search

BioJulia / GenomicFeatures.jl

Tools for genomic features in Julia.
Other
32 stars 13 forks source link

Release/v2.1.0 #41

Closed CiaranOMara closed 2 years ago

CiaranOMara commented 3 years ago

This PR attempts to include all non-breaking features from https://github.com/BioJulia/GenomicFeatures.jl/tree/pu/v3.0.0.

Briefly, this PR:

github-actions[bot] commented 3 years ago
Benchmark result # Judge result # Benchmark Report for */home/runner/work/GenomicFeatures.jl/GenomicFeatures.jl* ## Job Properties * Time of benchmarks: - Target: 25 Jun 2021 - 16:21 - Baseline: 25 Jun 2021 - 16:22 * Package commits: - Target: 18c2c8 - Baseline: d6de93 * Julia commits: - Target: 6aaede - Baseline: 6aaede * 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 | |---------------------------------------------------------------------------|------------------------------|---------------| | `["accessors", "Vector{Interval{Int64}}", "leftposition"]` | 0.84 (5%) :white_check_mark: | 1.00 (1%) | | `["accessors", "Vector{Interval{Int64}}", "seqname"]` | 0.88 (5%) :white_check_mark: | 1.00 (1%) | | `["eachoverlap", "IntervalCollection{Int64}, IntervalCollection{Int64}"]` | 0.94 (5%) :white_check_mark: | 1.00 (1%) | | `["eachoverlap", "IntervalCollection{Int64}, Vector{Interval{Int64}}"]` | 1.02 (5%) | 1.05 (1%) :x: | | `["insert", "shorthand"]` | 0.84 (5%) :white_check_mark: | 1.00 (1%) | | `["insert", "type"]` | 0.92 (5%) :white_check_mark: | 1.00 (1%) | | `["push", "Vector{Interval{Int64}}"]` | 0.93 (5%) :white_check_mark: | 1.00 (1%) | ## Benchmark Group List Here's a list of all the benchmark groups executed by this job: - `["accessors", "Vector{Interval{Int64}}"]` - `["eachoverlap"]` - `["insert"]` - `["push"]` - `["sort"]` ## Julia versioninfo ### Target ``` Julia Version 1.6.1 Commit 6aaedecc44 (2021-04-23 05:59 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 20.04.2 LTS uname: Linux 5.8.0-1033-azure #35~20.04.1-Ubuntu SMP Wed May 19 06:46:04 UTC 2021 x86_64 x86_64 CPU: Intel(R) Xeon(R) CPU E5-2673 v4 @ 2.30GHz: speed user nice sys idle irq #1 2294 MHz 1603 s 1 s 208 s 835 s 0 s #2 2294 MHz 871 s 1 s 140 s 1671 s 0 s Memory: 6.790924072265625 GB (3505.1015625 MB free) Uptime: 273.0 sec Load Avg: 1.08 0.81 0.37 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-11.0.1 (ORCJIT, broadwell) ``` ### Baseline ``` Julia Version 1.6.1 Commit 6aaedecc44 (2021-04-23 05:59 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 20.04.2 LTS uname: Linux 5.8.0-1033-azure #35~20.04.1-Ubuntu SMP Wed May 19 06:46:04 UTC 2021 x86_64 x86_64 CPU: Intel(R) Xeon(R) CPU E5-2673 v4 @ 2.30GHz: speed user nice sys idle irq #1 2294 MHz 2249 s 1 s 247 s 879 s 0 s #2 2294 MHz 921 s 1 s 143 s 2348 s 0 s Memory: 6.790924072265625 GB (3530.7734375 MB free) Uptime: 346.0 sec Load Avg: 1.02 0.86 0.42 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-11.0.1 (ORCJIT, broadwell) ``` --- # Target result # Benchmark Report for */home/runner/work/GenomicFeatures.jl/GenomicFeatures.jl* ## Job Properties * Time of benchmark: 25 Jun 2021 - 16:21 * Package commit: 18c2c8 * Julia commit: 6aaede * 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 | |---------------------------------------------------------------------------|----------------:|----------:|----------------:|------------:| | `["accessors", "Vector{Interval{Int64}}", "leftposition"]` | 1.130 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "metadata"]` | 1.160 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "rightposition"]` | 1.100 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "seqname"]` | 1.922 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "strand"]` | 871.154 ns (5%) | | 1.06 KiB (1%) | 1 | | `["eachoverlap", "IntervalCollection{Int64}, IntervalCollection{Int64}"]` | 418.800 ms (5%) | 8.428 ms | 99.91 MiB (1%) | 591412 | | `["eachoverlap", "IntervalCollection{Int64}, Vector{Interval{Int64}}"]` | 131.308 ms (5%) | 28.999 ms | 227.44 MiB (1%) | 2036657 | | `["eachoverlap", "Vector{Interval{Int64}}, IntervalCollection{Int64}"]` | 35.548 ms (5%) | 6.222 ms | 81.86 MiB (1%) | 295706 | | `["eachoverlap", "Vector{Interval{Int64}}, Vector{Interval{Int64}}"]` | 108.371 ms (5%) | 21.120 ms | 211.00 MiB (1%) | 2035654 | | `["insert", "shorthand"]` | 35.200 μs (5%) | | 78.81 KiB (1%) | 96 | | `["insert", "type"]` | 36.900 μs (5%) | | 78.81 KiB (1%) | 96 | | `["push", "Vector{Interval{Int64}}"]` | 258.602 μs (5%) | | 129.16 KiB (1%) | 1725 | | `["sort", "Vector{Interval{Int64}}"]` | 162.201 μs (5%) | | 58.84 KiB (1%) | 4 | ## Benchmark Group List Here's a list of all the benchmark groups executed by this job: - `["accessors", "Vector{Interval{Int64}}"]` - `["eachoverlap"]` - `["insert"]` - `["push"]` - `["sort"]` ## Julia versioninfo ``` Julia Version 1.6.1 Commit 6aaedecc44 (2021-04-23 05:59 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 20.04.2 LTS uname: Linux 5.8.0-1033-azure #35~20.04.1-Ubuntu SMP Wed May 19 06:46:04 UTC 2021 x86_64 x86_64 CPU: Intel(R) Xeon(R) CPU E5-2673 v4 @ 2.30GHz: speed user nice sys idle irq #1 2294 MHz 1603 s 1 s 208 s 835 s 0 s #2 2294 MHz 871 s 1 s 140 s 1671 s 0 s Memory: 6.790924072265625 GB (3505.1015625 MB free) Uptime: 273.0 sec Load Avg: 1.08 0.81 0.37 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-11.0.1 (ORCJIT, broadwell) ``` --- # Baseline result # Benchmark Report for */home/runner/work/GenomicFeatures.jl/GenomicFeatures.jl* ## Job Properties * Time of benchmark: 25 Jun 2021 - 16:22 * Package commit: d6de93 * Julia commit: 6aaede * 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 | |---------------------------------------------------------------------------|----------------:|----------:|----------------:|------------:| | `["accessors", "Vector{Interval{Int64}}", "leftposition"]` | 1.340 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "metadata"]` | 1.200 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "rightposition"]` | 1.120 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "seqname"]` | 2.189 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "strand"]` | 903.865 ns (5%) | | 1.06 KiB (1%) | 1 | | `["eachoverlap", "IntervalCollection{Int64}, IntervalCollection{Int64}"]` | 446.387 ms (5%) | 7.365 ms | 99.91 MiB (1%) | 591412 | | `["eachoverlap", "IntervalCollection{Int64}, Vector{Interval{Int64}}"]` | 129.111 ms (5%) | 20.192 ms | 217.44 MiB (1%) | 2036657 | | `["eachoverlap", "Vector{Interval{Int64}}, IntervalCollection{Int64}"]` | 36.389 ms (5%) | 6.074 ms | 81.86 MiB (1%) | 295706 | | `["eachoverlap", "Vector{Interval{Int64}}, Vector{Interval{Int64}}"]` | 110.062 ms (5%) | 20.876 ms | 211.00 MiB (1%) | 2035654 | | `["insert", "shorthand"]` | 41.700 μs (5%) | | 78.81 KiB (1%) | 96 | | `["insert", "type"]` | 40.300 μs (5%) | | 78.81 KiB (1%) | 96 | | `["push", "Vector{Interval{Int64}}"]` | 278.702 μs (5%) | | 129.16 KiB (1%) | 1725 | | `["sort", "Vector{Interval{Int64}}"]` | 159.200 μs (5%) | | 58.84 KiB (1%) | 4 | ## Benchmark Group List Here's a list of all the benchmark groups executed by this job: - `["accessors", "Vector{Interval{Int64}}"]` - `["eachoverlap"]` - `["insert"]` - `["push"]` - `["sort"]` ## Julia versioninfo ``` Julia Version 1.6.1 Commit 6aaedecc44 (2021-04-23 05:59 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 20.04.2 LTS uname: Linux 5.8.0-1033-azure #35~20.04.1-Ubuntu SMP Wed May 19 06:46:04 UTC 2021 x86_64 x86_64 CPU: Intel(R) Xeon(R) CPU E5-2673 v4 @ 2.30GHz: speed user nice sys idle irq #1 2294 MHz 2249 s 1 s 247 s 879 s 0 s #2 2294 MHz 921 s 1 s 143 s 2348 s 0 s Memory: 6.790924072265625 GB (3530.7734375 MB free) Uptime: 346.0 sec Load Avg: 1.02 0.86 0.42 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-11.0.1 (ORCJIT, broadwell) ``` --- # 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 Address sizes: 46 bits physical, 48 bits virtual 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: 79 Model name: Intel(R) Xeon(R) CPU E5-2673 v4 @ 2.30GHz Stepping: 1 CPU MHz: 2294.685 BogoMIPS: 4589.37 Hypervisor vendor: Microsoft Virtualization type: full L1d cache: 64 KiB L1i cache: 64 KiB L2 cache: 512 KiB L3 cache: 50 MiB NUMA node0 CPU(s): 0,1 Vulnerability Itlb multihit: KVM: Mitigation: VMX unsupported Vulnerability L1tf: Mitigation; PTE Inversion Vulnerability Mds: Mitigation; Clear CPU buffers; SMT Host state unknown Vulnerability Meltdown: Mitigation; PTI Vulnerability Spec store bypass: Vulnerable Vulnerability Spectre v1: Mitigation; usercopy/swapgs barriers and __user pointer sanitization Vulnerability Spectre v2: Mitigation; Full generic retpoline, STIBP disabled, RSB filling Vulnerability Srbds: Not affected Vulnerability Tsx async abort: Mitigation; Clear CPU buffers; SMT Host state unknown 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 rdseed adx smap xsaveopt md_clear | Cpu Property | Value | |:------------------ |:------------------------------------------------------- | | Brand | Intel(R) Xeon(R) CPU E5-2673 v4 @ 2.30GHz | | Vendor | :Intel | | Architecture | :Broadwell | | Model | Family: 0x06, Model: 0x4f, Stepping: 0x01, Type: 0x00 | | Cores | 2 physical cores, 2 logical cores (on executing CPU) | | | No Hyperthreading hardware capability detected | | Clock Frequencies | Not supported by CPU | | Data Cache | Level 1:3 : (32, 256, 51200) kbytes | | | 64 byte cache line size | | Address Size | 48 bits virtual, 46 bits physical | | SIMD | 256 bit = 32 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 |
github-actions[bot] commented 2 years ago
Benchmark result # Judge result # Benchmark Report for */home/runner/work/GenomicFeatures.jl/GenomicFeatures.jl* ## Job Properties * Time of benchmarks: - Target: 13 Nov 2021 - 13:18 - Baseline: 13 Nov 2021 - 13:19 * Package commits: - Target: a01e21 - Baseline: d6de93 * Julia commits: - Target: ae8452 - Baseline: ae8452 * 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 | |---------------------------------------------------------------------------|------------------------------|---------------| | `["accessors", "Vector{Interval{Int64}}", "metadata"]` | 0.90 (5%) :white_check_mark: | 1.00 (1%) | | `["eachoverlap", "IntervalCollection{Int64}, IntervalCollection{Int64}"]` | 1.10 (5%) :x: | 1.00 (1%) | | `["eachoverlap", "IntervalCollection{Int64}, Vector{Interval{Int64}}"]` | 1.08 (5%) :x: | 1.05 (1%) :x: | | `["eachoverlap", "Vector{Interval{Int64}}, Vector{Interval{Int64}}"]` | 1.10 (5%) :x: | 1.00 (1%) | | `["insert", "shorthand"]` | 1.15 (5%) :x: | 1.00 (1%) | | `["insert", "type"]` | 1.06 (5%) :x: | 1.00 (1%) | | `["push", "Vector{Interval{Int64}}"]` | 0.93 (5%) :white_check_mark: | 1.00 (1%) | ## Benchmark Group List Here's a list of all the benchmark groups executed by this job: - `["accessors", "Vector{Interval{Int64}}"]` - `["eachoverlap"]` - `["insert"]` - `["push"]` - `["sort"]` ## Julia versioninfo ### Target ``` Julia Version 1.6.3 Commit ae8452a9e0 (2021-09-23 17:34 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 20.04.3 LTS uname: Linux 5.11.0-1020-azure #21~20.04.1-Ubuntu SMP Mon Oct 11 18:54:28 UTC 2021 x86_64 x86_64 CPU: Intel(R) Xeon(R) CPU E5-2673 v3 @ 2.40GHz: speed user nice sys idle irq #1 2394 MHz 730 s 2 s 142 s 1919 s 0 s #2 2394 MHz 1906 s 0 s 259 s 655 s 0 s Memory: 6.788990020751953 GB (3415.30078125 MB free) Uptime: 286.0 sec Load Avg: 1.04 0.79 0.36 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-11.0.1 (ORCJIT, haswell) ``` ### Baseline ``` Julia Version 1.6.3 Commit ae8452a9e0 (2021-09-23 17:34 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 20.04.3 LTS uname: Linux 5.11.0-1020-azure #21~20.04.1-Ubuntu SMP Mon Oct 11 18:54:28 UTC 2021 x86_64 x86_64 CPU: Intel(R) Xeon(R) CPU E5-2673 v3 @ 2.40GHz: speed user nice sys idle irq #1 2394 MHz 1363 s 2 s 182 s 2014 s 0 s #2 2394 MHz 2010 s 0 s 263 s 1314 s 0 s Memory: 6.788990020751953 GB (3402.46875 MB free) Uptime: 363.0 sec Load Avg: 1.07 0.85 0.42 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-11.0.1 (ORCJIT, haswell) ``` --- # Target result # Benchmark Report for */home/runner/work/GenomicFeatures.jl/GenomicFeatures.jl* ## Job Properties * Time of benchmark: 13 Nov 2021 - 13:18 * Package commit: a01e21 * Julia commit: ae8452 * 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 | |---------------------------------------------------------------------------|----------------:|----------:|----------------:|------------:| | `["accessors", "Vector{Interval{Int64}}", "leftposition"]` | 1.410 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "metadata"]` | 1.260 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "rightposition"]` | 1.370 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "seqname"]` | 2.056 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "strand"]` | 1.000 μs (5%) | | 1.06 KiB (1%) | 1 | | `["eachoverlap", "IntervalCollection{Int64}, IntervalCollection{Int64}"]` | 460.099 ms (5%) | 7.513 ms | 99.91 MiB (1%) | 591412 | | `["eachoverlap", "IntervalCollection{Int64}, Vector{Interval{Int64}}"]` | 132.774 ms (5%) | 27.772 ms | 227.44 MiB (1%) | 2036657 | | `["eachoverlap", "Vector{Interval{Int64}}, IntervalCollection{Int64}"]` | 32.034 ms (5%) | 5.726 ms | 81.86 MiB (1%) | 295706 | | `["eachoverlap", "Vector{Interval{Int64}}, Vector{Interval{Int64}}"]` | 123.950 ms (5%) | 24.952 ms | 211.00 MiB (1%) | 2035654 | | `["insert", "shorthand"]` | 42.600 μs (5%) | | 78.81 KiB (1%) | 96 | | `["insert", "type"]` | 39.700 μs (5%) | | 78.81 KiB (1%) | 96 | | `["push", "Vector{Interval{Int64}}"]` | 293.002 μs (5%) | | 129.16 KiB (1%) | 1725 | | `["sort", "Vector{Interval{Int64}}"]` | 185.701 μs (5%) | | 58.84 KiB (1%) | 4 | ## Benchmark Group List Here's a list of all the benchmark groups executed by this job: - `["accessors", "Vector{Interval{Int64}}"]` - `["eachoverlap"]` - `["insert"]` - `["push"]` - `["sort"]` ## Julia versioninfo ``` Julia Version 1.6.3 Commit ae8452a9e0 (2021-09-23 17:34 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 20.04.3 LTS uname: Linux 5.11.0-1020-azure #21~20.04.1-Ubuntu SMP Mon Oct 11 18:54:28 UTC 2021 x86_64 x86_64 CPU: Intel(R) Xeon(R) CPU E5-2673 v3 @ 2.40GHz: speed user nice sys idle irq #1 2394 MHz 730 s 2 s 142 s 1919 s 0 s #2 2394 MHz 1906 s 0 s 259 s 655 s 0 s Memory: 6.788990020751953 GB (3415.30078125 MB free) Uptime: 286.0 sec Load Avg: 1.04 0.79 0.36 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-11.0.1 (ORCJIT, haswell) ``` --- # Baseline result # Benchmark Report for */home/runner/work/GenomicFeatures.jl/GenomicFeatures.jl* ## Job Properties * Time of benchmark: 13 Nov 2021 - 13:19 * Package commit: d6de93 * Julia commit: ae8452 * 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 | |---------------------------------------------------------------------------|----------------:|----------:|----------------:|------------:| | `["accessors", "Vector{Interval{Int64}}", "leftposition"]` | 1.360 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "metadata"]` | 1.400 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "rightposition"]` | 1.380 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "seqname"]` | 2.022 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "strand"]` | 960.000 ns (5%) | | 1.06 KiB (1%) | 1 | | `["eachoverlap", "IntervalCollection{Int64}, IntervalCollection{Int64}"]` | 417.126 ms (5%) | 7.134 ms | 99.91 MiB (1%) | 591412 | | `["eachoverlap", "IntervalCollection{Int64}, Vector{Interval{Int64}}"]` | 123.174 ms (5%) | 22.809 ms | 217.44 MiB (1%) | 2036657 | | `["eachoverlap", "Vector{Interval{Int64}}, IntervalCollection{Int64}"]` | 31.755 ms (5%) | 5.365 ms | 81.86 MiB (1%) | 295706 | | `["eachoverlap", "Vector{Interval{Int64}}, Vector{Interval{Int64}}"]` | 112.582 ms (5%) | 23.981 ms | 211.00 MiB (1%) | 2035654 | | `["insert", "shorthand"]` | 37.200 μs (5%) | | 78.81 KiB (1%) | 96 | | `["insert", "type"]` | 37.500 μs (5%) | | 78.81 KiB (1%) | 96 | | `["push", "Vector{Interval{Int64}}"]` | 313.402 μs (5%) | | 129.16 KiB (1%) | 1725 | | `["sort", "Vector{Interval{Int64}}"]` | 184.701 μs (5%) | | 58.84 KiB (1%) | 4 | ## Benchmark Group List Here's a list of all the benchmark groups executed by this job: - `["accessors", "Vector{Interval{Int64}}"]` - `["eachoverlap"]` - `["insert"]` - `["push"]` - `["sort"]` ## Julia versioninfo ``` Julia Version 1.6.3 Commit ae8452a9e0 (2021-09-23 17:34 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 20.04.3 LTS uname: Linux 5.11.0-1020-azure #21~20.04.1-Ubuntu SMP Mon Oct 11 18:54:28 UTC 2021 x86_64 x86_64 CPU: Intel(R) Xeon(R) CPU E5-2673 v3 @ 2.40GHz: speed user nice sys idle irq #1 2394 MHz 1363 s 2 s 182 s 2014 s 0 s #2 2394 MHz 2010 s 0 s 263 s 1314 s 0 s Memory: 6.788990020751953 GB (3402.46875 MB free) Uptime: 363.0 sec Load Avg: 1.07 0.85 0.42 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-11.0.1 (ORCJIT, haswell) ``` --- # 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 Address sizes: 46 bits physical, 48 bits virtual 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: 63 Model name: Intel(R) Xeon(R) CPU E5-2673 v3 @ 2.40GHz Stepping: 2 CPU MHz: 2394.455 BogoMIPS: 4788.91 Hypervisor vendor: Microsoft Virtualization type: full L1d cache: 64 KiB L1i cache: 64 KiB L2 cache: 512 KiB L3 cache: 30 MiB NUMA node0 CPU(s): 0,1 Vulnerability Itlb multihit: KVM: Mitigation: VMX unsupported Vulnerability L1tf: Mitigation; PTE Inversion Vulnerability Mds: Mitigation; Clear CPU buffers; SMT Host state unknown Vulnerability Meltdown: Mitigation; PTI Vulnerability Spec store bypass: Vulnerable Vulnerability Spectre v1: Mitigation; usercopy/swapgs barriers and __user pointer sanitization Vulnerability Spectre v2: Mitigation; Full generic retpoline, STIBP disabled, RSB filling Vulnerability Srbds: Not affected Vulnerability Tsx async abort: Not affected 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 invpcid_single pti fsgsbase bmi1 avx2 smep bmi2 erms invpcid xsaveopt md_clear | Cpu Property | Value | |:------------------ |:------------------------------------------------------- | | Brand | Intel(R) Xeon(R) CPU E5-2673 v3 @ 2.40GHz | | Vendor | :Intel | | Architecture | :Haswell | | Model | Family: 0x06, Model: 0x3f, Stepping: 0x02, Type: 0x00 | | Cores | 2 physical cores, 2 logical cores (on executing CPU) | | | No Hyperthreading hardware capability detected | | Clock Frequencies | Not supported by CPU | | Data Cache | Level 1:3 : (32, 256, 30720) kbytes | | | 64 byte cache line size | | Address Size | 48 bits virtual, 46 bits physical | | SIMD | 256 bit = 32 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 |
github-actions[bot] commented 2 years ago
Benchmark result # Judge result # Benchmark Report for */home/runner/work/GenomicFeatures.jl/GenomicFeatures.jl* ## Job Properties * Time of benchmarks: - Target: 15 Nov 2021 - 02:21 - Baseline: 15 Nov 2021 - 02:22 * Package commits: - Target: 8e4859 - Baseline: d6de93 * Julia commits: - Target: ae8452 - Baseline: ae8452 * 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 | |---------------------------------------------------------------------------|---------------|---------------| | `["accessors", "Vector{Interval{Int64}}", "seqname"]` | 1.27 (5%) :x: | 1.00 (1%) | | `["eachoverlap", "IntervalCollection{Int64}, IntervalCollection{Int64}"]` | 1.11 (5%) :x: | 1.00 (1%) | | `["eachoverlap", "IntervalCollection{Int64}, Vector{Interval{Int64}}"]` | 1.02 (5%) | 1.05 (1%) :x: | ## Benchmark Group List Here's a list of all the benchmark groups executed by this job: - `["accessors", "Vector{Interval{Int64}}"]` - `["eachoverlap"]` - `["insert"]` - `["push"]` - `["sort"]` ## Julia versioninfo ### Target ``` Julia Version 1.6.3 Commit ae8452a9e0 (2021-09-23 17:34 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 20.04.3 LTS uname: Linux 5.11.0-1020-azure #21~20.04.1-Ubuntu SMP Mon Oct 11 18:54:28 UTC 2021 x86_64 x86_64 CPU: Intel(R) Xeon(R) Platinum 8272CL CPU @ 2.60GHz: speed user nice sys idle irq #1 2593 MHz 1593 s 1 s 218 s 1511 s 0 s #2 2593 MHz 664 s 1 s 131 s 2535 s 0 s Memory: 6.788990020751953 GB (3399.35546875 MB free) Uptime: 337.0 sec Load Avg: 1.03 0.65 0.28 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-11.0.1 (ORCJIT, skylake-avx512) ``` ### Baseline ``` Julia Version 1.6.3 Commit ae8452a9e0 (2021-09-23 17:34 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 20.04.3 LTS uname: Linux 5.11.0-1020-azure #21~20.04.1-Ubuntu SMP Mon Oct 11 18:54:28 UTC 2021 x86_64 x86_64 CPU: Intel(R) Xeon(R) Platinum 8272CL CPU @ 2.60GHz: speed user nice sys idle irq #1 2593 MHz 1674 s 1 s 221 s 2090 s 0 s #2 2593 MHz 1213 s 1 s 174 s 2609 s 0 s Memory: 6.788990020751953 GB (3394.27734375 MB free) Uptime: 403.0 sec Load Avg: 1.04 0.73 0.34 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-11.0.1 (ORCJIT, skylake-avx512) ``` --- # Target result # Benchmark Report for */home/runner/work/GenomicFeatures.jl/GenomicFeatures.jl* ## Job Properties * Time of benchmark: 15 Nov 2021 - 2:21 * Package commit: 8e4859 * Julia commit: ae8452 * 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 | |---------------------------------------------------------------------------|----------------:|----------:|----------------:|------------:| | `["accessors", "Vector{Interval{Int64}}", "leftposition"]` | 1.340 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "metadata"]` | 1.330 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "rightposition"]` | 1.340 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "seqname"]` | 2.888 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "strand"]` | 935.000 ns (5%) | | 1.06 KiB (1%) | 1 | | `["eachoverlap", "IntervalCollection{Int64}, IntervalCollection{Int64}"]` | 421.115 ms (5%) | 7.598 ms | 99.91 MiB (1%) | 591412 | | `["eachoverlap", "IntervalCollection{Int64}, Vector{Interval{Int64}}"]` | 114.650 ms (5%) | 25.092 ms | 227.44 MiB (1%) | 2036657 | | `["eachoverlap", "Vector{Interval{Int64}}, IntervalCollection{Int64}"]` | 34.607 ms (5%) | 5.084 ms | 81.86 MiB (1%) | 295706 | | `["eachoverlap", "Vector{Interval{Int64}}, Vector{Interval{Int64}}"]` | 111.156 ms (5%) | 24.763 ms | 211.00 MiB (1%) | 2035654 | | `["insert", "shorthand"]` | 37.601 μs (5%) | | 78.81 KiB (1%) | 96 | | `["insert", "type"]` | 37.400 μs (5%) | | 78.81 KiB (1%) | 96 | | `["push", "Vector{Interval{Int64}}"]` | 292.501 μs (5%) | | 129.16 KiB (1%) | 1725 | | `["sort", "Vector{Interval{Int64}}"]` | 193.401 μs (5%) | | 58.84 KiB (1%) | 4 | ## Benchmark Group List Here's a list of all the benchmark groups executed by this job: - `["accessors", "Vector{Interval{Int64}}"]` - `["eachoverlap"]` - `["insert"]` - `["push"]` - `["sort"]` ## Julia versioninfo ``` Julia Version 1.6.3 Commit ae8452a9e0 (2021-09-23 17:34 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 20.04.3 LTS uname: Linux 5.11.0-1020-azure #21~20.04.1-Ubuntu SMP Mon Oct 11 18:54:28 UTC 2021 x86_64 x86_64 CPU: Intel(R) Xeon(R) Platinum 8272CL CPU @ 2.60GHz: speed user nice sys idle irq #1 2593 MHz 1593 s 1 s 218 s 1511 s 0 s #2 2593 MHz 664 s 1 s 131 s 2535 s 0 s Memory: 6.788990020751953 GB (3399.35546875 MB free) Uptime: 337.0 sec Load Avg: 1.03 0.65 0.28 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-11.0.1 (ORCJIT, skylake-avx512) ``` --- # Baseline result # Benchmark Report for */home/runner/work/GenomicFeatures.jl/GenomicFeatures.jl* ## Job Properties * Time of benchmark: 15 Nov 2021 - 2:22 * Package commit: d6de93 * Julia commit: ae8452 * 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 | |---------------------------------------------------------------------------|----------------:|----------:|----------------:|------------:| | `["accessors", "Vector{Interval{Int64}}", "leftposition"]` | 1.310 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "metadata"]` | 1.310 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "rightposition"]` | 1.310 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "seqname"]` | 2.275 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "strand"]` | 910.000 ns (5%) | | 1.06 KiB (1%) | 1 | | `["eachoverlap", "IntervalCollection{Int64}, IntervalCollection{Int64}"]` | 378.768 ms (5%) | 8.163 ms | 99.91 MiB (1%) | 591412 | | `["eachoverlap", "IntervalCollection{Int64}, Vector{Interval{Int64}}"]` | 111.890 ms (5%) | 20.947 ms | 217.44 MiB (1%) | 2036657 | | `["eachoverlap", "Vector{Interval{Int64}}, IntervalCollection{Int64}"]` | 33.791 ms (5%) | 4.813 ms | 81.86 MiB (1%) | 295706 | | `["eachoverlap", "Vector{Interval{Int64}}, Vector{Interval{Int64}}"]` | 108.947 ms (5%) | 24.107 ms | 211.00 MiB (1%) | 2035654 | | `["insert", "shorthand"]` | 39.200 μs (5%) | | 78.81 KiB (1%) | 96 | | `["insert", "type"]` | 39.300 μs (5%) | | 78.81 KiB (1%) | 96 | | `["push", "Vector{Interval{Int64}}"]` | 305.402 μs (5%) | | 129.16 KiB (1%) | 1725 | | `["sort", "Vector{Interval{Int64}}"]` | 189.099 μs (5%) | | 58.84 KiB (1%) | 4 | ## Benchmark Group List Here's a list of all the benchmark groups executed by this job: - `["accessors", "Vector{Interval{Int64}}"]` - `["eachoverlap"]` - `["insert"]` - `["push"]` - `["sort"]` ## Julia versioninfo ``` Julia Version 1.6.3 Commit ae8452a9e0 (2021-09-23 17:34 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 20.04.3 LTS uname: Linux 5.11.0-1020-azure #21~20.04.1-Ubuntu SMP Mon Oct 11 18:54:28 UTC 2021 x86_64 x86_64 CPU: Intel(R) Xeon(R) Platinum 8272CL CPU @ 2.60GHz: speed user nice sys idle irq #1 2593 MHz 1674 s 1 s 221 s 2090 s 0 s #2 2593 MHz 1213 s 1 s 174 s 2609 s 0 s Memory: 6.788990020751953 GB (3394.27734375 MB free) Uptime: 403.0 sec Load Avg: 1.04 0.73 0.34 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-11.0.1 (ORCJIT, skylake-avx512) ``` --- # 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 Address sizes: 46 bits physical, 48 bits virtual 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 8272CL CPU @ 2.60GHz Stepping: 7 CPU MHz: 2593.906 BogoMIPS: 5187.81 Hypervisor vendor: Microsoft Virtualization type: full L1d cache: 64 KiB L1i cache: 64 KiB L2 cache: 2 MiB L3 cache: 35.8 MiB NUMA node0 CPU(s): 0,1 Vulnerability Itlb multihit: KVM: Mitigation: VMX unsupported Vulnerability L1tf: Mitigation; PTE Inversion Vulnerability Mds: Mitigation; Clear CPU buffers; SMT Host state unknown Vulnerability Meltdown: Mitigation; PTI Vulnerability Spec store bypass: Vulnerable Vulnerability Spectre v1: Mitigation; usercopy/swapgs barriers and __user pointer sanitization Vulnerability Spectre v2: Mitigation; Full generic retpoline, STIBP disabled, RSB filling Vulnerability Srbds: Not affected Vulnerability Tsx async abort: Mitigation; Clear CPU buffers; SMT Host state unknown 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 8272CL CPU @ 2.60GHz | | Vendor | :Intel | | Architecture | :Skylake | | Model | Family: 0x06, Model: 0x55, Stepping: 0x07, Type: 0x00 | | Cores | 2 physical cores, 2 logical cores (on executing CPU) | | | No Hyperthreading hardware capability 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, 46 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 |
github-actions[bot] commented 2 years ago
Benchmark result # Judge result # Benchmark Report for */home/runner/work/GenomicFeatures.jl/GenomicFeatures.jl* ## Job Properties * Time of benchmarks: - Target: 16 Nov 2021 - 02:46 - Baseline: 16 Nov 2021 - 02:48 * Package commits: - Target: efd908 - Baseline: d6de93 * Julia commits: - Target: ae8452 - Baseline: ae8452 * 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 | |---------------------------------------------------------------------------|------------------------------|---------------| | `["accessors", "Vector{Interval{Int64}}", "rightposition"]` | 1.10 (5%) :x: | 1.00 (1%) | | `["accessors", "Vector{Interval{Int64}}", "strand"]` | 1.14 (5%) :x: | 1.00 (1%) | | `["eachoverlap", "IntervalCollection{Int64}, IntervalCollection{Int64}"]` | 0.92 (5%) :white_check_mark: | 1.00 (1%) | | `["eachoverlap", "IntervalCollection{Int64}, Vector{Interval{Int64}}"]` | 1.04 (5%) | 1.05 (1%) :x: | | `["eachoverlap", "Vector{Interval{Int64}}, IntervalCollection{Int64}"]` | 1.06 (5%) :x: | 1.00 (1%) | | `["push", "Vector{Interval{Int64}}"]` | 0.93 (5%) :white_check_mark: | 1.00 (1%) | | `["sort", "Vector{Interval{Int64}}"]` | 1.05 (5%) :x: | 1.00 (1%) | ## Benchmark Group List Here's a list of all the benchmark groups executed by this job: - `["accessors", "Vector{Interval{Int64}}"]` - `["eachoverlap"]` - `["insert"]` - `["push"]` - `["sort"]` ## Julia versioninfo ### Target ``` Julia Version 1.6.3 Commit ae8452a9e0 (2021-09-23 17:34 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 20.04.3 LTS uname: Linux 5.11.0-1020-azure #21~20.04.1-Ubuntu SMP Mon Oct 11 18:54:28 UTC 2021 x86_64 x86_64 CPU: Intel(R) Xeon(R) CPU E5-2673 v4 @ 2.30GHz: speed user nice sys idle irq #1 2294 MHz 665 s 1 s 178 s 4316 s 0 s #2 2294 MHz 1963 s 1 s 257 s 2959 s 0 s Memory: 6.788990020751953 GB (3384.4609375 MB free) Uptime: 523.0 sec Load Avg: 1.1 0.81 0.4 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-11.0.1 (ORCJIT, broadwell) ``` ### Baseline ``` Julia Version 1.6.3 Commit ae8452a9e0 (2021-09-23 17:34 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 20.04.3 LTS uname: Linux 5.11.0-1020-azure #21~20.04.1-Ubuntu SMP Mon Oct 11 18:54:28 UTC 2021 x86_64 x86_64 CPU: Intel(R) Xeon(R) CPU E5-2673 v4 @ 2.30GHz: speed user nice sys idle irq #1 2294 MHz 1254 s 1 s 217 s 4464 s 0 s #2 2294 MHz 2118 s 1 s 263 s 3572 s 0 s Memory: 6.788990020751953 GB (3379.125 MB free) Uptime: 601.0 sec Load Avg: 1.02 0.86 0.45 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-11.0.1 (ORCJIT, broadwell) ``` --- # Target result # Benchmark Report for */home/runner/work/GenomicFeatures.jl/GenomicFeatures.jl* ## Job Properties * Time of benchmark: 16 Nov 2021 - 2:46 * Package commit: efd908 * Julia commit: ae8452 * 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 | |---------------------------------------------------------------------------|----------------:|----------:|----------------:|------------:| | `["accessors", "Vector{Interval{Int64}}", "leftposition"]` | 1.210 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "metadata"]` | 1.370 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "rightposition"]` | 1.480 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "seqname"]` | 2.010 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "strand"]` | 976.923 ns (5%) | | 1.06 KiB (1%) | 1 | | `["eachoverlap", "IntervalCollection{Int64}, IntervalCollection{Int64}"]` | 460.943 ms (5%) | 7.908 ms | 99.91 MiB (1%) | 591412 | | `["eachoverlap", "IntervalCollection{Int64}, Vector{Interval{Int64}}"]` | 133.899 ms (5%) | 23.284 ms | 227.44 MiB (1%) | 2036657 | | `["eachoverlap", "Vector{Interval{Int64}}, IntervalCollection{Int64}"]` | 38.319 ms (5%) | 6.061 ms | 81.86 MiB (1%) | 295706 | | `["eachoverlap", "Vector{Interval{Int64}}, Vector{Interval{Int64}}"]` | 123.948 ms (5%) | 23.782 ms | 211.00 MiB (1%) | 2035654 | | `["insert", "shorthand"]` | 39.300 μs (5%) | | 78.81 KiB (1%) | 96 | | `["insert", "type"]` | 37.200 μs (5%) | | 78.81 KiB (1%) | 96 | | `["push", "Vector{Interval{Int64}}"]` | 263.701 μs (5%) | | 129.16 KiB (1%) | 1725 | | `["sort", "Vector{Interval{Int64}}"]` | 167.001 μs (5%) | | 58.84 KiB (1%) | 4 | ## Benchmark Group List Here's a list of all the benchmark groups executed by this job: - `["accessors", "Vector{Interval{Int64}}"]` - `["eachoverlap"]` - `["insert"]` - `["push"]` - `["sort"]` ## Julia versioninfo ``` Julia Version 1.6.3 Commit ae8452a9e0 (2021-09-23 17:34 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 20.04.3 LTS uname: Linux 5.11.0-1020-azure #21~20.04.1-Ubuntu SMP Mon Oct 11 18:54:28 UTC 2021 x86_64 x86_64 CPU: Intel(R) Xeon(R) CPU E5-2673 v4 @ 2.30GHz: speed user nice sys idle irq #1 2294 MHz 665 s 1 s 178 s 4316 s 0 s #2 2294 MHz 1963 s 1 s 257 s 2959 s 0 s Memory: 6.788990020751953 GB (3384.4609375 MB free) Uptime: 523.0 sec Load Avg: 1.1 0.81 0.4 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-11.0.1 (ORCJIT, broadwell) ``` --- # Baseline result # Benchmark Report for */home/runner/work/GenomicFeatures.jl/GenomicFeatures.jl* ## Job Properties * Time of benchmark: 16 Nov 2021 - 2:48 * Package commit: d6de93 * Julia commit: ae8452 * 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 | |---------------------------------------------------------------------------|----------------:|----------:|----------------:|------------:| | `["accessors", "Vector{Interval{Int64}}", "leftposition"]` | 1.250 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "metadata"]` | 1.330 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "rightposition"]` | 1.340 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "seqname"]` | 2.040 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "strand"]` | 856.410 ns (5%) | | 1.06 KiB (1%) | 1 | | `["eachoverlap", "IntervalCollection{Int64}, IntervalCollection{Int64}"]` | 500.379 ms (5%) | 9.423 ms | 99.91 MiB (1%) | 591412 | | `["eachoverlap", "IntervalCollection{Int64}, Vector{Interval{Int64}}"]` | 128.418 ms (5%) | 21.561 ms | 217.44 MiB (1%) | 2036657 | | `["eachoverlap", "Vector{Interval{Int64}}, IntervalCollection{Int64}"]` | 36.232 ms (5%) | 5.569 ms | 81.86 MiB (1%) | 295706 | | `["eachoverlap", "Vector{Interval{Int64}}, Vector{Interval{Int64}}"]` | 129.468 ms (5%) | 23.013 ms | 211.00 MiB (1%) | 2035654 | | `["insert", "shorthand"]` | 40.200 μs (5%) | | 78.81 KiB (1%) | 96 | | `["insert", "type"]` | 35.800 μs (5%) | | 78.81 KiB (1%) | 96 | | `["push", "Vector{Interval{Int64}}"]` | 282.502 μs (5%) | | 129.16 KiB (1%) | 1725 | | `["sort", "Vector{Interval{Int64}}"]` | 158.701 μs (5%) | | 58.84 KiB (1%) | 4 | ## Benchmark Group List Here's a list of all the benchmark groups executed by this job: - `["accessors", "Vector{Interval{Int64}}"]` - `["eachoverlap"]` - `["insert"]` - `["push"]` - `["sort"]` ## Julia versioninfo ``` Julia Version 1.6.3 Commit ae8452a9e0 (2021-09-23 17:34 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 20.04.3 LTS uname: Linux 5.11.0-1020-azure #21~20.04.1-Ubuntu SMP Mon Oct 11 18:54:28 UTC 2021 x86_64 x86_64 CPU: Intel(R) Xeon(R) CPU E5-2673 v4 @ 2.30GHz: speed user nice sys idle irq #1 2294 MHz 1254 s 1 s 217 s 4464 s 0 s #2 2294 MHz 2118 s 1 s 263 s 3572 s 0 s Memory: 6.788990020751953 GB (3379.125 MB free) Uptime: 601.0 sec Load Avg: 1.02 0.86 0.45 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-11.0.1 (ORCJIT, broadwell) ``` --- # 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 Address sizes: 46 bits physical, 48 bits virtual 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: 79 Model name: Intel(R) Xeon(R) CPU E5-2673 v4 @ 2.30GHz Stepping: 1 CPU MHz: 2294.684 BogoMIPS: 4589.36 Hypervisor vendor: Microsoft Virtualization type: full L1d cache: 64 KiB L1i cache: 64 KiB L2 cache: 512 KiB L3 cache: 50 MiB NUMA node0 CPU(s): 0,1 Vulnerability Itlb multihit: KVM: Mitigation: VMX unsupported Vulnerability L1tf: Mitigation; PTE Inversion Vulnerability Mds: Mitigation; Clear CPU buffers; SMT Host state unknown Vulnerability Meltdown: Mitigation; PTI Vulnerability Spec store bypass: Vulnerable Vulnerability Spectre v1: Mitigation; usercopy/swapgs barriers and __user pointer sanitization Vulnerability Spectre v2: Mitigation; Full generic retpoline, STIBP disabled, RSB filling Vulnerability Srbds: Not affected Vulnerability Tsx async abort: Mitigation; Clear CPU buffers; SMT Host state unknown 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 rdseed adx smap xsaveopt md_clear | Cpu Property | Value | |:------------------ |:------------------------------------------------------- | | Brand | Intel(R) Xeon(R) CPU E5-2673 v4 @ 2.30GHz | | Vendor | :Intel | | Architecture | :Broadwell | | Model | Family: 0x06, Model: 0x4f, Stepping: 0x01, Type: 0x00 | | Cores | 2 physical cores, 2 logical cores (on executing CPU) | | | No Hyperthreading hardware capability detected | | Clock Frequencies | Not supported by CPU | | Data Cache | Level 1:3 : (32, 256, 51200) kbytes | | | 64 byte cache line size | | Address Size | 48 bits virtual, 46 bits physical | | SIMD | 256 bit = 32 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 |