From f2951f267f966718f6c56cc067aa598a9bb132b7 Mon Sep 17 00:00:00 2001 From: Ulrich Bauer Date: Sat, 21 May 2016 17:57:56 +0200 Subject: benchmarks --- benchmarks/sphere_3_192/dionysus.txt | 28 ++++ benchmarks/sphere_3_192/dipha.txt | 58 ++++++++ benchmarks/sphere_3_192/gudhi.txt | 18 +++ benchmarks/sphere_3_192/phat.txt | 17 +++ benchmarks/sphere_3_192/ripser.txt | 268 +++++++++++++++++++++++++++++++++++ 5 files changed, 389 insertions(+) create mode 100644 benchmarks/sphere_3_192/dionysus.txt create mode 100644 benchmarks/sphere_3_192/dipha.txt create mode 100644 benchmarks/sphere_3_192/gudhi.txt create mode 100644 benchmarks/sphere_3_192/phat.txt create mode 100644 benchmarks/sphere_3_192/ripser.txt (limited to 'benchmarks/sphere_3_192') diff --git a/benchmarks/sphere_3_192/dionysus.txt b/benchmarks/sphere_3_192/dionysus.txt new file mode 100644 index 0000000..56e23d1 --- /dev/null +++ b/benchmarks/sphere_3_192/dionysus.txt @@ -0,0 +1,28 @@ +uli:Dionysus uli$ /usr/bin/time -l ~/Source/Dionysus/examples/cohomology/rips-pairwise-cohomology -s3 -p2 ~/Bitbucket/phat-paper/benchmark/point\ cloud/sphere_3_192_points.dat +Boundary matrix: +Cocycles: *.ccl +Vertices: +Diagram: +Simplex vector generated, size: 56050288 + +0% 10 20 30 40 50 60 70 80 90 100% +|----|----|----|----|----|----|----|----|----|----| +*************************************************** +Rips timer : Elapsed time [393.20] seconds +Persistence timer : Elapsed time [322.41] seconds +Total timer : Elapsed time [807.98] seconds + 843.40 real 787.80 user 26.13 sys +3240779776 maximum resident set size + 0 average shared memory size + 0 average unshared data size + 0 average unshared stack size + 4808144 page reclaims + 0 page faults + 0 swaps + 11 block input operations + 0 block output operations + 0 messages sent + 0 messages received + 0 signals received + 11585 voluntary context switches + 691823 involuntary context switches diff --git a/benchmarks/sphere_3_192/dipha.txt b/benchmarks/sphere_3_192/dipha.txt new file mode 100644 index 0000000..38cc112 --- /dev/null +++ b/benchmarks/sphere_3_192/dipha.txt @@ -0,0 +1,58 @@ +uli:dipha uli$ /usr/bin/time -l ~/Bitbucket/dipha/dipha --benchmark --upper_dim 3 --dual ~/Bitbucket/phat-paper/benchmark/dipha/sphere_3_192.complex /dev/null + +Input filename: +/Users/uli/Bitbucket/phat-paper/benchmark/dipha/sphere_3_192.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 4 MB 0 MB complex.load_binary( input_filename, upper_dim ); + +Number of cells in input: +56050288 + 20.1s 4 MB 1714 MB 0 MB get_filtration_to_cell_map( complex, dualize, filtration_to_cell_map ); + 11.5s 431 MB 2756 MB 855 MB get_cell_to_filtration_map( complex.get_num_cells(), filtration_to_cell_map, cell_to_filtration_map ); + 1.9s 1713 MB 2756 MB 0 MB generate_unreduced_columns( complex, filtration_to_cell_map, cell_to_filtration_map, cur_dim, dualize, unreduced_columns ); + 0.0s 2144 MB 2756 MB 0 MB reduction_kernel( complex.get_num_cells(), unreduced_columns, reduced_columns ); + 1.7s 2145 MB 2756 MB 53 MB generate_unreduced_columns( complex, filtration_to_cell_map, cell_to_filtration_map, cur_dim, dualize, unreduced_columns ); + 0.1s 2226 MB 2756 MB 0 MB reduction_kernel( complex.get_num_cells(), unreduced_columns, reduced_columns ); + 35.9s 2244 MB 2809 MB 3349 MB generate_unreduced_columns( complex, filtration_to_cell_map, cell_to_filtration_map, cur_dim, dualize, unreduced_columns ); + 17.1s 1359 MB 2809 MB 0 MB reduction_kernel( complex.get_num_cells(), unreduced_columns, reduced_columns ); + 14.9s 943 MB 3638 MB 106 MB dipha::outputs::save_persistence_diagram( output_filename, complex, filtration_to_cell_map, reduced_columns, dualize, upper_dim ); + +Overall running time in seconds: +104.5 + +Reduction kernel running time in seconds: +17.2 + +Overall peak mem in GB of all ranks: +3.6 + +Individual peak mem in GB of per rank: +3.6 + +Maximal communication traffic (without sorting) in GB between any pair of nodes: +4.3 + +Total communication traffic (without sorting) in GB between all pairs of nodes: +4.3 + 104.51 real 71.06 user 25.97 sys +3815686144 maximum resident set size + 0 average shared memory size + 0 average unshared data size + 0 average unshared stack size + 8788553 page reclaims + 0 page faults + 0 swaps + 0 block input operations + 4 block output operations + 0 messages sent + 0 messages received + 0 signals received + 2337 voluntary context switches + 238131 involuntary context switches diff --git a/benchmarks/sphere_3_192/gudhi.txt b/benchmarks/sphere_3_192/gudhi.txt new file mode 100644 index 0000000..87763c8 --- /dev/null +++ b/benchmarks/sphere_3_192/gudhi.txt @@ -0,0 +1,18 @@ +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_192_points.dat -o/dev/null +The complex contains 56050288 simplices + and has dimension 3 + 71.98 real 120.27 user 5.86 sys +2905890816 maximum resident set size + 0 average shared memory size + 0 average unshared data size + 0 average unshared stack size + 1535169 page reclaims + 129 page faults + 0 swaps + 0 block input operations + 0 block output operations + 0 messages sent + 0 messages received + 0 signals received + 1957 voluntary context switches + 168798 involuntary context switches diff --git a/benchmarks/sphere_3_192/phat.txt b/benchmarks/sphere_3_192/phat.txt new file mode 100644 index 0000000..3ebcfff --- /dev/null +++ b/benchmarks/sphere_3_192/phat.txt @@ -0,0 +1,17 @@ +uli:phat uli$ /usr/bin/time -l ~/Bitbucket/phat/benchmark --primal --bit_tree_pivot_column --twist ~/Bitbucket/phat-paper/benchmark/sphere_3_192_coboundary.phat +/Users/uli/Bitbucket/phat-paper/benchmark/sphere_3_192_coboundary.phat, bit_tree_pivot_column, twist, primal, Reduction time: 2.649s + 16.91 real 12.22 user 4.38 sys +3742277632 maximum resident set size + 0 average shared memory size + 0 average unshared data size + 0 average unshared stack size + 1568913 page reclaims + 8 page faults + 0 swaps + 10 block input operations + 0 block output operations + 0 messages sent + 0 messages received + 0 signals received + 20 voluntary context switches + 13471 involuntary context switches diff --git a/benchmarks/sphere_3_192/ripser.txt b/benchmarks/sphere_3_192/ripser.txt new file mode 100644 index 0000000..60b7939 --- /dev/null +++ b/benchmarks/sphere_3_192/ripser.txt @@ -0,0 +1,268 @@ +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 --top_dim 2 ~/Bitbucket/phat-paper/benchmark/dipha/sphere_3_192.complex +distance matrix with 192 points +distance matrix transformed to lower triangular form +value range: [0.00367531,2] +persistence intervals in dim 0: + [0,0.145018) + [0,0.0831521) + [0,0.115939) + [0,0.202564) + [0,0.0217315) + [0,0.127383) + [0,0.0387451) + [0,0.0623736) + [0,0.282169) + [0,0.126595) + [0,0.195722) + [0,0.0792212) + [0,0.149226) + [0,0.2286) + [0,0.197377) + [0,0.0651112) + [0,0.138674) + [0,0.147427) + [0,0.124774) + [0,0.293466) + [0,0.17493) + [0,0.131438) + [0,0.151643) + [0,0.208063) + [0,0.129741) + [0,0.127864) + [0,0.131638) + [0,0.0959033) + [0,0.150747) + [0,0.119187) + [0,0.0870489) + [0,0.165592) + [0,0.121955) + [0,0.1569) + [0,0.0433426) + [0,0.280629) + [0,0.0487061) + [0,0.0746054) + [0,0.0728647) + [0,0.0471186) + [0,0.0988752) + [0,0.111131) + [0,0.141823) + [0,0.249345) + [0,0.283881) + [0,0.0522132) + [0,0.157293) + [0,0.0496187) + [0,0.143151) + [0,0.135402) + [0,0.192733) + [0,0.057488) + [0,0.0311057) + [0,0.159282) + [0,0.109526) + [0,0.234112) + [0,0.084341) + [0,0.0593071) + [0,0.133033) + [0,0.240632) + [0,0.248879) + [0,0.134886) + [0,0.228917) + [0,0.249339) + [0,0.204544) + [0,0.048826) + [0,0.143085) + [0,0.231675) + [0,0.191661) + [0,0.0637053) + [0,0.0560443) + [0,0.142537) + [0,0.00367531) + [0,0.257997) + [0,0.037954) + [0,0.204208) + [0,0.201961) + [0,0.215759) + [0,0.162464) + [0,0.0692368) + [0,0.145725) + [0,0.205389) + [0,0.203812) + [0,0.15587) + [0,0.123527) + [0,0.108768) + [0,0.165314) + [0,0.0782455) + [0,0.0173134) + [0,0.176306) + [0,0.0741239) + [0,0.0831358) + [0,0.266592) + [0,0.0515157) + [0,0.223232) + [0,0.0120098) + [0,0.122089) + [0,0.147203) + [0,0.283562) + [0,0.304062) + [0,0.253227) + [0,0.164809) + [0,0.149017) + [0,0.133525) + [0,0.237571) + [0,0.0743236) + [0,0.0672609) + [0,0.218526) + [0,0.0559886) + [0,0.165907) + [0,0.0800348) + [0,0.192356) + [0,0.164815) + [0,0.142834) + [0,0.174172) + [0,0.0714516) + [0,0.227933) + [0,0.0702075) + [0,0.18428) + [0,0.0970981) + [0,0.133722) + [0,0.0753955) + [0,0.0884133) + [0,0.15244) + [0,0.157373) + [0,0.234969) + [0,0.173412) + [0,0.193791) + [0,0.147289) + [0,0.111798) + [0,0.277191) + [0,0.167455) + [0,0.189106) + [0,0.179609) + [0,0.297053) + [0,0.158413) + [0,0.165494) + [0,0.199673) + [0,0.227524) + [0,0.076909) + [0,0.332695) + [0,0.0802451) + [0,0.0994522) + [0,0.154095) + [0,0.274611) + [0,0.24348) + [0,0.207016) + [0,0.218561) + [0,0.270996) + [0,0.214018) + [0,0.323964) + [0,0.184757) + [0,0.193804) + [0,0.276431) + [0,0.175016) + [0,0.142152) + [0,0.0857401) + [0,0.207714) + [0,0.00391946) + [0,0.168587) + [0,0.192406) + [0,0.246491) + [0,0.148506) + [0,0.25725) + [0,0.165202) + [0,0.0814685) + [0,0.247042) + [0,0.0633425) + [0,0.253163) + [0,0.157251) + [0,0.285416) + [0,0.173586) + [0,0.210372) + [0,0.266635) + [0,0.316023) + [0,0.287316) + [0,0.264334) + [0,0.208851) + [0,0.277582) + [0,0.288591) + [0,0.231179) + [0,0.190642) + [0,0.24509) + [0,0.319493) + [0,0.207261) + [0,0.173684) + [0,0.264483) + [0,0.289189) + [0,0.23879) + [0,0.297933) + [0,0.268806) + [0, ) +persistence intervals in dim 1: + [0.542696,0.558863) + [0.531636,0.578093) + [0.530723,0.576869) + [0.463389,0.505345) + [0.445398,0.448892) + [0.443911,0.54761) + [0.431628,0.477277) + [0.413789,0.487379) + [0.412572,0.46308) + [0.411549,0.471715) + [0.409968,0.478461) + [0.386278,0.4922) + [0.381084,0.421374) + [0.377729,0.514046) + [0.377147,0.414788) + [0.377019,0.434385) + [0.374531,0.477153) + [0.370051,0.483155) + [0.361715,0.403181) + [0.354747,0.454956) + [0.352356,0.541947) + [0.350913,0.369543) + [0.35058,0.580726) + [0.347806,0.638039) + [0.347388,0.559978) + [0.344005,0.387193) + [0.34298,0.65758) + [0.339394,0.463666) + [0.33836,0.350411) + [0.33392,0.35111) + [0.33364,0.3797) + [0.331259,0.356381) + [0.329066,0.386148) + [0.324571,0.343083) + [0.324159,0.399094) + [0.322683,0.482958) + [0.318032,0.417462) + [0.317521,0.349622) + [0.316534,0.682559) + [0.309419,0.37151) + [0.309336,0.310216) + [0.308779,0.346297) + [0.304761,0.647803) + [0.301986,0.478334) + [0.301045,0.303943) + [0.29997,0.311993) + [0.298341,0.360737) + [0.279016,0.301331) + [0.2576,0.373749) + [0.253337,0.292286) + [0.24546,0.248903) + [0.240869,0.288747) + [0.189652,0.197515) +persistence intervals in dim 2: + [0.720484,1.65562) + 2.22 real 2.09 user 0.11 sys + 182439936 maximum resident set size + 0 average shared memory size + 0 average unshared data size + 0 average unshared stack size + 44546 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 + 1307 involuntary context switches -- cgit v1.2.3