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Improve cycle reconstruction performance #173

Merged
merged 3 commits into from
Dec 19, 2024
Merged

Improve cycle reconstruction performance #173

merged 3 commits into from
Dec 19, 2024

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mtsch
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@mtsch mtsch commented Dec 19, 2024

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Update src/extra/cycles.jl
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Benchmark result

Judge result

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

Job Properties

  • Time of benchmarks:
    • Target: 19 Dec 2024 - 08:49
    • Baseline: 19 Dec 2024 - 08:52
  • Package commits:
    • Target: 2146fe
    • Baseline: 8b296a
  • Julia commits:
    • Target: 5e9a32
    • Baseline: 5e9a32
  • 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
["rips", "dense", "dragon2000.pts"] 1.06 (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 1.11.2
Commit 5e9a32e7af2 (2024-12-01 20:02 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 24.04.1 LTS
  uname: Linux 6.8.0-1017-azure #20-Ubuntu SMP Tue Oct 22 03:43:13 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1     0 MHz       1136 s          0 s        123 s       2973 s          0 s
       #2     0 MHz       1303 s          0 s        132 s       2771 s          0 s
       #3     0 MHz       1036 s          0 s        108 s       3041 s          0 s
       #4     0 MHz       1279 s          0 s         92 s       2843 s          0 s
  Memory: 15.615280151367188 GB (13395.859375 MB free)
  Uptime: 429.36 sec
  Load Avg:  1.16  1.24  0.65
  WORD_SIZE: 64
  LLVM: libLLVM-16.0.6 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)

Baseline

Julia Version 1.11.2
Commit 5e9a32e7af2 (2024-12-01 20:02 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 24.04.1 LTS
  uname: Linux 6.8.0-1017-azure #20-Ubuntu SMP Tue Oct 22 03:43:13 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1     0 MHz       1433 s          0 s        134 s       4486 s          0 s
       #2     0 MHz       2591 s          0 s        156 s       3282 s          0 s
       #3     0 MHz       1122 s          0 s        127 s       4757 s          0 s
       #4     0 MHz       1428 s          0 s        115 s       4492 s          0 s
  Memory: 15.615280151367188 GB (13325.921875 MB free)
  Uptime: 611.69 sec
  Load Avg:  1.0  1.12  0.72
  WORD_SIZE: 64
  LLVM: libLLVM-16.0.6 (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: 19 Dec 2024 - 8:49
  • Package commit: 2146fe
  • Julia commit: 5e9a32
  • 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"] 7.523 s (5%) 544.198 ms 2.83 GiB (1%) 44120166
["alpha", "torus10k.pts"] 2.169 s (5%) 71.557 ms 872.05 MiB (1%) 13516872
["cubical", "bonsai64.dipha"] 1.501 s (5%) 53.700 ms 384.74 MiB (1%) 546437
["cubical", "lena2048.dipha"] 4.037 s (5%) 435.894 ms 2.02 GiB (1%) 8470105
["homology", "klein200.pts"] 7.587 ms (5%) 3.10 MiB (1%) 8951
["homology", "lena1024.dipha"] 1.814 s (5%) 340.712 ms 618.92 MiB (1%) 1203673
["homology", "sphere100.pts"] 100.854 ms (5%) 38.88 MiB (1%) 135715
["rips", "dense", "dragon2000.pts"] 2.164 s (5%) 185.208 ms 402.53 MiB (1%) 13480
["rips", "dense", "fract-r.dist"] 12.671 s (5%) 368.633 ms 2.56 GiB (1%) 5705
["rips", "dense", "o3_1024.pts"] 2.570 s (5%) 18.753 ms 359.83 MiB (1%) 5202
["rips", "sparse", "alpha_4_sphere_2000.spdist"] 4.281 s (5%) 196.713 ms 463.59 MiB (1%) 8786
["rips", "sparse", "dragon2000.pts"] 2.204 s (5%) 177.013 ms 432.98 MiB (1%) 11482
["rips", "sparse", "fract-r.dist"] 14.345 s (5%) 376.760 ms 2.56 GiB (1%) 5195
["rips", "sparse", "o3_1024.pts"] 1.820 s (5%) 6.067 ms 367.80 MiB (1%) 4179

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 1.11.2
Commit 5e9a32e7af2 (2024-12-01 20:02 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 24.04.1 LTS
  uname: Linux 6.8.0-1017-azure #20-Ubuntu SMP Tue Oct 22 03:43:13 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1     0 MHz       1136 s          0 s        123 s       2973 s          0 s
       #2     0 MHz       1303 s          0 s        132 s       2771 s          0 s
       #3     0 MHz       1036 s          0 s        108 s       3041 s          0 s
       #4     0 MHz       1279 s          0 s         92 s       2843 s          0 s
  Memory: 15.615280151367188 GB (13395.859375 MB free)
  Uptime: 429.36 sec
  Load Avg:  1.16  1.24  0.65
  WORD_SIZE: 64
  LLVM: libLLVM-16.0.6 (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: 19 Dec 2024 - 8:52
  • Package commit: 8b296a
  • Julia commit: 5e9a32
  • 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"] 7.538 s (5%) 545.110 ms 2.83 GiB (1%) 44120166
["alpha", "torus10k.pts"] 2.136 s (5%) 69.405 ms 872.05 MiB (1%) 13516872
["cubical", "bonsai64.dipha"] 1.518 s (5%) 55.176 ms 384.74 MiB (1%) 546437
["cubical", "lena2048.dipha"] 4.031 s (5%) 439.884 ms 2.02 GiB (1%) 8470105
["homology", "klein200.pts"] 7.684 ms (5%) 3.10 MiB (1%) 8951
["homology", "lena1024.dipha"] 1.815 s (5%) 334.128 ms 618.92 MiB (1%) 1203673
["homology", "sphere100.pts"] 99.169 ms (5%) 38.88 MiB (1%) 135715
["rips", "dense", "dragon2000.pts"] 2.051 s (5%) 174.689 ms 402.53 MiB (1%) 13480
["rips", "dense", "fract-r.dist"] 12.577 s (5%) 367.917 ms 2.56 GiB (1%) 5705
["rips", "dense", "o3_1024.pts"] 2.522 s (5%) 18.982 ms 359.83 MiB (1%) 5202
["rips", "sparse", "alpha_4_sphere_2000.spdist"] 4.146 s (5%) 194.482 ms 463.59 MiB (1%) 8786
["rips", "sparse", "dragon2000.pts"] 2.200 s (5%) 181.612 ms 432.98 MiB (1%) 11482
["rips", "sparse", "fract-r.dist"] 14.417 s (5%) 370.960 ms 2.56 GiB (1%) 5195
["rips", "sparse", "o3_1024.pts"] 1.816 s (5%) 6.208 ms 367.80 MiB (1%) 4179

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 1.11.2
Commit 5e9a32e7af2 (2024-12-01 20:02 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 24.04.1 LTS
  uname: Linux 6.8.0-1017-azure #20-Ubuntu SMP Tue Oct 22 03:43:13 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1     0 MHz       1433 s          0 s        134 s       4486 s          0 s
       #2     0 MHz       2591 s          0 s        156 s       3282 s          0 s
       #3     0 MHz       1122 s          0 s        127 s       4757 s          0 s
       #4     0 MHz       1428 s          0 s        115 s       4492 s          0 s
  Memory: 15.615280151367188 GB (13325.921875 MB free)
  Uptime: 611.69 sec
  Load Avg:  1.0  1.12  0.72
  WORD_SIZE: 64
  LLVM: libLLVM-16.0.6 (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 vmmcall fsgsbase bmi1 avx2 smep bmi2 erms invpcid rdseed adx smap clflushopt clwb sha_ni xsaveopt xsavec xgetbv1 xsaves user_shstk 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 Reg file data sampling: 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; BHI 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
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coveralls commented Dec 19, 2024 •
edited
Loading

Pull Request Test Coverage Report for Build 12409292057

Details

  • 11 of 11 (100.0%) changed or added relevant lines in 1 file are covered.
  • 13 unchanged lines in 8 files lost coverage.
  • Overall coverage decreased (-0.7%) to 95.558%
Files with Coverage Reduction New Missed Lines %
src/base/primefield.jl 1 92.31%
src/base/abstractcell.jl 1 80.95%
src/base/abstractfiltration.jl 1 85.71%
src/filtrations/edgecollapse.jl 1 99.07%
src/filtrations/cubical.jl 1 98.03%
src/computation/cohomology.jl 2 97.47%
src/base/chainelement.jl 3 92.21%
src/extra/cycles.jl 3 94.32%
Totals Coverage Status
Change from base Build 9361292240: -0.7%
Covered Lines: 1721
Relevant Lines: 1801
💛 - Coveralls

@github-actions GitHub Actions
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Contributor

Benchmark result

Judge result

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

Job Properties

  • Time of benchmarks:
    • Target: 19 Dec 2024 - 08:54
    • Baseline: 19 Dec 2024 - 08:57
  • Package commits:
    • Target: 46f409
    • Baseline: 8b296a
  • Julia commits:
    • Target: 5e9a32
    • Baseline: 5e9a32
  • 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", "lena1024.dipha"] 0.86 (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 1.11.2
Commit 5e9a32e7af2 (2024-12-01 20:02 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 24.04.1 LTS
  uname: Linux 6.8.0-1017-azure #20-Ubuntu SMP Tue Oct 22 03:43:13 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1     0 MHz        814 s          0 s         97 s       3403 s          0 s
       #2     0 MHz        974 s          0 s        113 s       3260 s          0 s
       #3     0 MHz       1632 s          0 s        116 s       2532 s          0 s
       #4     0 MHz       1235 s          0 s         94 s       2963 s          0 s
  Memory: 15.615280151367188 GB (13277.02734375 MB free)
  Uptime: 438.85 sec
  Load Avg:  1.14  1.15  0.6
  WORD_SIZE: 64
  LLVM: libLLVM-16.0.6 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)

Baseline

Julia Version 1.11.2
Commit 5e9a32e7af2 (2024-12-01 20:02 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 24.04.1 LTS
  uname: Linux 6.8.0-1017-azure #20-Ubuntu SMP Tue Oct 22 03:43:13 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1     0 MHz       1037 s          0 s        112 s       4951 s          0 s
       #2     0 MHz       1791 s          0 s        134 s       4207 s          0 s
       #3     0 MHz       1870 s          0 s        130 s       4064 s          0 s
       #4     0 MHz       1738 s          0 s        110 s       4230 s          0 s
  Memory: 15.615280151367188 GB (13349.15625 MB free)
  Uptime: 617.57 sec
  Load Avg:  1.0  1.08  0.68
  WORD_SIZE: 64
  LLVM: libLLVM-16.0.6 (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: 19 Dec 2024 - 8:54
  • Package commit: 46f409
  • Julia commit: 5e9a32
  • 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"] 7.294 s (5%) 525.145 ms 2.83 GiB (1%) 44120166
["alpha", "torus10k.pts"] 2.050 s (5%) 67.434 ms 872.05 MiB (1%) 13516872
["cubical", "bonsai64.dipha"] 1.465 s (5%) 53.499 ms 384.74 MiB (1%) 546437
["cubical", "lena2048.dipha"] 3.918 s (5%) 428.083 ms 2.02 GiB (1%) 8470105
["homology", "klein200.pts"] 7.569 ms (5%) 3.10 MiB (1%) 8951
["homology", "lena1024.dipha"] 1.495 s (5%) 52.150 ms 618.92 MiB (1%) 1203673
["homology", "sphere100.pts"] 101.819 ms (5%) 38.88 MiB (1%) 135715
["rips", "dense", "dragon2000.pts"] 2.006 s (5%) 174.397 ms 402.53 MiB (1%) 13480
["rips", "dense", "fract-r.dist"] 12.291 s (5%) 351.770 ms 2.56 GiB (1%) 5705
["rips", "dense", "o3_1024.pts"] 2.436 s (5%) 19.111 ms 359.83 MiB (1%) 5202
["rips", "sparse", "alpha_4_sphere_2000.spdist"] 4.054 s (5%) 192.195 ms 463.59 MiB (1%) 8786
["rips", "sparse", "dragon2000.pts"] 2.151 s (5%) 173.425 ms 432.98 MiB (1%) 11482
["rips", "sparse", "fract-r.dist"] 14.019 s (5%) 359.073 ms 2.56 GiB (1%) 5195
["rips", "sparse", "o3_1024.pts"] 1.736 s (5%) 5.851 ms 367.80 MiB (1%) 4179

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 1.11.2
Commit 5e9a32e7af2 (2024-12-01 20:02 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 24.04.1 LTS
  uname: Linux 6.8.0-1017-azure #20-Ubuntu SMP Tue Oct 22 03:43:13 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1     0 MHz        814 s          0 s         97 s       3403 s          0 s
       #2     0 MHz        974 s          0 s        113 s       3260 s          0 s
       #3     0 MHz       1632 s          0 s        116 s       2532 s          0 s
       #4     0 MHz       1235 s          0 s         94 s       2963 s          0 s
  Memory: 15.615280151367188 GB (13277.02734375 MB free)
  Uptime: 438.85 sec
  Load Avg:  1.14  1.15  0.6
  WORD_SIZE: 64
  LLVM: libLLVM-16.0.6 (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: 19 Dec 2024 - 8:57
  • Package commit: 8b296a
  • Julia commit: 5e9a32
  • 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"] 7.366 s (5%) 526.847 ms 2.83 GiB (1%) 44120166
["alpha", "torus10k.pts"] 2.056 s (5%) 63.515 ms 872.05 MiB (1%) 13516872
["cubical", "bonsai64.dipha"] 1.467 s (5%) 53.477 ms 384.74 MiB (1%) 546437
["cubical", "lena2048.dipha"] 3.947 s (5%) 449.387 ms 2.02 GiB (1%) 8470105
["homology", "klein200.pts"] 7.780 ms (5%) 3.10 MiB (1%) 8951
["homology", "lena1024.dipha"] 1.746 s (5%) 326.806 ms 618.92 MiB (1%) 1203673
["homology", "sphere100.pts"] 98.583 ms (5%) 38.88 MiB (1%) 135715
["rips", "dense", "dragon2000.pts"] 2.050 s (5%) 172.773 ms 402.53 MiB (1%) 13480
["rips", "dense", "fract-r.dist"] 12.540 s (5%) 355.194 ms 2.56 GiB (1%) 5705
["rips", "dense", "o3_1024.pts"] 2.444 s (5%) 18.987 ms 359.83 MiB (1%) 5202
["rips", "sparse", "alpha_4_sphere_2000.spdist"] 4.069 s (5%) 192.447 ms 463.59 MiB (1%) 8786
["rips", "sparse", "dragon2000.pts"] 2.186 s (5%) 175.750 ms 432.98 MiB (1%) 11482
["rips", "sparse", "fract-r.dist"] 14.131 s (5%) 355.166 ms 2.56 GiB (1%) 5195
["rips", "sparse", "o3_1024.pts"] 1.790 s (5%) 6.233 ms 367.80 MiB (1%) 4179

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 1.11.2
Commit 5e9a32e7af2 (2024-12-01 20:02 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 24.04.1 LTS
  uname: Linux 6.8.0-1017-azure #20-Ubuntu SMP Tue Oct 22 03:43:13 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1     0 MHz       1037 s          0 s        112 s       4951 s          0 s
       #2     0 MHz       1791 s          0 s        134 s       4207 s          0 s
       #3     0 MHz       1870 s          0 s        130 s       4064 s          0 s
       #4     0 MHz       1738 s          0 s        110 s       4230 s          0 s
  Memory: 15.615280151367188 GB (13349.15625 MB free)
  Uptime: 617.57 sec
  Load Avg:  1.0  1.08  0.68
  WORD_SIZE: 64
  LLVM: libLLVM-16.0.6 (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:                             4890.85
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 vmmcall fsgsbase bmi1 avx2 smep bmi2 erms invpcid rdseed adx smap clflushopt clwb sha_ni xsaveopt xsavec xgetbv1 xsaves user_shstk 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 Reg file data sampling: 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; BHI 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

@mtsch mtsch changed the title Improve cycle reconstruction Improve cycle reconstruction performance Dec 19, 2024
@mtsch mtsch marked this pull request as ready for review December 19, 2024 09:10
@mtsch mtsch merged commit 6859825 into master Dec 19, 2024
8 checks passed
@mtsch mtsch deleted the improve-cycle-reconstruction branch December 19, 2024 09:10
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