diff options
Diffstat (limited to 'benchmarks/sphere_3_64')
-rw-r--r-- | benchmarks/sphere_3_64/dionysus.txt | 28 | ||||
-rw-r--r-- | benchmarks/sphere_3_64/dipha.txt | 58 | ||||
-rw-r--r-- | benchmarks/sphere_3_64/gudhi.txt | 18 | ||||
-rw-r--r-- | benchmarks/sphere_3_64/phat.txt | 17 | ||||
-rw-r--r-- | benchmarks/sphere_3_64/ripser.txt | 103 |
5 files changed, 224 insertions, 0 deletions
diff --git a/benchmarks/sphere_3_64/dionysus.txt b/benchmarks/sphere_3_64/dionysus.txt new file mode 100644 index 0000000..52b879d --- /dev/null +++ b/benchmarks/sphere_3_64/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_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 new file mode 100644 index 0000000..67534d6 --- /dev/null +++ b/benchmarks/sphere_3_64/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_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 new file mode 100644 index 0000000..ee69c4a --- /dev/null +++ b/benchmarks/sphere_3_64/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_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 new file mode 100644 index 0000000..0dff324 --- /dev/null +++ b/benchmarks/sphere_3_64/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_64_coboundary.phat +/Users/uli/Bitbucket/phat-paper/benchmark/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 new file mode 100644 index 0000000..016143d --- /dev/null +++ b/benchmarks/sphere_3_64/ripser.txt @@ -0,0 +1,103 @@ +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_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 |