benchmarks

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