benchmarks/output/sphere_3_192.ripser-no-emergent.txt deleted file mode 100644 index 37134ce..0000000 --- a/benchmarks/output/sphere_3_192.ripser-no-emergent.txt +++ /dev/null @@ -1,23 +0,0 @@ - Command being timed: "ripser sphere_3_192_points.dat --format point-cloud --dim 2" - User time (seconds): 5.49 - System time (seconds): 0.06 - Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:05.56 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 201136 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 66913 - Voluntary context switches: 1 - Involuntary context switches: 62 - Swaps: 0 - File system inputs: 0 - File system outputs: 0 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 0 diff --git a/benchmarks/output/sphere_3_192.ripser-store-reduced.txt b/benchmarks/output/sphere_3_192.ripser-store-reduced.txt deleted file mode 100644 index 22e6702..0000000 --- a/benchmarks/output/sphere_3_192.ripser-store-reduced.txt +++ /dev/null @@ -1,23 +0,0 @@ - Command being timed: "ripser sphere_3_192_points.dat --format point-cloud --dim 2" - User time (seconds): 13.80 - System time (seconds): 1.77 - Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:15.57 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 4288268 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 1860885 - Voluntary context switches: 1 - Involuntary context switches: 240 - Swaps: 0 - File system inputs: 0 - File system outputs: 0 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 0 diff --git a/benchmarks/output/sphere_3_192.ripser-use-reduced.txt b/benchmarks/output/sphere_3_192.ripser-use-reduced.txt deleted file mode 100644 index 66d80ac..0000000 --- a/benchmarks/output/sphere_3_192.ripser-use-reduced.txt +++ /dev/null @@ -1,23 +0,0 @@ - Command being timed: "ripser sphere_3_192_points.dat --format point-cloud --dim 2" - User time (seconds): 13.58 - System time (seconds): 1.76 - Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:15.34 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 4288276 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 1865102 - Voluntary context switches: 1 - Involuntary context switches: 193 - Swaps: 0 - File system inputs: 0 - File system outputs: 0 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 0 diff --git a/benchmarks/output/sphere_3_192.ripser.txt b/benchmarks/output/sphere_3_192.ripser.txt deleted file mode 100644 index d6f9446..0000000 --- a/benchmarks/output/sphere_3_192.ripser.txt +++ /dev/null @@ -1,23 +0,0 @@ - Command being timed: "ripser sphere_3_192_points.dat --format point-cloud --dim 2" - User time (seconds): 1.04 - System time (seconds): 0.04 - Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:01.08 - Average shared text size (kbytes): 0 - Average unshared data size (kbytes): 0 - Average stack size (kbytes): 0 - Average total size (kbytes): 0 - Maximum resident set size (kbytes): 201136 - Average resident set size (kbytes): 0 - Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 66924 - Voluntary context switches: 1 - Involuntary context switches: 57 - Swaps: 0 - File system inputs: 0 - File system outputs: 0 - Socket messages sent: 0 - Socket messages received: 0 - Signals delivered: 0 - Page size (bytes): 4096 - Exit status: 0 diff --git a/examples/almostlinear4.lower_distance_matrix b/examples/almostlinear4.lower_distance_matrix deleted file mode 100644 index 0992677..0000000 --- a/examples/almostlinear4.lower_distance_matrix +++ /dev/null @@ -1,3 +0,0 @@ -1, -2,1, -1,1.9,1 diff --git a/examples/almostlinear4a.lower_distance_matrix b/examples/almostlinear4a.lower_distance_matrix deleted file mode 100644 index c0e94e6..0000000 --- a/examples/almostlinear4a.lower_distance_matrix +++ /dev/null @@ -1,3 +0,0 @@ -1, -2,1, -3,4,5 diff --git a/examples/almostlinear4b.lower_distance_matrix b/examples/almostlinear4b.lower_distance_matrix deleted file mode 100644 index c990b9b..0000000 --- a/examples/almostlinear4b.lower_distance_matrix +++ /dev/null @@ -1,3 +0,0 @@ -1, -2,1, -3,5,4 diff --git a/examples/almostlinear4c.lower_distance_matrix b/examples/almostlinear4c.lower_distance_matrix deleted file mode 100644 index da2bb0f..0000000 --- a/examples/almostlinear4c.lower_distance_matrix +++ /dev/null @@ -1,3 +0,0 @@ -1, -2,1, -4,3,5 diff --git a/examples/linear5.lower_distance_matrix b/examples/linear5.lower_distance_matrix deleted file mode 100644 index 9a6f670..0000000 --- a/examples/linear5.lower_distance_matrix +++ /dev/null @@ -1,4 +0,0 @@ -1, -2,1, -3,4,5, - diff --git a/examples/test.lower_distance_matrix b/examples/test.lower_distance_matrix deleted file mode 100644 index e1aac02..0000000 --- a/examples/test.lower_distance_matrix +++ /dev/null @@ -1,4 +0,0 @@ -1, -2,3, -4,5,6, -7,8,9,10 diff --git a/examples/test.upper_distance_matrix b/examples/test.upper_distance_matrix deleted file mode 100644 index 274f252..0000000 --- a/examples/test.upper_distance_matrix +++ /dev/null @@ -1,5 +0,0 @@ -1, -3,4 -4,3,1, -3,4,3,1 -1,3,4,3,1 diff --git a/examples/test2.lower_distance_matrix b/examples/test2.lower_distance_matrix deleted file mode 100644 index 4bb81a4..0000000 --- a/examples/test2.lower_distance_matrix +++ /dev/null @@ -1,5 +0,0 @@ -1, -3,1, -4,3,1, -3,4,3,1, -1,3,4,3,1 diff --git a/examples/test2.upper_distance_matrix b/examples/test2.upper_distance_matrix deleted file mode 100644 index 9d4e39e..0000000 --- a/examples/test2.upper_distance_matrix +++ /dev/null @@ -1,5 +0,0 @@ -1,3,4,3,1, - 1,3,4,3, - 1,3,4, - 1,3, - 1 diff --git a/prettyprint.hpp b/prettyprint.hpp deleted file mode 100644 index 6bf2543..0000000 --- a/prettyprint.hpp +++ /dev/null @@ -1,445 +0,0 @@ -// Copyright Louis Delacroix 2010 - 2014. -// Distributed under the Boost Software License, Version 1.0. -// (See accompanying file LICENSE_1_0.txt or copy at -// http://www.boost.org/LICENSE_1_0.txt) -// -// A pretty printing library for C++ -// -// Usage: -// Include this header, and operator<< will "just work". - -#ifndef H_PRETTY_PRINT -#define H_PRETTY_PRINT - -#include <cstddef> -#include <iterator> -#include <memory> -#include <ostream> -#include <set> -#include <tuple> -#include <type_traits> -#include <unordered_set> -#include <utility> -#include <valarray> - -namespace pretty_print -{ - namespace detail - { - // SFINAE type trait to detect whether T::const_iterator exists. - - struct sfinae_base - { - using yes = char; - using no = yes[2]; - }; - - template <typename T> - struct has_const_iterator : private sfinae_base - { - private: - template <typename C> static yes & test(typename C::const_iterator*); - template <typename C> static no & test(...); - public: - static const bool value = sizeof(test<T>(nullptr)) == sizeof(yes); - using type = T; - }; - - template <typename T> - struct has_begin_end : private sfinae_base - { - private: - template <typename C> - static yes & f(typename std::enable_if< - std::is_same<decltype(static_cast<typename C::const_iterator(C::*)() const>(&C::begin)), - typename C::const_iterator(C::*)() const>::value>::type *); - - template <typename C> static no & f(...); - - template <typename C> - static yes & g(typename std::enable_if< - std::is_same<decltype(static_cast<typename C::const_iterator(C::*)() const>(&C::end)), - typename C::const_iterator(C::*)() const>::value, void>::type*); - - template <typename C> static no & g(...); - - public: - static bool const beg_value = sizeof(f<T>(nullptr)) == sizeof(yes); - static bool const end_value = sizeof(g<T>(nullptr)) == sizeof(yes); - }; - - } // namespace detail - - - // Holds the delimiter values for a specific character type - - template <typename TChar> - struct delimiters_values - { - using char_type = TChar; - const char_type * prefix; - const char_type * delimiter; - const char_type * postfix; - }; - - - // Defines the delimiter values for a specific container and character type - - template <typename T, typename TChar> - struct delimiters - { - using type = delimiters_values<TChar>; - static const type values; - }; - - - // Functor to print containers. You can use this directly if you want - // to specificy a non-default delimiters type. The printing logic can - // be customized by specializing the nested template. - - template <typename T, - typename TChar = char, - typename TCharTraits = ::std::char_traits<TChar>, - typename TDelimiters = delimiters<T, TChar>> - struct print_container_helper - { - using delimiters_type = TDelimiters; - using ostream_type = std::basic_ostream<TChar, TCharTraits>; - - template <typename U> - struct printer - { - static void print_body(const U & c, ostream_type & stream) - { - using std::begin; - using std::end; - - auto it = begin(c); - const auto the_end = end(c); - - if (it != the_end) - { - for ( ; ; ) - { - stream << *it; - - if (++it == the_end) break; - - if (delimiters_type::values.delimiter != NULL) - stream << delimiters_type::values.delimiter; - } - } - } - }; - - print_container_helper(const T & container) - : container_(container) - { } - - inline void operator()(ostream_type & stream) const - { - if (delimiters_type::values.prefix != NULL) - stream << delimiters_type::values.prefix; - - printer<T>::print_body(container_, stream); - - if (delimiters_type::values.postfix != NULL) - stream << delimiters_type::values.postfix; - } - - private: - const T & container_; - }; - - // Specialization for pairs - - template <typename T, typename TChar, typename TCharTraits, typename TDelimiters> - template <typename T1, typename T2> - struct print_container_helper<T, TChar, TCharTraits, TDelimiters>::printer<std::pair<T1, T2>> - { - using ostream_type = print_container_helper<T, TChar, TCharTraits, TDelimiters>::ostream_type; - - static void print_body(const std::pair<T1, T2> & c, ostream_type & stream) - { - stream << c.first; - if (print_container_helper<T, TChar, TCharTraits, TDelimiters>::delimiters_type::values.delimiter != NULL) - stream << print_container_helper<T, TChar, TCharTraits, TDelimiters>::delimiters_type::values.delimiter; - stream << c.second; - } - }; - - // Specialization for tuples - - template <typename T, typename TChar, typename TCharTraits, typename TDelimiters> - template <typename ...Args> - struct print_container_helper<T, TChar, TCharTraits, TDelimiters>::printer<std::tuple<Args...>> - { - using ostream_type = print_container_helper<T, TChar, TCharTraits, TDelimiters>::ostream_type; - using element_type = std::tuple<Args...>; - - template <std::size_t I> struct Int { }; - - static void print_body(const element_type & c, ostream_type & stream) - { - tuple_print(c, stream, Int<0>()); - } - - static void tuple_print(const element_type &, ostream_type &, Int<sizeof...(Args)>) - { - } - - static void tuple_print(const element_type & c, ostream_type & stream, - typename std::conditional<sizeof...(Args) != 0, Int<0>, std::nullptr_t>::type) - { - stream << std::get<0>(c); - tuple_print(c, stream, Int<1>()); - } - - template <std::size_t N> - static void tuple_print(const element_type & c, ostream_type & stream, Int<N>) - { - if (print_container_helper<T, TChar, TCharTraits, TDelimiters>::delimiters_type::values.delimiter != NULL) - stream << print_container_helper<T, TChar, TCharTraits, TDelimiters>::delimiters_type::values.delimiter; - - stream << std::get<N>(c); - - tuple_print(c, stream, Int<N + 1>()); - } - }; - - // Prints a print_container_helper to the specified stream. - - template<typename T, typename TChar, typename TCharTraits, typename TDelimiters> - inline std::basic_ostream<TChar, TCharTraits> & operator<<( - std::basic_ostream<TChar, TCharTraits> & stream, - const print_container_helper<T, TChar, TCharTraits, TDelimiters> & helper) - { - helper(stream); - return stream; - } - - - // Basic is_container template; specialize to derive from std::true_type for all desired container types - - template <typename T> - struct is_container : public std::integral_constant<bool, - detail::has_const_iterator<T>::value && - detail::has_begin_end<T>::beg_value && - detail::has_begin_end<T>::end_value> { }; - - template <typename T, std::size_t N> - struct is_container<T[N]> : std::true_type { }; - - template <std::size_t N> - struct is_container<char[N]> : std::false_type { }; - - template <typename T> - struct is_container<std::valarray<T>> : std::true_type { }; - - template <typename T1, typename T2> - struct is_container<std::pair<T1, T2>> : std::true_type { }; - - template <typename ...Args> - struct is_container<std::tuple<Args...>> : std::true_type { }; - - - // Default delimiters - - template <typename T> struct delimiters<T, char> { static const delimiters_values<char> values; }; - template <typename T> const delimiters_values<char> delimiters<T, char>::values = { "[", ", ", "]" }; - template <typename T> struct delimiters<T, wchar_t> { static const delimiters_values<wchar_t> values; }; - template <typename T> const delimiters_values<wchar_t> delimiters<T, wchar_t>::values = { L"[", L", ", L"]" }; - - - // Delimiters for (multi)set and unordered_(multi)set - - template <typename T, typename TComp, typename TAllocator> - struct delimiters< ::std::set<T, TComp, TAllocator>, char> { static const delimiters_values<char> values; }; - - template <typename T, typename TComp, typename TAllocator> - const delimiters_values<char> delimiters< ::std::set<T, TComp, TAllocator>, char>::values = { "{", ", ", "}" }; - - template <typename T, typename TComp, typename TAllocator> - struct delimiters< ::std::set<T, TComp, TAllocator>, wchar_t> { static const delimiters_values<wchar_t> values; }; - - template <typename T, typename TComp, typename TAllocator> - const delimiters_values<wchar_t> delimiters< ::std::set<T, TComp, TAllocator>, wchar_t>::values = { L"{", L", ", L"}" }; - - template <typename T, typename TComp, typename TAllocator> - struct delimiters< ::std::multiset<T, TComp, TAllocator>, char> { static const delimiters_values<char> values; }; - - template <typename T, typename TComp, typename TAllocator> - const delimiters_values<char> delimiters< ::std::multiset<T, TComp, TAllocator>, char>::values = { "{", ", ", "}" }; - - template <typename T, typename TComp, typename TAllocator> - struct delimiters< ::std::multiset<T, TComp, TAllocator>, wchar_t> { static const delimiters_values<wchar_t> values; }; - - template <typename T, typename TComp, typename TAllocator> - const delimiters_values<wchar_t> delimiters< ::std::multiset<T, TComp, TAllocator>, wchar_t>::values = { L"{", L", ", L"}" }; - - template <typename T, typename THash, typename TEqual, typename TAllocator> - struct delimiters< ::std::unordered_set<T, THash, TEqual, TAllocator>, char> { static const delimiters_values<char> values; }; - - template <typename T, typename THash, typename TEqual, typename TAllocator> - const delimiters_values<char> delimiters< ::std::unordered_set<T, THash, TEqual, TAllocator>, char>::values = { "{", ", ", "}" }; - - template <typename T, typename THash, typename TEqual, typename TAllocator> - struct delimiters< ::std::unordered_set<T, THash, TEqual, TAllocator>, wchar_t> { static const delimiters_values<wchar_t> values; }; - - template <typename T, typename THash, typename TEqual, typename TAllocator> - const delimiters_values<wchar_t> delimiters< ::std::unordered_set<T, THash, TEqual, TAllocator>, wchar_t>::values = { L"{", L", ", L"}" }; - - template <typename T, typename THash, typename TEqual, typename TAllocator> - struct delimiters< ::std::unordered_multiset<T, THash, TEqual, TAllocator>, char> { static const delimiters_values<char> values; }; - - template <typename T, typename THash, typename TEqual, typename TAllocator> - const delimiters_values<char> delimiters< ::std::unordered_multiset<T, THash, TEqual, TAllocator>, char>::values = { "{", ", ", "}" }; - - template <typename T, typename THash, typename TEqual, typename TAllocator> - struct delimiters< ::std::unordered_multiset<T, THash, TEqual, TAllocator>, wchar_t> { static const delimiters_values<wchar_t> values; }; - - template <typename T, typename THash, typename TEqual, typename TAllocator> - const delimiters_values<wchar_t> delimiters< ::std::unordered_multiset<T, THash, TEqual, TAllocator>, wchar_t>::values = { L"{", L", ", L"}" }; - - - // Delimiters for pair and tuple - - template <typename T1, typename T2> struct delimiters<std::pair<T1, T2>, char> { static const delimiters_values<char> values; }; - template <typename T1, typename T2> const delimiters_values<char> delimiters<std::pair<T1, T2>, char>::values = { "(", ", ", ")" }; - template <typename T1, typename T2> struct delimiters< ::std::pair<T1, T2>, wchar_t> { static const delimiters_values<wchar_t> values; }; - template <typename T1, typename T2> const delimiters_values<wchar_t> delimiters< ::std::pair<T1, T2>, wchar_t>::values = { L"(", L", ", L")" }; - - template <typename ...Args> struct delimiters<std::tuple<Args...>, char> { static const delimiters_values<char> values; }; - template <typename ...Args> const delimiters_values<char> delimiters<std::tuple<Args...>, char>::values = { "(", ", ", ")" }; - template <typename ...Args> struct delimiters< ::std::tuple<Args...>, wchar_t> { static const delimiters_values<wchar_t> values; }; - template <typename ...Args> const delimiters_values<wchar_t> delimiters< ::std::tuple<Args...>, wchar_t>::values = { L"(", L", ", L")" }; - - - // Type-erasing helper class for easy use of custom delimiters. - // Requires TCharTraits = std::char_traits<TChar> and TChar = char or wchar_t, and MyDelims needs to be defined for TChar. - // Usage: "cout << pretty_print::custom_delims<MyDelims>(x)". - - struct custom_delims_base - { - virtual ~custom_delims_base() { } - virtual std::ostream & stream(::std::ostream &) = 0; - virtual std::wostream & stream(::std::wostream &) = 0; - }; - - template <typename T, typename Delims> - struct custom_delims_wrapper : custom_delims_base - { - custom_delims_wrapper(const T & t_) : t(t_) { } - - std::ostream & stream(std::ostream & s) - { - return s << print_container_helper<T, char, std::char_traits<char>, Delims>(t); - } - - std::wostream & stream(std::wostream & s) - { - return s << print_container_helper<T, wchar_t, std::char_traits<wchar_t>, Delims>(t); - } - - private: - const T & t; - }; - - template <typename Delims> - struct custom_delims - { - template <typename Container> - custom_delims(const Container & c) : base(new custom_delims_wrapper<Container, Delims>(c)) { } - - std::unique_ptr<custom_delims_base> base; - }; - - template <typename TChar, typename TCharTraits, typename Delims> - inline std::basic_ostream<TChar, TCharTraits> & operator<<(std::basic_ostream<TChar, TCharTraits> & s, const custom_delims<Delims> & p) - { - return p.base->stream(s); - } - - - // A wrapper for a C-style array given as pointer-plus-size. - // Usage: std::cout << pretty_print_array(arr, n) << std::endl; - - template<typename T> - struct array_wrapper_n - { - typedef const T * const_iterator; - typedef T value_type; - - array_wrapper_n(const T * const a, size_t n) : _array(a), _n(n) { } - inline const_iterator begin() const { return _array; } - inline const_iterator end() const { return _array + _n; } - - private: - const T * const _array; - size_t _n; - }; - - - // A wrapper for hash-table based containers that offer local iterators to each bucket. - // Usage: std::cout << bucket_print(m, 4) << std::endl; (Prints bucket 5 of container m.) - - template <typename T> - struct bucket_print_wrapper - { - typedef typename T::const_local_iterator const_iterator; - typedef typename T::size_type size_type; - - const_iterator begin() const - { - return m_map.cbegin(n); - } - - const_iterator end() const - { - return m_map.cend(n); - } - - bucket_print_wrapper(const T & m, size_type bucket) : m_map(m), n(bucket) { } - - private: - const T & m_map; - const size_type n; - }; - -} // namespace pretty_print - - -// Global accessor functions for the convenience wrappers - -template<typename T> -inline pretty_print::array_wrapper_n<T> pretty_print_array(const T * const a, size_t n) -{ - return pretty_print::array_wrapper_n<T>(a, n); -} - -template <typename T> pretty_print::bucket_print_wrapper<T> -bucket_print(const T & m, typename T::size_type n) -{ - return pretty_print::bucket_print_wrapper<T>(m, n); -} - - -// Main magic entry point: An overload snuck into namespace std. -// Can we do better? - -namespace std -{ - // Prints a container to the stream using default delimiters - - template<typename T, typename TChar, typename TCharTraits> - inline typename enable_if< ::pretty_print::is_container<T>::value, - basic_ostream<TChar, TCharTraits> &>::type - operator<<(basic_ostream<TChar, TCharTraits> & stream, const T & container) - { - return stream << ::pretty_print::print_container_helper<T, TChar, TCharTraits>(container); - } -} - - - -#endif // H_PRETTY_PRINT @@ -962,10 +962,15 @@ enum file_format { BINARY }; +static const uint16_t endian_check(0xff00); +static const bool is_big_endian = *reinterpret_cast<const uint8_t*>(&endian_check); + template <typename T> T read(std::istream& input_stream) { T result; - input_stream.read(reinterpret_cast<char*>(&result), sizeof(T)); - return result; // on little endian: boost::endian::little_to_native(result); + char* p = reinterpret_cast<char*>(&result); + if (input_stream.read(p, sizeof(T)).gcount() != sizeof(T)) return T(); + if (is_big_endian) std::reverse(p, p + sizeof(T)); + return result; } compressed_lower_distance_matrix read_point_cloud(std::istream& input_stream) { diff --git a/ripser.xcodeproj/project.pbxproj b/ripser.xcodeproj/project.pbxproj deleted file mode 100644 index 316b1b2..0000000 --- a/ripser.xcodeproj/project.pbxproj +++ /dev/null @@ -1,276 +0,0 @@ -// !$*UTF8*$! -{ - archiveVersion = 1; - classes = { - }; - objectVersion = 46; - objects = { - -/* Begin PBXBuildFile section */ - 55E113311BD63CF3002B6F51 /* ripser.cpp in Sources */ = {isa = PBXBuildFile; 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