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mtsch / Ripserer.jl

Flexible and efficient persistent homology computation.
https://mtsch.github.io/Ripserer.jl/dev/
MIT License
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Add information about other Julia packages #95

Closed mtsch closed 4 years ago

mtsch commented 4 years ago

Related issue: #94

codecov[bot] commented 4 years ago

Codecov Report

Merging #95 into master will not change coverage. The diff coverage is n/a.

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@@           Coverage Diff           @@
##           master      #95   +/-   ##
=======================================
  Coverage   95.90%   95.90%           
=======================================
  Files          13       13           
  Lines         929      929           
=======================================
  Hits          891      891           
  Misses         38       38

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github-actions[bot] commented 4 years ago
Benchmark result # Judge result # Benchmark Report for */home/runner/work/Ripserer.jl/Ripserer.jl* ## Job Properties * Time of benchmarks: - Target: 30 Aug 2020 - 03:19 - Baseline: 30 Aug 2020 - 03:23 * Package commits: - Target: ba3f7e - Baseline: ad4262 * Julia commits: - Target: 44fa15 - Baseline: 44fa15 * 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 | |----------------------------------------------------------------|---------------|--------------| | `["coboundary", "sparse, 50% full"]` | 1.12 (5%) :x: | 1.00 (1%) | | `["image", "bonsai"]` | 1.05 (5%) :x: | 1.00 (1%) | | `["torus", "n=1024, dim_max=1, modulus=7, threshold=nothing"]` | 1.07 (5%) :x: | 1.00 (1%) | ## Benchmark Group List Here's a list of all the benchmark groups executed by this job: - `["coboundary"]` - `["image"]` - `["sparse"]` - `["torus"]` ## Julia versioninfo ### Target ``` Julia Version 1.4.2 Commit 44fa15b150* (2020-05-23 18:35 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 18.04.5 LTS uname: Linux 5.3.0-1034-azure #35~18.04.1-Ubuntu SMP Mon Jul 13 12:54:45 UTC 2020 x86_64 x86_64 CPU: Intel(R) Xeon(R) Platinum 8171M CPU @ 2.60GHz: speed user nice sys idle irq #1 2095 MHz 9745 s 0 s 1718 s 33568 s 0 s #2 2095 MHz 30331 s 0 s 3437 s 11405 s 0 s Memory: 6.764881134033203 GB (1956.0546875 MB free) Uptime: 470.0 sec Load Avg: 1.0 0.91357421875 0.50439453125 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-8.0.1 (ORCJIT, skylake) ``` ### Baseline ``` Julia Version 1.4.2 Commit 44fa15b150* (2020-05-23 18:35 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 18.04.5 LTS uname: Linux 5.3.0-1034-azure #35~18.04.1-Ubuntu SMP Mon Jul 13 12:54:45 UTC 2020 x86_64 x86_64 CPU: Intel(R) Xeon(R) Platinum 8171M CPU @ 2.60GHz: speed user nice sys idle irq #1 2095 MHz 25471 s 0 s 2582 s 40909 s 0 s #2 2095 MHz 36960 s 0 s 4198 s 27932 s 0 s Memory: 6.764881134033203 GB (1925.0859375 MB free) Uptime: 710.0 sec Load Avg: 1.00244140625 0.984375 0.6376953125 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-8.0.1 (ORCJIT, skylake) ``` --- # Target result # Benchmark Report for */home/runner/work/Ripserer.jl/Ripserer.jl* ## Job Properties * Time of benchmark: 30 Aug 2020 - 3:19 * Package commit: ba3f7e * Julia commit: 44fa15 * 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 | |----------------------------------------------------------------|----------------:|-----------:|----------------:|------------:| | `["coboundary", "full, no threshold"]` | 5.433 s (5%) | | 3.05 MiB (1%) | 50000 | | `["coboundary", "full, threshold=1"]` | 3.893 s (5%) | | 3.05 MiB (1%) | 50000 | | `["coboundary", "sparse, 25% full"]` | 202.006 ms (5%) | | 4.27 MiB (1%) | 40000 | | `["coboundary", "sparse, 50% full"]` | 978.753 ms (5%) | | 2.14 MiB (1%) | 20000 | | `["coboundary", "sparse, 75% full"]` | 1.342 s (5%) | | 1.07 MiB (1%) | 10000 | | `["image", "bonsai"]` | 2.436 s (5%) | 54.479 ms | 311.45 MiB (1%) | 4091823 | | `["image", "hubble"]` | 6.148 s (5%) | 252.074 ms | 1.75 GiB (1%) | 34001155 | | `["sparse", "20 tori with 100 points, dim_max=2, modulus=3"]` | 5.320 s (5%) | 84.919 ms | 1.07 GiB (1%) | 7848622 | | `["sparse", "20 tori with 300 points, dim_max=1, modulus=3"]` | 7.776 s (5%) | | 445.85 MiB (1%) | 4875937 | | `["sparse", "20 tori with 50 points, dim_max=3, modulus=2"]` | 7.091 s (5%) | 91.558 ms | 1.47 GiB (1%) | 11376330 | | `["sparse", "30 tori with 200 points, dim_max=1, modulus=2"]` | 3.037 s (5%) | 44.101 ms | 256.17 MiB (1%) | 3243174 | | `["torus", "n=1024, dim_max=1, modulus=2, threshold=1"]` | 10.377 s (5%) | | 466.16 MiB (1%) | 1138984 | | `["torus", "n=1024, dim_max=1, modulus=7, threshold=nothing"]` | 37.312 s (5%) | 26.964 ms | 1.55 GiB (1%) | 2444931 | | `["torus", "n=256, dim_max=2, modulus=2, threshold=nothing"]` | 2.960 s (5%) | 32.621 ms | 594.87 MiB (1%) | 5233276 | | `["torus", "n=256, dim_max=2, modulus=7, threshold=1"]` | 2.012 s (5%) | 31.374 ms | 336.17 MiB (1%) | 2819276 | | `["torus", "n=64, dim_max=4, modulus=2, threshold=nothing"]` | 5.952 s (5%) | 97.406 ms | 1.18 GiB (1%) | 10982105 | | `["torus", "n=81, dim_max=4, modulus=3, threshold=1"]` | 9.168 s (5%) | 113.030 ms | 1.36 GiB (1%) | 14858586 | ## Benchmark Group List Here's a list of all the benchmark groups executed by this job: - `["coboundary"]` - `["image"]` - `["sparse"]` - `["torus"]` ## Julia versioninfo ``` Julia Version 1.4.2 Commit 44fa15b150* (2020-05-23 18:35 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 18.04.5 LTS uname: Linux 5.3.0-1034-azure #35~18.04.1-Ubuntu SMP Mon Jul 13 12:54:45 UTC 2020 x86_64 x86_64 CPU: Intel(R) Xeon(R) Platinum 8171M CPU @ 2.60GHz: speed user nice sys idle irq #1 2095 MHz 9745 s 0 s 1718 s 33568 s 0 s #2 2095 MHz 30331 s 0 s 3437 s 11405 s 0 s Memory: 6.764881134033203 GB (1956.0546875 MB free) Uptime: 470.0 sec Load Avg: 1.0 0.91357421875 0.50439453125 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-8.0.1 (ORCJIT, skylake) ``` --- # Baseline result # Benchmark Report for */home/runner/work/Ripserer.jl/Ripserer.jl* ## Job Properties * Time of benchmark: 30 Aug 2020 - 3:23 * Package commit: ad4262 * Julia commit: 44fa15 * 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 | |----------------------------------------------------------------|----------------:|-----------:|----------------:|------------:| | `["coboundary", "full, no threshold"]` | 5.386 s (5%) | | 3.05 MiB (1%) | 50000 | | `["coboundary", "full, threshold=1"]` | 3.961 s (5%) | | 3.05 MiB (1%) | 50000 | | `["coboundary", "sparse, 25% full"]` | 198.811 ms (5%) | | 4.27 MiB (1%) | 40000 | | `["coboundary", "sparse, 50% full"]` | 877.222 ms (5%) | | 2.14 MiB (1%) | 20000 | | `["coboundary", "sparse, 75% full"]` | 1.317 s (5%) | | 1.07 MiB (1%) | 10000 | | `["image", "bonsai"]` | 2.319 s (5%) | 53.429 ms | 311.45 MiB (1%) | 4091823 | | `["image", "hubble"]` | 6.039 s (5%) | 264.762 ms | 1.75 GiB (1%) | 34001155 | | `["sparse", "20 tori with 100 points, dim_max=2, modulus=3"]` | 5.321 s (5%) | 85.125 ms | 1.07 GiB (1%) | 7848621 | | `["sparse", "20 tori with 300 points, dim_max=1, modulus=3"]` | 7.553 s (5%) | | 445.85 MiB (1%) | 4875937 | | `["sparse", "20 tori with 50 points, dim_max=3, modulus=2"]` | 7.232 s (5%) | 92.033 ms | 1.47 GiB (1%) | 11376330 | | `["sparse", "30 tori with 200 points, dim_max=1, modulus=2"]` | 3.069 s (5%) | 43.499 ms | 256.17 MiB (1%) | 3243174 | | `["torus", "n=1024, dim_max=1, modulus=2, threshold=1"]` | 10.366 s (5%) | | 466.16 MiB (1%) | 1138984 | | `["torus", "n=1024, dim_max=1, modulus=7, threshold=nothing"]` | 35.022 s (5%) | 25.580 ms | 1.55 GiB (1%) | 2444932 | | `["torus", "n=256, dim_max=2, modulus=2, threshold=nothing"]` | 2.943 s (5%) | 31.136 ms | 594.87 MiB (1%) | 5233276 | | `["torus", "n=256, dim_max=2, modulus=7, threshold=1"]` | 2.005 s (5%) | 33.766 ms | 336.17 MiB (1%) | 2819276 | | `["torus", "n=64, dim_max=4, modulus=2, threshold=nothing"]` | 5.971 s (5%) | 101.174 ms | 1.18 GiB (1%) | 10982123 | | `["torus", "n=81, dim_max=4, modulus=3, threshold=1"]` | 9.089 s (5%) | 115.001 ms | 1.36 GiB (1%) | 14858567 | ## Benchmark Group List Here's a list of all the benchmark groups executed by this job: - `["coboundary"]` - `["image"]` - `["sparse"]` - `["torus"]` ## Julia versioninfo ``` Julia Version 1.4.2 Commit 44fa15b150* (2020-05-23 18:35 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 18.04.5 LTS uname: Linux 5.3.0-1034-azure #35~18.04.1-Ubuntu SMP Mon Jul 13 12:54:45 UTC 2020 x86_64 x86_64 CPU: Intel(R) Xeon(R) Platinum 8171M CPU @ 2.60GHz: speed user nice sys idle irq #1 2095 MHz 25471 s 0 s 2582 s 40909 s 0 s #2 2095 MHz 36960 s 0 s 4198 s 27932 s 0 s Memory: 6.764881134033203 GB (1925.0859375 MB free) Uptime: 710.0 sec Load Avg: 1.00244140625 0.984375 0.6376953125 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-8.0.1 (ORCJIT, skylake) ``` --- # Runtime information | Runtime Info | | |:--|:--| | BLAS #threads | 2 | | `BLAS.vendor()` | `openblas64` | | `Sys.CPU_THREADS` | 2 | `lscpu` output: Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit Byte Order: Little Endian CPU(s): 2 On-line CPU(s) list: 0,1 Thread(s) per core: 1 Core(s) per socket: 2 Socket(s): 1 NUMA node(s): 1 Vendor ID: GenuineIntel CPU family: 6 Model: 85 Model name: Intel(R) Xeon(R) Platinum 8171M CPU @ 2.60GHz Stepping: 4 CPU MHz: 2095.246 BogoMIPS: 4190.49 Hypervisor vendor: Microsoft Virtualization type: full L1d cache: 32K L1i cache: 32K L2 cache: 1024K L3 cache: 36608K NUMA node0 CPU(s): 0,1 Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ss ht syscall nx pdpe1gb rdtscp lm constant_tsc rep_good nopl xtopology cpuid pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand hypervisor lahf_lm abm 3dnowprefetch invpcid_single pti fsgsbase bmi1 hle avx2 smep bmi2 erms invpcid rtm mpx avx512f avx512dq rdseed adx smap clflushopt avx512cd avx512bw avx512vl xsaveopt xsavec xsaves md_clear | Cpu Property | Value | |:------------------ |:------------------------------------------------------- | | Brand | Intel(R) Xeon(R) Platinum 8171M CPU @ 2.60GHz | | Vendor | :Intel | | Architecture | :Skylake | | Model | Family: 0x06, Model: 0x55, Stepping: 0x04, Type: 0x00 | | Cores | 2 physical cores, 2 logical cores (on executing CPU) | | | No Hyperthreading detected | | Clock Frequencies | Not supported by CPU | | Data Cache | Level 1:3 : (32, 1024, 36608) kbytes | | | 64 byte cache line size | | Address Size | 48 bits virtual, 44 bits physical | | SIMD | 512 bit = 64 byte max. SIMD vector size | | Time Stamp Counter | TSC is accessible via `rdtsc` | | | TSC increased at every clock cycle (non-invariant TSC) | | Perf. Monitoring | Performance Monitoring Counters (PMC) are not supported | | Hypervisor | Yes, Microsoft |