From 93b0e7c84f936ad65152339af07c3ecbb2fd5a8a Mon Sep 17 00:00:00 2001 From: Ulrich Bauer Date: Sun, 11 Aug 2019 16:24:15 +0200 Subject: benchmark moved to repository "ripser-benchmark" --- benchmarks/sphere_3_64/dionysus.txt | 28 ------- benchmarks/sphere_3_64/dipha.txt | 58 --------------- benchmarks/sphere_3_64/gudhi.txt | 18 ----- benchmarks/sphere_3_64/phat.txt | 17 ----- benchmarks/sphere_3_64/ripser.txt | 103 -------------------------- benchmarks/sphere_3_64/sphere_3_64_points.dat | 64 ---------------- 6 files changed, 288 deletions(-) delete mode 100644 benchmarks/sphere_3_64/dionysus.txt delete mode 100644 benchmarks/sphere_3_64/dipha.txt delete mode 100644 benchmarks/sphere_3_64/gudhi.txt delete mode 100644 benchmarks/sphere_3_64/phat.txt delete mode 100644 benchmarks/sphere_3_64/ripser.txt delete mode 100644 benchmarks/sphere_3_64/sphere_3_64_points.dat (limited to 'benchmarks/sphere_3_64') diff --git a/benchmarks/sphere_3_64/dionysus.txt b/benchmarks/sphere_3_64/dionysus.txt deleted file mode 100644 index 52b879d..0000000 --- a/benchmarks/sphere_3_64/dionysus.txt +++ /dev/null @@ -1,28 +0,0 @@ -uli:Dionysus uli$ /usr/bin/time -l ~/Source/Dionysus/examples/cohomology/rips-pairwise-cohomology -s3 -p2 ~/Bitbucket/phat-paper/benchmark/point\ cloud/sphere_3_64_points.dat -Boundary matrix: -Cocycles: *.ccl -Vertices: -Diagram: -Simplex vector generated, size: 679120 - -0% 10 20 30 40 50 60 70 80 90 100% -|----|----|----|----|----|----|----|----|----|----| -*************************************************** -Rips timer : Elapsed time [3.01] seconds -Persistence timer : Elapsed time [1.98] seconds -Total timer : Elapsed time [5.85] seconds - 5.94 real 5.85 user 0.05 sys - 76812288 maximum resident set size - 0 average shared memory size - 0 average unshared data size - 0 average unshared stack size - 18766 page reclaims - 0 page faults - 0 swaps - 0 block input operations - 0 block output operations - 0 messages sent - 0 messages received - 0 signals received - 0 voluntary context switches - 2160 involuntary context switches diff --git a/benchmarks/sphere_3_64/dipha.txt b/benchmarks/sphere_3_64/dipha.txt deleted file mode 100644 index 67534d6..0000000 --- a/benchmarks/sphere_3_64/dipha.txt +++ /dev/null @@ -1,58 +0,0 @@ -uli:dipha uli$ /usr/bin/time -l ~/Bitbucket/dipha/dipha --benchmark --upper_dim 3 --dual ~/Bitbucket/phat-paper/benchmark/dipha/sphere_3_64.complex /dev/null - -Input filename: -/Users/uli/Bitbucket/phat-paper/benchmark/dipha/sphere_3_64.complex - -upper_dim: 3 - -Number of processes used: -1 - -Detailed information for rank 0: - time prior mem peak mem bytes recv - 0.0s 3 MB 3 MB 0 MB complex.load_binary( input_filename, upper_dim ); - -Number of cells in input: -679120 - 0.2s 3 MB 24 MB 0 MB get_filtration_to_cell_map( complex, dualize, filtration_to_cell_map ); - 0.1s 24 MB 69 MB 10 MB get_cell_to_filtration_map( complex.get_num_cells(), filtration_to_cell_map, cell_to_filtration_map ); - 0.0s 84 MB 85 MB 0 MB generate_unreduced_columns( complex, filtration_to_cell_map, cell_to_filtration_map, cur_dim, dualize, unreduced_columns ); - 0.0s 85 MB 85 MB 0 MB reduction_kernel( complex.get_num_cells(), unreduced_columns, reduced_columns ); - 0.0s 85 MB 88 MB 1 MB generate_unreduced_columns( complex, filtration_to_cell_map, cell_to_filtration_map, cur_dim, dualize, unreduced_columns ); - 0.0s 88 MB 89 MB 0 MB reduction_kernel( complex.get_num_cells(), unreduced_columns, reduced_columns ); - 0.3s 89 MB 122 MB 38 MB generate_unreduced_columns( complex, filtration_to_cell_map, cell_to_filtration_map, cur_dim, dualize, unreduced_columns ); - 0.1s 102 MB 142 MB 0 MB reduction_kernel( complex.get_num_cells(), unreduced_columns, reduced_columns ); - 0.1s 141 MB 142 MB 3 MB dipha::outputs::save_persistence_diagram( output_filename, complex, filtration_to_cell_map, reduced_columns, dualize, upper_dim ); - -Overall running time in seconds: -0.8 - -Reduction kernel running time in seconds: -0.1 - -Overall peak mem in GB of all ranks: -0.1 - -Individual peak mem in GB of per rank: -0.1 - -Maximal communication traffic (without sorting) in GB between any pair of nodes: -0.1 - -Total communication traffic (without sorting) in GB between all pairs of nodes: -0.1 - 0.81 real 0.65 user 0.13 sys - 149577728 maximum resident set size - 0 average shared memory size - 0 average unshared data size - 0 average unshared stack size - 51467 page reclaims - 0 page faults - 0 swaps - 0 block input operations - 1 block output operations - 0 messages sent - 0 messages received - 0 signals received - 7 voluntary context switches - 1069 involuntary context switches diff --git a/benchmarks/sphere_3_64/gudhi.txt b/benchmarks/sphere_3_64/gudhi.txt deleted file mode 100644 index ee69c4a..0000000 --- a/benchmarks/sphere_3_64/gudhi.txt +++ /dev/null @@ -1,18 +0,0 @@ -uli:Gudhi_library_1.3.0 uli$ /usr/bin/time -l ~/Source/Gudhi_library_1.3.0/example/Persistent_cohomology/rips_persistence -d3 -p2 ~/Bitbucket/phat-paper/benchmark/point\ cloud/sphere_3_64_points.dat -o/dev/null -The complex contains 679120 simplices - and has dimension 3 - 0.45 real 0.75 user 0.02 sys - 37740544 maximum resident set size - 0 average shared memory size - 0 average unshared data size - 0 average unshared stack size - 9124 page reclaims - 122 page faults - 0 swaps - 1 block input operations - 0 block output operations - 0 messages sent - 0 messages received - 0 signals received - 14 voluntary context switches - 2324 involuntary context switches diff --git a/benchmarks/sphere_3_64/phat.txt b/benchmarks/sphere_3_64/phat.txt deleted file mode 100644 index 40c18fe..0000000 --- a/benchmarks/sphere_3_64/phat.txt +++ /dev/null @@ -1,17 +0,0 @@ -uli:phat uli$ /usr/bin/time -l ~/Bitbucket/phat/benchmark --primal --bit_tree_pivot_column --twist ~/Bitbucket/phat-paper/benchmark/phat/sphere_3_64_coboundary.phat -/Users/uli/Bitbucket/phat-paper/benchmark/phat/sphere_3_64_coboundary.phat, bit_tree_pivot_column, twist, primal, Reduction time: 0.019s - 0.22 real 0.15 user 0.04 sys - 47742976 maximum resident set size - 0 average shared memory size - 0 average unshared data size - 0 average unshared stack size - 11669 page reclaims - 2 page faults - 0 swaps - 2 block input operations - 0 block output operations - 0 messages sent - 0 messages received - 0 signals received - 4 voluntary context switches - 106 involuntary context switches diff --git a/benchmarks/sphere_3_64/ripser.txt b/benchmarks/sphere_3_64/ripser.txt deleted file mode 100644 index 761403c..0000000 --- a/benchmarks/sphere_3_64/ripser.txt +++ /dev/null @@ -1,103 +0,0 @@ -uli:ripser uli$ c++ -std=c++11 ripser.cpp -o ripser -Ofast -D NDEBUG -D FILE_FORMAT_DIPHA -D PRINT_PERSISTENCE_PAIRS && /usr/bin/time -l ./ripser --dim 2 ~/Bitbucket/phat-paper/benchmark/dipha/sphere_3_64.complex -distance matrix with 64 points -distance matrix transformed to lower triangular form -value range: [0.00391946,1.99927] -persistence intervals in dim 0: - [0,0.147289) - [0,0.111798) - [0,0.279354) - [0,0.379849) - [0,0.217485) - [0,0.179609) - [0,0.297053) - [0,0.227524) - [0,0.334523) - [0,0.205129) - [0,0.266643) - [0,0.076909) - [0,0.424333) - [0,0.0802451) - [0,0.141103) - [0,0.154095) - [0,0.280747) - [0,0.561426) - [0,0.255364) - [0,0.218561) - [0,0.344005) - [0,0.457212) - [0,0.339394) - [0,0.184757) - [0,0.193804) - [0,0.276431) - [0,0.276383) - [0,0.273482) - [0,0.162738) - [0,0.208851) - [0,0.00391946) - [0,0.168587) - [0,0.231288) - [0,0.370337) - [0,0.151879) - [0,0.336643) - [0,0.176636) - [0,0.0814685) - [0,0.287316) - [0,0.0633425) - [0,0.46675) - [0,0.169115) - [0,0.387245) - [0,0.354112) - [0,0.236525) - [0,0.377019) - [0,0.396994) - [0,0.58991) - [0,0.374531) - [0,0.374138) - [0,0.439977) - [0,0.487279) - [0,0.231179) - [0,0.200333) - [0,0.401576) - [0,0.574945) - [0,0.252863) - [0,0.173684) - [0,0.284319) - [0,0.355419) - [0,0.23879) - [0,0.381084) - [0,0.532104) - [0, ) -persistence intervals in dim 1: - [0.84172,1.04196) - [0.763446,0.863406) - [0.727244,0.74155) - [0.708398,0.757279) - [0.655113,0.849319) - [0.62495,0.753672) - [0.60904,0.682559) - [0.607973,0.672219) - [0.606907,0.829538) - [0.588045,1.04527) - [0.57698,0.769491) - [0.559498,0.586113) - [0.525224,0.645181) - [0.445398,0.448892) - [0.412572,0.478334) - [0.376457,0.63549) -persistence intervals in dim 2: - [1.10328,1.67029) - 0.05 real 0.05 user 0.00 sys - 4300800 maximum resident set size - 0 average shared memory size - 0 average unshared data size - 0 average unshared stack size - 1054 page reclaims - 9 page faults - 0 swaps - 0 block input operations - 0 block output operations - 0 messages sent - 0 messages received - 0 signals received - 1 voluntary context switches - 10 involuntary context switches diff --git a/benchmarks/sphere_3_64/sphere_3_64_points.dat b/benchmarks/sphere_3_64/sphere_3_64_points.dat deleted file mode 100644 index f2e07c2..0000000 --- a/benchmarks/sphere_3_64/sphere_3_64_points.dat +++ /dev/null @@ -1,64 +0,0 @@ - 1.6967853e-001 6.9526921e-001 -6.9843391e-001 - 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