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BioJulia / GenomicFeatures.jl

Tools for genomic features in Julia.
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Release/v3.0.0 #50

Closed CiaranOMara closed 1 year ago

CiaranOMara commented 1 year ago

This PR refactors GenomicFeatures to make use of abstract types.

This PR contains the following breaking changes.

github-actions[bot] commented 1 year ago
Benchmark result # Judge result # Benchmark Report for */home/runner/work/GenomicFeatures.jl/GenomicFeatures.jl* ## Job Properties * Time of benchmarks: - Target: 20 Apr 2023 - 15:46 - Baseline: 20 Apr 2023 - 15:47 * Package commits: - Target: 5dffa7 - Baseline: b99efc * Julia commits: - Target: 17cfb8 - Baseline: 17cfb8 * 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 | |---------------------------|---------------|---------------| | `["insert", "type"]` | 2.51 (5%) :x: | 1.77 (1%) :x: | ## Benchmark Group List Here's a list of all the benchmark groups executed by this job: - `["insert"]` ## Julia versioninfo ### Target ``` Julia Version 1.8.5 Commit 17cfb8e65ea (2023-01-08 06:45 UTC) Platform Info: OS: Linux (x86_64-linux-gnu) Ubuntu 22.04.2 LTS uname: Linux 5.15.0-1035-azure #42-Ubuntu SMP Tue Feb 28 19:41:23 UTC 2023 x86_64 x86_64 CPU: Intel(R) Xeon(R) Platinum 8272CL CPU @ 2.60GHz: speed user nice sys idle irq #1 2593 MHz 1460 s 0 s 245 s 1071 s 0 s #2 2593 MHz 488 s 0 s 141 s 2134 s 0 s Memory: 6.781211853027344 GB (5241.19140625 MB free) Uptime: 281.84 sec Load Avg: 1.07 0.82 0.38 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-13.0.1 (ORCJIT, skylake-avx512) Threads: 1 on 2 virtual cores ``` ### Baseline ``` Julia Version 1.8.5 Commit 17cfb8e65ea (2023-01-08 06:45 UTC) Platform Info: OS: Linux (x86_64-linux-gnu) Ubuntu 22.04.2 LTS uname: Linux 5.15.0-1035-azure #42-Ubuntu SMP Tue Feb 28 19:41:23 UTC 2023 x86_64 x86_64 CPU: Intel(R) Xeon(R) Platinum 8272CL CPU @ 2.60GHz: speed user nice sys idle irq #1 2593 MHz 1739 s 0 s 264 s 1293 s 0 s #2 2593 MHz 681 s 0 s 180 s 2422 s 0 s Memory: 6.781211853027344 GB (5251.9609375 MB free) Uptime: 333.89 sec Load Avg: 1.03 0.85 0.42 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-13.0.1 (ORCJIT, skylake-avx512) Threads: 1 on 2 virtual cores ``` --- # Target result # Benchmark Report for */home/runner/work/GenomicFeatures.jl/GenomicFeatures.jl* ## Job Properties * Time of benchmark: 20 Apr 2023 - 15:46 * Package commit: 5dffa7 * Julia commit: 17cfb8 * 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{GenomicInterval{Int64}}", "groupname"]` | 3.063 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{GenomicInterval{Int64}}", "leftposition"]` | 1.300 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{GenomicInterval{Int64}}", "metadata"]` | 1.300 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{GenomicInterval{Int64}}", "rightposition"]` | 1.310 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{GenomicInterval{Int64}}", "strand"]` | 953.885 ns (5%) | | 1.06 KiB (1%) | 1 | | `["eachoverlap", "GenomicIntervalCollection{GenomicInterval{Int64}}, GenomicIntervalCollection{GenomicInterval{Int64}}"]` | 35.295 ms (5%) | 2.495 ms | 104.03 MiB (1%) | 589881 | | `["eachoverlap", "GenomicIntervalCollection{GenomicInterval{Int64}}, Vector{GenomicInterval{Int64}}"]` | 115.012 ms (5%) | 25.014 ms | 232.40 MiB (1%) | 2061663 | | `["eachoverlap", "Vector{GenomicInterval{Int64}}, GenomicIntervalCollection{GenomicInterval{Int64}}"]` | 29.767 ms (5%) | | 86.02 MiB (1%) | 294939 | | `["eachoverlap", "Vector{GenomicInterval{Int64}}, Vector{GenomicInterval{Int64}}"]` | 108.184 ms (5%) | 17.664 ms | 215.91 MiB (1%) | 2061659 | | `["insert", "shorthand"]` | 37.901 μs (5%) | | 76.48 KiB (1%) | 96 | | `["insert", "type"]` | 99.203 μs (5%) | | 135.28 KiB (1%) | 100 | | `["push", "Vector{GenomicInterval{Int64}}"]` | 238.906 μs (5%) | | 105.91 KiB (1%) | 148 | | `["sort", "Vector{GenomicInterval{Int64}}"]` | 180.905 μs (5%) | | 58.80 KiB (1%) | 4 | ## Benchmark Group List Here's a list of all the benchmark groups executed by this job: - `["accessors", "Vector{GenomicInterval{Int64}}"]` - `["eachoverlap"]` - `["insert"]` - `["push"]` - `["sort"]` ## Julia versioninfo ``` Julia Version 1.8.5 Commit 17cfb8e65ea (2023-01-08 06:45 UTC) Platform Info: OS: Linux (x86_64-linux-gnu) Ubuntu 22.04.2 LTS uname: Linux 5.15.0-1035-azure #42-Ubuntu SMP Tue Feb 28 19:41:23 UTC 2023 x86_64 x86_64 CPU: Intel(R) Xeon(R) Platinum 8272CL CPU @ 2.60GHz: speed user nice sys idle irq #1 2593 MHz 1460 s 0 s 245 s 1071 s 0 s #2 2593 MHz 488 s 0 s 141 s 2134 s 0 s Memory: 6.781211853027344 GB (5241.19140625 MB free) Uptime: 281.84 sec Load Avg: 1.07 0.82 0.38 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-13.0.1 (ORCJIT, skylake-avx512) Threads: 1 on 2 virtual cores ``` --- # Baseline result # Benchmark Report for */home/runner/work/GenomicFeatures.jl/GenomicFeatures.jl* ## Job Properties * Time of benchmark: 20 Apr 2023 - 15:47 * Package commit: b99efc * Julia commit: 17cfb8 * 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"]` | 1.100 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"]` | 1.200 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "seqname"]` | 2.500 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "strand"]` | 900.000 ns (5%) | | 1.06 KiB (1%) | 1 | | `["eachoverlap", "IntervalCollection{Int64}, IntervalCollection{Int64}"]` | 35.406 ms (5%) | 2.344 ms | 104.03 MiB (1%) | 589881 | | `["eachoverlap", "IntervalCollection{Int64}, Vector{Interval{Int64}}"]` | 115.445 ms (5%) | 19.703 ms | 227.87 MiB (1%) | 2061663 | | `["eachoverlap", "Vector{Interval{Int64}}, IntervalCollection{Int64}"]` | 29.886 ms (5%) | | 86.02 MiB (1%) | 294939 | | `["eachoverlap", "Vector{Interval{Int64}}, Vector{Interval{Int64}}"]` | 110.280 ms (5%) | 21.296 ms | 215.91 MiB (1%) | 2061659 | | `["insert", "shorthand"]` | 39.600 μs (5%) | | 76.48 KiB (1%) | 96 | | `["insert", "type"]` | 39.601 μs (5%) | | 76.48 KiB (1%) | 96 | | `["push", "Vector{Interval{Int64}}"]` | 246.507 μs (5%) | | 105.91 KiB (1%) | 148 | | `["sort", "Vector{Interval{Int64}}"]` | 185.105 μs (5%) | | 58.80 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 1.8.5 Commit 17cfb8e65ea (2023-01-08 06:45 UTC) Platform Info: OS: Linux (x86_64-linux-gnu) Ubuntu 22.04.2 LTS uname: Linux 5.15.0-1035-azure #42-Ubuntu SMP Tue Feb 28 19:41:23 UTC 2023 x86_64 x86_64 CPU: Intel(R) Xeon(R) Platinum 8272CL CPU @ 2.60GHz: speed user nice sys idle irq #1 2593 MHz 1739 s 0 s 264 s 1293 s 0 s #2 2593 MHz 681 s 0 s 180 s 2422 s 0 s Memory: 6.781211853027344 GB (5251.9609375 MB free) Uptime: 333.89 sec Load Avg: 1.03 0.85 0.42 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-13.0.1 (ORCJIT, skylake-avx512) Threads: 1 on 2 virtual cores ``` --- # Runtime information | Runtime Info | | |:--|:--| | BLAS #threads | 1 | | `BLAS.vendor()` | `openblas64` | | `Sys.CPU_THREADS` | 2 | `lscpu` output: Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit Address sizes: 46 bits physical, 48 bits virtual Byte Order: Little Endian CPU(s): 2 On-line CPU(s) list: 0,1 Vendor ID: GenuineIntel Model name: Intel(R) Xeon(R) Platinum 8272CL CPU @ 2.60GHz CPU family: 6 Model: 85 Thread(s) per core: 1 Core(s) per socket: 2 Socket(s): 1 Stepping: 7 BogoMIPS: 5187.81 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 avx512f avx512dq rdseed adx smap clflushopt avx512cd avx512bw avx512vl xsaveopt xsavec xsaves md_clear Hypervisor vendor: Microsoft Virtualization type: full L1d cache: 64 KiB (2 instances) L1i cache: 64 KiB (2 instances) L2 cache: 2 MiB (2 instances) L3 cache: 35.8 MiB (1 instance) NUMA node(s): 1 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 Mmio stale data: Vulnerable: Clear CPU buffers attempted, no microcode; SMT Host state unknown Vulnerability Retbleed: Vulnerable Vulnerability Spec store bypass: Vulnerable Vulnerability Spectre v1: Mitigation; usercopy/swapgs barriers and __user pointer sanitization Vulnerability Spectre v2: Mitigation; Retpolines, STIBP disabled, RSB filling, PBRSB-eIBRS Not affected Vulnerability Srbds: Not affected Vulnerability Tsx async abort: Mitigation; Clear CPU buffers; SMT Host state unknown | 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 |
CiaranOMara commented 1 year ago

@kescobo, this PR is now ready for review again. I think I addressed your comment and tidied up a few loose ends.

github-actions[bot] commented 1 year ago
Benchmark result # Judge result # Benchmark Report for */home/runner/work/GenomicFeatures.jl/GenomicFeatures.jl* ## Job Properties * Time of benchmarks: - Target: 29 Apr 2023 - 02:33 - Baseline: 29 Apr 2023 - 02:34 * Package commits: - Target: 464597 - Baseline: b99efc * Julia commits: - Target: 17cfb8 - Baseline: 17cfb8 * 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 | |---------------------------|------------------------------|---------------| | `["insert", "shorthand"]` | 0.80 (5%) :white_check_mark: | 1.00 (1%) | | `["insert", "type"]` | 2.13 (5%) :x: | 1.77 (1%) :x: | ## Benchmark Group List Here's a list of all the benchmark groups executed by this job: - `["insert"]` ## Julia versioninfo ### Target ``` Julia Version 1.8.5 Commit 17cfb8e65ea (2023-01-08 06:45 UTC) Platform Info: OS: Linux (x86_64-linux-gnu) Ubuntu 22.04.2 LTS uname: Linux 5.15.0-1036-azure #43-Ubuntu SMP Wed Mar 29 16:11:05 UTC 2023 x86_64 x86_64 CPU: Intel(R) Xeon(R) CPU E5-2673 v4 @ 2.30GHz: speed user nice sys idle irq #1 2294 MHz 701 s 0 s 213 s 2490 s 0 s #2 2294 MHz 1534 s 0 s 224 s 1606 s 0 s Memory: 6.781208038330078 GB (5320.34375 MB free) Uptime: 346.24 sec Load Avg: 1.1 0.78 0.37 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-13.0.1 (ORCJIT, broadwell) Threads: 1 on 2 virtual cores ``` ### Baseline ``` Julia Version 1.8.5 Commit 17cfb8e65ea (2023-01-08 06:45 UTC) Platform Info: OS: Linux (x86_64-linux-gnu) Ubuntu 22.04.2 LTS uname: Linux 5.15.0-1036-azure #43-Ubuntu SMP Wed Mar 29 16:11:05 UTC 2023 x86_64 x86_64 CPU: Intel(R) Xeon(R) CPU E5-2673 v4 @ 2.30GHz: speed user nice sys idle irq #1 2294 MHz 743 s 0 s 217 s 3004 s 0 s #2 2294 MHz 2010 s 0 s 272 s 1644 s 0 s Memory: 6.781208038330078 GB (5218.80078125 MB free) Uptime: 402.32 sec Load Avg: 1.07 0.84 0.42 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-13.0.1 (ORCJIT, broadwell) Threads: 1 on 2 virtual cores ``` --- # Target result # Benchmark Report for */home/runner/work/GenomicFeatures.jl/GenomicFeatures.jl* ## Job Properties * Time of benchmark: 29 Apr 2023 - 2:33 * Package commit: 464597 * Julia commit: 17cfb8 * 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{GenomicInterval{Int64}}", "groupname"]` | 1.550 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{GenomicInterval{Int64}}", "leftposition"]` | 1.110 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{GenomicInterval{Int64}}", "metadata"]` | 1.100 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{GenomicInterval{Int64}}", "rightposition"]` | 1.110 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{GenomicInterval{Int64}}", "strand"]` | 835.078 ns (5%) | | 1.06 KiB (1%) | 1 | | `["eachoverlap", "GenomicIntervalCollection{GenomicInterval{Int64}}, GenomicIntervalCollection{GenomicInterval{Int64}}"]` | 38.620 ms (5%) | 3.609 ms | 104.03 MiB (1%) | 589881 | | `["eachoverlap", "GenomicIntervalCollection{GenomicInterval{Int64}}, Vector{GenomicInterval{Int64}}"]` | 122.732 ms (5%) | 22.415 ms | 232.40 MiB (1%) | 2061663 | | `["eachoverlap", "Vector{GenomicInterval{Int64}}, GenomicIntervalCollection{GenomicInterval{Int64}}"]` | 35.726 ms (5%) | 4.306 ms | 86.02 MiB (1%) | 294939 | | `["eachoverlap", "Vector{GenomicInterval{Int64}}, Vector{GenomicInterval{Int64}}"]` | 124.712 ms (5%) | 25.562 ms | 215.91 MiB (1%) | 2061659 | | `["insert", "shorthand"]` | 33.301 μs (5%) | | 76.48 KiB (1%) | 96 | | `["insert", "type"]` | 86.101 μs (5%) | | 135.28 KiB (1%) | 100 | | `["push", "Vector{GenomicInterval{Int64}}"]` | 214.800 μs (5%) | | 105.91 KiB (1%) | 148 | | `["sort", "Vector{GenomicInterval{Int64}}"]` | 155.900 μs (5%) | | 58.80 KiB (1%) | 4 | ## Benchmark Group List Here's a list of all the benchmark groups executed by this job: - `["accessors", "Vector{GenomicInterval{Int64}}"]` - `["eachoverlap"]` - `["insert"]` - `["push"]` - `["sort"]` ## Julia versioninfo ``` Julia Version 1.8.5 Commit 17cfb8e65ea (2023-01-08 06:45 UTC) Platform Info: OS: Linux (x86_64-linux-gnu) Ubuntu 22.04.2 LTS uname: Linux 5.15.0-1036-azure #43-Ubuntu SMP Wed Mar 29 16:11:05 UTC 2023 x86_64 x86_64 CPU: Intel(R) Xeon(R) CPU E5-2673 v4 @ 2.30GHz: speed user nice sys idle irq #1 2294 MHz 701 s 0 s 213 s 2490 s 0 s #2 2294 MHz 1534 s 0 s 224 s 1606 s 0 s Memory: 6.781208038330078 GB (5320.34375 MB free) Uptime: 346.24 sec Load Avg: 1.1 0.78 0.37 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-13.0.1 (ORCJIT, broadwell) Threads: 1 on 2 virtual cores ``` --- # Baseline result # Benchmark Report for */home/runner/work/GenomicFeatures.jl/GenomicFeatures.jl* ## Job Properties * Time of benchmark: 29 Apr 2023 - 2:34 * Package commit: b99efc * Julia commit: 17cfb8 * 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"]` | 1.100 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"]` | 1.200 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "seqname"]` | 1.500 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "strand"]` | 800.000 ns (5%) | | 1.06 KiB (1%) | 1 | | `["eachoverlap", "IntervalCollection{Int64}, IntervalCollection{Int64}"]` | 41.648 ms (5%) | 3.238 ms | 104.03 MiB (1%) | 589881 | | `["eachoverlap", "IntervalCollection{Int64}, Vector{Interval{Int64}}"]` | 137.419 ms (5%) | 24.603 ms | 227.87 MiB (1%) | 2061663 | | `["eachoverlap", "Vector{Interval{Int64}}, IntervalCollection{Int64}"]` | 37.710 ms (5%) | 4.445 ms | 86.02 MiB (1%) | 294939 | | `["eachoverlap", "Vector{Interval{Int64}}, Vector{Interval{Int64}}"]` | 118.223 ms (5%) | 14.144 ms | 215.91 MiB (1%) | 2061659 | | `["insert", "shorthand"]` | 41.400 μs (5%) | | 76.48 KiB (1%) | 96 | | `["insert", "type"]` | 40.500 μs (5%) | | 76.48 KiB (1%) | 96 | | `["push", "Vector{Interval{Int64}}"]` | 217.001 μs (5%) | | 105.91 KiB (1%) | 148 | | `["sort", "Vector{Interval{Int64}}"]` | 155.201 μs (5%) | | 58.80 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 1.8.5 Commit 17cfb8e65ea (2023-01-08 06:45 UTC) Platform Info: OS: Linux (x86_64-linux-gnu) Ubuntu 22.04.2 LTS uname: Linux 5.15.0-1036-azure #43-Ubuntu SMP Wed Mar 29 16:11:05 UTC 2023 x86_64 x86_64 CPU: Intel(R) Xeon(R) CPU E5-2673 v4 @ 2.30GHz: speed user nice sys idle irq #1 2294 MHz 743 s 0 s 217 s 3004 s 0 s #2 2294 MHz 2010 s 0 s 272 s 1644 s 0 s Memory: 6.781208038330078 GB (5218.80078125 MB free) Uptime: 402.32 sec Load Avg: 1.07 0.84 0.42 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-13.0.1 (ORCJIT, broadwell) Threads: 1 on 2 virtual cores ``` --- # Runtime information | Runtime Info | | |:--|:--| | BLAS #threads | 1 | | `BLAS.vendor()` | `openblas64` | | `Sys.CPU_THREADS` | 2 | `lscpu` output: Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit Address sizes: 46 bits physical, 48 bits virtual Byte Order: Little Endian CPU(s): 2 On-line CPU(s) list: 0,1 Vendor ID: GenuineIntel Model name: Intel(R) Xeon(R) CPU E5-2673 v4 @ 2.30GHz CPU family: 6 Model: 79 Thread(s) per core: 1 Core(s) per socket: 2 Socket(s): 1 Stepping: 1 BogoMIPS: 4589.37 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 Hypervisor vendor: Microsoft Virtualization type: full L1d cache: 64 KiB (2 instances) L1i cache: 64 KiB (2 instances) L2 cache: 512 KiB (2 instances) L3 cache: 50 MiB (1 instance) NUMA node(s): 1 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 Mmio stale data: Vulnerable: Clear CPU buffers attempted, no microcode; SMT Host state unknown Vulnerability Retbleed: Not affected Vulnerability Spec store bypass: Vulnerable Vulnerability Spectre v1: Mitigation; usercopy/swapgs barriers and __user pointer sanitization Vulnerability Spectre v2: Mitigation; Retpolines, STIBP disabled, RSB filling, PBRSB-eIBRS Not affected Vulnerability Srbds: Not affected Vulnerability Tsx async abort: Mitigation; Clear CPU buffers; SMT Host state unknown | 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 1 year ago
Benchmark result # Judge result # Benchmark Report for */home/runner/work/GenomicFeatures.jl/GenomicFeatures.jl* ## Job Properties * Time of benchmarks: - Target: 29 Apr 2023 - 02:59 - Baseline: 29 Apr 2023 - 03:00 * Package commits: - Target: 8ddc14 - Baseline: b99efc * Julia commits: - Target: 17cfb8 - Baseline: 17cfb8 * 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 | |---------------------------|------------------------------|---------------| | `["insert", "shorthand"]` | 0.94 (5%) :white_check_mark: | 1.00 (1%) | | `["insert", "type"]` | 2.50 (5%) :x: | 1.77 (1%) :x: | ## Benchmark Group List Here's a list of all the benchmark groups executed by this job: - `["insert"]` ## Julia versioninfo ### Target ``` Julia Version 1.8.5 Commit 17cfb8e65ea (2023-01-08 06:45 UTC) Platform Info: OS: Linux (x86_64-linux-gnu) Ubuntu 22.04.2 LTS uname: Linux 5.15.0-1036-azure #43-Ubuntu SMP Wed Mar 29 16:11:05 UTC 2023 x86_64 x86_64 CPU: Intel(R) Xeon(R) CPU E5-2673 v4 @ 2.30GHz: speed user nice sys idle irq #1 2294 MHz 1679 s 0 s 279 s 2019 s 0 s #2 2294 MHz 799 s 0 s 190 s 2966 s 0 s Memory: 6.781208038330078 GB (5298.90625 MB free) Uptime: 404.47 sec Load Avg: 1.04 0.85 0.43 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-13.0.1 (ORCJIT, broadwell) Threads: 1 on 2 virtual cores ``` ### Baseline ``` Julia Version 1.8.5 Commit 17cfb8e65ea (2023-01-08 06:45 UTC) Platform Info: OS: Linux (x86_64-linux-gnu) Ubuntu 22.04.2 LTS uname: Linux 5.15.0-1036-azure #43-Ubuntu SMP Wed Mar 29 16:11:05 UTC 2023 x86_64 x86_64 CPU: Intel(R) Xeon(R) CPU E5-2673 v4 @ 2.30GHz: speed user nice sys idle irq #1 2294 MHz 1974 s 0 s 287 s 2326 s 0 s #2 2294 MHz 1074 s 0 s 230 s 3260 s 0 s Memory: 6.781208038330078 GB (5207.24609375 MB free) Uptime: 465.64 sec Load Avg: 1.01 0.88 0.47 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-13.0.1 (ORCJIT, broadwell) Threads: 1 on 2 virtual cores ``` --- # Target result # Benchmark Report for */home/runner/work/GenomicFeatures.jl/GenomicFeatures.jl* ## Job Properties * Time of benchmark: 29 Apr 2023 - 2:59 * Package commit: 8ddc14 * Julia commit: 17cfb8 * 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{GenomicInterval{Int64}}", "groupname"]` | 2.250 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{GenomicInterval{Int64}}", "leftposition"]` | 1.470 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{GenomicInterval{Int64}}", "metadata"]` | 1.440 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{GenomicInterval{Int64}}", "rightposition"]` | 1.370 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{GenomicInterval{Int64}}", "strand"]` | 941.176 ns (5%) | | 1.06 KiB (1%) | 1 | | `["eachoverlap", "GenomicIntervalCollection{GenomicInterval{Int64}}, GenomicIntervalCollection{GenomicInterval{Int64}}"]` | 42.809 ms (5%) | 3.192 ms | 104.03 MiB (1%) | 589881 | | `["eachoverlap", "GenomicIntervalCollection{GenomicInterval{Int64}}, Vector{GenomicInterval{Int64}}"]` | 145.573 ms (5%) | 26.765 ms | 232.40 MiB (1%) | 2061663 | | `["eachoverlap", "Vector{GenomicInterval{Int64}}, GenomicIntervalCollection{GenomicInterval{Int64}}"]` | 40.677 ms (5%) | 4.970 ms | 86.02 MiB (1%) | 294939 | | `["eachoverlap", "Vector{GenomicInterval{Int64}}, Vector{GenomicInterval{Int64}}"]` | 132.675 ms (5%) | 15.228 ms | 215.91 MiB (1%) | 2061659 | | `["insert", "shorthand"]` | 43.700 μs (5%) | | 76.48 KiB (1%) | 96 | | `["insert", "type"]` | 113.098 μs (5%) | | 135.28 KiB (1%) | 100 | | `["push", "Vector{GenomicInterval{Int64}}"]` | 244.096 μs (5%) | | 105.91 KiB (1%) | 148 | | `["sort", "Vector{GenomicInterval{Int64}}"]` | 185.197 μs (5%) | | 58.80 KiB (1%) | 4 | ## Benchmark Group List Here's a list of all the benchmark groups executed by this job: - `["accessors", "Vector{GenomicInterval{Int64}}"]` - `["eachoverlap"]` - `["insert"]` - `["push"]` - `["sort"]` ## Julia versioninfo ``` Julia Version 1.8.5 Commit 17cfb8e65ea (2023-01-08 06:45 UTC) Platform Info: OS: Linux (x86_64-linux-gnu) Ubuntu 22.04.2 LTS uname: Linux 5.15.0-1036-azure #43-Ubuntu SMP Wed Mar 29 16:11:05 UTC 2023 x86_64 x86_64 CPU: Intel(R) Xeon(R) CPU E5-2673 v4 @ 2.30GHz: speed user nice sys idle irq #1 2294 MHz 1679 s 0 s 279 s 2019 s 0 s #2 2294 MHz 799 s 0 s 190 s 2966 s 0 s Memory: 6.781208038330078 GB (5298.90625 MB free) Uptime: 404.47 sec Load Avg: 1.04 0.85 0.43 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-13.0.1 (ORCJIT, broadwell) Threads: 1 on 2 virtual cores ``` --- # Baseline result # Benchmark Report for */home/runner/work/GenomicFeatures.jl/GenomicFeatures.jl* ## Job Properties * Time of benchmark: 29 Apr 2023 - 3:0 * Package commit: b99efc * Julia commit: 17cfb8 * 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"]` | 1.399 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "metadata"]` | 1.499 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "rightposition"]` | 1.599 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "seqname"]` | 1.900 μs (5%) | | 7.94 KiB (1%) | 1 | | `["accessors", "Vector{Interval{Int64}}", "strand"]` | 999.000 ns (5%) | | 1.06 KiB (1%) | 1 | | `["eachoverlap", "IntervalCollection{Int64}, IntervalCollection{Int64}"]` | 44.747 ms (5%) | 3.438 ms | 104.03 MiB (1%) | 589881 | | `["eachoverlap", "IntervalCollection{Int64}, Vector{Interval{Int64}}"]` | 153.520 ms (5%) | 27.342 ms | 227.87 MiB (1%) | 2061663 | | `["eachoverlap", "Vector{Interval{Int64}}, IntervalCollection{Int64}"]` | 39.986 ms (5%) | 4.446 ms | 86.02 MiB (1%) | 294939 | | `["eachoverlap", "Vector{Interval{Int64}}, Vector{Interval{Int64}}"]` | 156.714 ms (5%) | 28.328 ms | 215.91 MiB (1%) | 2061659 | | `["insert", "shorthand"]` | 46.499 μs (5%) | | 76.48 KiB (1%) | 96 | | `["insert", "type"]` | 45.299 μs (5%) | | 76.48 KiB (1%) | 96 | | `["push", "Vector{Interval{Int64}}"]` | 244.796 μs (5%) | | 105.91 KiB (1%) | 148 | | `["sort", "Vector{Interval{Int64}}"]` | 182.198 μs (5%) | | 58.80 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 1.8.5 Commit 17cfb8e65ea (2023-01-08 06:45 UTC) Platform Info: OS: Linux (x86_64-linux-gnu) Ubuntu 22.04.2 LTS uname: Linux 5.15.0-1036-azure #43-Ubuntu SMP Wed Mar 29 16:11:05 UTC 2023 x86_64 x86_64 CPU: Intel(R) Xeon(R) CPU E5-2673 v4 @ 2.30GHz: speed user nice sys idle irq #1 2294 MHz 1974 s 0 s 287 s 2326 s 0 s #2 2294 MHz 1074 s 0 s 230 s 3260 s 0 s Memory: 6.781208038330078 GB (5207.24609375 MB free) Uptime: 465.64 sec Load Avg: 1.01 0.88 0.47 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-13.0.1 (ORCJIT, broadwell) Threads: 1 on 2 virtual cores ``` --- # Runtime information | Runtime Info | | |:--|:--| | BLAS #threads | 1 | | `BLAS.vendor()` | `openblas64` | | `Sys.CPU_THREADS` | 2 | `lscpu` output: Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit Address sizes: 46 bits physical, 48 bits virtual Byte Order: Little Endian CPU(s): 2 On-line CPU(s) list: 0,1 Vendor ID: GenuineIntel Model name: Intel(R) Xeon(R) CPU E5-2673 v4 @ 2.30GHz CPU family: 6 Model: 79 Thread(s) per core: 1 Core(s) per socket: 2 Socket(s): 1 Stepping: 1 BogoMIPS: 4589.37 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 Hypervisor vendor: Microsoft Virtualization type: full L1d cache: 64 KiB (2 instances) L1i cache: 64 KiB (2 instances) L2 cache: 512 KiB (2 instances) L3 cache: 50 MiB (1 instance) NUMA node(s): 1 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 Mmio stale data: Vulnerable: Clear CPU buffers attempted, no microcode; SMT Host state unknown Vulnerability Retbleed: Not affected Vulnerability Spec store bypass: Vulnerable Vulnerability Spectre v1: Mitigation; usercopy/swapgs barriers and __user pointer sanitization Vulnerability Spectre v2: Mitigation; Retpolines, STIBP disabled, RSB filling, PBRSB-eIBRS Not affected Vulnerability Srbds: Not affected Vulnerability Tsx async abort: Mitigation; Clear CPU buffers; SMT Host state unknown | 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 |
CiaranOMara commented 1 year ago

Thanks @kescobo.