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mtsch / Ripserer.jl

Flexible and efficient persistent homology computation.
https://mtsch.github.io/Ripserer.jl/dev/
MIT License
66 stars 8 forks source link

Better homology #166

Open mtsch opened 7 months ago

mtsch commented 7 months ago
github-actions[bot] commented 7 months ago
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 :x:), while a ratio less than `1.0` denotes a possible improvement (marked with :white_check_mark:). 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%) :white_check_mark: | | `["homology", "lena1024.dipha"]` | 1.12 (5%) :x: | 0.96 (1%) :white_check_mark: | | `["homology", "sphere100.pts"]` | 1.01 (5%) | 0.95 (1%) :white_check_mark: | ## 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[bot] commented 7 months ago
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 :x:), while a ratio less than `1.0` denotes a possible improvement (marked with :white_check_mark:). 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%) :white_check_mark: | | `["homology", "lena1024.dipha"]` | 1.05 (5%) :x: | 0.96 (1%) :white_check_mark: | | `["homology", "sphere100.pts"]` | 0.95 (5%) :white_check_mark: | 0.95 (1%) :white_check_mark: | | `["rips", "dense", "o3_1024.pts"]` | 0.94 (5%) :white_check_mark: | 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 |
github-actions[bot] commented 7 months ago
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 :x:), while a ratio less than `1.0` denotes a possible improvement (marked with :white_check_mark:). 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%) :white_check_mark: | 1.00 (1%) | | `["cubical", "lena2048.dipha"]` | 0.79 (5%) :white_check_mark: | 1.00 (1%) | | `["homology", "klein200.pts"]` | 1.01 (5%) | 0.92 (1%) :white_check_mark: | | `["homology", "lena1024.dipha"]` | 1.00 (5%) | 0.96 (1%) :white_check_mark: | | `["homology", "sphere100.pts"]` | 0.97 (5%) | 0.95 (1%) :white_check_mark: | | `["rips", "sparse", "dragon2000.pts"]` | 0.87 (5%) :white_check_mark: | 1.00 (1%) | | `["rips", "sparse", "fract-r.dist"]` | 0.90 (5%) :white_check_mark: | 1.00 (1%) | | `["rips", "sparse", "o3_1024.pts"]` | 0.92 (5%) :white_check_mark: | 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 commented 7 months ago

Pull Request Test Coverage Report for Build 8545078607

Details

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%
<!-- Total: 245 250 98.0% -->
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%
<!-- Total: 3 -->
Totals Coverage Status
Change from base Build 3797140729: 0.09%
Covered Lines: 1770
Relevant Lines: 1834
💛 - Coveralls