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Better homology #166

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mtsch
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@mtsch mtsch commented Apr 3, 2024

  • Improvements to the homology algorithm:
    • compute infinite intervals by tracking potential birth simplex candidates.
    • use these candidates to stop the reduction early if possible.
  • Some code reorganization.

github-actions[bot]
github-actions bot reviewed Apr 3, 2024
View reviewed changes
test/filtrations/rips.jl
Comment on lines +327 to 332
@test ripserer(
Rips(cycle; threshold=2); alg=:homology, implicit=true
)[2][1] == (1.0, Inf)
@test_broken ripserer(
@test ripserer(
Rips, cycle; alg=:homology, threshold=2, implicit=false
)[2][1] == (1.0, Inf)
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[JuliaFormatter] reported by reviewdog 🐶

Suggested change
@test ripserer(
Rips(cycle; threshold=2); alg=:homology, implicit=true
)[2][1] == (1.0, Inf)
@test_broken ripserer(
@test ripserer(
Rips, cycle; alg=:homology, threshold=2, implicit=false
)[2][1] == (1.0, Inf)
@test ripserer(Rips(cycle; threshold=2); alg=:homology, implicit=true)[2][1] ==
(1.0, Inf)
@test ripserer(Rips, cycle; alg=:homology, threshold=2, implicit=false)[2][1] ==
(1.0, Inf)

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github-actions bot commented Apr 3, 2024

Benchmark result

Judge result

Benchmark Report for /home/runner/work/Ripserer.jl/Ripserer.jl

Job Properties

  • Time of benchmarks:
    • Target: 3 Apr 2024 - 11:49
    • Baseline: 3 Apr 2024 - 11:52
  • Package commits:
    • Target: b8bcc5
    • Baseline: 3f2d63
  • Julia commits:
    • Target: bd47ec
    • Baseline: bd47ec
  • Julia command flags:
    • Target: None
    • Baseline: None
  • Environment variables:
    • Target: None
    • Baseline: None

Results

A ratio greater than 1.0 denotes a possible regression (marked with ❌), while a ratio less
than 1.0 denotes a possible improvement (marked with ✅). Only significant results - results
that indicate possible regressions or improvements - are shown below (thus, an empty table means that all
benchmark results remained invariant between builds).

ID time ratio memory ratio
["homology", "klein200.pts"] 0.99 (5%) 0.92 (1%) ✅
["homology", "lena1024.dipha"] 1.12 (5%) ❌ 0.96 (1%) ✅
["homology", "sphere100.pts"] 1.01 (5%) 0.95 (1%) ✅

Benchmark Group List

Here's a list of all the benchmark groups executed by this job:

  • ["alpha"]
  • ["cubical"]
  • ["homology"]
  • ["rips", "dense"]
  • ["rips", "sparse"]

Julia versioninfo

Target

Julia Version 1.10.2
Commit bd47eca2c8a (2024-03-01 10:14 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.4 LTS
  uname: Linux 6.5.0-1016-azure #16~22.04.1-Ubuntu SMP Fri Feb 16 15:42:02 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  3242 MHz        959 s          0 s        106 s       3429 s          0 s
       #2  3225 MHz        975 s          0 s        103 s       3414 s          0 s
       #3  2445 MHz       1233 s          0 s        127 s       3125 s          0 s
       #4  2445 MHz        846 s          0 s        108 s       3533 s          0 s
  Memory: 15.606498718261719 GB (13659.140625 MB free)
  Uptime: 451.75 sec
  Load Avg:  1.1  0.95  0.45
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)

Baseline

Julia Version 1.10.2
Commit bd47eca2c8a (2024-03-01 10:14 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.4 LTS
  uname: Linux 6.5.0-1016-azure #16~22.04.1-Ubuntu SMP Fri Feb 16 15:42:02 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  3240 MHz       1424 s          0 s        129 s       4676 s          0 s
       #2  2601 MHz       1544 s          0 s        124 s       4559 s          0 s
       #3  2445 MHz       1652 s          0 s        147 s       4420 s          0 s
       #4  3243 MHz       1106 s          0 s        126 s       4989 s          0 s
  Memory: 15.606498718261719 GB (13653.24609375 MB free)
  Uptime: 625.43 sec
  Load Avg:  1.07  0.99  0.56
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)

Target result

Benchmark Report for /home/runner/work/Ripserer.jl/Ripserer.jl

Job Properties

  • Time of benchmark: 3 Apr 2024 - 11:49
  • Package commit: b8bcc5
  • Julia commit: bd47ec
  • Julia command flags: None
  • Environment variables: None

Results

Below is a table of this job's results, obtained by running the benchmarks.
The values listed in the ID column have the structure [parent_group, child_group, ..., key], and can be used to
index into the BaseBenchmarks suite to retrieve the corresponding benchmarks.
The percentages accompanying time and memory values in the below table are noise tolerances. The "true"
time/memory value for a given benchmark is expected to fall within this percentage of the reported value.
An empty cell means that the value was zero.

ID time GC time memory allocations
["alpha", "klein500.pts"] 7.421 s (5%) 193.447 ms 2.72 GiB (1%) 25741846
["alpha", "torus10k.pts"] 2.146 s (5%) 37.549 ms 828.85 MiB (1%) 7915108
["cubical", "bonsai64.dipha"] 1.435 s (5%) 16.900 ms 299.73 MiB (1%) 284200
["cubical", "lena2048.dipha"] 4.023 s (5%) 322.999 ms 1.62 GiB (1%) 4275722
["homology", "klein200.pts"] 8.120 ms (5%) 2.87 MiB (1%) 9101
["homology", "lena1024.dipha"] 1.827 s (5%) 150.267 ms 446.60 MiB (1%) 1201341
["homology", "sphere100.pts"] 108.167 ms (5%) 34.44 MiB (1%) 135726
["rips", "dense", "dragon2000.pts"] 2.073 s (5%) 132.218 ms 281.87 MiB (1%) 11410
["rips", "dense", "fract-r.dist"] 12.679 s (5%) 270.361 ms 1.98 GiB (1%) 5106
["rips", "dense", "o3_1024.pts"] 2.576 s (5%) 26.745 ms 288.30 MiB (1%) 6123
["rips", "sparse", "alpha_4_sphere_2000.spdist"] 4.143 s (5%) 366.54 MiB (1%) 8662
["rips", "sparse", "dragon2000.pts"] 2.368 s (5%) 126.077 ms 312.23 MiB (1%) 7407
["rips", "sparse", "fract-r.dist"] 14.534 s (5%) 277.619 ms 1.98 GiB (1%) 4079
["rips", "sparse", "o3_1024.pts"] 1.975 s (5%) 135.032 ms 296.22 MiB (1%) 4070

Benchmark Group List

Here's a list of all the benchmark groups executed by this job:

  • ["alpha"]
  • ["cubical"]
  • ["homology"]
  • ["rips", "dense"]
  • ["rips", "sparse"]

Julia versioninfo

Julia Version 1.10.2
Commit bd47eca2c8a (2024-03-01 10:14 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.4 LTS
  uname: Linux 6.5.0-1016-azure #16~22.04.1-Ubuntu SMP Fri Feb 16 15:42:02 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  3242 MHz        959 s          0 s        106 s       3429 s          0 s
       #2  3225 MHz        975 s          0 s        103 s       3414 s          0 s
       #3  2445 MHz       1233 s          0 s        127 s       3125 s          0 s
       #4  2445 MHz        846 s          0 s        108 s       3533 s          0 s
  Memory: 15.606498718261719 GB (13659.140625 MB free)
  Uptime: 451.75 sec
  Load Avg:  1.1  0.95  0.45
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)

Baseline result

Benchmark Report for /home/runner/work/Ripserer.jl/Ripserer.jl

Job Properties

  • Time of benchmark: 3 Apr 2024 - 11:52
  • Package commit: 3f2d63
  • Julia commit: bd47ec
  • Julia command flags: None
  • Environment variables: None

Results

Below is a table of this job's results, obtained by running the benchmarks.
The values listed in the ID column have the structure [parent_group, child_group, ..., key], and can be used to
index into the BaseBenchmarks suite to retrieve the corresponding benchmarks.
The percentages accompanying time and memory values in the below table are noise tolerances. The "true"
time/memory value for a given benchmark is expected to fall within this percentage of the reported value.
An empty cell means that the value was zero.

ID time GC time memory allocations
["alpha", "klein500.pts"] 7.502 s (5%) 202.511 ms 2.72 GiB (1%) 25741846
["alpha", "torus10k.pts"] 2.099 s (5%) 35.666 ms 828.85 MiB (1%) 7915108
["cubical", "bonsai64.dipha"] 1.457 s (5%) 17.191 ms 299.73 MiB (1%) 284200
["cubical", "lena2048.dipha"] 4.063 s (5%) 327.377 ms 1.62 GiB (1%) 4275722
["homology", "klein200.pts"] 8.200 ms (5%) 3.11 MiB (1%) 9100
["homology", "lena1024.dipha"] 1.632 s (5%) 35.319 ms 466.16 MiB (1%) 1201338
["homology", "sphere100.pts"] 106.862 ms (5%) 36.06 MiB (1%) 135724
["rips", "dense", "dragon2000.pts"] 2.080 s (5%) 134.606 ms 281.87 MiB (1%) 11410
["rips", "dense", "fract-r.dist"] 12.748 s (5%) 276.644 ms 1.98 GiB (1%) 5106
["rips", "dense", "o3_1024.pts"] 2.619 s (5%) 137.419 ms 288.30 MiB (1%) 6123
["rips", "sparse", "alpha_4_sphere_2000.spdist"] 4.118 s (5%) 366.54 MiB (1%) 8662
["rips", "sparse", "dragon2000.pts"] 2.353 s (5%) 118.978 ms 312.23 MiB (1%) 7407
["rips", "sparse", "fract-r.dist"] 14.573 s (5%) 276.561 ms 1.98 GiB (1%) 4079
["rips", "sparse", "o3_1024.pts"] 1.990 s (5%) 136.552 ms 296.22 MiB (1%) 4070

Benchmark Group List

Here's a list of all the benchmark groups executed by this job:

  • ["alpha"]
  • ["cubical"]
  • ["homology"]
  • ["rips", "dense"]
  • ["rips", "sparse"]

Julia versioninfo

Julia Version 1.10.2
Commit bd47eca2c8a (2024-03-01 10:14 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.4 LTS
  uname: Linux 6.5.0-1016-azure #16~22.04.1-Ubuntu SMP Fri Feb 16 15:42:02 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  3240 MHz       1424 s          0 s        129 s       4676 s          0 s
       #2  2601 MHz       1544 s          0 s        124 s       4559 s          0 s
       #3  2445 MHz       1652 s          0 s        147 s       4420 s          0 s
       #4  3243 MHz       1106 s          0 s        126 s       4989 s          0 s
  Memory: 15.606498718261719 GB (13653.24609375 MB free)
  Uptime: 625.43 sec
  Load Avg:  1.07  0.99  0.56
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)

Runtime information

Runtime Info
BLAS #threads 2
BLAS.vendor() lbt
Sys.CPU_THREADS 4

lscpu output:

Architecture:                       x86_64
CPU op-mode(s):                     32-bit, 64-bit
Address sizes:                      48 bits physical, 48 bits virtual
Byte Order:                         Little Endian
CPU(s):                             4
On-line CPU(s) list:                0-3
Vendor ID:                          AuthenticAMD
Model name:                         AMD EPYC 7763 64-Core Processor
CPU family:                         25
Model:                              1
Thread(s) per core:                 2
Core(s) per socket:                 2
Socket(s):                          1
Stepping:                           1
BogoMIPS:                           4890.84
Flags:                              fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl tsc_reliable nonstop_tsc cpuid extd_apicid aperfmperf pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand hypervisor lahf_lm cmp_legacy svm cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw topoext invpcid_single vmmcall fsgsbase bmi1 avx2 smep bmi2 erms invpcid rdseed adx smap clflushopt clwb sha_ni xsaveopt xsavec xgetbv1 xsaves clzero xsaveerptr rdpru arat npt nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold v_vmsave_vmload umip vaes vpclmulqdq rdpid fsrm
Virtualization:                     AMD-V
Hypervisor vendor:                  Microsoft
Virtualization type:                full
L1d cache:                          64 KiB (2 instances)
L1i cache:                          64 KiB (2 instances)
L2 cache:                           1 MiB (2 instances)
L3 cache:                           32 MiB (1 instance)
NUMA node(s):                       1
NUMA node0 CPU(s):                  0-3
Vulnerability Gather data sampling: Not affected
Vulnerability Itlb multihit:        Not affected
Vulnerability L1tf:                 Not affected
Vulnerability Mds:                  Not affected
Vulnerability Meltdown:             Not affected
Vulnerability Mmio stale data:      Not affected
Vulnerability Retbleed:             Not affected
Vulnerability Spec rstack overflow: Vulnerable: Safe RET, no microcode
Vulnerability Spec store bypass:    Vulnerable
Vulnerability Spectre v1:           Mitigation; usercopy/swapgs barriers and __user pointer sanitization
Vulnerability Spectre v2:           Mitigation; Retpolines, STIBP disabled, RSB filling, PBRSB-eIBRS Not affected
Vulnerability Srbds:                Not affected
Vulnerability Tsx async abort:      Not affected
Cpu Property Value
Brand AMD EPYC 7763 64-Core Processor
Vendor :AMD
Architecture :Unknown
Model Family: 0xaf, Model: 0x01, Stepping: 0x01, Type: 0x00
Cores 16 physical cores, 16 logical cores (on executing CPU)
No Hyperthreading hardware capability detected
Clock Frequencies Not supported by CPU
Data Cache Level 1:3 : (32, 512, 32768) kbytes
64 byte cache line size
Address Size 48 bits virtual, 48 bits physical
SIMD 256 bit = 32 byte max. SIMD vector size
Time Stamp Counter TSC is accessible via rdtsc
TSC runs at constant rate (invariant from clock frequency)
Perf. Monitoring Performance Monitoring Counters (PMC) are not supported
Hypervisor Yes, Microsoft

@github-actions GitHub Actions
Copy link
Contributor

github-actions bot commented Apr 3, 2024

Benchmark result

Judge result

Benchmark Report for /home/runner/work/Ripserer.jl/Ripserer.jl

Job Properties

  • Time of benchmarks:
    • Target: 3 Apr 2024 - 11:57
    • Baseline: 3 Apr 2024 - 12:00
  • Package commits:
    • Target: f56efb
    • Baseline: 3f2d63
  • Julia commits:
    • Target: bd47ec
    • Baseline: bd47ec
  • Julia command flags:
    • Target: None
    • Baseline: None
  • Environment variables:
    • Target: None
    • Baseline: None

Results

A ratio greater than 1.0 denotes a possible regression (marked with ❌), while a ratio less
than 1.0 denotes a possible improvement (marked with ✅). Only significant results - results
that indicate possible regressions or improvements - are shown below (thus, an empty table means that all
benchmark results remained invariant between builds).

ID time ratio memory ratio
["homology", "klein200.pts"] 0.98 (5%) 0.92 (1%) ✅
["homology", "lena1024.dipha"] 1.05 (5%) ❌ 0.96 (1%) ✅
["homology", "sphere100.pts"] 0.95 (5%) ✅ 0.95 (1%) ✅
["rips", "dense", "o3_1024.pts"] 0.94 (5%) ✅ 1.00 (1%)

Benchmark Group List

Here's a list of all the benchmark groups executed by this job:

  • ["alpha"]
  • ["cubical"]
  • ["homology"]
  • ["rips", "dense"]
  • ["rips", "sparse"]

Julia versioninfo

Target

Julia Version 1.10.2
Commit bd47eca2c8a (2024-03-01 10:14 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.4 LTS
  uname: Linux 6.5.0-1016-azure #16~22.04.1-Ubuntu SMP Fri Feb 16 15:42:02 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  2445 MHz       1068 s          0 s        103 s       2485 s          0 s
       #2  2445 MHz       1347 s          0 s        120 s       2190 s          0 s
       #3  3270 MHz        963 s          0 s        127 s       2580 s          0 s
       #4  3242 MHz        707 s          0 s        103 s       2848 s          0 s
  Memory: 15.606498718261719 GB (13683.07421875 MB free)
  Uptime: 369.09 sec
  Load Avg:  1.19  1.04  0.51
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)

Baseline

Julia Version 1.10.2
Commit bd47eca2c8a (2024-03-01 10:14 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.4 LTS
  uname: Linux 6.5.0-1016-azure #16~22.04.1-Ubuntu SMP Fri Feb 16 15:42:02 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  2582 MHz       1283 s          0 s        116 s       4037 s          0 s
       #2  2445 MHz       1603 s          0 s        144 s       3691 s          0 s
       #3  2445 MHz       1725 s          0 s        146 s       3581 s          0 s
       #4  3241 MHz       1235 s          0 s        129 s       4075 s          0 s
  Memory: 15.606498718261719 GB (13635.31640625 MB free)
  Uptime: 547.48 sec
  Load Avg:  1.03  1.03  0.61
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)

Target result

Benchmark Report for /home/runner/work/Ripserer.jl/Ripserer.jl

Job Properties

  • Time of benchmark: 3 Apr 2024 - 11:57
  • Package commit: f56efb
  • Julia commit: bd47ec
  • Julia command flags: None
  • Environment variables: None

Results

Below is a table of this job's results, obtained by running the benchmarks.
The values listed in the ID column have the structure [parent_group, child_group, ..., key], and can be used to
index into the BaseBenchmarks suite to retrieve the corresponding benchmarks.
The percentages accompanying time and memory values in the below table are noise tolerances. The "true"
time/memory value for a given benchmark is expected to fall within this percentage of the reported value.
An empty cell means that the value was zero.

ID time GC time memory allocations
["alpha", "klein500.pts"] 7.630 s (5%) 199.761 ms 2.72 GiB (1%) 25741846
["alpha", "torus10k.pts"] 2.164 s (5%) 39.933 ms 828.85 MiB (1%) 7915108
["cubical", "bonsai64.dipha"] 1.489 s (5%) 21.423 ms 299.73 MiB (1%) 284200
["cubical", "lena2048.dipha"] 4.103 s (5%) 333.912 ms 1.62 GiB (1%) 4275722
["homology", "klein200.pts"] 8.027 ms (5%) 2.87 MiB (1%) 9101
["homology", "lena1024.dipha"] 1.779 s (5%) 151.255 ms 446.60 MiB (1%) 1201341
["homology", "sphere100.pts"] 105.618 ms (5%) 34.44 MiB (1%) 135726
["rips", "dense", "dragon2000.pts"] 2.107 s (5%) 145.828 ms 281.87 MiB (1%) 11410
["rips", "dense", "fract-r.dist"] 13.659 s (5%) 287.129 ms 1.98 GiB (1%) 5106
["rips", "dense", "o3_1024.pts"] 2.533 s (5%) 29.541 ms 288.30 MiB (1%) 6123
["rips", "sparse", "alpha_4_sphere_2000.spdist"] 4.100 s (5%) 366.54 MiB (1%) 8662
["rips", "sparse", "dragon2000.pts"] 2.353 s (5%) 123.388 ms 312.23 MiB (1%) 7407
["rips", "sparse", "fract-r.dist"] 14.847 s (5%) 286.042 ms 1.98 GiB (1%) 4079
["rips", "sparse", "o3_1024.pts"] 2.065 s (5%) 143.599 ms 296.22 MiB (1%) 4070

Benchmark Group List

Here's a list of all the benchmark groups executed by this job:

  • ["alpha"]
  • ["cubical"]
  • ["homology"]
  • ["rips", "dense"]
  • ["rips", "sparse"]

Julia versioninfo

Julia Version 1.10.2
Commit bd47eca2c8a (2024-03-01 10:14 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.4 LTS
  uname: Linux 6.5.0-1016-azure #16~22.04.1-Ubuntu SMP Fri Feb 16 15:42:02 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  2445 MHz       1068 s          0 s        103 s       2485 s          0 s
       #2  2445 MHz       1347 s          0 s        120 s       2190 s          0 s
       #3  3270 MHz        963 s          0 s        127 s       2580 s          0 s
       #4  3242 MHz        707 s          0 s        103 s       2848 s          0 s
  Memory: 15.606498718261719 GB (13683.07421875 MB free)
  Uptime: 369.09 sec
  Load Avg:  1.19  1.04  0.51
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)

Baseline result

Benchmark Report for /home/runner/work/Ripserer.jl/Ripserer.jl

Job Properties

  • Time of benchmark: 3 Apr 2024 - 12:0
  • Package commit: 3f2d63
  • Julia commit: bd47ec
  • Julia command flags: None
  • Environment variables: None

Results

Below is a table of this job's results, obtained by running the benchmarks.
The values listed in the ID column have the structure [parent_group, child_group, ..., key], and can be used to
index into the BaseBenchmarks suite to retrieve the corresponding benchmarks.
The percentages accompanying time and memory values in the below table are noise tolerances. The "true"
time/memory value for a given benchmark is expected to fall within this percentage of the reported value.
An empty cell means that the value was zero.

ID time GC time memory allocations
["alpha", "klein500.pts"] 7.581 s (5%) 223.598 ms 2.72 GiB (1%) 25741846
["alpha", "torus10k.pts"] 2.115 s (5%) 39.649 ms 828.85 MiB (1%) 7915108
["cubical", "bonsai64.dipha"] 1.499 s (5%) 16.636 ms 299.73 MiB (1%) 284200
["cubical", "lena2048.dipha"] 4.290 s (5%) 337.823 ms 1.62 GiB (1%) 4275722
["homology", "klein200.pts"] 8.193 ms (5%) 3.11 MiB (1%) 9100
["homology", "lena1024.dipha"] 1.691 s (5%) 35.135 ms 466.16 MiB (1%) 1201338
["homology", "sphere100.pts"] 111.525 ms (5%) 36.06 MiB (1%) 135724
["rips", "dense", "dragon2000.pts"] 2.146 s (5%) 142.872 ms 281.87 MiB (1%) 11410
["rips", "dense", "fract-r.dist"] 13.388 s (5%) 294.759 ms 1.98 GiB (1%) 5106
["rips", "dense", "o3_1024.pts"] 2.687 s (5%) 145.082 ms 288.30 MiB (1%) 6123
["rips", "sparse", "alpha_4_sphere_2000.spdist"] 4.284 s (5%) 366.54 MiB (1%) 8662
["rips", "sparse", "dragon2000.pts"] 2.344 s (5%) 121.669 ms 312.23 MiB (1%) 7407
["rips", "sparse", "fract-r.dist"] 14.991 s (5%) 298.351 ms 1.98 GiB (1%) 4079
["rips", "sparse", "o3_1024.pts"] 2.099 s (5%) 143.919 ms 296.22 MiB (1%) 4070

Benchmark Group List

Here's a list of all the benchmark groups executed by this job:

  • ["alpha"]
  • ["cubical"]
  • ["homology"]
  • ["rips", "dense"]
  • ["rips", "sparse"]

Julia versioninfo

Julia Version 1.10.2
Commit bd47eca2c8a (2024-03-01 10:14 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.4 LTS
  uname: Linux 6.5.0-1016-azure #16~22.04.1-Ubuntu SMP Fri Feb 16 15:42:02 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  2582 MHz       1283 s          0 s        116 s       4037 s          0 s
       #2  2445 MHz       1603 s          0 s        144 s       3691 s          0 s
       #3  2445 MHz       1725 s          0 s        146 s       3581 s          0 s
       #4  3241 MHz       1235 s          0 s        129 s       4075 s          0 s
  Memory: 15.606498718261719 GB (13635.31640625 MB free)
  Uptime: 547.48 sec
  Load Avg:  1.03  1.03  0.61
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)

Runtime information

Runtime Info
BLAS #threads 2
BLAS.vendor() lbt
Sys.CPU_THREADS 4

lscpu output:

Architecture:                       x86_64
CPU op-mode(s):                     32-bit, 64-bit
Address sizes:                      48 bits physical, 48 bits virtual
Byte Order:                         Little Endian
CPU(s):                             4
On-line CPU(s) list:                0-3
Vendor ID:                          AuthenticAMD
Model name:                         AMD EPYC 7763 64-Core Processor
CPU family:                         25
Model:                              1
Thread(s) per core:                 2
Core(s) per socket:                 2
Socket(s):                          1
Stepping:                           1
BogoMIPS:                           4890.86
Flags:                              fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl tsc_reliable nonstop_tsc cpuid extd_apicid aperfmperf pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand hypervisor lahf_lm cmp_legacy svm cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw topoext invpcid_single vmmcall fsgsbase bmi1 avx2 smep bmi2 erms invpcid rdseed adx smap clflushopt clwb sha_ni xsaveopt xsavec xgetbv1 xsaves clzero xsaveerptr rdpru arat npt nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold v_vmsave_vmload umip vaes vpclmulqdq rdpid fsrm
Virtualization:                     AMD-V
Hypervisor vendor:                  Microsoft
Virtualization type:                full
L1d cache:                          64 KiB (2 instances)
L1i cache:                          64 KiB (2 instances)
L2 cache:                           1 MiB (2 instances)
L3 cache:                           32 MiB (1 instance)
NUMA node(s):                       1
NUMA node0 CPU(s):                  0-3
Vulnerability Gather data sampling: Not affected
Vulnerability Itlb multihit:        Not affected
Vulnerability L1tf:                 Not affected
Vulnerability Mds:                  Not affected
Vulnerability Meltdown:             Not affected
Vulnerability Mmio stale data:      Not affected
Vulnerability Retbleed:             Not affected
Vulnerability Spec rstack overflow: Vulnerable: Safe RET, no microcode
Vulnerability Spec store bypass:    Vulnerable
Vulnerability Spectre v1:           Mitigation; usercopy/swapgs barriers and __user pointer sanitization
Vulnerability Spectre v2:           Mitigation; Retpolines, STIBP disabled, RSB filling, PBRSB-eIBRS Not affected
Vulnerability Srbds:                Not affected
Vulnerability Tsx async abort:      Not affected
Cpu Property Value
Brand AMD EPYC 7763 64-Core Processor
Vendor :AMD
Architecture :Unknown
Model Family: 0xaf, Model: 0x01, Stepping: 0x01, Type: 0x00
Cores 16 physical cores, 16 logical cores (on executing CPU)
No Hyperthreading hardware capability detected
Clock Frequencies Not supported by CPU
Data Cache Level 1:3 : (32, 512, 32768) kbytes
64 byte cache line size
Address Size 48 bits virtual, 48 bits physical
SIMD 256 bit = 32 byte max. SIMD vector size
Time Stamp Counter TSC is accessible via rdtsc
TSC runs at constant rate (invariant from clock frequency)
Perf. Monitoring Performance Monitoring Counters (PMC) are not supported
Hypervisor Yes, Microsoft

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github-actions bot commented Apr 3, 2024

Benchmark result

Judge result

Benchmark Report for /home/runner/work/Ripserer.jl/Ripserer.jl

Job Properties

  • Time of benchmarks:
    • Target: 3 Apr 2024 - 20:31
    • Baseline: 3 Apr 2024 - 20:34
  • Package commits:
    • Target: 1b04ee
    • Baseline: 3f2d63
  • Julia commits:
    • Target: bd47ec
    • Baseline: bd47ec
  • Julia command flags:
    • Target: None
    • Baseline: None
  • Environment variables:
    • Target: None
    • Baseline: None

Results

A ratio greater than 1.0 denotes a possible regression (marked with ❌), while a ratio less
than 1.0 denotes a possible improvement (marked with ✅). Only significant results - results
that indicate possible regressions or improvements - are shown below (thus, an empty table means that all
benchmark results remained invariant between builds).

ID time ratio memory ratio
["cubical", "bonsai64.dipha"] 0.85 (5%) ✅ 1.00 (1%)
["cubical", "lena2048.dipha"] 0.79 (5%) ✅ 1.00 (1%)
["homology", "klein200.pts"] 1.01 (5%) 0.92 (1%) ✅
["homology", "lena1024.dipha"] 1.00 (5%) 0.96 (1%) ✅
["homology", "sphere100.pts"] 0.97 (5%) 0.95 (1%) ✅
["rips", "sparse", "dragon2000.pts"] 0.87 (5%) ✅ 1.00 (1%)
["rips", "sparse", "fract-r.dist"] 0.90 (5%) ✅ 1.00 (1%)
["rips", "sparse", "o3_1024.pts"] 0.92 (5%) ✅ 1.00 (1%)

Benchmark Group List

Here's a list of all the benchmark groups executed by this job:

  • ["alpha"]
  • ["cubical"]
  • ["homology"]
  • ["rips", "dense"]
  • ["rips", "sparse"]

Julia versioninfo

Target

Julia Version 1.10.2
Commit bd47eca2c8a (2024-03-01 10:14 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.4 LTS
  uname: Linux 6.5.0-1016-azure #16~22.04.1-Ubuntu SMP Fri Feb 16 15:42:02 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  3242 MHz       1168 s          0 s        111 s       3594 s          0 s
       #2  3267 MHz       1111 s          0 s        112 s       3667 s          0 s
       #3  2445 MHz        973 s          0 s        119 s       3785 s          0 s
       #4  2589 MHz        802 s          0 s        120 s       3966 s          0 s
  Memory: 15.606498718261719 GB (13602.51171875 MB free)
  Uptime: 491.41 sec
  Load Avg:  1.14  1.0  0.47
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)

Baseline

Julia Version 1.10.2
Commit bd47eca2c8a (2024-03-01 10:14 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.4 LTS
  uname: Linux 6.5.0-1016-azure #16~22.04.1-Ubuntu SMP Fri Feb 16 15:42:02 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  3162 MHz       2085 s          0 s        136 s       4485 s          0 s
       #2  2445 MHz       1826 s          0 s        131 s       4765 s          0 s
       #3  3229 MHz       1124 s          0 s        133 s       5451 s          0 s
       #4  3243 MHz        832 s          0 s        144 s       5743 s          0 s
  Memory: 15.606498718261719 GB (13597.375 MB free)
  Uptime: 674.81 sec
  Load Avg:  1.04  1.02  0.58
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)

Target result

Benchmark Report for /home/runner/work/Ripserer.jl/Ripserer.jl

Job Properties

  • Time of benchmark: 3 Apr 2024 - 20:31
  • Package commit: 1b04ee
  • Julia commit: bd47ec
  • Julia command flags: None
  • Environment variables: None

Results

Below is a table of this job's results, obtained by running the benchmarks.
The values listed in the ID column have the structure [parent_group, child_group, ..., key], and can be used to
index into the BaseBenchmarks suite to retrieve the corresponding benchmarks.
The percentages accompanying time and memory values in the below table are noise tolerances. The "true"
time/memory value for a given benchmark is expected to fall within this percentage of the reported value.
An empty cell means that the value was zero.

ID time GC time memory allocations
["alpha", "klein500.pts"] 7.470 s (5%) 264.297 ms 2.72 GiB (1%) 25741846
["alpha", "torus10k.pts"] 2.112 s (5%) 38.700 ms 828.85 MiB (1%) 7915108
["cubical", "bonsai64.dipha"] 1.500 s (5%) 40.600 ms 299.73 MiB (1%) 284200
["cubical", "lena2048.dipha"] 4.089 s (5%) 336.289 ms 1.62 GiB (1%) 4275722
["homology", "klein200.pts"] 8.377 ms (5%) 2.87 MiB (1%) 9101
["homology", "lena1024.dipha"] 1.811 s (5%) 154.752 ms 446.60 MiB (1%) 1201341
["homology", "sphere100.pts"] 106.693 ms (5%) 34.44 MiB (1%) 135726
["rips", "dense", "dragon2000.pts"] 2.084 s (5%) 137.886 ms 281.87 MiB (1%) 11410
["rips", "dense", "fract-r.dist"] 12.981 s (5%) 283.632 ms 1.98 GiB (1%) 5106
["rips", "dense", "o3_1024.pts"] 2.483 s (5%) 28.189 ms 288.30 MiB (1%) 6123
["rips", "sparse", "alpha_4_sphere_2000.spdist"] 4.110 s (5%) 366.54 MiB (1%) 8662
["rips", "sparse", "dragon2000.pts"] 2.363 s (5%) 123.547 ms 312.23 MiB (1%) 7407
["rips", "sparse", "fract-r.dist"] 14.621 s (5%) 285.797 ms 1.98 GiB (1%) 4079
["rips", "sparse", "o3_1024.pts"] 1.986 s (5%) 138.836 ms 296.22 MiB (1%) 4070

Benchmark Group List

Here's a list of all the benchmark groups executed by this job:

  • ["alpha"]
  • ["cubical"]
  • ["homology"]
  • ["rips", "dense"]
  • ["rips", "sparse"]

Julia versioninfo

Julia Version 1.10.2
Commit bd47eca2c8a (2024-03-01 10:14 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.4 LTS
  uname: Linux 6.5.0-1016-azure #16~22.04.1-Ubuntu SMP Fri Feb 16 15:42:02 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  3242 MHz       1168 s          0 s        111 s       3594 s          0 s
       #2  3267 MHz       1111 s          0 s        112 s       3667 s          0 s
       #3  2445 MHz        973 s          0 s        119 s       3785 s          0 s
       #4  2589 MHz        802 s          0 s        120 s       3966 s          0 s
  Memory: 15.606498718261719 GB (13602.51171875 MB free)
  Uptime: 491.41 sec
  Load Avg:  1.14  1.0  0.47
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)

Baseline result

Benchmark Report for /home/runner/work/Ripserer.jl/Ripserer.jl

Job Properties

  • Time of benchmark: 3 Apr 2024 - 20:34
  • Package commit: 3f2d63
  • Julia commit: bd47ec
  • Julia command flags: None
  • Environment variables: None

Results

Below is a table of this job's results, obtained by running the benchmarks.
The values listed in the ID column have the structure [parent_group, child_group, ..., key], and can be used to
index into the BaseBenchmarks suite to retrieve the corresponding benchmarks.
The percentages accompanying time and memory values in the below table are noise tolerances. The "true"
time/memory value for a given benchmark is expected to fall within this percentage of the reported value.
An empty cell means that the value was zero.

ID time GC time memory allocations
["alpha", "klein500.pts"] 7.683 s (5%) 441.825 ms 2.72 GiB (1%) 25741846
["alpha", "torus10k.pts"] 2.127 s (5%) 37.902 ms 828.85 MiB (1%) 7915108
["cubical", "bonsai64.dipha"] 1.763 s (5%) 21.381 ms 299.73 MiB (1%) 284200
["cubical", "lena2048.dipha"] 5.168 s (5%) 426.174 ms 1.62 GiB (1%) 4275722
["homology", "klein200.pts"] 8.291 ms (5%) 3.11 MiB (1%) 9100
["homology", "lena1024.dipha"] 1.811 s (5%) 153.981 ms 466.16 MiB (1%) 1201338
["homology", "sphere100.pts"] 109.512 ms (5%) 36.06 MiB (1%) 135724
["rips", "dense", "dragon2000.pts"] 2.090 s (5%) 147.300 ms 281.87 MiB (1%) 11410
["rips", "dense", "fract-r.dist"] 13.068 s (5%) 305.215 ms 1.98 GiB (1%) 5106
["rips", "dense", "o3_1024.pts"] 2.613 s (5%) 148.274 ms 288.30 MiB (1%) 6123
["rips", "sparse", "alpha_4_sphere_2000.spdist"] 4.297 s (5%) 366.54 MiB (1%) 8662
["rips", "sparse", "dragon2000.pts"] 2.703 s (5%) 177.690 ms 312.23 MiB (1%) 7407
["rips", "sparse", "fract-r.dist"] 16.256 s (5%) 344.683 ms 1.98 GiB (1%) 4079
["rips", "sparse", "o3_1024.pts"] 2.155 s (5%) 154.842 ms 296.22 MiB (1%) 4070

Benchmark Group List

Here's a list of all the benchmark groups executed by this job:

  • ["alpha"]
  • ["cubical"]
  • ["homology"]
  • ["rips", "dense"]
  • ["rips", "sparse"]

Julia versioninfo

Julia Version 1.10.2
Commit bd47eca2c8a (2024-03-01 10:14 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.4 LTS
  uname: Linux 6.5.0-1016-azure #16~22.04.1-Ubuntu SMP Fri Feb 16 15:42:02 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  3162 MHz       2085 s          0 s        136 s       4485 s          0 s
       #2  2445 MHz       1826 s          0 s        131 s       4765 s          0 s
       #3  3229 MHz       1124 s          0 s        133 s       5451 s          0 s
       #4  3243 MHz        832 s          0 s        144 s       5743 s          0 s
  Memory: 15.606498718261719 GB (13597.375 MB free)
  Uptime: 674.81 sec
  Load Avg:  1.04  1.02  0.58
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)

Runtime information

Runtime Info
BLAS #threads 2
BLAS.vendor() lbt
Sys.CPU_THREADS 4

lscpu output:

Architecture:                       x86_64
CPU op-mode(s):                     32-bit, 64-bit
Address sizes:                      48 bits physical, 48 bits virtual
Byte Order:                         Little Endian
CPU(s):                             4
On-line CPU(s) list:                0-3
Vendor ID:                          AuthenticAMD
Model name:                         AMD EPYC 7763 64-Core Processor
CPU family:                         25
Model:                              1
Thread(s) per core:                 2
Core(s) per socket:                 2
Socket(s):                          1
Stepping:                           1
BogoMIPS:                           4890.86
Flags:                              fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl tsc_reliable nonstop_tsc cpuid extd_apicid aperfmperf pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand hypervisor lahf_lm cmp_legacy svm cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw topoext invpcid_single vmmcall fsgsbase bmi1 avx2 smep bmi2 erms invpcid rdseed adx smap clflushopt clwb sha_ni xsaveopt xsavec xgetbv1 xsaves clzero xsaveerptr rdpru arat npt nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold v_vmsave_vmload umip vaes vpclmulqdq rdpid fsrm
Virtualization:                     AMD-V
Hypervisor vendor:                  Microsoft
Virtualization type:                full
L1d cache:                          64 KiB (2 instances)
L1i cache:                          64 KiB (2 instances)
L2 cache:                           1 MiB (2 instances)
L3 cache:                           32 MiB (1 instance)
NUMA node(s):                       1
NUMA node0 CPU(s):                  0-3
Vulnerability Gather data sampling: Not affected
Vulnerability Itlb multihit:        Not affected
Vulnerability L1tf:                 Not affected
Vulnerability Mds:                  Not affected
Vulnerability Meltdown:             Not affected
Vulnerability Mmio stale data:      Not affected
Vulnerability Retbleed:             Not affected
Vulnerability Spec rstack overflow: Vulnerable: Safe RET, no microcode
Vulnerability Spec store bypass:    Vulnerable
Vulnerability Spectre v1:           Mitigation; usercopy/swapgs barriers and __user pointer sanitization
Vulnerability Spectre v2:           Mitigation; Retpolines, STIBP disabled, RSB filling, PBRSB-eIBRS Not affected
Vulnerability Srbds:                Not affected
Vulnerability Tsx async abort:      Not affected
Cpu Property Value
Brand AMD EPYC 7763 64-Core Processor
Vendor :AMD
Architecture :Unknown
Model Family: 0xaf, Model: 0x01, Stepping: 0x01, Type: 0x00
Cores 16 physical cores, 16 logical cores (on executing CPU)
No Hyperthreading hardware capability detected
Clock Frequencies Not supported by CPU
Data Cache Level 1:3 : (32, 512, 32768) kbytes
64 byte cache line size
Address Size 48 bits virtual, 48 bits physical
SIMD 256 bit = 32 byte max. SIMD vector size
Time Stamp Counter TSC is accessible via rdtsc
TSC runs at constant rate (invariant from clock frequency)
Perf. Monitoring Performance Monitoring Counters (PMC) are not supported
Hypervisor Yes, Microsoft

@coveralls
Copy link

Pull Request Test Coverage Report for Build 8545078607

Details

  • 245 of 250 (98.0%) changed or added relevant lines in 5 files are covered.
  • 3 unchanged lines in 3 files lost coverage.
  • Overall coverage increased (+0.09%) to 96.51%
Changes Missing Coverage Covered Lines Changed/Added Lines %
src/computation/homology.jl 62 63 98.41%
src/filtrations/rips.jl 2 3 66.67%
src/computation/involuted.jl 42 45 93.33%
Files with Coverage Reduction New Missed Lines %
src/filtrations/cubical.jl 1 98.03%
src/base/simplexrecipes.jl 1 66.13%
src/computation/utils.jl 1 88.89%
Totals Coverage Status
Change from base Build 3797140729: 0.09%
Covered Lines: 1770
Relevant Lines: 1834
💛 - Coveralls

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