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BioJulia / GenomicFeatures.jl

Tools for genomic features in Julia.
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Release/v2.0.5 #47

Closed CiaranOMara closed 2 years ago

CiaranOMara commented 2 years ago

Briefly, this PR:

There are no new features.

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: 23 Nov 2021 - 22:34 - Baseline: 23 Nov 2021 - 22:35 * Package commits: - Target: d8d3e5 - Baseline: d6de93 * Julia commits: - Target: 35f0c9 - Baseline: 35f0c9 * 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"]` | 0.92 (5%) :white_check_mark: | 1.00 (1%) | | `["eachoverlap", "IntervalCollection{Int64}, Vector{Interval{Int64}}"]` | 0.99 (5%) | 1.05 (1%) :x: | | `["eachoverlap", "Vector{Interval{Int64}}, IntervalCollection{Int64}"]` | 0.92 (5%) :white_check_mark: | 1.00 (1%) | | `["insert", "shorthand"]` | 0.91 (5%) :white_check_mark: | 1.00 (1%) | | `["insert", "type"]` | 1.08 (5%) :x: | 1.00 (1%) | | `["push", "Vector{Interval{Int64}}"]` | 0.85 (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 1.6.4 Commit 35f0c911f4 (2021-11-19 03:54 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 20.04.3 LTS uname: Linux 5.11.0-1021-azure #22~20.04.1-Ubuntu SMP Fri Oct 29 01:11:25 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 1703 s 1 s 232 s 2134 s 0 s #2 2294 MHz 820 s 1 s 159 s 3098 s 0 s Memory: 6.788982391357422 GB (3513.72265625 MB free) Uptime: 413.65 sec Load Avg: 1.22 0.79 0.36 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-11.0.1 (ORCJIT, broadwell) ``` ### Baseline ``` Julia Version 1.6.4 Commit 35f0c911f4 (2021-11-19 03:54 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 20.04.3 LTS uname: Linux 5.11.0-1021-azure #22~20.04.1-Ubuntu SMP Fri Oct 29 01:11:25 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 1798 s 1 s 237 s 2764 s 0 s #2 2294 MHz 1425 s 1 s 199 s 3184 s 0 s Memory: 6.788982391357422 GB (3481.72265625 MB free) Uptime: 486.82 sec Load Avg: 1.06 0.84 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: 23 Nov 2021 - 22:34 * Package commit: d8d3e5 * Julia commit: 35f0c9 * 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"]` | 1.140 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "metadata"]` | 1.130 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"]` | 1.633 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "strand"]` | 862.963 ns (5%) | | 1.06 KiB (1%) | 1 | | `["eachoverlap", "IntervalCollection{Int64}, IntervalCollection{Int64}"]` | 456.231 ms (5%) | 7.815 ms | 99.91 MiB (1%) | 591412 | | `["eachoverlap", "IntervalCollection{Int64}, Vector{Interval{Int64}}"]` | 123.867 ms (5%) | 21.836 ms | 227.44 MiB (1%) | 2036657 | | `["eachoverlap", "Vector{Interval{Int64}}, IntervalCollection{Int64}"]` | 35.405 ms (5%) | 5.602 ms | 81.86 MiB (1%) | 295706 | | `["eachoverlap", "Vector{Interval{Int64}}, Vector{Interval{Int64}}"]` | 122.882 ms (5%) | 22.904 ms | 211.00 MiB (1%) | 2035654 | | `["insert", "shorthand"]` | 33.200 μs (5%) | | 78.81 KiB (1%) | 96 | | `["insert", "type"]` | 38.000 μs (5%) | | 78.81 KiB (1%) | 96 | | `["push", "Vector{Interval{Int64}}"]` | 257.402 μs (5%) | | 129.16 KiB (1%) | 1725 | | `["sort", "Vector{Interval{Int64}}"]` | 157.401 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 1.6.4 Commit 35f0c911f4 (2021-11-19 03:54 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 20.04.3 LTS uname: Linux 5.11.0-1021-azure #22~20.04.1-Ubuntu SMP Fri Oct 29 01:11:25 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 1703 s 1 s 232 s 2134 s 0 s #2 2294 MHz 820 s 1 s 159 s 3098 s 0 s Memory: 6.788982391357422 GB (3513.72265625 MB free) Uptime: 413.65 sec Load Avg: 1.22 0.79 0.36 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: 23 Nov 2021 - 22:35 * Package commit: d6de93 * Julia commit: 35f0c9 * 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"]` | 1.180 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "metadata"]` | 1.100 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "rightposition"]` | 1.200 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "seqname"]` | 1.689 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "strand"]` | 825.926 ns (5%) | | 1.06 KiB (1%) | 1 | | `["eachoverlap", "IntervalCollection{Int64}, IntervalCollection{Int64}"]` | 477.474 ms (5%) | 9.498 ms | 99.91 MiB (1%) | 591412 | | `["eachoverlap", "IntervalCollection{Int64}, Vector{Interval{Int64}}"]` | 124.657 ms (5%) | 20.968 ms | 217.44 MiB (1%) | 2036657 | | `["eachoverlap", "Vector{Interval{Int64}}, IntervalCollection{Int64}"]` | 38.673 ms (5%) | 6.310 ms | 81.86 MiB (1%) | 295706 | | `["eachoverlap", "Vector{Interval{Int64}}, Vector{Interval{Int64}}"]` | 127.206 ms (5%) | 24.672 ms | 211.00 MiB (1%) | 2035654 | | `["insert", "shorthand"]` | 36.600 μs (5%) | | 78.81 KiB (1%) | 96 | | `["insert", "type"]` | 35.100 μs (5%) | | 78.81 KiB (1%) | 96 | | `["push", "Vector{Interval{Int64}}"]` | 301.702 μs (5%) | | 129.16 KiB (1%) | 1725 | | `["sort", "Vector{Interval{Int64}}"]` | 157.701 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 1.6.4 Commit 35f0c911f4 (2021-11-19 03:54 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 20.04.3 LTS uname: Linux 5.11.0-1021-azure #22~20.04.1-Ubuntu SMP Fri Oct 29 01:11:25 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 1798 s 1 s 237 s 2764 s 0 s #2 2294 MHz 1425 s 1 s 199 s 3184 s 0 s Memory: 6.788982391357422 GB (3481.72265625 MB free) Uptime: 486.82 sec Load Avg: 1.06 0.84 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: 2294.684 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 |
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: 23 Nov 2021 - 22:47 - Baseline: 23 Nov 2021 - 22:48 * Package commits: - Target: d58843 - Baseline: d6de93 * Julia commits: - Target: 35f0c9 - Baseline: 35f0c9 * 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"]` | 0.82 (5%) :white_check_mark: | 1.00 (1%) | | `["accessors", "Vector{Interval{Int64}}", "seqname"]` | 1.08 (5%) :x: | 1.00 (1%) | | `["eachoverlap", "IntervalCollection{Int64}, Vector{Interval{Int64}}"]` | 1.03 (5%) | 1.05 (1%) :x: | | `["insert", "shorthand"]` | 1.06 (5%) :x: | 1.00 (1%) | | `["push", "Vector{Interval{Int64}}"]` | 0.95 (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 1.6.4 Commit 35f0c911f4 (2021-11-19 03:54 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 20.04.3 LTS uname: Linux 5.11.0-1021-azure #22~20.04.1-Ubuntu SMP Fri Oct 29 01:11:25 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 1776 s 2 s 235 s 730 s 0 s #2 2294 MHz 820 s 2 s 155 s 1766 s 0 s Memory: 6.788982391357422 GB (3561.3515625 MB free) Uptime: 280.49 sec Load Avg: 1.14 0.86 0.39 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-11.0.1 (ORCJIT, broadwell) ``` ### Baseline ``` Julia Version 1.6.4 Commit 35f0c911f4 (2021-11-19 03:54 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 20.04.3 LTS uname: Linux 5.11.0-1021-azure #22~20.04.1-Ubuntu SMP Fri Oct 29 01:11:25 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 2376 s 2 s 274 s 860 s 0 s #2 2294 MHz 958 s 2 s 161 s 2389 s 0 s Memory: 6.788982391357422 GB (3529.734375 MB free) Uptime: 357.43 sec Load Avg: 1.04 0.9 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: 23 Nov 2021 - 22:47 * Package commit: d58843 * Julia commit: 35f0c9 * 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"]` | 1.230 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "metadata"]` | 1.410 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"]` | 2.367 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "strand"]` | 930.000 ns (5%) | | 1.06 KiB (1%) | 1 | | `["eachoverlap", "IntervalCollection{Int64}, IntervalCollection{Int64}"]` | 444.171 ms (5%) | 8.202 ms | 99.91 MiB (1%) | 591412 | | `["eachoverlap", "IntervalCollection{Int64}, Vector{Interval{Int64}}"]` | 135.180 ms (5%) | 24.155 ms | 227.44 MiB (1%) | 2036657 | | `["eachoverlap", "Vector{Interval{Int64}}, IntervalCollection{Int64}"]` | 37.948 ms (5%) | 6.550 ms | 81.86 MiB (1%) | 295706 | | `["eachoverlap", "Vector{Interval{Int64}}, Vector{Interval{Int64}}"]` | 135.769 ms (5%) | 19.394 ms | 211.00 MiB (1%) | 2035654 | | `["insert", "shorthand"]` | 42.300 μs (5%) | | 78.81 KiB (1%) | 96 | | `["insert", "type"]` | 40.800 μs (5%) | | 78.81 KiB (1%) | 96 | | `["push", "Vector{Interval{Int64}}"]` | 267.002 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 1.6.4 Commit 35f0c911f4 (2021-11-19 03:54 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 20.04.3 LTS uname: Linux 5.11.0-1021-azure #22~20.04.1-Ubuntu SMP Fri Oct 29 01:11:25 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 1776 s 2 s 235 s 730 s 0 s #2 2294 MHz 820 s 2 s 155 s 1766 s 0 s Memory: 6.788982391357422 GB (3561.3515625 MB free) Uptime: 280.49 sec Load Avg: 1.14 0.86 0.39 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: 23 Nov 2021 - 22:48 * Package commit: d6de93 * Julia commit: 35f0c9 * 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"]` | 1.500 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "metadata"]` | 1.440 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "rightposition"]` | 1.440 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "seqname"]` | 2.200 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "strand"]` | 930.000 ns (5%) | | 1.06 KiB (1%) | 1 | | `["eachoverlap", "IntervalCollection{Int64}, IntervalCollection{Int64}"]` | 429.796 ms (5%) | 7.840 ms | 99.91 MiB (1%) | 591412 | | `["eachoverlap", "IntervalCollection{Int64}, Vector{Interval{Int64}}"]` | 130.997 ms (5%) | 26.114 ms | 217.44 MiB (1%) | 2036657 | | `["eachoverlap", "Vector{Interval{Int64}}, IntervalCollection{Int64}"]` | 38.746 ms (5%) | 6.385 ms | 81.86 MiB (1%) | 295706 | | `["eachoverlap", "Vector{Interval{Int64}}, Vector{Interval{Int64}}"]` | 130.544 ms (5%) | 27.492 ms | 211.00 MiB (1%) | 2035654 | | `["insert", "shorthand"]` | 40.000 μs (5%) | | 78.81 KiB (1%) | 96 | | `["insert", "type"]` | 39.300 μs (5%) | | 78.81 KiB (1%) | 96 | | `["push", "Vector{Interval{Int64}}"]` | 282.201 μs (5%) | | 129.16 KiB (1%) | 1725 | | `["sort", "Vector{Interval{Int64}}"]` | 159.301 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 1.6.4 Commit 35f0c911f4 (2021-11-19 03:54 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 20.04.3 LTS uname: Linux 5.11.0-1021-azure #22~20.04.1-Ubuntu SMP Fri Oct 29 01:11:25 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 2376 s 2 s 274 s 860 s 0 s #2 2294 MHz 958 s 2 s 161 s 2389 s 0 s Memory: 6.788982391357422 GB (3529.734375 MB free) Uptime: 357.43 sec Load Avg: 1.04 0.9 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: 2294.690 BogoMIPS: 4589.38 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: 25 Nov 2021 - 00:46 - Baseline: 25 Nov 2021 - 00:47 * Package commits: - Target: c36dbf - Baseline: d6de93 * Julia commits: - Target: 35f0c9 - Baseline: 35f0c9 * 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"]` | 1.28 (5%) :x: | 1.00 (1%) | | `["eachoverlap", "IntervalCollection{Int64}, IntervalCollection{Int64}"]` | 0.89 (5%) :white_check_mark: | 1.00 (1%) | | `["eachoverlap", "IntervalCollection{Int64}, Vector{Interval{Int64}}"]` | 1.05 (5%) :x: | 1.05 (1%) :x: | | `["push", "Vector{Interval{Int64}}"]` | 0.95 (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 1.6.4 Commit 35f0c911f4 (2021-11-19 03:54 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 20.04.3 LTS uname: Linux 5.11.0-1021-azure #22~20.04.1-Ubuntu SMP Fri Oct 29 01:11:25 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 1596 s 2 s 212 s 3559 s 0 s #2 2593 MHz 636 s 1 s 134 s 4630 s 0 s Memory: 6.788982391357422 GB (3511.05078125 MB free) Uptime: 543.58 sec Load Avg: 1.07 0.76 0.36 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-11.0.1 (ORCJIT, skylake-avx512) ``` ### Baseline ``` Julia Version 1.6.4 Commit 35f0c911f4 (2021-11-19 03:54 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 20.04.3 LTS uname: Linux 5.11.0-1021-azure #22~20.04.1-Ubuntu SMP Fri Oct 29 01:11:25 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 2107 s 2 s 252 s 3659 s 0 s #2 2593 MHz 742 s 1 s 138 s 5170 s 0 s Memory: 6.788982391357422 GB (3467.17578125 MB free) Uptime: 608.78 sec Load Avg: 1.02 0.81 0.41 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: 25 Nov 2021 - 0:46 * Package commit: c36dbf * Julia commit: 35f0c9 * 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"]` | 1.350 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"]` | 1.350 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "seqname"]` | 2.938 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "strand"]` | 936.000 ns (5%) | | 1.06 KiB (1%) | 1 | | `["eachoverlap", "IntervalCollection{Int64}, IntervalCollection{Int64}"]` | 370.985 ms (5%) | 8.226 ms | 99.91 MiB (1%) | 591412 | | `["eachoverlap", "IntervalCollection{Int64}, Vector{Interval{Int64}}"]` | 114.269 ms (5%) | 22.143 ms | 227.44 MiB (1%) | 2036657 | | `["eachoverlap", "Vector{Interval{Int64}}, IntervalCollection{Int64}"]` | 34.889 ms (5%) | 4.957 ms | 81.86 MiB (1%) | 295706 | | `["eachoverlap", "Vector{Interval{Int64}}, Vector{Interval{Int64}}"]` | 112.404 ms (5%) | 25.102 ms | 211.00 MiB (1%) | 2035654 | | `["insert", "shorthand"]` | 37.101 μs (5%) | | 78.81 KiB (1%) | 96 | | `["insert", "type"]` | 38.400 μs (5%) | | 78.81 KiB (1%) | 96 | | `["push", "Vector{Interval{Int64}}"]` | 289.403 μs (5%) | | 129.16 KiB (1%) | 1725 | | `["sort", "Vector{Interval{Int64}}"]` | 190.302 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 1.6.4 Commit 35f0c911f4 (2021-11-19 03:54 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 20.04.3 LTS uname: Linux 5.11.0-1021-azure #22~20.04.1-Ubuntu SMP Fri Oct 29 01:11:25 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 1596 s 2 s 212 s 3559 s 0 s #2 2593 MHz 636 s 1 s 134 s 4630 s 0 s Memory: 6.788982391357422 GB (3511.05078125 MB free) Uptime: 543.58 sec Load Avg: 1.07 0.76 0.36 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: 25 Nov 2021 - 0:47 * Package commit: d6de93 * Julia commit: 35f0c9 * 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"]` | 1.290 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"]` | 2.300 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "strand"]` | 936.000 ns (5%) | | 1.06 KiB (1%) | 1 | | `["eachoverlap", "IntervalCollection{Int64}, IntervalCollection{Int64}"]` | 418.301 ms (5%) | 7.948 ms | 99.91 MiB (1%) | 591412 | | `["eachoverlap", "IntervalCollection{Int64}, Vector{Interval{Int64}}"]` | 108.783 ms (5%) | 21.864 ms | 217.44 MiB (1%) | 2036657 | | `["eachoverlap", "Vector{Interval{Int64}}, IntervalCollection{Int64}"]` | 34.063 ms (5%) | 4.787 ms | 81.86 MiB (1%) | 295706 | | `["eachoverlap", "Vector{Interval{Int64}}, Vector{Interval{Int64}}"]` | 108.335 ms (5%) | 24.107 ms | 211.00 MiB (1%) | 2035654 | | `["insert", "shorthand"]` | 37.500 μs (5%) | | 78.81 KiB (1%) | 96 | | `["insert", "type"]` | 36.901 μs (5%) | | 78.81 KiB (1%) | 96 | | `["push", "Vector{Interval{Int64}}"]` | 304.903 μs (5%) | | 129.16 KiB (1%) | 1725 | | `["sort", "Vector{Interval{Int64}}"]` | 190.702 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 1.6.4 Commit 35f0c911f4 (2021-11-19 03:54 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 20.04.3 LTS uname: Linux 5.11.0-1021-azure #22~20.04.1-Ubuntu SMP Fri Oct 29 01:11:25 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 2107 s 2 s 252 s 3659 s 0 s #2 2593 MHz 742 s 1 s 138 s 5170 s 0 s Memory: 6.788982391357422 GB (3467.17578125 MB free) Uptime: 608.78 sec Load Avg: 1.02 0.81 0.41 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 |