From 0dc8dc9c9dd444951928dcf6c59967f9f617f488 Mon Sep 17 00:00:00 2001 From: Ulrich Bauer Date: Mon, 9 Jan 2017 11:56:45 +0100 Subject: benchmark H^1 --- benchmarks/sphere_3_192/run_benchmarks.sh | 4 ++++ benchmarks/sphere_3_192/run_dionysus.sh | 1 + benchmarks/sphere_3_192/run_dipha.sh | 1 + benchmarks/sphere_3_192/run_gudhi.sh | 1 + benchmarks/sphere_3_192/run_ripser.sh | 1 + 5 files changed, 8 insertions(+) create mode 100644 benchmarks/sphere_3_192/run_benchmarks.sh create mode 100644 benchmarks/sphere_3_192/run_dionysus.sh create mode 100644 benchmarks/sphere_3_192/run_dipha.sh create mode 100644 benchmarks/sphere_3_192/run_gudhi.sh create mode 100644 benchmarks/sphere_3_192/run_ripser.sh diff --git a/benchmarks/sphere_3_192/run_benchmarks.sh b/benchmarks/sphere_3_192/run_benchmarks.sh new file mode 100644 index 0000000..14cac6c --- /dev/null +++ b/benchmarks/sphere_3_192/run_benchmarks.sh @@ -0,0 +1,4 @@ +. run_dionysus.sh +. run_dipha.sh +. run_gudhi.sh +. run_ripser.sh diff --git a/benchmarks/sphere_3_192/run_dionysus.sh b/benchmarks/sphere_3_192/run_dionysus.sh new file mode 100644 index 0000000..1e5c7d3 --- /dev/null +++ b/benchmarks/sphere_3_192/run_dionysus.sh @@ -0,0 +1 @@ +/usr/bin/time -l ~/Source/Dionysus/examples/cohomology/rips-pairwise-cohomology -s2 -p2 ~/Bitbucket/phat-paper/benchmark/point\ cloud/sphere_3_192_points.dat 2>&1 | tee dionysus.out.txt diff --git a/benchmarks/sphere_3_192/run_dipha.sh b/benchmarks/sphere_3_192/run_dipha.sh new file mode 100644 index 0000000..312bcd7 --- /dev/null +++ b/benchmarks/sphere_3_192/run_dipha.sh @@ -0,0 +1 @@ +/usr/bin/time -l ~/Bitbucket/dipha/dipha --benchmark --upper_dim 2 --dual ~/Bitbucket/phat-paper/benchmark/dipha/sphere_3_192.complex /dev/null 2>&1 | tee dipha.out.txt diff --git a/benchmarks/sphere_3_192/run_gudhi.sh b/benchmarks/sphere_3_192/run_gudhi.sh new file mode 100644 index 0000000..a4c6c51 --- /dev/null +++ b/benchmarks/sphere_3_192/run_gudhi.sh @@ -0,0 +1 @@ +/usr/bin/time -l ~/Source/Gudhi_library_1.3.1/example/Persistent_cohomology/rips_persistence -d2 -p2 ~/Bitbucket/phat-paper/benchmark/point\ cloud/sphere_3_192_points.dat -o/dev/null 2>&1 | tee gudhi.out.txt diff --git a/benchmarks/sphere_3_192/run_ripser.sh b/benchmarks/sphere_3_192/run_ripser.sh new file mode 100644 index 0000000..209c410 --- /dev/null +++ b/benchmarks/sphere_3_192/run_ripser.sh @@ -0,0 +1 @@ +/usr/bin/time -l ~/Bitbucket/ripser/ripser ~/Bitbucket/ripser/examples/sphere_3_192.lower_distance_matrix 2>&1 | tee ripser.out.txt -- cgit v1.2.3 From 3c3f3e74e26a1534202cf0235956c8a7924085ed Mon Sep 17 00:00:00 2001 From: Ulrich Bauer Date: Wed, 11 Jan 2017 13:16:58 +0100 Subject: gudhi benchmark output --- benchmarks/sphere_3_192/run_gudhi.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/benchmarks/sphere_3_192/run_gudhi.sh b/benchmarks/sphere_3_192/run_gudhi.sh index a4c6c51..80ae403 100644 --- a/benchmarks/sphere_3_192/run_gudhi.sh +++ b/benchmarks/sphere_3_192/run_gudhi.sh @@ -1 +1 @@ -/usr/bin/time -l ~/Source/Gudhi_library_1.3.1/example/Persistent_cohomology/rips_persistence -d2 -p2 ~/Bitbucket/phat-paper/benchmark/point\ cloud/sphere_3_192_points.dat -o/dev/null 2>&1 | tee gudhi.out.txt +/usr/bin/time -l ~/Source/Gudhi_library_1.3.1/example/Persistent_cohomology/rips_persistence -d2 -p2 ~/Bitbucket/phat-paper/benchmark/point\ cloud/sphere_3_192_points.dat 2>&1 | tee gudhi.out.txt -- cgit v1.2.3 From f84042ed1b0b1de7f66e57d9a516cf60736af91a Mon Sep 17 00:00:00 2001 From: Ulrich Bauer Date: Wed, 11 Jan 2017 13:22:21 +0100 Subject: benchmark results --- benchmarks/sphere_3_192/dionysus.out.txt | 27 ++++ benchmarks/sphere_3_192/dipha.out.txt | 55 +++++++ benchmarks/sphere_3_192/gudhi.out.txt | 262 ++++++++++++++++++++++++++++++ benchmarks/sphere_3_192/ripser.out.txt | 264 +++++++++++++++++++++++++++++++ 4 files changed, 608 insertions(+) create mode 100644 benchmarks/sphere_3_192/dionysus.out.txt create mode 100644 benchmarks/sphere_3_192/dipha.out.txt create mode 100644 benchmarks/sphere_3_192/gudhi.out.txt create mode 100644 benchmarks/sphere_3_192/ripser.out.txt diff --git a/benchmarks/sphere_3_192/dionysus.out.txt b/benchmarks/sphere_3_192/dionysus.out.txt new file mode 100644 index 0000000..3191f98 --- /dev/null +++ b/benchmarks/sphere_3_192/dionysus.out.txt @@ -0,0 +1,27 @@ +Boundary matrix: +Cocycles: *.ccl +Vertices: +Diagram: +Simplex vector generated, size: 1179808 + +0% 10 20 30 40 50 60 70 80 90 100% +|----|----|----|----|----|----|----|----|----|----| +*************************************************** +Rips timer : Elapsed time [4.39] seconds +Persistence timer : Elapsed time [2.55] seconds +Total timer : Elapsed time [7.88] seconds + 7.99 real 7.88 user 0.08 sys + 141664256 maximum resident set size + 0 average shared memory size + 0 average unshared data size + 0 average unshared stack size + 34606 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 + 2629 involuntary context switches diff --git a/benchmarks/sphere_3_192/dipha.out.txt b/benchmarks/sphere_3_192/dipha.out.txt new file mode 100644 index 0000000..bae5fc7 --- /dev/null +++ b/benchmarks/sphere_3_192/dipha.out.txt @@ -0,0 +1,55 @@ + +Input filename: +/Users/uli/Bitbucket/phat-paper/benchmark/dipha/sphere_3_192.complex + +upper_dim: 2 + +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: +1179808 + 0.2s 4 MB 40 MB 0 MB get_filtration_to_cell_map( complex, dualize, filtration_to_cell_map ); + 0.1s 40 MB 127 MB 18 MB get_cell_to_filtration_map( complex.get_num_cells(), filtration_to_cell_map, cell_to_filtration_map ); + 0.0s 154 MB 156 MB 0 MB generate_unreduced_columns( complex, filtration_to_cell_map, cell_to_filtration_map, cur_dim, dualize, unreduced_columns ); + 0.0s 153 MB 156 MB 0 MB reduction_kernel( complex.get_num_cells(), unreduced_columns, reduced_columns ); + 0.3s 151 MB 165 MB 53 MB generate_unreduced_columns( complex, filtration_to_cell_map, cell_to_filtration_map, cur_dim, dualize, unreduced_columns ); + 0.1s 136 MB 169 MB 0 MB reduction_kernel( complex.get_num_cells(), unreduced_columns, reduced_columns ); + 0.1s 167 MB 169 MB 1 MB dipha::outputs::save_persistence_diagram( output_filename, complex, filtration_to_cell_map, reduced_columns, dualize, upper_dim ); + +Overall running time in seconds: +0.9 + +Reduction kernel running time in seconds: +0.1 + +Overall peak mem in GB of all ranks: +0.2 + +Individual peak mem in GB of per rank: +0.2 + +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 + 0.94 real 0.75 user 0.16 sys + 177598464 maximum resident set size + 0 average shared memory size + 0 average unshared data size + 0 average unshared stack size + 78159 page reclaims + 0 page faults + 0 swaps + 0 block input operations + 0 block output operations + 0 messages sent + 0 messages received + 0 signals received + 5 voluntary context switches + 333 involuntary context switches diff --git a/benchmarks/sphere_3_192/gudhi.out.txt b/benchmarks/sphere_3_192/gudhi.out.txt new file mode 100644 index 0000000..1a0cddf --- /dev/null +++ b/benchmarks/sphere_3_192/gudhi.out.txt @@ -0,0 +1,262 @@ +The complex contains 1179808 simplices + and has dimension 2 +2 0 0 inf +2 1 0.316534 0.682559 +2 1 0.304761 0.647803 +2 0 0 0.332695 +2 0 0 0.323964 +2 0 0 0.319493 +2 0 0 0.316023 +2 1 0.34298 0.65758 +2 0 0 0.304062 +2 0 0 0.297933 +2 0 0 0.297053 +2 0 0 0.293466 +2 1 0.347806 0.638039 +2 0 0 0.289189 +2 0 0 0.288591 +2 0 0 0.287316 +2 0 0 0.285416 +2 0 0 0.283881 +2 0 0 0.283562 +2 0 0 0.282169 +2 0 0 0.280629 +2 0 0 0.277582 +2 0 0 0.277191 +2 0 0 0.276431 +2 0 0 0.274611 +2 0 0 0.270996 +2 0 0 0.268806 +2 0 0 0.266635 +2 0 0 0.266592 +2 0 0 0.264483 +2 0 0 0.264334 +2 0 0 0.257997 +2 0 0 0.25725 +2 0 0 0.253227 +2 0 0 0.253163 +2 0 0 0.249345 +2 0 0 0.249339 +2 0 0 0.248879 +2 0 0 0.247042 +2 0 0 0.246491 +2 0 0 0.24509 +2 0 0 0.24348 +2 0 0 0.240632 +2 0 0 0.23879 +2 0 0 0.237571 +2 0 0 0.234969 +2 0 0 0.234112 +2 0 0 0.231675 +2 0 0 0.231179 +2 1 0.35058 0.580726 +2 0 0 0.228917 +2 0 0 0.2286 +2 0 0 0.227933 +2 0 0 0.227524 +2 0 0 0.223232 +2 0 0 0.218561 +2 0 0 0.218526 +2 0 0 0.215759 +2 0 0 0.214018 +2 1 0.347388 0.559978 +2 0 0 0.210372 +2 0 0 0.208851 +2 0 0 0.208063 +2 0 0 0.207714 +2 0 0 0.207261 +2 0 0 0.207016 +2 0 0 0.205389 +2 0 0 0.204544 +2 0 0 0.204208 +2 0 0 0.203812 +2 0 0 0.202564 +2 0 0 0.201961 +2 0 0 0.199673 +2 0 0 0.197377 +2 0 0 0.195722 +2 0 0 0.193804 +2 0 0 0.193791 +2 0 0 0.192733 +2 0 0 0.192406 +2 0 0 0.192356 +2 0 0 0.191661 +2 0 0 0.190642 +2 1 0.352356 0.541947 +2 0 0 0.189106 +2 0 0 0.184757 +2 0 0 0.18428 +2 0 0 0.179609 +2 1 0.301986 0.478334 +2 0 0 0.176306 +2 0 0 0.175016 +2 0 0 0.17493 +2 0 0 0.174172 +2 0 0 0.173684 +2 0 0 0.173586 +2 0 0 0.173412 +2 0 0 0.168587 +2 0 0 0.167455 +2 0 0 0.165907 +2 0 0 0.165592 +2 0 0 0.165494 +2 0 0 0.165314 +2 0 0 0.165202 +2 0 0 0.164815 +2 0 0 0.164809 +2 0 0 0.162464 +2 1 0.322683 0.482958 +2 0 0 0.159282 +2 0 0 0.158413 +2 0 0 0.157373 +2 0 0 0.157293 +2 0 0 0.157251 +2 0 0 0.1569 +2 0 0 0.15587 +2 0 0 0.154095 +2 0 0 0.15244 +2 0 0 0.151643 +2 0 0 0.150747 +2 0 0 0.149226 +2 0 0 0.149017 +2 0 0 0.148506 +2 0 0 0.147427 +2 0 0 0.147289 +2 0 0 0.147203 +2 0 0 0.145725 +2 0 0 0.145018 +2 0 0 0.143151 +2 0 0 0.143085 +2 0 0 0.142834 +2 0 0 0.142537 +2 0 0 0.142152 +2 0 0 0.141823 +2 0 0 0.138674 +2 1 0.377729 0.514046 +2 0 0 0.135402 +2 0 0 0.134886 +2 0 0 0.133722 +2 0 0 0.133525 +2 0 0 0.133033 +2 0 0 0.131638 +2 0 0 0.131438 +2 0 0 0.129741 +2 0 0 0.127864 +2 0 0 0.127383 +2 0 0 0.126595 +2 0 0 0.124774 +2 1 0.339394 0.463666 +2 0 0 0.123527 +2 0 0 0.122089 +2 0 0 0.121955 +2 0 0 0.119187 +2 1 0.2576 0.373749 +2 0 0 0.115939 +2 1 0.370051 0.483155 +2 0 0 0.111798 +2 0 0 0.111131 +2 0 0 0.109526 +2 0 0 0.108768 +2 1 0.386278 0.4922 +2 1 0.443911 0.54761 +2 1 0.374531 0.477153 +2 1 0.354747 0.454956 +2 0 0 0.0994522 +2 1 0.318032 0.417462 +2 0 0 0.0988752 +2 0 0 0.0970981 +2 0 0 0.0959033 +2 0 0 0.0884133 +2 0 0 0.0870489 +2 0 0 0.0857401 +2 0 0 0.084341 +2 0 0 0.0831521 +2 0 0 0.0831358 +2 0 0 0.0814685 +2 0 0 0.0802451 +2 0 0 0.0800348 +2 0 0 0.0792212 +2 0 0 0.0782455 +2 0 0 0.076909 +2 0 0 0.0753955 +2 1 0.324159 0.399094 +2 0 0 0.0746054 +2 0 0 0.0743236 +2 0 0 0.0741239 +2 1 0.413789 0.487379 +2 0 0 0.0728647 +2 0 0 0.0714516 +2 0 0 0.0702075 +2 0 0 0.0692368 +2 1 0.409968 0.478461 +2 0 0 0.0672609 +2 0 0 0.0651112 +2 0 0 0.0637053 +2 0 0 0.0633425 +2 1 0.298341 0.360737 +2 0 0 0.0623736 +2 1 0.309419 0.37151 +2 1 0.411549 0.471715 +2 0 0 0.0593071 +2 0 0 0.057488 +2 1 0.377019 0.434385 +2 1 0.329066 0.386148 +2 0 0 0.0560443 +2 0 0 0.0559886 +2 0 0 0.0522132 +2 0 0 0.0515157 +2 1 0.412572 0.46308 +2 0 0 0.0496187 +2 0 0 0.048826 +2 0 0 0.0487061 +2 1 0.240869 0.288747 +2 0 0 0.0471186 +2 1 0.531636 0.578093 +2 1 0.530723 0.576869 +2 1 0.33364 0.3797 +2 1 0.431628 0.477277 +2 0 0 0.0433426 +2 1 0.344005 0.387193 +2 1 0.463389 0.505345 +2 1 0.361715 0.403181 +2 1 0.381084 0.421374 +2 1 0.253337 0.292286 +2 0 0 0.0387451 +2 0 0 0.037954 +2 1 0.377147 0.414788 +2 1 0.308779 0.346297 +2 1 0.317521 0.349622 +2 0 0 0.0311057 +2 1 0.331259 0.356381 +2 1 0.279016 0.301331 +2 0 0 0.0217315 +2 1 0.350913 0.369543 +2 1 0.324571 0.343083 +2 0 0 0.0173134 +2 1 0.33392 0.35111 +2 1 0.542696 0.558863 +2 1 0.33836 0.350411 +2 1 0.29997 0.311993 +2 0 0 0.0120098 +2 1 0.189652 0.197515 +2 0 0 0.00391946 +2 0 0 0.0036753 +2 1 0.445398 0.448892 +2 1 0.24546 0.248903 +2 1 0.301045 0.303943 +2 1 0.309336 0.310216 + 0.59 real 0.56 user 0.02 sys + 69210112 maximum resident set size + 0 average shared memory size + 0 average unshared data size + 0 average unshared stack size + 16916 page reclaims + 0 page faults + 0 swaps + 0 block input operations + 0 block output operations + 0 messages sent + 0 messages received + 0 signals received + 10 voluntary context switches + 125 involuntary context switches diff --git a/benchmarks/sphere_3_192/ripser.out.txt b/benchmarks/sphere_3_192/ripser.out.txt new file mode 100644 index 0000000..bc741ae --- /dev/null +++ b/benchmarks/sphere_3_192/ripser.out.txt @@ -0,0 +1,264 @@ +distance matrix with 192 points +value range: [0.00367531,2] +persistence intervals in dim 0: + [0,0.00367531) + [0,0.00391946) + [0,0.0120098) + [0,0.0173134) + [0,0.0217315) + [0,0.0311057) + [0,0.037954) + [0,0.0387451) + [0,0.0433426) + [0,0.0471186) + [0,0.0487061) + [0,0.048826) + [0,0.0496187) + [0,0.0515157) + [0,0.0522132) + [0,0.0559886) + [0,0.0560443) + [0,0.057488) + [0,0.0593071) + [0,0.0623736) + [0,0.0633425) + [0,0.0637053) + [0,0.0651112) + [0,0.0672609) + [0,0.0692368) + [0,0.0702075) + [0,0.0714516) + [0,0.0728647) + [0,0.0741239) + [0,0.0743236) + [0,0.0746054) + [0,0.0753955) + [0,0.076909) + [0,0.0782455) + [0,0.0792212) + [0,0.0800348) + [0,0.0802451) + [0,0.0814685) + [0,0.0831358) + [0,0.0831521) + [0,0.084341) + [0,0.0857401) + [0,0.0870489) + [0,0.0884133) + [0,0.0959033) + [0,0.0970981) + [0,0.0988752) + [0,0.0994522) + [0,0.108768) + [0,0.109526) + [0,0.111131) + [0,0.111798) + [0,0.115939) + [0,0.119187) + [0,0.121955) + [0,0.122089) + [0,0.123527) + [0,0.124774) + [0,0.126595) + [0,0.127383) + [0,0.127864) + [0,0.129741) + [0,0.131438) + [0,0.131638) + [0,0.133033) + [0,0.133525) + [0,0.133722) + [0,0.134886) + [0,0.135402) + [0,0.138674) + [0,0.141823) + [0,0.142152) + [0,0.142537) + [0,0.142834) + [0,0.143085) + [0,0.143151) + [0,0.145018) + [0,0.145725) + [0,0.147203) + [0,0.147289) + [0,0.147427) + [0,0.148506) + [0,0.149017) + [0,0.149226) + [0,0.150747) + [0,0.151643) + [0,0.15244) + [0,0.154095) + [0,0.15587) + [0,0.1569) + [0,0.157251) + [0,0.157293) + [0,0.157373) + [0,0.158413) + [0,0.159282) + [0,0.162464) + [0,0.164809) + [0,0.164815) + [0,0.165202) + [0,0.165314) + [0,0.165494) + [0,0.165592) + [0,0.165907) + [0,0.167455) + [0,0.168587) + [0,0.173412) + [0,0.173586) + [0,0.173684) + [0,0.174172) + [0,0.17493) + [0,0.175016) + [0,0.176306) + [0,0.179609) + [0,0.18428) + [0,0.184757) + [0,0.189106) + [0,0.190642) + [0,0.191661) + [0,0.192356) + [0,0.192406) + [0,0.192733) + [0,0.193791) + [0,0.193804) + [0,0.195722) + [0,0.197377) + [0,0.199673) + [0,0.201961) + [0,0.202564) + [0,0.203812) + [0,0.204208) + [0,0.204544) + [0,0.205389) + [0,0.207016) + [0,0.207261) + [0,0.207714) + [0,0.208063) + [0,0.208851) + [0,0.210372) + [0,0.214018) + [0,0.215759) + [0,0.218526) + [0,0.218561) + [0,0.223232) + [0,0.227524) + [0,0.227933) + [0,0.2286) + [0,0.228917) + [0,0.231179) + [0,0.231675) + [0,0.234112) + [0,0.234969) + [0,0.237571) + [0,0.23879) + [0,0.240632) + [0,0.24348) + [0,0.24509) + [0,0.246491) + [0,0.247042) + [0,0.248879) + [0,0.249339) + [0,0.249345) + [0,0.253163) + [0,0.253227) + [0,0.25725) + [0,0.257997) + [0,0.264334) + [0,0.264483) + [0,0.266592) + [0,0.266635) + [0,0.268806) + [0,0.270996) + [0,0.274611) + [0,0.276431) + [0,0.277191) + [0,0.277582) + [0,0.280629) + [0,0.282169) + [0,0.283562) + [0,0.283881) + [0,0.285416) + [0,0.287316) + [0,0.288591) + [0,0.289189) + [0,0.293466) + [0,0.297053) + [0,0.297933) + [0,0.304062) + [0,0.316023) + [0,0.319493) + [0,0.323964) + [0,0.332695) + [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) + 0.03 real 0.03 user 0.00 sys + 3276800 maximum resident set size + 0 average shared memory size + 0 average unshared data size + 0 average unshared stack size + 819 page reclaims + 0 page faults + 0 swaps + 0 block input operations + 0 block output operations + 0 messages sent + 0 messages received + 0 signals received + 7 voluntary context switches + 119 involuntary context switches -- cgit v1.2.3 From eb8a0a7d92c1b3260ff33e8f213b7369dd038d0b Mon Sep 17 00:00:00 2001 From: Ulrich Bauer Date: Wed, 22 Feb 2017 12:55:07 +0100 Subject: typo in readme --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 0c5a2e6..4aae03d 100644 --- a/README.md +++ b/README.md @@ -74,7 +74,7 @@ The input is given either in a file whose name is passed as an argument, or thro - `--format`: use the specified file format for the input. The following formats are supported: - `lower-distance` (default if no format is specified): lower triangular distance matrix; a comma (or whitespace, or other non-numerical character) separated list of the distance matrix entries below the diagonal, sorted lexicographically by row index, then column index - `upper-distance`: upper triangular distance matrix; similar to the previous, but for the entries above the diagonal; suitable for output from the MATLAB functions `pdist` or `seqpdist`, exported to a CSV file - - `distances`: full distance matrix; similar to the above, but for all entries of the distance matrix + - `distance`: full distance matrix; similar to the above, but for all entries of the distance matrix - `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 - `--dim k`: compute persistent homology up to dimension *k* -- cgit v1.2.3